10-K

UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington D.C. 20549

FORM 10-K

(Mark One)

x ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

For the fiscal year ended December 31, 2012

OR

¨ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

For the Transition Period from to

Commission File Number: 001-34885

AMYRIS, INC.

(Exact name of registrant as specified in its charter)

Delaware	55-0856151
(State or other jurisdiction of incorporation or organization)	(I.R.S. Employer Identification No.)

5885 Hollis Street, Suite 100, Emeryville, California	94608
(Address of principal executive office)	(Zip Code)

(510) 450-0761

(Registrant’s telephone number, including area code)

Securities registered pursuant to Section 12(b) of the Act:

Title of each class	Name of each exchange on which registered
Common Stock, $0.0001 par value per share	The NASDAQ Stock Market LLC (NASDAQ Global Select Market)

Securities registered pursuant to Section 12(g) of the Act: None

Indicate by check mark if the registrant is a well-known seasoned issuer, as defined in Rule 405 of the Securities Act.    Yes  ¨    No  x

Indicate by check mark if the registrant is not required to file reports pursuant to Section 13 or Section 15(d) of the Act.    Yes  ¨    No  x

Indicate by check mark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days.    Yes  x    No  ¨

Indicate by check mark whether the registrant has submitted electronically and posted on its corporate Web site, if any, every Interactive Data File required to be submitted and posted pursuant to Rule 405 of Regulation S-T (§232.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was required to submit and post such files).    Yes  x    No  ¨

Indicate by check mark if disclosure of delinquent filers pursuant to Item 405 of Regulation S-K is not contained herein, and will not be contained, to the best of registrant’s knowledge, in definitive proxy or information statements incorporated by reference in Part III of this Form 10-K or any amendment to this Form 10-K.  x

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, or a non-accelerated filer. See definition of “large accelerated filer”, “accelerated filer” and “smaller reporting company” in Rule 12b-2 of the Exchange Act. (Check one.)

Large accelerated filer	¨	Accelerated filer	x
Non-accelerated filer	¨(Do not check if a smaller reporting company)	Smaller reporting company	¨

Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act.):    Yes  ¨    No  x

As of June 29, 2012, the last business day of the registrant’s most recently completed second fiscal quarter, the aggregate market value of the voting stock held by non-affiliates of the registrant was approximately $154.3 million, based on the closing price of the registrant’s common stock on the NASDAQ Global Select Market on such date.

73,876,289 shares of the Registrant’s common stock, par value $0.0001 per share, were outstanding as of March 1, 2013.

DOCUMENTS INCORPORATED BY REFERENCE

Portions of registrant’s proxy statement to be delivered to stockholders in connection with the registrant’s 2013 Annual Meeting of Stockholders to be held on or about May 9, 2013 are incorporated by reference into Part III of this Form 10-K. The registrant intends to file its proxy statement within 120 days after its fiscal year end.

AMYRIS, INC.

ANNUAL REPORT ON FORM 10-K

For the Fiscal Year Ended December 31, 2012

INDEX

		Page
	PART I
Item 1.	Business	2
Item 1A.	Risk Factors	12
	Executive Officers of the Registrant	32
Item 1B	Unresolved Staff Comments	33
Item 2.	Properties	33
Item 3.	Legal Proceedings	34
Item 4.	Mine Safety Disclosures	34
	PART II
Item 5.	Market for the Registrant’s Common Equity, Related Stockholder Matters and Issuer Purchases of Equity Securities	35
Item 6.	Selected Financial Data	38
Item 7.	Management’s Discussion and Analysis of Financial Condition and Results of Operations	39
Item 7A.	Quantitative and Qualitative Disclosures About Market Risk	57
Item 8.	Financial Statements and Supplementary Data	59
Item 9.	Changes in and Disagreements with Accountants on Accounting and Financial Disclosure	118
Item 9A.	Controls and Procedures	118
Item 9B.	Other Information	119
	PART III
Item 10.	Directors, Executive Officers and Corporate Governance	120
Item 11.	Executive Compensation	120
Item 12.	Security Ownership of Certain Beneficial Owners and Management and Related Stockholder Matters	120
Item 13.	Certain Relationships and Related Transactions, and Director Independence	120
Item 14.	Principal Accounting Fees and Services	120
	PART IV
Item 15.	Exhibits, Financial Statement Schedules	121
	Signatures	129

FORWARD-LOOKING STATEMENTS

This report on Form 10-K, including the sections entitled “Item 1. Business,” “Item 1A. Risk Factors,” and “Item 7. Management’s Discussion and Analysis of Financial Condition and Results of Operations,” contains forward-looking statements reflecting our current expectations that involve risks and uncertainties and which are subject to safe harbors under the Securities Act of 1933, as amended, or the Securities Act, and the Securities Exchange Act of 1934, as amended. These forward-looking statements include, but are not limited to, statements concerning our strategy, future production capacity and other aspects of our future operations, ability to improve our production efficiencies, future financial position, future revenues, projected costs, expectations regarding demand and acceptance for our technologies, growth opportunities and trends in the market in which we operate, prospects and plans and objectives of management. The words “anticipates,” “believes,” “estimates,” “expects,” “intends,” “may,” “plans,” “projects,” “will,” “would” and similar expressions are intended to identify forward-looking statements, although not all forward-looking statements contain these identifying words. We may not actually achieve the plans, intentions or expectations disclosed in our forward-looking statements and you should not place undue reliance on our forward-looking statements. These forward-looking statements involve risks and uncertainties that could cause our actual results to differ materially from those in the forward-looking statements, including, without limitation, the risks set forth in Part I, Item 1A, “Risk Factors” in this Annual Report on Form 10-K and in our other filings with the Securities and Exchange Commission. We do not assume any obligation to update any forward-looking statements.

TRADEMARKS

Amyris^®, the Amyris logo, Biofene^® and No Compromise^® are trademarks or registered trademarks of Amyris, Inc. This report also contains trademarks and trade names of other business that are the property of their respective holders.

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PART I

ITEM 1. BUSINESS

Overview

Amyris is a renewable products company focused on providing sustainable alternatives to a broad range of petroleum-sourced products. We developed innovative microbial engineering and screening technologies that modify the way microorganisms process sugars. We are using our proprietary synthetic biology platform to design microbes, primarily yeast, and use them as living factories in established fermentation processes to convert plant-sourced sugars into renewable hydrocarbons. We are developing, and, in some cases, already commercializing, products from these hydrocarbons in several target markets, including cosmetics, lubricants, flavors and fragrances, polymers and plastic additives, home and personal care products, and transportation fuels. We call these No Compromise^® products because we design them to perform comparably to, or better than, currently available products.

We were founded in 2003 in the San Francisco Bay Area by a group of scientists from the University of California, Berkeley. Our first major milestone came in 2005 when, through a grant from the Bill & Melinda Gates Foundation, our scientists developed technology capable of creating microbial strains to produce artemisinic acid - a precursor of artemisinin, an effective anti-malarial drug. In 2008, we granted a royalty-free license to this technology to Sanofi-Aventis, which currently expects to begin distributing artemisinin-based anti-malarial drugs made through our technology in 2013.

Building on our success with semi-synthetic artemisinin to combat malaria, Amyris has been applying its industrial synthetic biology platform to provide alternatives to a broad range of petroleum-sourced products. Amyris has focused its development efforts on the production of Biofene^®, Amyris's brand of renewable farnesene, a long-chain, branched liquid hydrocarbon molecule. Using Biofene as a building block molecule, we are developing a wide range of renewable products for our target markets.

While our platform is able to utilize a wide variety of feedstocks, we are focusing our large-scale production plans primarily on the use of Brazilian sugarcane as our feedstock because of its abundance, low cost and relative price stability. By locating our production facilities in Brazil, we are leveraging a mature sugarcane growing and fermentation infrastructure, reducing our production costs, and accessing feedstock that is somewhat insulated from price volatility. We have also produced Biofene from other feedstocks such as sugar beets, corn dextrose, sweet sorghum and cellulosic sugars.

Amyris's first purpose-built, large-scale Biofene production plant commenced operations in southeastern Brazil in December 2012. This plant is in Brotas in the state of São Paulo and is adjacent to an existing sugar and ethanol mill, Paraíso Bioenergia. Amyris has also advanced initial construction of a second large-scale production plant in Brazil, located at the Usina São Martinho sugar and ethanol mill (also in the state of São Paulo), which we intend to complete when production economics support start-up of that plant. To satisfy initial demand for our products until our own facilities are operating, we have leveraged contract-manufacturing capabilities of established companies.

Our business strategy is to focus our direct commercialization efforts on higher-value, lower-volume markets while moving lower-margin, higher-volume commodity products, including our fuels and base oil lubricants products, into joint venture arrangements with established industry leaders. We believe this approach will permit access to the capital and resources necessary to support large-scale production and global distribution for our large-market commodity products.

Amyris is focused on building its renewable-product leadership position initially with squalane in cosmetics, niche fuel opportunities, fragrance oils, and farnesene for liquid polymers applications. We believe that success in these early markets will pave the way to accessing larger markets and having a more significant impact in the longer term.

We were incorporated in 2003. We have two operating subsidiaries, Amyris Brasil Ltda. (formerly Amyris Brasil S.A.), or Amyris Brasil, and Amyris Fuels LLC, or Amyris Fuels. Amyris Brasil oversees the establishment and expansion of our production in Brazil. Amyris Fuels was originally established to help us develop fuel distribution capabilities in the U.S.

We began selling fuels through Amyris Fuels in June 2008. Amyris Fuels generated revenue from the sale of ethanol and reformulated ethanol-blended gasoline to wholesale customers through a network of terminals in the eastern U.S. We completed our planned transition out of the ethanol and ethanol-blended gasoline business in the third quarter of 2012. In 2012, we generated $73.7 million in revenues, including $38.8 million from sales of ethanol and ethanol-blended gasoline by Amyris Fuels, $24.1 million from grants and collaborations, and $10.8 million from product sales of our renewable products.

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Our Business Strategy

Petroleum is a fundamental building block for many products, such as consumer products, chemicals, plastics and transportation fuels that are essential to modern economies. Recently, the increased demand for petroleum in the face of limited supply, supply chain uncertainties and negative environmental impacts have created challenges to the current petroleum infrastructure. As a result, there have been many attempts to create products comparable to petroleum derivatives without these drawbacks. However, initial approaches have faced a number of challenges that have limited their success, including exposure to volatile feedstock pricing, questionable environmental sustainability, limited product portfolio, and dependency on government policy.

Our objective is to become the leading provider of renewable, high-performance alternatives to selected petroleum-sourced chemicals and fuels. By leveraging our synthetic biology platform, our partners' know-how, and our experience in industrial fermentation, our products are designed to enable our customers to reduce the environmental impact of their products without compromising performance, and, in some cases, our renewable products provide superior performance to the petroleum-sourced products they are replacing.

Key elements of our strategy include:

1. Leveraging our technology platform to improve efficiency. We continue applying synthetic biology, primarily our strain engineering platform, to lower the cost of production of our products through improvements in yields and other production process efficiencies. We do this with our industrial platform for yeast strain development at our world-class laboratories. We also support scale up to commercial production in two pilot plant facilities and a demonstration production facility, as well as at various contract manufacturing locations.

2. Accelerating development through collaborations. In order to accelerate the development of new technologies, production methods or products, we enter into collaborative research, development and commercialization agreements, such as our existing agreements with Total Gas & Power USA SAS, or Total, Firmenich SA, or Firmenich, Givaudan Schweiz AG, or Givaudan, Cosan Indústria e Comércio S.A., or Cosan, Kuraray Co., Ltd., or Kuraray, M&G Finanziaria S.R.L, or M&G, Method Home Products, Inc., or Method, and Manufacture Francaise de Pneumatiques Michelin, or Michelin. We have also entered into partnerships with the U.S. government to develop certain technologies and processes capable of improving our ability of producing alternatives to petroleum-sourced products.

3. Delivering cost efficient manufacturing. Building on our breakthrough technology and experience gained from production through third party contract manufacturing, we built, commissioned and are now operating our own large-scale Biofene production plant in Brotas, in the state of São Paulo, Brazil. We opted to focus on Brazilian sugarcane as the feedstock to support our production ramp because of its abundance, low-cost and relative price stability. As we develop cost efficient manufacturing in our first production facility, we expect to seek to work selectively with other Brazilian sugar and ethanol producers to build additional facilities adjacent to their existing mills, thereby reducing the capital required to establish and scale our production operations.

4. Targeting product markets to maximize returns. We have begun to commercialize our products derived from Biofene primarily in select specialty chemical markets characterized by higher-margin, lower-volume products, where we believe we can earn positive gross margins with current production process efficiencies. For example, in 2011 we initiated sales of a cosmetic emollient, squalane, produced from Biofene. We have also established sales channels to certain niche diesel markets in metropolitan bus fleets in Brazil. As we lower our production costs through technological and manufacturing improvements, we intend to expand into broader, lower-margin, higher volume commodity product markets, such as the broad-based fuels market and base oil lubricants markets, through joint venture arrangements.

Our Breakthrough Technology

Our synthetic biology platform enables us to modify the genetic pathways of microorganisms, primarily yeast, to turn them into living factories to produce target molecules for which we believe there may be significant market opportunities. In addition to using our synthetic biology platform to identify and improve strains of microbes to produce target molecules, we are using our technology platform to develop production processes that we believe will allow us to scale to commercial levels.

The primary biological pathway within the microbe that we currently use to produce our target molecules is the isoprenoid pathway. Isoprenoids constitute a large, diverse class of organic chemicals with current product applications in a wide range of industries, including specialty chemicals and fuels. With this pathway, we can potentially produce thousands of different isoprenoid molecules.

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The key steps in our strain engineering and scale-up process have been as follows:

Identifying target molecules. We start our process by identifying a commercial application where we can deliver a No Compromise solution that we want to pursue. We identify the key molecular properties that are essential to product performance in a specific commercial application and then analyze the chemical structures that drive those key performance characteristics. Finally, we identify target molecules or derivatives of molecules that are comprised of these key chemical structures and that may be produced by our yeast strains.

Developing initial strains. Once we have chosen a target molecule, we identify the steps required for its production in a biological pathway. We then seek to design a pathway to produce the target, either directly or by producing a molecule that can, through simple chemical steps, be synthesized, or converted, into the target. Once this pathway is identified, we undertake to engineer it into our yeast strains by employing the processes discussed below.

Improving strain performance and process development. After we have established a pathway and verified that it can produce the target molecule, the yeast strain must be improved to increase the level of efficiency of production. Initially, we focus primarily on yield, a measure of the amount of product produced by a defined amount of sugar as the means to improve strain output. As we advance in our scale up and commercial scale process development, we also seek to improve production output through improvements in strain productivity, the rate at which our product is produced by a given yeast strain, and titer, the concentration of product in the fermentation broth. In addition, we seek to develop processes to improve production recovery efficiency, including separation efficiency, which is the amount of product that is captured from a fermentation run, cycle-time, which is the time needed to run a full fermentation cycle, and the evolution of batch process methods to semi-continuous and continuous production methods.

Moving production from lab to commercial scale. Once we have established a pathway and verified that it can produce the target molecule, the yeast strain must be improved to increase the level of efficiency of production. We design our lab scale two-liter fermenters to mimic the conditions found in larger scale fermentation so that our findings may translate predictably from lab scale to pilot, demonstration and commercial scale. In addition to our lab scale fermenters, we have operating pilot plants in our facilities in Emeryville, California and Campinas, Brazil, as well as two 5,000-liter fermenters in our Campinas demonstration facility. To date, most of our efforts have focused on developing yeast strains to produce Biofene and, to a lesser extent, flavors and fragrances, with significant development efforts devoted to chemical synthesis of other products from Biofene. Though our technology platform allows us to develop yeast strains engineered to produce other target molecules, we expect to continue focusing most of our strain-engineering efforts on Biofene production and, to a lesser extent, selected specialty chemical ingredients, for the foreseeable future.

Our Industrial Production

Our industrial production operations generally involve two major steps. First, we produce a target molecule by means of an industrial fermentation process. In some cases this target molecule is itself the desired end product. In other cases, it must be converted into the desired end product by a second step where we use chemical synthesis of the initial target molecule to produce a final target molecule.

Commercial Production of Target Fermentation Molecules

We have initiated commercial production of Biofene, our initial fermentation molecule, at our purpose-built, large-scale Biofene production plant in Brotas, in the State of São Paulo, Brazil. Our Biofene production plant in Brotas is adjacent to an existing sugar and ethanol mill, Paraíso Bioenergia. Under our agreement with Paraíso Bioenergia S.A., or Paraíso Bioenergia, they will supply sugarcane juice and other utilities and we were responsible for construction (which commenced in August 2011) and operation of our Biofene production facility. Our Biofene production plant has six 200,000 liter production fermenters and was designed to process sugarcane juice, or its equivalent, from up to one million tons of raw sugarcane annually. In December 2012, following a successful commissioning phase, we began production of Biofene at the facility. Our first shipment of Biofene produced at the facility occurred on February 1, 2013.

Prior to operating our own facility, we relied on multiple contract manufacturing facilities in the U.S., Brazil and Spain, which used 100,000 to 240,000 liter fermenters and multiple kinds of feedstock.

We have also advanced initial construction of a second large-scale production plant in Brazil, located at the Usina São Martinho sugar and ethanol mill also in the state of São Paulo, which we intend to complete when production economics support start-up of that plant. We entered into agreements with Usina São Martinho S.A., or Usina São Martinho, a subsidiary of São

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Martinho S.A., to establish the facility at Usina São Martinho, and the plant is being built by a joint venture (SMA Indústria Química S.A., or SMA). We formed SMA in 2010, and commenced site preparation in December 2010 and civil construction in February 2011. In early 2012, we suspended construction at SMA pending completion and operation of our Brotas facility. The SMA plant is intended to provide a large-scale production facility to support our longer-term production plans.

Following the completion of our SMA plant, we expect to seek to expand our large-scale production capacity of intermediate molecules by entering into agreements with owners of additional sugar and ethanol mills in Brazil.

Chemical Finishing Process

In some cases, we perform additional chemical finishing steps to convert initial target molecules into other finished products, such as renewable squalane, lubricants, polymers and diesel. We have established an agreement with Glycotech Inc., or Glycotech, for use of the Leland, North Carolina facility of Salisbury Partners, LLC to convert Biofene into squalane and other final products. We expect to enter into additional agreements with other chemical companies for finishing services to access flexible capacity and an array of services as we develop additional products.

Our Products

We are focused on developing a broad range of products to address six identified markets: cosmetics, lubricants, flavors and fragrances, polymers, consumer products and transportation fuels.

Cosmetics

Through simple chemical finishing steps, we are able to convert Biofene into squalane. Squalane is used today as a moisturizing ingredient in cosmetics and other personal care products. Squalane traditionally has been manufactured from olive oil or extracted from shark liver oil. We believe Amyris-produced squalane offers a purity that is equal or superior to squalane derived from conventional sources. The relatively high price of squalane to date has meant that its use has been limited to small quantities in mass-market product formulations or to use in luxury products. We believe that we are capable of producing squalane at a price that would permit formulators to use squalane more broadly. To initially market and distribute squalane, we established a relationship with Soliance, a leading distributor of renewable cosmetics ingredients based in the Champagne-Ardenne region in France. We also have agreements with Nikko Chemicals Co. Ltd., or Nikko, a distributor in Japan, and Centerchem, Inc., or Centerchem, a distributor in North America. We anticipate identifying additional distributors in 2013.

Lubricants

Base oils are the building blocks of lubricating oils and are currently derived from the crude oil refining process. Additives are materials added to base oils to change their properties, characteristics, or performance (e.g., anti-foam, anti-wear, corrosion inhibitor, detergent, dispersant, pour point depressant, anti-oxidant, or friction modifier). Lubricants are manufactured by combining a base oil with additives required by lubricant product applications, including engine oils, gear oils, hydraulic oils and turbine oils. Biofene may be chemically modified to serve as a base oil, additive, and/or lubricant. We believe the high-purity, synthetic base oil and additive molecules that can be made from Biofene could enable lubricant products to perform in harsh environments under extremes of temperature, moisture, dirt and wear.

In December 2010, we entered into an agreement with Cosan and its affiliates to establish a joint venture for the worldwide development, production and commercialization of renewable base oils for the automotive, industrial and commercial lubricants markets. In March 2013, we expanded this collaboration to also include additives and lubricants for the automotive, industrial and commercial lubricants markets. The joint venture is operated through Novvi LLC. We anticipate that Novvi LLC will source Biofene for its products initially from Amyris production facilities, and Amyris and Cosan, as co-owners of Novvi LLC, would share its development, marketing and operating costs.

Flavors and Fragrances

We believe we are well situated to cost-effectively and sustainably produce natural oils and aroma chemicals that are commonly used in the flavors and fragrances market. Many of the natural ingredients used in flavors and fragrances market are expensive because there is limited supply and the synthetic alternatives require complex chemical conversions. Amyris intends to offer flavors and fragrances companies a natural route to procure these ingredients without sacrificing cost or quality.

Currently, we are working with partners to develop a variety of flavors and fragrances ingredients that are either direct fermentation target molecules or derivatives of fermentation target molecules.

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We plan to participate in the flavors and fragrance market by providing sustainable replacements that are high quality, reliably available, and competitively priced. To begin to develop our product offerings in this area, we have established the following partnerships:

• A collaboration and joint development arrangement with Firmenich, a global flavors and fragrances company headquartered in Geneva, Switzerland. Under a March 2013 master collaboration agreement (which superseded prior arrangements with Firmenich), we will research and develop flavors and fragrances compounds and grant Firmenich exclusive access to such compounds in exchange for research and development funding and a profit sharing arrangement. The new agreement superseded and expanded a prior collaboration agreement with Firmenich for joint development and commercialization of specific ingredients within the flavors and fragrances field.

• A co-development agreement with Givaudan, a global flavors and fragrance company headquartered in Vernier, Switzerland. Under the agreement, we will develop a derivative of Biofene to be used as a building block for one of the proprietary fragrance ingredients in Givaudan's portfolio. Under the agreement, upon achievement of certain success criteria, we would supply Biofene to Givaudan to derive the proprietary ingredient for the global fragrances and flavors market and share in the economic value created from the use of Biofene.

Polymers and Plastic Additives

Synthetic polymers are commonly used in the manufacture of thousands of products that incorporate plastics and other polymeric materials, and we believe Biofene has the potential to provide significant opportunities for development of renewable products for the polymer market.

In July 2011, we entered into a collaboration agreement with Kuraray to develop polymers from Biofene. Under the agreement, Kuraray will use Biofene to replace petroleum-derived molecules such as butadiene and isoprene in the production of specified classes of high-performing polymers. Upon successful completion of the technical development program for the first polymer, Amyris and Kuraray would enter into a supply agreement for Kuraray's exclusive use of Biofene in the manufacturing and commercialization of these polymer products.

Home & Personal Care Products

Biofene also offers a platform for development of sustainable, high-performing and cost-competitive ingredients for the fabric and home care (such as detergents, fabric softener, dish soap, and household cleaning products) and the personal care (such as hair care and body care) markets. We have entered into some evaluation and collaboration agreements with certain producers of home and personal care products to explore opportunities in these markets.

Transportation Fuels

We have selected diesel as our primary area of focus within the transportation fuels market because of its projected global demand growth, the lack of a scalable, competitive renewable product, and our belief that our fuel product has properties superior to those of existing renewable alternatives. In general, we will produce our renewable diesel by the simple chemical step of hydrogenating our Biofene. Hydrogenation is a common chemical process currently used in the production of numerous products, such as saturation of vegetable oils to make margarine.

In July 2011, we entered into an agreement with Petrobras Distribuidora S.A., or Petrobras, to sell diesel derived from Biofene to Petrobras to blend with fuel supplied and distributed by Petrobras to city bus fleets of São Paulo and Rio de Janeiro, Brazil. In November 2011 and July 2012, we entered into amendments of our technology license, development, research and collaboration agreement with Total to establish a renewable diesel development program as described in more detail below under "Total Collaboration Products."

We have completed significant steps to validate our ability to produce a market-accepted diesel product. By design, our product is a hydrocarbon of similar size to many of the hydrocarbons in petroleum-sourced diesel fuel. Due to the similarity of its chemical composition to that of existing petroleum-sourced diesel, our product has the properties required of diesel fuel and thereby satisfies the ASTM D975 Table 1 specifications for petroleum-derived diesel fuel oils. The Environmental Protection Agency, or EPA, has registered our diesel for use as a 35% blend with petroleum diesel in highway vehicles and non-road equipment and we are working to obtain registration for a higher blend with petroleum diesel, as opposed to the typical 3-10% blend of other bio-diesel products with petroleum diesel. We have received required approvals with Brazilian ANP (Agência Nacional do Petróleo,

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Gas Natural e Biocombustíveis) for specific uses of our fuel in the country, and are pursuing Diesel Fuel registration with the CARB (California Air Resources Board) and other relevant regulatory bodies.

Our ability to enter the diesel market is also dependent upon our ability to continue to achieve the required regulatory approvals in the global markets in which we will seek to sell our diesel products. These approvals primarily involve clearance by the relevant environmental agencies in the particular jurisdiction. We must also be certified by a sufficient number of diesel engine manufacturers, vehicle manufacturers or operators of large trucking fleets so that our diesel will have an appropriately large and accessible addressable market. These certification processes include fuel analysis modeling and the testing of engines and their components to ensure that the use of our diesel fuel does not degrade performance or reduce the lifecycle of the engine or cause it to fail to meet emissions standards.

We have completed successful engine testing of our diesel fuel with Cummins Engine Company, or Cummins, and Mercedes-Benz Brasil at a blend of up to 10%, and our renewable diesel has received OEM engine warranties from Cummins, Volkswagen AG and Mercedes-Benz Brasil for demonstration purposes. We continue to work with other diesel engine manufacturers to qualify our product for use in their engines.

Total Collaboration Products

We have a license, development, research and collaboration agreement with Total that sets forth the terms for the research, development, production and commercialization of chemical and/or fuels products to be agreed on by the parties. The agreement establishes a multi-phased process through which compounds are identified, screened, selected for product feasibility study, and then ultimately selected as a lead compound for development. To commercialize any strains and compounds that are developed, Amyris and Total expect to form one or more joint ventures, the first of which we expect will be the fuels joint venture described below. Both Amyris and Total retain certain rights to make covered products independently subject to making royalty payments to the non-producing party, and Total has certain rights to require Amyris to work on non-collaboration projects. We have retained rights to produce and commercialize products in the following markets: flavors and fragrances; cosmetics, pharmaceuticals, consumer packaged goods, food additives, and pesticides. The first programs we are focusing on with Total relate to renewable diesel and jet fuel and industrial lubricants; however, we and Total retain the right to propose product development programs under these agreements in the future.

In November 2011, we entered into an amendment of the collaboration agreement with Total with respect to development and commercialization of Biofene for diesel. This represented an expansion of the initial collaboration that the parties established in 2010, and established a global, exclusive collaboration for the development of Biofene for diesel and a framework for the creation of a joint venture to manufacture and commercialize Biofene for diesel. In addition, a limited number of other potential products were subject to development for the joint venture on a non-exclusive basis. In July 2012, we entered into a further amendment of the collaboration agreement with Total that expanded Total's investment in the Biofene collaboration, incorporated the development of certain joint venture products for use in diesel and jet fuel into the scope of the collaboration, and changed the structure of the funding from Total to include a convertible debt mechanism.

Product Distribution and Sales

We intend to distribute and sell our products either directly, through joint ventures, or with partners, depending on the market. For most chemical applications, we intend to sell directly to specialty chemical and consumer products companies. For example, we would expect to sell directly to Firmenich, Givaudan, Kuraray, M&G, Method and Michelin under our agreements with them. Generally, our collaboration agreements such as these do not include any specific purchase obligations, and sales are contingent upon achievement of technical and commercial milestones. In addition, we expect to commercialize certain products, including fuels and base oils through joint venture arrangements with Total and Cosan, respectively.

Commencing in 2008, we began developing a fuels distribution network and distribution capabilities in the U.S. through Amyris Fuels. Through mid-2012, we purchased ethanol produced by third parties and gasoline and sold both pure ethanol and reformulated ethanol-blended gasoline to wholesale customers. For 2012, Mansfield Oil Company accounted for more than 10% of our reported revenues by virtue of its purchases of ethanol and reformulated ethanol-blended gasoline from Amyris Fuels. Collaboration revenues from Total also accounted for more than 10% of our reported revenues in 2012. Customers purchased ethanol and ethanol-blended gasoline from us under short-term agreements and spot transactions, and we generally did not have any contractual commitments from customers to purchase ethanol and ethanol-blended gasoline from us over any period of time.

Nearly all of our customer revenue through the third quarter of 2012 came from the sale of ethanol and reformulated ethanol-blended gasoline, with the remainder of our revenues coming from collaborations and government grants and, more recently, sales of our renewable products. In the third quarter of 2012, we transitioned out of the ethanol and ethanol-blended gasoline

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business. We do not expect to be able to replace much of the revenue lost as a result of this transition, particularly in 2013, while we continue our efforts to establish a renewable products business.

Intellectual Property

Our success depends in large part upon our ability to obtain and maintain proprietary protection for our products and technologies, and to operate without infringing the proprietary rights of others. We seek to avoid the latter by monitoring patents and publications in our product areas and technologies to be aware of developments that may affect our business, and to the extent we identify such developments, evaluate and take appropriate courses of action. With respect to the former, our policy is to protect our proprietary position by, among other methods, filing for patent applications on inventions that are important to the development and conduct of our business with the U.S. Patent and Trademark Office, or the USPTO, and its foreign counterparts.

As of March 1, 2013, we had 202 issued U.S. and foreign patents and 302 pending U.S. and foreign patent applications that are owned by or licensed to us.We also use other forms of protection (such as trademark, copyright, and trade secret) to protect our intellectual property, particularly where we do not believe patent protection is appropriate or obtainable. We aim to take advantage of all of the intellectual property rights that are available to us and believe that this comprehensive approach provides us with a strong proprietary position.

We have obtained patents for various fuel products: U.S. Patent No. 7,399,323 directed to our renewable diesel fuel composition; U.S. Patent No. 7,540,888 directed to our renewable gasoline fuel composition; and U.S. Patents No. 7,589,243 and No. 7,671,245, which are directed to our renewable jet products. Since obtaining our fuels patents, we have expanded the use of this program to our chemicals portfolio and have recently obtained U.S. Patent Nos. 7,592,295 and 7,691,792 for our lubricant products, and U.S. Patent Nos. 7,655,739 and 7,759,444 for our adhesive and polymer products.

Patents extend for varying periods according to the date of patent filing or grant and the legal term of patents in various countries where patent protection is obtained. The actual protection afforded by patent, which can vary from country to country, depends on the type of patent, the scope of its coverage and the availability of legal remedies in the country. See “Risk Factors-Risks Relating to Our Business-Our proprietary rights may not adequately protect our technologies and product candidates.”

We also protect our proprietary information by requiring our employees, consultants, contractors and other advisers to execute nondisclosure and assignment of invention agreements upon commencement of their respective employment or engagement. Agreements with our employees also prevent them from bringing the proprietary rights of third parties to us. In addition, we also require confidentiality or material transfer agreements from third parties that receive our confidential data or materials.

Competition

We expect that our renewable products will compete with both the traditional, largely petroleum-based specialty chemical and fuels products that are currently being used in our target markets and with the alternatives to these existing products that established enterprises and new companies are seeking to produce.

Chemical Products

In the specialty chemical markets that we are initially seeking to enter, and in other chemical markets that we may seek to enter in the future, we will compete with the established providers of chemicals currently used in these products. Producers of these incumbent products include global oil companies, large international chemical companies and companies specializing in specific products, such as squalane or essential oils. We may also compete in one or more of these markets with products that are offered as alternatives to the traditional petroleum-based or other traditional products being offered in these markets.

Transportation Fuel Products

In the transportation fuels market, we expect to compete with independent and integrated oil refiners, advanced biofuels companies and biodiesel companies. Refiners compete with us by selling traditional fuel products and some are also pursuing hydrocarbon fuel production using non-renewable feedstocks, such as natural gas and coal, as well as processes using renewable feedstocks, such as vegetable oil and biomass. We also expect to compete with companies that are developing the capacity to produce diesel and other transportation fuels from renewable resources in other ways. These include advanced biofuels companies using specific enzymes that they have developed to convert cellulosic biomass, which is non-food plant material such as wood chips, corn stalks and sugarcane bagasse, into fermentable sugars. Similar to us, some companies are seeking to use engineered enzymes to convert sugars, in some cases from cellulosic biomass and in others from natural sugar sources, into renewable diesel

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and other fuels. Biodiesel companies convert vegetable oils and animal oils into diesel fuel and some are seeking to produce diesel and other transportation fuels using thermochemical methods to convert biomass into renewable fuels.

With the emergence of many new companies seeking to produce chemicals and fuels from alternative sources, we may face increasing competition from alternative fuels and chemicals companies. As they emerge, some of these companies may be able to establish production capacity and commercial partnerships to compete with us.

Competitive Factors

We believe the primary competitive factors in both the chemicals and fuels markets are:

• product price;

• product performance and other measures of quality;

• infrastructure compatibility of products;

• sustainability; and

• dependability of supply.

We believe that for our chemical products to succeed in the market, we must demonstrate that our products are comparable alternatives to existing products and to any alternative products that are being developed for the same markets based on some combination of product cost, availability, performance, and consumer preference characteristics. With respect to our diesel and other transportation fuels products, we believe that our product must perform as effectively as petroleum-based fuel, or alternative fuels, and be available on a cost-competitive basis. In addition, with the wide range of renewable fuels products under development, we must be successful in reaching potential customers and convincing them that ours are effective and reliable alternatives.

Environmental and Other Regulatory Matters

Our development and production processes involve the use, generation, handling, storage, transportation and disposal of hazardous chemicals and radioactive and biological materials. We are subject to a variety of federal, state, local and international laws, regulations and permit requirements governing the use, generation, manufacture, transportation, storage, handling and disposal of these materials in the U.S., Brazil and other countries where we operate or may operate or sell our products in the future. These laws, regulations and permits can require expensive fees, pollution control equipment or operational changes to limit actual or potential impact of our technology on the environment and violation of these laws could result in significant fines, civil sanctions, permit revocation or costs from environmental remediation. We believe we are currently in substantial compliance with applicable environmental regulations and permitting. However, future developments including our commencement of commercial manufacturing of one or more of our products, more stringent environmental regulation, policies and enforcement, the implementation of new laws and regulations or the discovery of unknown environmental conditions may require expenditures that could have a material adverse effect on our business, results of operations or financial condition. See “Risk Factors-Risks Relating to Our Business-We may incur significant costs complying with environmental laws and regulations, and failure to comply with these laws and regulations could expose us to significant liabilities.”

The use of genetically-modified microorganisms, or GMMs, such as our yeast strains, is subject to laws and regulations in many countries. In the U.S., the EPA regulates the commercial use of GMMs as well as potential products produced from the GMMs. Various states within the U.S. could choose to regulate products made with GMMs as well. While the strain of genetically modified yeast that we use, S. cerevisiae, is eligible for exemption from EPA review because the EPA recognizes it as posing a low risk we must satisfy certain criteria to achieve this exemption, including but not limited to use of compliant containment structures and safety procedures. In Brazil, GMMs are regulated by CTNBio under its Biosafety Law No. 11.105-2005. We have obtained approval from CTNBio to generally use GMMs under specific conditions in our Campinas facilities and our production plant in Brotas for research and development purposes. In addition, we have received CTNBio approval for commercial use of a specific strain in our Brotas plant.

We expect to encounter GMM regulations in most if not all of the countries in which we may seek to make our products, however, the scope and nature of these regulations will likely be different from country to country. If we cannot meet the applicable requirements in countries in which we intend to produce our products using our yeast strains, then our business will be adversely affected. See “Risk Factors-Risks Related to Our Business-Our use of genetically-modified feedstocks and yeast strains to produce our products subjects us to risks of regulatory limitations and rejection of our products.”

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Our renewable chemical products may be subject to regulation by government agencies in our target markets. The EPA administers the requirements of the Toxic Substances Control Act, or the TSCA, which regulates the commercial use of chemicals. Before an entity can manufacture a chemical, it needs to determine whether that chemical is listed in the TSCA inventory. If the substance is listed, then manufacture can commence immediately. If not, then in most cases a “Chemical Abstracts Service” number registration and pre-manufacture notice must be filed with the EPA, which has up to 180 days to review the filing.

Our diesel fuel is subject to regulation by various government agencies. In the U.S., this includes the EPA and the CARB. In Brazil, this includes ANP. To date we have obtained registration with the EPA for the use of our diesel in the U.S. at a 35% blend rate with petroleum diesel. In addition, ANP has authorized the use of our diesel fuel at blend rates of 10% and 30% for specific bus fleets. We are also currently in the process of registering our fuel with the CARB and the European Commission. Registration with each of these bodies is required for the sale and use of our fuels within their respective jurisdictions. In addition, for us to achieve full access to the U.S. fuels market for our fuel products, we will need to obtain EPA and CARB (and potentially other state agencies) certifications for our feedstock pathway and production facility, including certification of a feedstock lifecycle analysis relating to greenhouse gas emissions. Any delay in obtaining these additional certifications could impair our ability to sell our renewable fuels to refiners, importers, blenders and other parties that produce transportation fuels as they comply with federal and state requirements to include certified renewable fuels in their products. See “Risk Factors-Risks Relating to Our Business-We may not be able to obtain regulatory approval for the sale of our renewable products.”

Amyris Fuels is subject to various U.S. federal regulations relating to its marketing and distribution of ethanol and ethanol-blended gasoline, and it is registered with the EPA in connection with its use of ethanol as a fuel additive. In addition, Amyris Fuels is subject to various state regulations, including regulations regarding excise tax payments and the posting of surety bonds.

Research and Development

We devote substantial resources to our research and development efforts. As of March 1, 2013, our research and development organization included approximately 209 employees, 63 of whom held Ph.D.s.Our technology development is currently focused primarily on improving the performance of our production strains and on developing strains that produce new molecules. To facilitate the transfer of our fermentation technology to production, we operate pilot-scale fermentation facilities in both Emeryville, California and Campinas, Brazil, and transfer strains on a regular basis. Our process consists of a number of discrete steps including:

• identifying new target molecules

• creating new microbial strains capable of producing the target molecule

• increasing product yield and productivity from microbial strains through strain modification or fermentation improvements

• increasing efficiency of product separation and purification

• continuous translation of these steps from lab to commercial scale production.

Our research and development expenditures were approximately $73.6 million, $87.3 million, and $55.2 million and for the fiscal years ended December 31, 2012, 2011 and 2010, respectively.

Employees

As of March 1, 2013, we had 397 full-time employees. Of these employees, 254 were in the U.S. and 143 were in Brazil.Except for labor union representation for Brazil-based employees based on labor code requirements in Brazil, none of our employees is represented by a labor union or is covered by a collective bargaining agreement. We have never experienced any employment-related work stoppages and consider relations with our employees to be good.

Financial Information About Geographic Areas

Financial information regarding revenues and long-lived assets by geographic area is included in Note 17 "Reporting Segments” in “Notes to Consolidated Financial Statements” included in this Form 10-K.

Business Background and Available Information

We organized our business in July 2003 as a California corporation under the name Amyris Biotechnologies, Inc. and have maintained our headquarters and research facilities in the San Francisco Bay Area since that time. In June 2010, we reincorporated

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in Delaware and changed our name to Amyris, Inc. We commenced research activities in 2005, focusing on the development of an alternative source of artemisinic acid for the treatment of malaria and launched research efforts for production of Biofene in 2006. In 2008, we began to sell third party ethanol to wholesale customers through our Amyris Fuels subsidiary. In the third quarter of 2012, we transitioned out of the ethanol and reformulated ethanol-blended gasoline business, though we continue to maintain the Amyris Fuels subsidiary for activities related to renewable fuel sales. We first established a presence in Brazil in 2008 through the opening of laboratories in Campinas. Our corporate headquarters are located at 5885 Hollis Street, Suite 100, Emeryville, CA 94608, and our telephone number is (510) 450-0761. Our website address is www.amyris.com. The information contained in or accessible through our website or contained on other websites is not deemed to be part of this report on Form 10-K.

We are subject to the filing requirements of the Securities Exchange Act of 1934. Therefore, we file periodic reports, proxy statements and other information with the Securities and Exchange Commission. Such reports, proxy statements and other information may be obtained by visiting the Public Reference Room of the Securities and Exchange Commission at 100 F Street, NE, Washington, D.C. 20549. You may obtain information regarding the operation of the Public Reference Room by calling the Securities and Exchange Commission at 1-800-SEC-0330. In addition, the Securities and Exchange Commission maintains a website (www.sec.gov) that contains reports, proxy and information statements, and other information regarding issuers that file electronically.

We make our annual reports on Form 10-K, quarterly reports on Form 10-Q, current reports on Form 8-K and all amendments to such reports filed or furnished pursuant to Section 13(a) or 15(d) of the Securities Exchange Act of 1934 available free of charge through a link on the Investors section of our website located at www.amyris.com (under “Financial Information-SEC Filings”) as soon as reasonably practicable after they are filed with or furnished to the Securities and Exchange Commission.

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ITEM 1A. RISK FACTORS

Investing in our common stock involves a high degree of risk. You should carefully consider the risks and uncertainties described below, together with all of the other information set forth in this Annual Report on Form 10-K, which could materially affect our business, financial condition or future results. If any of the following risks actually occurs, our business, financial condition, results of operations and future prospects could be materially and adversely harmed. The trading price of our common stock could decline due to any of these risks, and, as a result, you may lose all or part of your investment.

Risks Related to Our Business

We have incurred losses to date, anticipate continuing to incur losses in the future and may never achieve or sustain profitability.

We have incurred significant losses in each year since our inception and believe that we will continue to incur losses and negative cash flow from operations into at least 2014. As of December 31, 2012, we had an accumulated deficit of $586.3 million and had cash, cash equivalents and short term investments of $30.7 million. We have significant outstanding debt and contractual obligations related to purchase commitments, as well as capital and operating leases. As of December 31, 2012, our debt totaled $104.2 million, of which $3.3 million matures within the next twelve months. In addition, our debt agreements contain various covenants, including restrictions on business that could cause us to be at risk of defaults. We expect to incur additional costs and expenses related to the continued development and expansion of our business, including construction and operation of our manufacturing facilities, our research and development operations, continued operation of our pilot plants and demonstration facility, and engineering and design work. Further, we expect to incur costs related to contract manufacturing arrangements. There can be no assurance that we will ever achieve or sustain profitability on a quarterly or annual basis.

We have limited experience producing our products at commercial scale and may not be able to commercialize our products to the extent necessary to sustain and grow our current business.

To commercialize our products, we must be successful in using our yeast strains to produce target molecules at commercial scale and at a commercially viable cost. Such production will require that our technology and processes be scaled from laboratory, pilot and demonstration projects to commercial-scale production. If we cannot achieve commercially-viable production economics, we will be unable to achieve a sustainable integrated renewable products business. Most of our commercial manufacturing experience to date has been at contract manufacturing facilities. For the future, we are focused on developing most of our production capacity through purpose-built, large-scale production plants in Brazil, which is a time-consuming, costly, uncertain and expensive process. Given our limited experience commissioning and operating our own manufacturing facilities and our limited financial resources, we cannot be sure that we will be successful in commissioning and scaling up production at these larger-scale plants, either in a timely manner or with production economics that allow us to meet our plans for commercialization. Even to the extent we successfully complete product development in our laboratories and pilot and demonstration facilities, and at contract manufacturing facilities, we may be unable to translate such success to large-scale, purpose-built plants. If this occurs, our ability to commercialize our technology will be adversely affected and we may be unable to produce and sell any significant volumes of our products. Also, with respect to products that we are able to bring to market, we may not be able to lower the cost of production, which would adversely affect our ability to sell such products profitably.

We will require additional financing to fund our anticipated operations and may not be able to obtain such financing on favorable terms, if at all.

Our planned 2013 working capital needs and our planned operating and capital expenditures for 2013 are dependent on significant inflows of cash from existing collaboration partners, as well as additional funding from new collaborations, equity or debt offerings, credit facilities or loans, or combinations of these sources. We will continue to need to fund our research and development and related activities and to provide working capital to fund production, storage, distribution and other aspects of its business. Our operating plan contemplates capital expenditures of approximately $10.0 million in 2013 and we expect to continue to incur costs in connection with our existing contract manufacturing arrangements. Furthermore, we are expecting additional funding in 2013 from collaborations, equity or debt offerings, or combinations of these sources. Our operating plan contemplates securing a portion of this additional funding in the second quarter of 2013. However, as of the date of this filing, we have not yet secured this additional funding and there can be no assurance that financing will be available on commercially acceptable terms or at all. For example, some of our existing anticipated financing sources, such as research and development collaborations, are subject to risk that we cannot meet milestones or are not yet subject to definitive agreements or mandatory

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funding commitments and we may not be able to secure additional equity or debt financing in a timely manner or on reasonable terms, if at all.

If we seek additional types of funding that involve the issuance of equity securities, our existing stockholders would suffer dilution. For example, in 2012, we completed private placements of our common stock that resulted in the issuance of approximately 26.1 million shares of our common stock of which approximately 5.0 million shares were issued in January 2013 following receipt of proceeds. We also issued approximately $78.3 million in unsecured senior convertible promissory notes that are convertible into common stock at an initial conversion price of $7.0682 per share. Through 2015, we expect to issue up to an aggregate of $51.7 million in additional unsecured senior convertible promissory notes under the agreements with Total described below under the caption, “Our relationship with our strategic partner, Total, may have a substantial impact on our company.” In addition to dilution, to the extent we issue convertible promissory notes and similar instruments, we would become subject to various covenants, including restrictions on our business, that could cause us to be at risk of defaults. For example, the convertible notes we issued in 2012 contained various covenants, including restrictions on the amount of debt we are permitted to incur.

If we are unable to raise additional financing, or if other expected sources of funding are delayed or not received, we would take the following actions as early as the second quarter of 2013 to support our liquidity needs through the remainder of 2013 and into 2014:

• Effect significant headcount reductions in the U.S. and in Brazil, particularly with respect to both general and administrative employees and other employees not connected to critical or contracted activities.

• Shift our focus to existing products and customers with significantly reduced investment in new product and commercial development efforts.

• Reduce our expenditures for third party contractors, including consultants, professional advisors and other vendors.

• Suspend operations at our pilot plants and demonstration facilities.

• Reduce or delay uncommitted capital expenditures, including non-essential lab equipment and information technology projects.

The contingency cash plan contemplating these actions is designed to save us an estimated $35 million to $40 million over the next twelve months. Implementing this plan could have a material negative impact on our ability to continue our business as currently contemplated, including, without limitation, delays or failures in our ability to:

• Achieve planned production levels;

• Develop and commercialize products within planned timelines or at planned scales; and

• Continue other core activities.

Furthermore, any inability to scale-back operations as necessary, and any unexpected liquidity needs, could create pressure to implement more severe measures. Such measures could have a material adverse effect on our ability to meet contractual requirements, including obligations to maintain manufacturing operations, and increase the severity of the consequences described above. We also may be forced to seek funding on terms that are not favorable to us. For example, in order to raise sufficient funds, we could be forced to issue preferred and discounted equity, agree to onerous covenants, grant security interests in our assets, enter into collaboration and licensing arrangements that require us to relinquish commercial rights or grant licenses on terms that are not favorable to us, or any or all of these.

If our major production facilities do not successfully commence operations, our customer relationships, business and results of operations may be adversely affected.

A substantial component of our planned production capacity in the near and long term depends on successful operations at our initial and planned large-scale production plants in Brazil. We are in the early stages of operating our first purpose-built, large-scale production plant in Brotas and may complete construction of certain other facilities in the coming years. Delays or problems in the construction, start-up or operation of these facilities will cause delays in our ramp-up of production and hamper our ability to reduce our production costs. Delays in construction can occur due to a variety of factors, including regulatory requirements and our ability to fund construction and commissioning costs. Once our large-scale production facilities are built, we must successfully commission them and they must perform as we have designed them. If we encounter significant delays, cost overruns, engineering

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issues, contamination problems, equipment supply constraints or other serious challenges in bringing these facilities online and operating them at commercial scale, we may be unable to produce our initial renewable products in the time frame we have planned. We may also need to continue to use contract manufacturing sources more than we expect, which would reduce our anticipated gross margins and may prevent us from accessing certain markets for our products. Further, if our efforts to complete and commence production at these facilities are not successful, other mill owners in Brazil may decide not to work with us to develop additional production facilities, demand more favorable terms or delay their commitment to invest capital in our production.

Our reliance on the large-scale production plant in Brotas subjects us to execution and economic risks.

Our decision to focus our efforts for production capacity on the manufacturing facility in Brotas means that we will have limited manufacturing sources for our products in 2013 and beyond. Accordingly, any failure to establish operations at that plant could have a significant negative impact on our business, including our ability to achieve commercial viability for our products. Construction and commissioning of the plant in Brotas was recently completed, and we cannot be sure that we will be able to successfully scale up and operate the plant at levels sufficient to supply farnesene previously produced at contract manufacturing facilities. Furthermore, while we are moving our production focus to our plant in Brotas based on an expectation that we will ultimately be able to produce farnesene at a lower cost using such facility, we cannot be sure when, or if, using such plant will in fact result in such lower production costs than contract manufacturing facilities. Also, with the facility in Brotas, we will, for the first time, be the operator of a commercial fermentation and separation facility. We are inexperienced at operating plants and may face unexpected difficulties associated with the operation of the plant. For example, we have in the past, at certain contract manufacturing facilities, encountered significant delays and difficulties in ramping up production based on contamination in the production process, problems with plant utilities, lack of automation and related human error, issues arising from process modifications to reduce costs and adjust product specifications, and other similar challenges. Such challenges could arise in our plant in Brotas, and we cannot be certain that we will be able to remedy them quickly or effectively enough to achieve commercially viable near-term production costs and volumes.

As part of our arrangement to build the plant in Brotas, we have an agreement with Paraíso Bioenergia to purchase from Paraíso Bioenergia sugarcane juice corresponding to a certain number of tons of sugarcane per year, along with specified water and vapor volumes. Until this annual volume is reached, we are restricted from purchasing sugarcane juice for processing in the facility from any third party, subject to limited exceptions, unless we pay the premium to Paraíso Bioenergia that we would have paid if we bought the juice from them. As such, we will be relying on Paraíso Bioenergia to supply such juice and utilities on a timely basis, in the volumes we need, and at competitive prices. If a third party can offer superior prices and Paraíso Bioenergia does not consent to our purchasing from such third party, we would be required to pay Paraíso Bioenergia the applicable premium, which would have a negative impact on our production cost. Furthermore, we agreed to pay a price for the juice that is based on the lower of the cost of two other products produced by Paraíso Bioenergia using such juice, plus a premium. Paraíso Bioenergia may not want to sell sugarcane juice to us if the price of one of the other products is substantially higher than the one setting the price for the juice we purchase. While the agreement provides that Paraíso Bioenergia would have to pay a penalty to us if it fails to supply the agreed-upon volume of juice for a given month, the penalty may not be enough to compensate us for the increased cost if third-party suppliers do not offer competitive prices. Also, if the prices of the other products produced by Paraíso Bioenergia increase, we could be forced to pay those increased prices for production without a related increase in the price at which we can sell our products, reducing or eliminating any margins we can otherwise achieve. If in the future these supply terms no longer provide a viable economic structure for the operation in Brotas, we may be required to renegotiate our agreement, which could result in manufacturing disruptions and delays.

Our joint venture with UsinaSão Martinho subjects us to certain legal and financial terms that could adversely affect us.

We have various agreements with Usina São Martinho that contemplate construction of another large-scale manufacturing facility in Brazil. Under these agreements, we are responsible for designing and managing the construction project, and are responsible for the initial construction costs. We projected the construction costs of the project to be approximately US$100 million. While we completed a significant portion of the construction of the plant before 2012, we delayed further construction and commissioning of the plant while we constructed and commissioned our production plant in Brotas, and we expect to continue to defer the project for the near term based on economic considerations and to allow us to focus on successful implementation at our production plant in Brotas. While Usina São Martinho was obligated to contribute up to approximately R$61.8 million (approximately US$30.2 million based on the exchange rate as of December 31, 2012) to the construction of the plant, such contributions depended on, among other things, successful commencement of operations at the plant. Based on our shifting manufacturing priorities and uncertainty regarding financing availability, we cannot currently predict when or if our facility at Usina São Martinho will be completed or commence commercial operations, which means that Usina São Martinho's anticipated contribution will be delayed and may never occur. Under our existing agreement with Usina São Martinho, if the joint venture fails to commence operations by the end of 2013, Usina São Martinho has the right to terminate the joint venture and to require us to buy Usina São Martinho's equity in the joint venture at its acquisition cost, and transfer the joint venture's assets at the Usina

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São Martinho site to another location. In that event, we would incur significant costs and be required to find alternative locations for the facility. In March 2013, we met with Usina São Martinho and the parties agreed in principle to a revised business plan for the joint venture with the plant becoming operational in 2016, and, while we are in the process of documenting that revised business plan as an amendment to the agreement, we may not be able to reach final agreement on the revised terms. In addition, if Amyris Brasil becomes controlled, directly or indirectly, by a competitor of Usina São Martinho, then Usina São Martinho has the right to acquire our interest in the joint venture and if Usina São Martinho becomes controlled, directly or indirectly, by a competitor of ours, then we have the right to sell our interest in the joint venture to Usina São Martinho. In either case, the purchase price is to be determined in accordance with the joint venture agreements, and we would continue to have the obligation to acquire products produced by the joint venture for the remainder of the term of the supply agreement then in effect even though we might no longer be involved in the joint venture's management.

If we are ultimately successful in establishing the plant at Usina São Martinho, the agreements governing the joint venture subject us to terms that may not be favorable to us under certain conditions. For example, we are required to purchase the output of the joint venture for the first four years at a price that guarantees the return of Usina São Martinho's investment plus a fixed interest rate. We may not be able to sell the output at a price that allows us to achieve anticipated, or any, level of profitability on the product we acquire under these terms. Similarly, the return that we are required to provide the joint venture for products after the first four years may have an adverse effect on the profitability we achieve from acquiring the mill's output. Additionally, our purchase obligation with the mill requires us to purchase the output regardless of whether we have a customer for such output, and our results of operations and financial condition would be adversely affected if we are unable to sell the output that we are required to purchase.

Our reliance on and relationships with contract manufacturers exposes us to risks relating to costs, contractual terms and logistics .

We commenced commercial production of Biofene and some specialty chemical products in 2011 through the use of contract manufacturers, and we anticipate that we will continue to use contract manufacturers for chemical conversion and production of end-products and, to mitigate cost and volume risks at our large-scale production facilities, for production of Biofene. Establishing and operating contract manufacturing facilities requires us to make significant capital expenditures, which reduces our cash and places this capital at risk. For example, based on an evaluation of our assets associated with contract manufacturing facilities and anticipated levels of use of such facilities, we recorded a loss on write off of production assets of approximately $5.5 million in the year ended December 31, 2012. Further write off of such assets may occur in future quarters as we continue to evaluate and adjust our priorities for production, including the levels of utilization of our current and planned manufacturing facilities, which would cause us to incur additional losses associated with such facilities in the future. Also, many of our contract manufacturing agreements contain terms that commit us to pay for capital expenditures and other costs incurred or expected to be earned by the plant operators and owners, which can result in contractual liability and losses for us even if we terminate a particular contract manufacturing arrangement or decide to reduce or stop production under such an arrangement. We incurred a $40.4 million loss in the year ended December 31, 2012 related to $10.0 million in facility modification costs and $30.4 million of fixed purchase commitment losses associated with a scale-back of production at certain facilities. Some of our contract manufacturing agreements have also contained requirements to pay bonuses for milestone achievements by the contractor, minimum offtake requirements with penalties for failure to purchase specified amounts in a given period, and other terms that created contingent liabilities or other obligations for us. Any failure to comply with such requirements could result in legal claims against us, resulting in additional liability and diverting management attention, which could have a material adverse effect on our business.

The locations of contract manufacturers can pose additional cost, logistics and feedstock challenges. If production capacity is available at a plant that is remote from usable chemical finishing or distribution facilities, or from customers, we will be required to incur additional expenses in shipping products to other locations. Such costs could include shipping costs, compliance with export and import controls, tariffs and additional taxes, among others. In addition, we may be required to use feedstock from a particular region for a given production facility. The feedstock available in a particular region may not be the least expensive or most effective feedstock for production, which could significantly raise our overall production cost until we are able to optimize the supply chain.

Loss or termination of contract manufacturing relationships could harm our ability to meet our production goals.

As we have focused on building and commissioning our own plant and improving our production economics, we have limited our use of contract manufacturing and have terminated relationships with some of our contract manufacturing partners. The failure to have multiple available supply options could create a risk for us if a single source or a limited number of sources of manufacturing runs into operational issues. In addition, if we are unable to secure the services of contract manufacturers when and as needed, we may lose customer opportunities and the growth of our business may be impaired. We cannot be sure that contract manufacturers will be available when we need their services, that they will be willing to dedicate a portion of their capacity to our projects, or

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that we will be able to reach acceptable price and other terms with them for the provision of their production services. If we shift priorities and stop or adjust anticipated production levels at contract manufacturing facilities, such adjustments could also result in disputes or otherwise harm our business relationships with contract manufacturers. In addition, reducing or stopping production at one facility while increasing or starting up production at another facility generally results in significant losses of production efficiency, which can persist for varying periods of time. Also, in order for production to commence under our contract manufacturing arrangements, we will generally have to provide equipment needed for the production of our products and we cannot be assured that such equipment can be ordered, or installed, on a timely basis, at acceptable costs, or at all. Further, in order to establish new manufacturing facilities, we need to transfer our yeast strains and production processes from lab to commercial plants controlled by third parties, which may pose technical or operational challenges that delay production or increase our costs.

If we are unable to decrease our production costs, we may not be able to produce our products at competitive prices and our ability to grow our business will be limited.

Currently, our costs of production are not low enough to allow us to offer many of our planned products at competitive prices. Our production costs depend on many factors that could have a negative effect on our ability to offer our planned products at competitive prices. Key factors beyond production scale and feedstock cost that impact our production costs include yield, productivity, separation efficiency and chemical process efficiency. Yield refers to the amount of the desired molecule that can be produced from a fixed amount of feedstock. Productivity represents the rate at which our product is produced by a given yeast strain. Separation efficiency refers to the amount of desired product produced in the fermentation process that we are able to extract and the time that it takes to do so. Chemical process efficiency refers to the cost and yield for the chemical finishing steps that convert our target molecule into a desired product. In order to successfully enter transportation fuels and certain chemical markets, we must produce those products at significantly lower costs, which will require both substantially higher yields than we have achieved to date and other significant improvements in production efficiency, including in productivity and in separation and chemical process efficiencies. There can be no assurance that we will be able to make these improvements or reduce our production costs sufficiently to offer our planned products at competitive prices, and any such failure could have a material adverse impact on our business and prospects.

Our ability to establish substantial commercial sales of our products is subject to many risks, any of which could prevent or delay revenue growth and adversely impact our customer relationships, business and results of operations.

There can be no assurance that our products will be approved or accepted by customers, that customers will choose our products over competing products, or that we will be able to sell our products profitably at prices and with features sufficient to establish demand. The markets we intend to enter first are primarily those for specialty chemical products used by large consumer products or specialty chemical companies. In entering these markets, we intend to sell our products as alternatives to chemicals currently in use, and in some cases the chemicals that we seek to replace have been used for many years. The potential customers for our molecules generally have well developed manufacturing processes and arrangements with suppliers of the chemical components of their products and may have a resistance to changing these processes and components. These potential customers frequently impose lengthy and complex product qualification procedures on their suppliers, influenced by consumer preference, manufacturing considerations such as process changes and capital and other costs associated with transitioning to alternative components, supplier operating history, regulatory issues, product liability and other factors, many of which are unknown to, or not well understood by, us. Satisfying these processes may take many months or years. If we are unable to convince these potential customers (and the consumers who purchase products containing such chemicals) that our products are comparable to the chemicals that they currently use or that the use of our products is otherwise to their benefits, we will not be successful in entering these markets and our business will be adversely affected.

In order for our diesel fuel to be accepted in various countries around the world, diesel engine manufacturers must determine that the use of our fuels in their equipment will not invalidate product warranties and that they otherwise regard our diesel fuel as an acceptable fuel. In addition, we must successfully demonstrate to these manufacturers that our fuel does not degrade the performance or reduce the life cycle of their engines or cause them to fail to meet emissions standards. Meeting these suitability standards can be a time consuming and expensive process, and we may invest substantial time and resources into such qualification efforts without ultimately securing approval. To date, our diesel fuel has achieved limited approvals from certain engine manufacturers, but we cannot be assured that other engine or vehicle manufacturers or fleet operators, will approve usage of our fuels. To distribute our diesel fuel, we must also meet requirements imposed by pipeline operators and fuel distributors. If these operators impose volume limitations on the transport of our fuels, our ability to sell our fuels may be impaired. Our ability to sell a jet fuel product is subject to similar types of qualification requirements as diesel, although we believe the qualification process will ultimately take longer and will be more expensive than the process for diesel.

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We expect to face competition for our specialty chemical and transportation fuels products from providers of petroleum-based products and from other companies seeking to provide alternatives to these products, and if we cannot compete effectively against these companies or products we may not be successful in bringing our products to market or further growing our business after we do so.

We expect that our renewable products will compete with both the traditional, largely petroleum-based specialty chemical and fuels products that are currently being used in our target markets and with the alternatives to these existing products that established enterprises and new companies are seeking to produce.

In the specialty chemical markets that we are initially seeking to enter, and in other chemical markets that we may seek to enter in the future, we will compete primarily with the established providers of chemicals currently used in these products. Producers of these incumbent products include global oil companies, large international chemical companies and companies specializing in specific products, such as squalane or essential oils. We may also compete in one or more of these markets with products that are offered as alternatives to the traditional petroleum-based or other traditional products being offered in these markets.

In the transportation fuels market, we expect to compete with independent and integrated oil refiners, advanced biofuels companies and biodiesel companies. Refiners compete with us by selling traditional fuel products and some are also pursuing hydrocarbon fuel production using non-renewable feedstocks, such as natural gas and coal, as well as processes using renewable feedstocks, such as vegetable oil and biomass. We also expect to compete with companies that are developing the capacity to produce diesel and other transportation fuels from renewable resources in other ways. These include advanced biofuels companies using specific enzymes that they have developed to convert cellulosic biomass, which is non-food plant material such as wood chips, corn stalks and sugarcane bagasse, into fermentable sugars. Similar to us, some companies are seeking to use engineered enzymes to convert sugars, in some cases from cellulosic biomass and in others from natural sugar sources, into renewable diesel and other fuels. Biodiesel companies convert vegetable oils and animal oils into diesel fuel and some are seeking to produce diesel and other transportation fuels using thermochemical methods to convert biomass into renewable fuels.

With the emergence of many new companies seeking to produce chemicals and fuels from alternative sources, we may face increasing competition from alternative fuels and chemicals companies. As they emerge, some of these companies may be able to establish production capacity and commercial partnerships to compete with us. If we are unable to establish production and sales channels that allow us to offer comparable products at attractive prices, we may not be able to compete effectively with these companies.

We believe the primary competitive factors in both the chemicals and fuels markets are:

• product price;

• product performance and other measures of quality;

• infrastructure compatibility of products;

• sustainability; and

• dependability of supply.

The oil companies, large chemical companies and well-established agricultural products companies with whom we compete are much larger than we are, have, in many cases, well developed distribution systems and networks for their products, have valuable historical relationships with the potential customers we are seeking to serve and have much more extensive sales and marketing programs in place to promote their products. In order to be successful, we must convince customers that our products are at least as effective as the traditional products they are seeking to replace and we must provide our products on a cost-competitive basis with these traditional products and other available alternatives. Some of our competitors may use their influence to impede the development and acceptance of renewable products of the type that we are seeking to produce.

We believe that for our chemical products to succeed in the market, we must demonstrate that our products are comparable alternatives to existing products and to any alternative products that are being developed for the same markets based on some combination of product cost, availability, performance, and consumer preference characteristics. With respect to our diesel and other transportation fuels products, we believe that our product must perform as effectively as petroleum-based fuel, or alternative fuels, and be available on a cost-competitive basis. In addition, with the wide range of renewable fuels products under development, we must be successful in reaching potential customers and convincing them that ours are effective and reliable alternatives.

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Our relationship with our strategic partner, Total, has a substantial impact on our company.

We have a license, development, research and collaboration agreement with Total, under which we may develop, produce and commercialize products with Total, that originally contemplated Total paying up to the first $50 million in research costs for selected research and development projects (which arrangement has been modified as described below). As of March 1, 2013, Total held approximately 18.4% of our outstanding common stock. Under the agreement, Total has a right of first negotiation with us with respect to exclusive commercialization arrangements that we would propose to enter into with certain third parties, as well as the right to purchase any of our products on terms not less favorable than those offered to or received by us from third parties in any market where Total or its affiliates have a significant market position. These rights might inhibit potential strategic partners or potential customers from entering into negotiations with us about future business opportunities. Total also has the right to terminate the collaboration agreement in the event we undergo a sale or change of control to certain entities, which could discourage a potential acquirer from making an offer to acquire us.

In November 2011, we entered into an amendment of the collaboration agreement with Total with respect to development and commercialization of Biofene for diesel. This represented an expansion of the initial collaboration that the parties established in 2010, and established a global, exclusive collaboration for the development of Biofene for diesel and a framework for the creation of a joint venture to manufacture and commercialize Biofene for diesel. In addition, a limited number of other potential products were subject to development for the joint venture on a non-exclusive basis. In July 2012, we entered into a further amendment of the collaboration agreement with Total that expanded Total's investment in the Biofene collaboration, incorporated the development of certain joint venture products for use in diesel and jet fuel into the scope of the collaboration, and changed the structure of the funding from Total to include a convertible debt mechanism. Under the new agreements, Total funded $30 million in new cash investment during the third quarter of 2012 and, in March 2013, agreed to provide an additional $30 million in 2013. Total may decide to provide further funding in 2014. Upon completion of the research and development program, we and Total would form a joint venture company that would have exclusive rights to produce and market renewable diesel and/or jet fuel. Should Total decide not to pursue commercialization, under certain conditions, it is eligible to recover up to $100 million, payable in March 2017, in the form of cash or in the form of common stock at a conversion price of $7.0682 per share (or, for notes issued in 2013, a lower price as determined under the March 2013 letter agreement as described below in MD&A-Overview-Total).

Under the agreements related to the July 2012 amendment, the $50 million in funding by Total originally contemplated under the collaboration agreement is deemed to be exhausted, so the funding under the most recent amendment is all the funding still contemplated by our agreements with Total. We cannot be certain that Total will choose to continue funding the research and development program or ultimately opt in to participate in the anticipated joint venture. Under the new agreements, Total may, at certain decision points through a final decision date following the earlier of completion of the research and development program or December 31, 2016, decide not to continue funding or participating in the program and, if it does, any notes issued to Total to date will remain outstanding and become payable or convertible into our common stock. If Total chooses to demand repayment of amounts advanced under the notes, we may not be able to repay them by the maturity date in March 2017, which could lead to defaults and our insolvency, and Total and other creditors could pursue collection claims against us. If the notes become convertible and Total chooses to convert them, the resulting issuance of common stock would be dilutive to other stockholders. Under the July 2012 agreements, Total also has a right to participate in our future equity or convertible debt financings through December 31, 2013 to preserve its pro rata ownership of us (and thereafter in limited circumstances). The agreements provided that the purchase price for the first $30 million of purchases under this pro rata right would be paid by cancellation of outstanding notes held by Total; Total canceled $5 million of an outstanding convertible promissory note in connection with a private placement in December 2012, which reduced the amount of notes it could cancel to exercise its pro rata rights by $5 million. Exercise by Total of this right by cancellation of notes reduces the cash proceeds we receive from any covered offering.

The new agreements provide that we will provide an exclusive license to our intellectual property related to the manufacture and commercialization of Biofene-based diesel and jet fuel to the above-mentioned fuels joint venture, and also contemplate providing an option to Total to buy out our interest in the joint venture under certain circumstances such as our insolvency. Furthermore, the new agreements contemplate that Total can, if there is a deadlock in finalizing various matters related to the formation of the joint venture, initiate a bidding process where the fair value of the proposed joint venture would be determined and we would be required to choose whether to (i) sell our joint venture assets to Total for 50% of the joint venture value, (ii) proceed with formation of the joint venture with Total as a 50% owner and accept Total's position regarding the funding requirements of the joint venture, or (iii) proceed with the formation of the joint venture with Total as a 50% owner, accepting Total's position regarding the funding requirements of the joint venture, and then sell all or a portion of our 50% interest in the joint venture to Total for a price equal to the fair value multiplied by the percentage ownership of the joint venture sold to Total. If we are forced to relinquish our rights with respect to diesel and jet fuel under these scenarios (or under an early exclusive license as described above), our ability to continue pursuing our fuels business will be impaired.

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If we do not meet technical, development and commercial milestones in our collaboration agreements, our future revenue and financial results will be adversely impacted.

We have entered into a number of agreements regarding the further development of certain of our products and, in some cases, for ultimate sale of certain products to the customer under the agreement. None of these agreements affirmatively obligates the other party to purchase specific quantities of any products at this time, and most contain important conditions that must be satisfied before additional research and development funding or product purchases would occur. These conditions include research and development milestones and technical specifications that must be achieved to the satisfaction of our collaborators, which we cannot be certain we will achieve. If we do not achieve these contractual milestones, our revenues and financial results will be harmed.

We are subject to risks related to our reliance on collaboration arrangements to fund development and commercialization of our products.

For most product markets we are trying to address, we either have or are seeking collaboration partners to fund the research and development, commercialization and production efforts required for the target products. Typically we provide limited exclusive rights and revenue sharing with respect to the production and sale of particular types of products in specific markets in exchange for such up-front funding. These exclusivity, revenue-sharing and other similar terms limit our ability to commercialize our products and technology, and may impact the size of our business or our profitability in ways that we do not currently envision. In addition, revenues from these types of relationships are a key part of our cash plan for 2013 and beyond. If we fail to collect expected collaboration revenues, or to identify and add sufficient additional collaborations to fund our planned operations, we may be unable to fund our operations or pursue development and commercialization of our planned products. To achieve our collaboration revenue targets from year to year, we may be forced to enter into agreements that contain less favorable terms, including broader exclusivity provisions for commercial partners and a smaller financial stake in any successful ventures resulting from collaborations.

Our manufacturing operations require sugar feedstock, and the inability to obtain such feedstock in sufficient quantities or in a timely manner, or at reasonable prices, may limit our ability to produce our products profitably, or at all.

We anticipate that the production of our products will require large volumes of feedstock. We have relied on a mixture of feedstock sources for use at our contract manufacturing operations, including cane sugar, corn-based dextrose and beet molasses. For our large-scale production facilities in Brazil, we are relying primarily on Brazilian sugarcane. We cannot predict the future availability or price of these various feedstocks, nor can we be sure that our mill partners, which we expect to supply the sugarcane feedstock necessary to produce our products in Brazil, will be able to supply it in sufficient quantities or in a timely manner. Furthermore, to the extent we are required to rely on sugar feedstock other than Brazilian sugarcane, the cost of such feedstock may be higher than we expect, increasing our anticipated production costs. Feedstock crop yields and sugar content depend on weather conditions, such as rainfall and temperature. Weather conditions have historically caused volatility in the ethanol and sugar industries by causing crop failures or reduced harvests. Excessive rainfall can adversely affect the supply of sugarcane and other sugar feedstock available for the production of our products by reducing the sucrose content and limiting growers' ability to harvest. Crop disease and pestilence can also occur from time to time and can adversely affect feedstock growth, potentially rendering useless or unusable all or a substantial portion of affected harvests. With respect to sugarcane, our initial primary feedstock, the limited amount of time during which it keeps its sugar content after harvest and the fact that sugarcane is not itself a traded commodity increases these risks and limits our ability to substitute supply in the event of such an occurrence. If production of sugarcane or any other feedstock we may use to produce our products is adversely affected by these or other conditions, our production will be impaired, and our business will be adversely affected.

The price of sugarcane and other feedstocks can be volatile as a result of changes in industry policy and may increase the cost of production of our products.

In Brazil, Conselho dos Produtores de Cana, Açúcar e Álcool (Council of Sugarcane, Sugar and Ethanol Producers), or Consecana, an industry association of producers of sugarcane, sugar and ethanol, sets market terms and prices for general supply, lease and partnership agreements for sugarcane. If Consecana makes changes to such terms and prices, this could result higher sugarcane prices and/or a significant decrease in the volume of sugarcane available for the production of our products. Furthermore, if Consecana were to cease to be involved in this process, such prices and terms could become more volatile. Similar principles apply to pricing of other feedstocks as well. Any of these events could adversely affect our business and results of operations.

Our large-scale commercial production capacity is centered in Brazil, and our business will be adversely affected if we do not operate effectively in that country.

For the foreseeable future, we will be subject to risks associated with the concentration of essential product sourcing and operations in Brazil. The Brazilian government has changed in the past, and may change in the future, monetary, taxation, credit,

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tariff and other policies to influence the course of Brazil's economy. For example, the government's actions to control inflation have at times involved setting wage and price controls, adjusting interest rates, imposing taxes and exchange controls and limiting imports into Brazil. We have no control over, and cannot predict, what policies or actions the Brazilian government may take in the future. Our business, financial performance and prospects may be adversely affected by, among others, the following factors:

• delays or failures in securing licenses, permits or other governmental approvals necessary to build and operate facilities and use our yeast strains to produce products;

• rapid consolidation in the sugar and ethanol industries in Brazil, which could result in a decrease in competition;

• political, economic, diplomatic or social instability in or affecting Brazil;

• changing interest rates;

• tax burden and policies;

• effects of changes in currency exchange rates;

• exchange controls and restrictions on remittances abroad;

• inflation;

• land reform movements;

• export or import restrictions that limit our ability to move our products out of Brazil or interfere with the import of essential materials into Brazil;

• changes in or interpretations of foreign regulations that may adversely affect our ability to sell our products or repatriate profits to the U.S.;

• tariffs, trade protection measures and other regulatory requirements;

• successful compliance with U.S. and foreign laws that regulate the conduct of business abroad;

• an inability, or reduced ability, to protect our intellectual property in Brazil including any effect of compulsory licensing imposed by government action; and

• difficulties and costs of staffing and managing foreign operations. 

We cannot predict whether the current or future Brazilian government will implement changes to existing policies on taxation, exchange controls, monetary strategy, social security and the like, nor can we estimate the impact of any such changes on the Brazilian economy or our operations.

Our international operations expose us to the risk of fluctuation in currency exchange rates and rates of foreign inflation, which could adversely affect our results of operations.

We currently incur significant costs and expenses in Brazilian reais and may in the future incur additional expenses in foreign currencies and derive a portion of our revenues in the local currencies of customers throughout the world. As a result, our revenues and results of operations are subject to foreign exchange fluctuations, which we may not be able to manage successfully. During the past few decades, the Brazilian currency in particular has faced frequent and substantial exchange rate fluctuations in relation to the U.S. dollar and other foreign currencies. There can be no assurance that the Brazilian real will not significantly appreciate or depreciate against the U.S. dollar in the future. We also bear the risk that the rate of inflation in the foreign countries where we incur costs and expenses or the decline in value of the U.S. dollar compared to those foreign currencies will increase our costs as expressed in U.S. dollars. For example, future measures by the Central Bank of Brazil to control inflation, including interest rate adjustments, intervention in the foreign exchange market and actions to fix the value of the real, may weaken the U.S. dollar in Brazil. Whether in Brazil or otherwise, we may not be able to adjust the prices of our products to offset the effects of inflation or foreign currency appreciation on our cost structure, which could increase our costs and reduce our net operating margins. If we do not successfully manage these risks through hedging or other mechanisms, our revenues and results of operations could be adversely affected.

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Our use of genetically-modified feedstocks and yeast strains to produce our products subjects us to risks of regulatory limitations and rejection of our products.

The use of genetically-modified microorganisms, or GMMs, such as our yeast strains, is subject to laws and regulations in many countries, some of which are new and some of which are still evolving. Public attitudes about the safety and environmental hazards of, and ethical concerns over, genetic research and GMMs could influence public acceptance of our technology and products. In the U.S., the Environmental Protection Agency, or EPA, regulates the commercial use of GMMs as well as potential products produced from the GMMs. Various states within the U.S. could choose to regulate products made with GMMs as well. While the strain of genetically modified yeast that we currently use for the development and anticipate using for the commercial production of our target molecules, S. cerevisiae, is eligible for exemption from EPA review because it is recognized as posing a low risk, we must satisfy certain criteria to achieve this exemption, including but not limited to use of compliant containment structures and safety procedures, and we cannot be sure that we will meet such criteria in a timely manner, or at all. If exemption of S. cerevisiae is not obtained, our business may be substantially harmed. In addition to S. cerevisiae, we may seek to use different GMMs in the future that will require EPA approval. If approval of different GMMs is not secured, our ability to grow our business could be adversely affected. In addition to the regulatory requirements relating directly to our yeast strains and products, we must satisfy the product specification requirements of our customers, which can include requirements that we use non-genetically modified feedstocks. For example, some cosmetics suppliers require that ingredients used in their cosmetics not be produced from any genetically-modified feedstocks.

In Brazil, GMMs are regulated by the National Biosafety Technical Commission, or CTNBio. We have obtained approval from CTNBio to use GMMs in a contained environment in our Campinas facilities for research and development purposes as well as at a contract manufacturing facility in Brazil. In addition, we have obtained initial commercial approval from CTNBio for one of our current yeast strains. As we continue to develop new yeast strains and deploy our technology at new production facilities in Brazil, we will be required to obtain further approvals from CTNBio in order to use these strains in commercial production in Brazil. We may not be able to obtain approvals from relevant Brazilian authorities on a timely basis, or at all, and if we do not, our ability to produce our products in Brazil would be impaired, which would adversely affect our results of operations and financial condition.

In addition to our production operations in the U.S. and Brazil, we have been party to contract manufacturing agreements with parties in other production locations around the world, including Europe. The use of GMM technology is strictly regulated in the European Union, which has established various directives for member states regarding regulation of the use of such technology, including notification processes for contained use of such technology. We expect to encounter GMM regulations in most, if not all, of the countries in which we may seek to establish production capabilities, and the scope and nature of these regulations will likely be different from country to country. If we cannot meet the applicable requirements in other countries in which we intend to produce products using our yeast strains, or if it takes longer than anticipated to obtain such approvals, our business could be adversely affected.

We may not be able to obtain regulatory approval for the sale of our renewable products.

Our renewable chemical products may be subject to government regulation in our target markets. In the U.S., the EPA administers the Toxic Substances Control Act, or TSCA, which regulates the commercial registration, distribution, and use of many chemicals. Before an entity can manufacture or distribute significant volumes of a chemical, it needs to determine whether that chemical is listed in the TSCA inventory. If the substance is listed, then manufacture or distribution can commence immediately. If not, then in most cases a “Chemical Abstracts Service” number registration and pre-manufacture notice must be filed with the EPA, which has up to 180 days to review the filing. Some of the products we produce or plan to produce, such as Biofene and squalane, are already in the TSCA inventory. Others, such as our farnesane (diesel) and new jet fuel molecules, are not yet listed. We may not be able to expediently receive approval from the EPA to list the molecules we would like to make on the TSCA registry, resulting in delays or significant increases in testing requirements. A similar program exists in the European Union, called REACH (Registration, Evaluation, Authorization, and Restriction of Chemical Substances). Under this program, we need to register our products, including Biofene, with the European Commission, and this process could cause delays or significant costs. To the extent that other geographies, such as Brazil, may rely on TSCA or REACH (or similar laws and programs) for chemical registration in their geographies, delays with the U.S. or European authorities may subsequently delay entry into these markets as well.

Our diesel fuel is subject to regulation by various government agencies, including the EPA and the CARB in the U.S. and ANP in Brazil. To date, we have obtained registration with the EPA for the use of our diesel fuel in the U.S. at a 35% blend rate with petroleum diesel. In addition, ANP has authorized the use our diesel fuel at blend rates of 10% and 30% for specific bus fleets. We are also currently in the process of registering our fuel with the CARB and the European Commission. Registration with each of these bodies is required for the sale and use of our fuels within their respective jurisdictions. In addition, for us to

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achieve full access to the U.S. fuels market for our fuel products, we will need to obtain EPA and CARB (and potentially other state agencies) certifications for our feedstock pathway and production facilities, including certification of a feedstock lifecycle analysis relating to greenhouse gas emissions. Any delay in obtaining these additional certifications could impair our ability to sell our renewable fuels to refiners, importers, blenders and other parties that produce transportation fuels as they comply with federal and state requirements to include certified renewable fuels in their products.

We expect to encounter regulations in most, if not all, of the countries in which we may seek to sell our renewable chemical and fuel products, and we cannot assure you that we will be able to obtain necessary approvals in a timely manner or at all. If our chemical and fuel products do not meet applicable regulatory requirements in a particular country or at all, then we may not be able to commercialize our products and our business will be adversely affected.

Changes in government regulations, including subsidies and economic incentives, could have a material adverse effect upon our business.

The market for renewable fuels is heavily influenced by foreign, federal, state and local government regulations and policies. Changes to existing or adoption of new domestic or foreign federal, state and local legislative initiatives that impact the production, distribution or sale of renewable fuels may harm our renewable fuels business. In the U.S. and in a number of other countries, regulations and policies encouraging production and use of alternative fuels have been modified in the past and may be modified again in the future. Any reduction in mandated requirements for fuel alternatives and additives to gasoline or diesel may cause demand for biofuels to decline and deter investment in the research and development of renewable fuels. The market uncertainty regarding this and future standards and policies may also affect our ability to develop new renewable products or to license our technologies to third parties and to sell products to our end customers. Any inability to address these requirements and any regulatory or policy changes could have a material adverse effect on our business, financial condition and results of operations.

Concerns associated with renewable fuels, including land usage, national security interests and food crop usage, continue to receive legislative, industry and public attention. This attention could result in future legislation, regulation and/or administrative action that could adversely affect our business. Any inability to address these requirements and any regulatory or policy changes could have a material adverse effect on our business, financial condition and results of operations.

Furthermore, the production of our products will depend on the availability of feedstock, especially sugarcane. Agricultural production and trade flows are subject to government policies and regulations. Governmental policies affecting the agricultural industry, such as taxes, tariffs, duties, subsidies, incentives and import and export restrictions on agricultural commodities and commodity products, can influence the planting of certain crops, the location and size of crop production, whether unprocessed or processed commodity products are traded, the volume and types of imports and exports, and the availability and competitiveness of feedstocks as raw materials. Future government policies may adversely affect the supply of feedstocks, restrict our ability to use sugarcane or other feedstocks to produce our products, and negatively impact our future revenues and results of operations.

We may incur significant costs complying with environmental laws and regulations, and failure to comply with these laws and regulations could expose us to significant liabilities.

We use hazardous chemicals and radioactive and biological materials in our business and such materials are subject to a variety of federal, state and local laws and regulations governing the use, generation, manufacture, storage, handling and disposal of these materials both in the U.S. and overseas. Although we have implemented safety procedures for handling and disposing of these materials and related waste products in an effort to comply with these laws and regulations, we cannot be sure that our safety measures will prevent accidental injury or contamination from the use, storage, handling or disposal of hazardous materials. In the event of contamination or injury, we could be held liable for any resulting damages, and any liability could exceed our insurance coverage. There can be no assurance that violations of environmental, health and safety laws will not occur in the future as a result of human error, accident, equipment failure or other causes. Compliance with applicable environmental laws and regulations may be expensive, and the failure to comply with past, present, or future laws could result in the imposition of fines, third party property damage, product liability and personal injury claims, investigation and remediation costs, the suspension of production, or a cessation of operations, and our liability may exceed our total assets. Liability under environmental laws can be joint and several and without regard to comparative fault. Environmental laws could become more stringent over time, imposing greater compliance costs and increasing risks and penalties associated with violations, which could impair our research, development or production efforts and harm our business.

A decline in the price of petroleum and petroleum-based products may reduce demand for many of our renewable products and may otherwise adversely affect our business.

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We anticipate that most of our renewable products, and in particular our fuels, will be marketed as alternatives to corresponding petroleum-based products. If the price of oil falls, we may be unable to produce products that are cost-effective alternatives to petroleum-based products. Declining oil prices, or the perception of a future decline in oil prices, may adversely affect the prices we can obtain from our potential customers or prevent potential customers from entering into agreements with us to buy our products. During sustained periods of lower oil prices we may be unable to sell some of our products, which could materially and adversely affect our operating results.

Our financial results could vary significantly from quarter to quarter and are difficult to predict.

Our revenues and results of operations could vary significantly from quarter to quarter because of a variety of factors, many of which are outside of our control. As a result, comparing our results of operations on a period-to-period basis may not be meaningful. Factors that could cause our quarterly results of operations to fluctuate include:

• achievement, or failure, with respect to technology, product development or manufacturing milestones needed to allow us to enter identified markets on a cost effective basis;

• delays or greater than anticipated expenses associated with the completion or commissioning of new production facilities, or the time to ramp up and stabilize production following completion of a new production facility;

• impairment of assets based on shifting business priorities and working capital limitations;

• disruptions in the production process at any manufacturing facility;

• losses associated with producing our products as we ramp to commercial production levels;

• failure to recover value added tax (VAT) that we currently reflect as recoverable in our financial statements (e.g., due to failure to meet conditions for reimbursement of VAT under local law);

• the timing, size and mix of sales to customers for our products;

• increases in price or decreases in availability of feedstock;

• the unavailability of contract manufacturing capacity altogether or at reasonable cost;

• fluctuations in foreign currency exchange rates;

• gains or losses associated with our hedging activities;

• fluctuations in the price of and demand for sugar, ethanol, and petroleum-based and other products for which our products are alternatives;

• seasonal variability in production and sales of our products;

• competitive pricing pressures, including decreases in average selling prices of our products;

• unanticipated expenses associated with changes in governmental regulations and environmental, health and safety requirements;

• reductions or changes to existing fuel and chemical regulations and policies;

• departure of executives or other key management employees resulting in transition and severance costs;

• our ability to use our net operating loss carryforwards to offset future taxable income;

• business interruptions such as earthquakes and other natural disasters;

• our ability to integrate businesses that we may acquire;

• risks associated with the international aspects of our business; and

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• changes in general economic, industry and market conditions, both domestically and in our foreign markets.

In addition, nearly all of our revenue through the third quarter of 2012 came from the sale of ethanol and reformulated ethanol-blended gasoline, with the remainder coming from collaborations and government grants and, more recently, sales of our renewable products. In the third quarter of 2012, we transitioned out of the ethanol and reformulated ethanol-blended gasoline business. We do not expect to be able to replace much of the revenue lost as a result of this transition, particularly in 2013 while we continue our efforts to establish a renewable products business.

As part of our operating plan for 2013, we are reducing our cost structure by improving efficiency in our operations and reducing non-critical expenditures. These efforts have included, and may include in the future, reductions to our workforce and adjustments to the timing and scope of planned capital expenditures.

Due to the factors described above, among others, the results of any quarterly or annual period may not meet our expectations or the expectations of our investors and may not be meaningful indications of our future performance.

Loss of key personnel, including key management personnel, and/or failure to attract and retain additional personnel could delay our product development programs and harm our research and development efforts and our ability to meet our business objectives.

Our business involves complex, global operations across a variety of markets and requires a management team and employee workforce that is knowledgeable in the many areas in which we operate. As we build our business, we will need to hire additional qualified research and development, management and other personnel to succeed. The process of hiring, training and successfully integrating qualified personnel into our operation, in both the U.S. and Brazil, is a lengthy and expensive one. The market for qualified personnel is very competitive because of the limited number of people available with the necessary technical skills and understanding of our technology and anticipated products, particularly in Brazil. Our failure to hire and retain qualified personnel could impair our ability to meet our research and development and business objectives and adversely affect our results of operations and financial condition.

The loss of any key member of our management or key technical and operational employees, or the failure to attract or retain such employees could prevent us from developing and commercializing our products for our target markets and executing our business strategy. We also may not be able to attract or retain qualified employees in the future due to the intense competition for qualified personnel among biotechnology and other technology-based businesses, particularly in the renewable chemicals and fuels area, or due to the availability of personnel with the qualifications or experience necessary for our business. In addition, reductions to our workforce as part of cost-saving measures may make it more difficult for us to attract and retain key employees. If do not maintain the necessary personnel to accomplish our business objectives, we may experience staffing constraints that will adversely affect our ability to meet the demands of our collaborators and customers in a timely fashion or to support our internal research and development programs and operations. In particular, our product and process development programs are dependent on our ability to attract and retain highly skilled technical and operational personnel. Competition for such personnel from numerous companies and academic and other research institutions may limit our ability to do so on acceptable terms. All of our employees are at-will employees, which mean that either the employee or we may terminate their employment at any time.

Growth may place significant demands on our management and our infrastructure.

We have experienced, and expect to continue to experience, expansion of our business as we continue to make efforts to develop and bring our products to market. We have grown from 18 employees at the end of 2005 to 397at March 1, 2013. Our growth and diversified operations have placed, and may continue to place, significant demands on our management and our operational and financial infrastructure. In particular, continued growth could strain our ability to:

• manage multiple research and development programs;

• operate multiple manufacturing facilities around the world;

• develop and improve our operational, financial and management controls;

• enhance our reporting systems and procedures;

• recruit, train and retain highly skilled personnel;

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• develop and maintain our relationships with existing and potential business partners;

• maintain our quality standards; and

• maintain customer satisfaction.

Managing our growth will require significant expenditures and allocation of valuable management resources. If we fail to achieve the necessary level of efficiency in our organization as it grows, our business, results of operations and financial condition would be adversely impacted.

Our proprietary rights may not adequately protect our technologies and product candidates.

Our commercial success will depend substantially on our ability to obtain patents and maintain adequate legal protection for our technologies and product candidates in the U.S. and other countries. As of March 1, 2013, we had 202 issued U.S. and foreign patents and 302 pending U.S. and foreign patent applications that were owned by or licensed to us. We will be able to protect our proprietary rights from unauthorized use by third parties only to the extent that our proprietary technologies and future products are covered by valid and enforceable patents or are effectively maintained as trade secrets.

We apply for patents covering both our technologies and product candidates, as we deem appropriate. However, we may fail to apply for patents on important technologies or product candidates in a timely fashion, or at all. Our existing and future patents may not be sufficiently broad to prevent others from practicing our technologies or from developing competing products or technologies. In addition, the patent positions of companies like ours are highly uncertain and involve complex legal and factual questions for which important legal principles remain unresolved. No consistent policy regarding the breadth of patent claims has emerged to date in the U.S. and the landscape is expected to become even more uncertain in view of recent rule changes by the Patent and Trademark Office, or USPTO, the introduction of patent reform legislation in Congress and recent decisions in patent law cases by the U.S. Supreme Court. In addition, we obtained certain key U.S. patents using a procedure for accelerated examination recently implemented by the USPTO which requires special activities and disclosures that may create additional risks related to the validity or enforceability of the U.S. patents so obtained. The patent situation outside of the U.S. is even less predictable. As a result, the validity and enforceability of patents cannot be predicted with certainty. Moreover, we cannot be certain whether:

• we or our licensors were the first to make the inventions covered by each of our issued patents and pending patent applications;

• we or our licensors were the first to file patent applications for these inventions;

• others will independently develop similar or alternative technologies or duplicate any of our technologies;

• any of our or our licensors' patents will be valid or enforceable;

• any patents issued to us or our licensors will provide us with any competitive advantages, or will be challenged by third parties;

• we will develop additional proprietary products or technologies that are patentable; or

• the patents of others will have an adverse effect on our business.

We do not know whether any of our patent applications or those patent applications that we license will result in the issuance of any patents. Even if patents are issued, they may not be sufficient to protect our technology or product candidates. The patents we own or license and those that may be issued in the future may be challenged, invalidated, rendered unenforceable, or circumvented, and the rights granted under any issued patents may not provide us with proprietary protection or competitive advantages. In particular, U.S. patents we obtained using the USPTO accelerated examination program may introduce additional risks to the validity or enforceability of some or all of these specially-obtained U.S. patents if validity or enforceability are challenged. Moreover, third parties could practice our inventions in territories where we do not have patent protection or in territories where they could obtain a compulsory license to our technology where patented. Such third parties may then try to import products made using our inventions into the U.S. or other territories. Additional uncertainty may result from potential passage of patent reform legislation by the U.S. Congress, legal precedent by the U.S. Federal Circuit and Supreme Court as they determine legal issues concerning the scope and construction of patent claims and inconsistent interpretation of patent laws by the lower courts. Accordingly, we cannot ensure that any of our pending patent applications will result in issued patents, or even if issued, predict the breadth, validity and enforceability of the claims upheld in our and other companies' patents.

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Unauthorized parties may attempt to copy or otherwise obtain and use our products or technology. Monitoring unauthorized use of our intellectual property is difficult, and we cannot be certain that the steps we have taken will prevent unauthorized use of our technology, particularly in certain foreign countries where the local laws may not protect our proprietary rights as fully as in the U.S. or may provide, today or in the future, for compulsory licenses. If competitors are able to use our technology, our ability to compete effectively could be harmed. Moreover, others may independently develop and obtain patents for technologies that are similar to, or superior to, our technologies. If that happens, we may need to license these technologies, and we may not be able to obtain licenses on reasonable terms, if at all, which could cause harm to our business.

We rely in part on trade secrets to protect our technology, and our failure to obtain or maintain trade secret protection could adversely affect our competitive business position.

We rely on trade secrets to protect some of our technology, particularly where we do not believe patent protection is appropriate or obtainable. However, trade secrets are difficult to maintain and protect. Our strategy for contract manufacturing and scale-up of commercial production requires us to share confidential information with our international business partners and other parties. Our product development collaborations with third parties, including with Total, require us to share confidential information, including with employees of Total who are seconded to Amyris during the term of the collaboration. While we use reasonable efforts to protect our trade secrets, our or our business partners' employees, consultants, contractors or scientific and other advisors may unintentionally or willfully disclose our proprietary information to competitors. Enforcement of claims that a third party has illegally obtained and is using trade secrets is expensive, time consuming and uncertain. In addition, foreign courts are sometimes less willing than U.S. courts to protect trade secrets. If our competitors independently develop equivalent knowledge, methods and know-how, we would not be able to assert our trade secrets against them.

We require new employees and consultants to execute confidentiality agreements upon the commencement of an employment or consulting arrangement with us. These agreements generally require that all confidential information developed by the individual or made known to the individual by us during the course of the individual's relationship with us be kept confidential and not disclosed to third parties. These agreements also generally provide that inventions conceived by the individual in the course of rendering services to us shall be our exclusive property. Nevertheless, our proprietary information may be disclosed, or these agreements may be unenforceable or difficult to enforce. Additionally, trade secret law in Brazil differs from that in the U.S. which requires us to take a different approach to protecting our trade secrets in Brazil. Some of these approaches to trade secret protection may be novel and untested under Brazilian law and we cannot guarantee that we would prevail if our trade secrets are contested in Brazil. If any of the above risks materializes, our failure to obtain or maintain trade secret protection could adversely affect our competitive business position.

Third parties may misappropriate our yeast strains.

Third parties, including contract manufacturers, sugar and ethanol mill owners, other contractors and shipping agents, often have custody or control of our yeast strains. If our yeast strains were stolen, misappropriated or reverse engineered, they could be used by other parties who may be able to reproduce the yeast strains for their own commercial gain. If this were to occur, it would be difficult for us to challenge and prevent this type of use, especially in countries where we have limited intellectual property protection or that do not have robust intellectual property law regimes.

If we are sued for infringing intellectual property rights or other proprietary rights of third parties, litigation could be costly and time consuming and could prevent us from developing or commercializing our future products.

Our commercial success depends on our ability to operate without infringing the patents and proprietary rights of other parties and without breaching any agreements we have entered into with regard to our technologies and product candidates. We cannot determine with certainty whether patents or patent applications of other parties may materially affect our ability to conduct our business. Our industry spans several sectors, including biotechnology, renewable fuels, renewable specialty chemicals and other renewable compounds, and is characterized by the existence of a significant number of patents and disputes regarding patent and other intellectual property rights. Because patent applications can take several years to issue, there may currently be pending applications, unknown to us, that may result in issued patents that cover our technologies or product candidates. We are aware of a significant number of patents and patent applications relating to aspects of our technologies filed by, and issued to, third parties. The existence of third-party patent applications and patents could significantly reduce the coverage of patents owned by or licensed to us and limit our ability to obtain meaningful patent protection. If we wish to make, use, sell, offer to sell, or import the technology or compound claimed in issued and unexpired patents owned by others, we will need to obtain a license from the owner, enter into litigation to challenge the validity of the patents or incur the risk of litigation in the event that the owner asserts that we infringe its patents. If patents containing competitive or conflicting claims are issued to third parties and these claims are ultimately

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determined to be valid, we may be enjoined from pursing research, development, or commercialization of products, or be required to obtain licenses to these patents, or to develop or obtain alternative technologies.

If a third-party asserts that we infringe upon its patents or other proprietary rights, we could face a number of issues that could seriously harm our competitive position, including:

• infringement and other intellectual property claims, which could be costly and time consuming to litigate, whether or not the claims have merit, and which could delay getting our products to market and divert management attention from our business;

• substantial damages for past infringement, which we may have to pay if a court determines that our product candidates or technologies infringe a third party's patent or other proprietary rights;

• a court prohibiting us from selling or licensing our technologies or future products unless the holder licenses the patent or other proprietary rights to us, which it is not required to do; and

• if a license is available from a third party, such third party may require us to pay substantial royalties or grant cross licenses to our patents or proprietary rights.

The industries in which we operate, and the biotechnology industry in particular, are characterized by frequent and extensive litigation regarding patents and other intellectual property rights. Many biotechnology companies have employed intellectual property litigation as a way to gain a competitive advantage. If any of our competitors have filed patent applications or obtained patents that claim inventions also claimed by us, we may have to participate in interference proceedings declared by the relevant patent regulatory agency to determine priority of invention and, thus, the right to the patents for these inventions in the U.S. These proceedings could result in substantial cost to us even if the outcome is favorable. Even if successful, an interference proceeding may result in loss of certain claims. Our involvement in litigation, interferences, opposition proceedings or other intellectual property proceedings inside and outside of the U.S., to defend our intellectual property rights or as a result of alleged infringement of the rights of others, may divert management time from focusing on business operations and could cause us to spend significant resources, all of which could harm our business and results of operations.

Many of our employees were previously employed at universities, biotechnology, specialty chemical or oil companies, including our competitors or potential competitors. We may be subject to claims that these employees or we have inadvertently or otherwise used or disclosed trade secrets or other proprietary information of their former employers. Litigation may be necessary to defend against these claims. If we fail in defending such claims, in addition to paying monetary damages, we may lose valuable intellectual property rights or personnel and be enjoined from certain activities. A loss of key research personnel or their work product could hamper or prevent our ability to commercialize our product candidates, which could severely harm our business. Even if we are successful in defending against these claims, litigation could result in substantial costs and demand on management resources.

We may need to commence litigation to enforce our intellectual property rights, which would divert resources and management's time and attention and the results of which would be uncertain.

Enforcement of claims that a third party is using our proprietary rights without permission is expensive, time consuming and uncertain. Significant litigation would result in substantial costs, even if the eventual outcome is favorable to us and would divert management's attention from our business objectives. In addition, an adverse outcome in litigation could result in a substantial loss of our proprietary rights and we may lose our ability to exclude others from practicing our technology or producing our product candidates.

The laws of some foreign countries do not protect intellectual property rights to the same extent as do the laws of the U.S. Many companies have encountered significant problems in protecting and defending intellectual property rights in certain foreign jurisdictions. The legal systems of certain countries, particularly certain developing countries, do not favor the enforcement of patents and other intellectual property protection, particularly those relating to biotechnology and/or bioindustrial technologies. This could make it difficult for us to stop the infringement of our patents or misappropriation of our other intellectual property rights. Proceedings to enforce our patent rights in foreign jurisdictions could result in substantial costs and divert our efforts and attention from other aspects of our business. Moreover, our efforts to protect our intellectual property rights in such countries may be inadequate.

Our products subject us to product-safety risks, and we may be sued for product liability.

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The design, development, production and sale of our products involve an inherent risk of product liability claims and the associated adverse publicity. Our potential products could be used by a wide variety of consumers with varying levels of sophistication. Although safety is a priority for us, we are not always in control of the final uses and formulations of the products we supply or their use as ingredients. Our products could have detrimental impacts or adverse impacts we cannot anticipate. Despite our efforts, negative publicity about Amyris, including product safety or similar concerns, whether real or perceived, could occur, and our products could face withdrawal, recall or other quality issues. In addition, we may be named directly in product liability suits relating to our products, even for defects resulting from errors of our commercial partners, contract manufacturers or chemical finishers. These claims could be brought by various parties, including customers who are purchasing products directly from us or other users who purchase products from our customers. We could also be named as co-parties in product liability suits that are brought against the contract manufacturers or Brazilian sugar and ethanol mills with whom we partner to produce our products. Insurance coverage is expensive, may be difficult to obtain and may not be available in the future on acceptable terms. We cannot be certain that our contract manufacturers or the sugar and ethanol producers who partner with us to produce our products will have adequate insurance coverage to cover against potential claims. Any insurance we do maintain may not provide adequate coverage against potential losses, and if claims or losses exceed our liability insurance coverage, our business would be adversely impacted. In addition, insurance coverage may become more expensive, which would harm our results of operations.

During the ordinary course of business, we may become subject to lawsuits or indemnity claims, which could materially and adversely affect our business and results of operations.

From time to time, we may in the ordinary course of business be named as a defendant in lawsuits, claims and other legal proceedings. These actions may seek, among other things, compensation for alleged personal injury, worker's compensation, employment discrimination, breach of contract, property damages, civil penalties and other losses of injunctive or declaratory relief. In the event that such actions or indemnities are ultimately resolved unfavorably at amounts exceeding our accrued liability, or at material amounts, the outcome could materially and adversely affect our reputation, business and results of operations. In addition, payments of significant amounts, even if reserved, could adversely affect our liquidity position.

If we fail to maintain an effective system of internal controls, we might not be able to report our financial results accurately or prevent fraud; in that case, our stockholders could lose confidence in our financial reporting, which would harm our business and could negatively impact the price of our stock.

Effective internal controls are necessary for us to provide reliable financial reports and prevent fraud. In addition, Section 404 of the Sarbanes-Oxley Act of 2002 requires us and our independent registered public accounting firm to evaluate and report on our internal control over financial reporting. The process of implementing our internal controls and complying with Section 404 is expensive and time consuming, and requires significant attention of management. We cannot be certain that these measures will ensure that we maintain adequate controls over our financial processes and reporting in the future. In addition, to the extent we create joint ventures or have any variable interest entities and the financial statements of such entities are not prepared by us, we will not have direct control over their financial statement preparation. As a result, we will, for our financial reporting, depend on what these entities report to us, which could result in us adding monitoring and audit processes and increase the difficulty of implementing and maintaining adequate controls over our financial processes and reporting in the future. This may be particularly true where we are establishing such entities with commercial partners that do not have sophisticated financial accounting processes in place, or where we are entering into new relationships at a rapid pace, straining our integration capacity. Additionally, if we do not receive the information from the joint venture or variable interest entity on a timely basis, this could cause delays in our external reporting. Even if we conclude, and our independent registered public accounting firm concurs, that our internal control over financial reporting provides reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles, because of its inherent limitations, internal control over financial reporting may not prevent or detect fraud or misstatements. Failure to implement required new or improved controls, or difficulties encountered in their implementation, could harm our results of operations or cause us to fail to meet our reporting obligations. If we or our independent registered public accounting firm discover a material weakness, the disclosure of that fact, even if quickly remedied, could reduce the market's confidence in our financial statements and harm our stock price. In addition, failure to comply with Section 404 could subject us to a variety of administrative sanctions, including SEC action, ineligibility for short form resale registration, the suspension or delisting of our common stock from the stock exchange on which it is listed, and the inability of registered broker-dealers to make a market in our common stock, which would further reduce our stock price and could harm our business.

If the value of our goodwill or other intangible assets becomes impaired, it could materially reduce the value of our assets and reduce our net income for the year in which the related impairment charges occur.

We apply the applicable accounting principles set forth in the U.S. Financial Accounting Standards Board's Accounting Standards Codification to our intangible assets (including goodwill), which prohibits the amortization of intangible assets with

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indefinite useful lives and requires that these assets be reviewed for impairment at least annually. There are several methods that can be used to determine the estimated fair value of the in-process research and development acquired in a business combination. We have used the “income method,” which applies a probability weighting that considers the risk of development and commercialization, to the estimated future net cash flows that are derived from projected sales revenues and estimated costs. These projections are based on factors such as relevant market size, pricing of similar products, and expected industry trends. The estimated future net cash flows are then discounted to the present value using an appropriate discount rate. These assets are treated as indefinite-lived intangible assets until completion or abandonment of the projects, at which time the assets will be amortized over the remaining useful life or written off, as appropriate.If the carrying amount of the assets is greater than the measures of fair value, impairment is considered to have occurred and a write-down of the asset is recorded. Any finding that the value of our intangible assets has been impaired would require us to write-down the impaired portion, which could reduce the value of our assets and reduce our net income for the year in which the related impairment charges occur.  As of December 31, 2012, we had a net carrying value of approximately $9.1 million million in in-process research and development and goodwill associated with our acquisition of Draths Corporation.

Our ability to use our net operating loss carryforwards to offset future taxable income may be subject to certain limitations.

In general, under Section 382 of the Internal Revenue Code, or Code, a corporation that undergoes an “ownership change” is subject to limitations on its ability to utilize its pre-change net operating loss carryforwards, or NOLs, to offset future taxable income. If the Internal Revenue Service challenges our analysis that our existing NOLs are not subject to limitations arising from previous ownership changes, or if we undergo an ownership change, our ability to utilize NOLs could be limited by Section 382 of the Code. Future changes in our stock ownership, some of which are outside of our control, could result in an ownership change under Section 382 of the Code. Furthermore, our ability to utilize NOLs of companies that we may acquire in the future may be subject to limitations. For these reasons, we may not be able to utilize a material portion of the NOLs carryforward as of December 31, 2012, even if we attain profitability.

Loss of government contract revenues could impair our research and development efforts.

In 2010, we were awarded an “Integrated Bio-Refinery” grant from the U.S. Department of Energy, or DOE. The terms of this grant make funds available to us to leverage and expand our existing Emeryville, California, pilot plant and support laboratories to develop U.S.-based production capabilities for renewable fuels and chemicals derived from sweet sorghum. In 2012, we entered into a Technology Investment Agreement with The Defense Advanced Research Projects Agency (DARPA), under which we are performing certain research and development activities funded in part by DARPA. Generally, these agreements have fixed terms and may be terminated, modified or recovered by the government agency under certain conditions (such as failure to comply with detailed reporting and governance processes or failure to achieve milestones). Under these agreements, we are also subject to audits, which can result in corrective action plans and penalties up to and including termination. If the DOE or DARPA terminate their agreements with us, in addition to reducing our revenues, our U.S.-based research and development activities could be impaired, which would harm our business.

Our headquarters and other facilities are located in an active earthquake zone, and an earthquake or other types of natural disasters affecting us or our suppliers could cause resource shortages and disrupt and harm our results of operations.

We conduct our primary research and development operations in the San Francisco Bay Area in an active earthquake zone, and certain of our suppliers conduct their operations in the same region or in other locations that are susceptible to natural disasters. In addition, California and some of the locations where certain of our suppliers are located have experienced shortages of water, electric power and natural gas from time to time. The occurrence of a natural disaster, such as an earthquake, drought or flood, or localized extended outages of critical utilities or transportation systems, or any critical resource shortages, affecting us or our suppliers could cause a significant interruption in our business, damage or destroy our facilities, production equipment or inventory or those of our suppliers and cause us to incur significant costs or result in limitations on the availability of our raw materials, any of which could harm our business, financial condition and results of operations. The insurance we maintain against fires, earthquakes and other natural disasters may not be adequate to cover our losses in any particular case.

Risks Related to Ownership of Our Common Stock

Our stock price may be volatile.

The market price of our common stock has been, and we expect it to continue to be, subject to significant volatility, and it has declined significantly from our initial public offering price. As of January 31, 2013, the reported closing price for our common stock on the NASDAQ Global Select Market was $3.04 per share. Market prices for securities of early stage companies have

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historically been particularly volatile. Such fluctuations could be in response to, among other things, the factors described in this “Risk Factors” section or elsewhere in this report, or other factors, some of which are beyond our control, such as:

• fluctuations in our financial results or outlook or those of companies perceived to be similar to us;

• changes in estimates of our financial results or recommendations by securities analysts;

• changes in market valuations of similar companies;

• changes in the prices of commodities associated with our business such as sugar, ethanol and petroleum;

• changes in our capital structure, such as future issuances of securities or the incurrence of debt;

• announcements by us or our competitors of significant contracts, acquisitions or strategic alliances;

• regulatory developments in the U.S., Brazil, and/or other foreign countries;

• litigation involving us, our general industry or both;

• additions or departures of key personnel;

• investors' general perception of us; and

• changes in general economic, industry and market conditions.

Furthermore, stock markets have experienced price and volume fluctuations that have affected, and continue to affect, the market prices of equity securities of many companies. These fluctuations often have been unrelated or disproportionate to the operating performance of those companies. These broad market fluctuations, as well as general economic, political and market conditions, such as recessions, interest rate changes and international currency fluctuations, may negatively affect the market price of our common stock.

In the past, many companies that have experienced volatility and sustained declines in the market price of their stock have become subject to securities class action litigation. We may be the target of this type of litigation in the future. Securities litigation against us could result in substantial costs and divert our management's attention from other business concerns, which could seriously harm our business.

The concentration of our capital stock ownership with insiders will limit your ability to influence corporate matters.

As of March 1, 2013:

• our executive officers and directors and their affiliates (including Total) together held approximately 36.5% of our outstanding common stock;

• Total held approximately 18.4% of our outstanding common stock; and

• our next two largest holders of outstanding common stock after Total (Maxwell Mauritius Pte. Ltd. and Biolding Investment SA, each of whom has a designee on our Board of Directors) together held approximately 22.1% of our outstanding common stock.

This significant concentration of share ownership may adversely affect the trading price for our common stock because investors often perceive disadvantages in owning stock in companies with controlling stockholders. Also, these stockholders, acting together, will be able to control our management and affairs and matters requiring stockholder approval, including the election of directors and the approval of significant corporate transactions, such as mergers, consolidations or the sale of substantially all of our assets. Consequently, this concentration of ownership may have the effect of delaying or preventing a change of control, including a merger, consolidation or other business combination involving us, or discouraging a potential acquirer from making a tender offer or otherwise attempting to obtain control, even if that change of control would benefit our other stockholders.

If securities or industry analysts do not publish or cease publishing research or reports about us, our business or our market, or if they change their recommendations regarding our stock adversely, our stock price and trading volume could decline.

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The trading market for our common stock will be influenced by the research and reports that industry or securities analysts may publish about us, our business, our market or our competitors. If any of the analysts who cover us change their recommendation regarding our stock adversely, or provide more favorable relative recommendations about our competitors, our stock price would likely decline. If any analyst who may cover us were to cease coverage of our company or fail to regularly publish reports on us, we could lose visibility in the financial markets, which in turn could cause our stock price or trading volume to decline.

We do not expect to declare any dividends in the foreseeable future.

We do not anticipate declaring any cash dividends to holders of our common stock in the foreseeable future. In addition, certain of our equipment leases and credit facilities currently restrict our ability to pay dividends. Consequently, investors may need to rely on sales of their common stock after price appreciation, which may never occur, as the only way to realize any future gains on their investment. Investors seeking cash dividends should not purchase our common stock.

Anti-takeover provisions contained in our certificate of incorporation and bylaws, as well as provisions of Delaware law, could impair a takeover attempt.

Our certificate of incorporation and bylaws contain provisions that could delay or prevent a change in control of our company. These provisions could also make it more difficult for stockholders to elect directors and take other corporate actions. These provisions include:

• staggered board of directors;

• authorizing the board to issue, without stockholder approval, preferred stock with rights senior to those of our common stock;

• authorizing the board to amend our bylaws and to fill board vacancies until the next annual meeting of the stockholders;

• prohibiting stockholder action by written consent;

• limiting the liability of, and providing indemnification to, our directors and officers;

• eliminating the ability of our stockholders to call special meetings; and

• requiring advance notification of stockholder nominations and proposals. 

Section 203 of the Delaware General Corporation Law prohibits, subject to some exceptions, “business combinations” between a Delaware corporation and an “interested stockholder,” which is generally defined as a stockholder who becomes a beneficial owner of 15% or more of a Delaware corporation's voting stock, for a three-year period following the date that the stockholder became an interested stockholder. We have agreed to opt out of Section 203 through our certificate of incorporation, but our certificate of incorporation contains substantially similar protections to our company and stockholders as those afforded under Section 203, except that we have agreed with Total that it and its affiliates will not be deemed to be “interested stockholders” under such protections.

In addition, we have an agreement with Total, which provides that, so long as Total holds at least 10% of our voting securities, we must inform Total of any offer to acquire us or any decision of our Board of Directors to sell our company, and we must provide Total with information about the contemplated transaction. In such events, Total will have an exclusive negotiating period of fifteen business days in the event the Board of Directors authorizes us to solicit offers to buy Amyris, or five business days in the event that we receive an unsolicited offer to purchase us. This exclusive negotiation period will be followed by an additional restricted negotiation period of ten business days, during which we are obligated to continue to negotiate with Total and will be prohibited from entering into an agreement with any other potential acquirer.

These and other provisions in our amended and restated certificate of incorporation and our amended and restated bylaws that became effective upon the completion of our initial public offering under Delaware law and in our agreement with Total could discourage potential takeover attempts, reduce the price that investors might be willing to pay in the future for shares of our common stock and result in the market price of our common stock being lower than it would be without these provisions.

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EXECUTIVE OFFICERS OF THE REGISTRANT

The following table provides the names, ages and offices of each of our executive officers as of March 5, 2013:

Name	Age	Position
Executive Officers:
John Melo	47	Director, President and Chief Executive Officer
Steven R. Mills	57	Chief Financial Officer
Peter Boynton	58	Chief Commercial Officer
Joel Cherry, Ph.D.	52	President of Research and Development
Paulo Diniz	55	Chief Executive Officer, Amyris Brasil Ltda.
Gary Loeb	43	Senior Vice President, General Counsel and Corporate Secretary
Zanna McFerson	47	Chief Business Officer
Key Employees:
Jack Newman, Ph.D.	46	Chief Scientific Officer

John Melo

John Melo has served as our President and Chief Executive Officer and a director since January 2007 and our President since January 2008. Before joining Amyris, Mr. Melo served in various senior management positions at BP Plc (formerly British Petroleum), one of the world’s largest energy firms, from 1997 to 2006, most recently as President of U.S. Fuels Operations from 2004 until December 2006, and previously as Chief Information Officer of the refining and marketing segment from 2001 to 2003, Senior Advisor for e-business strategy to Lord Browne, BP Chief Executive, from 2000 to 2001, and Director of Global Brand Development from 1999 to 2000. Before joining BP, Mr. Melo was with Ernst & Young, an accounting firm, from 1996 to 1997, and a member of the management teams of several startup companies, including Computer Aided Services, a management systems integration company, and Alldata Corporation, a provider of automobile repair software to the automotive service industry. Mr. Melo currently serves on the board of directors of U.S. Venture, Inc. and Renmatix Inc., and also serves as Vice Chairman of the Board of Directors of the Bay Area Biosciences Association (BayBio). Mr. Melo is an appointed member to the U.S. section of the U.S.-Brazil CEO Forum. Mr. Melo’s experience as a senior executive at one of the world’s largest energy companies provides critical leadership in designing the fuels value chain, shaping strategic direction and business transactions, and in building teams to drive innovation.

Steven R. Mills

Steven Mills has served as our Chief Financial Officer since May 2012. Prior to joining Amyris, Mr. Mills served as Senior Executive Vice President of Performance & Growth at Archer-Daniels-Midland Company (ADM), a global agricultural commodity processing company, from December 2010 to February 2012. Previously, he served as ADM’s Executive Vice President and Chief Financial Officer from March 2008 to December 2010. Mr. Mills joined ADM in 1979 and served in various senior accounting and treasury roles, including 12 years as Controller. He has been a director and a member of the audit committee of Black Hills Corporation, a diversified energy holding company, since October 2011. Mr. Mills also serves on the boards of Illinois College and Hickory Point Bank & Trust. He holds a Bachelor of Science degree in Mathematics from Illinois College in Jacksonville, Illinois.

Peter Boynton

Peter Boynton has served as our Chief Commercial Officer since December 2009. Mr. Boynton joined Amyris from Tate & Lyle Plc., a global food and agricultural ingredients company, where he served in various positions from 1999 to December 2009, most recently as Senior Vice President, Bio-products, and Fermentation. Previously, he held multiple positions at Cargill, Inc., a privately-held food and agriculture company, from 1980 to 1998, lastly as Vice President NACM. Mr. Boynton holds a Bachelor of Science degree in Economics from the University of Georgia.

Joel Cherry, Ph.D.

Dr. Joel Cherry has served as our President of Research and Development since July 2011 and previously as our Senior Vice President of Research Programs and Operations since November 2008. Before joining Amyris, Dr. Cherry was Senior Director of Bioenergy Biotechnology at Novozymes, a biotechnology company focusing on development and manufacture of industrial

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enzymes from 1992 to November 2008. At Novozymes, he served in a variety of R&D scientific and management positions, including membership in Novozymes’ International R&D Management team, and as Principal Investigator and Director of the BioEnergy Project, a U.S. Department of Energy-funded $18 million effort initiated in 2000. Dr. Cherry holds a Bachelor of Arts degree in Chemistry from Carleton College and a Doctor of Philosophy degree in Biochemistry from the University of New Hampshire.

Paulo Diniz

Paulo Diniz joined us as the CEO of Amyris Brasil in March 2011. Prior to joining Amyris, Mr. Diniz served as Chief Financial Officer of Bunge Brasil S.A., a wholly owned subsidiary of Bunge Ltd., an agribusiness and food company, from April 2009 to November 2010. From 2003 to April 2009, Mr. Diniz was Chief Financial Officer and a member of the board of directors of Cosan S.A., a renewable energy company. He received a Master of Business Administration degree from IMD in Switzerland, a B. of Sc. degree in Production Engineering from USP in Brazil, and did post graduate work in human resources at INSEAD in France.

Gary Loeb

Gary Loeb joined Amyris in March 2011 as Senior Corporate and Regulatory Counsel and became General Counsel and Corporate Secretary in May 2012. Previously, Mr. Loeb served as Vice President of Intellectual Property from March 2008 to May 2011 and as Head of Litigation, most recently as Associate General Counsel, from 2003 to March 2008 at Genentech, Inc., a biotechnology company. Prior to joining Genentech in 2000, Mr. Loeb practiced general intellectual property law in Los Angeles and San Francisco. Mr. Loeb holds a Doctor of Jurisprudence degree from Columbia Law School and a Bachelor of Science degree in Biological Sciences and Bachelor of Arts degree in English from Stanford University. Mr. Loeb also served as an Adjunct Professor at the University of San Francisco School of Law from 2006 through 2011, where he lectured on biotechnology law.

Zanna McFerson

Zanna McFerson joined us as our Chief Business Officer in March 2013. Prior to joining Amyris, Ms. McFerson was a Vice President at Cargill, Incorporated, a privately-held international producer and marketer of food, agricultural, financial and industrial products and services, where she served as Business Director, Truvia Enterprise, from August 2008 to February 2013. Previously, Ms. McFerson served as Business Director, Health and Nutrition - Truvia, at Cargill from May 2006 to July 2008. She joined Cargill in 1990 as a commodity trader and held various roles in sales, management, and new product development until joining the leadership team of Cargill Health and Nutrition in May 2005. Ms. McFerson received a Bachelor of Arts degree in Economics from the University of Illinois and a Master of Business Administration degree from the University of Iowa. She served on the Board of Directors for the International Stevia Council, is a member of the Finnish American Chamber of Commerce, and contributes to the American Swedish Institute in Minneapolis.

Key Employee

Jack Newman, Ph.D.

Dr. Jack Newman is a co-founder of Amyris and has served as our Chief Scientific Officer since July 2011 and previously as our Senior Vice President of Research since July 2007, and also served as our Director, Biology from 2004 to June 2007. Dr. Newman holds a Bachelor of Arts degree in Molecular and Cell Biology from the University of California, Berkeley and a Doctor of Philosophy degree from the University of Wisconsin-Madison in the field of microbial physiology and gene regulation.

Our executive officers are elected by, and serve at the discretion of, our Board of Directors. There are no family relationships among any of our directors and executive officers.

ITEM 1B. UNRESOLVED STAFF COMMENTS

Not applicable.

ITEM 2. PROPERTIES

We lease approximately 136,000 square feet of space in two adjacent buildings in Emeryville, California, pursuant to two leases. Of this space, we use approximately 113,000 square feet for general office purposes and lab space, and approximately 23,000 square feet comprise our pilot plant. Our leases expire in May 2018 and we have an option to extend these leases for five

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years. We also lease approximately 19,375 square feet of space in North Carolina under a month-to-month lease. This lease relates to manufacturing operations through Glycotech, one of our variable interest entities.

Amyris Brasil leases approximately 52,000 square feet of space in Campinas, Brazil, pursuant to two leases that will expire in October 2015 and November 2016. Of this space, approximately 36,000 square feet comprise a pilot plant and demonstration facility, and the remainder is general office and lab space. Amyris Brasil has a right of first refusal to purchase the space if the landlord elects to sell it and an option to extend the lease for five additional years.

Our first large-scale Biofene production plant commenced operations in December 2012 in Brotas in the state of São Paulo, Brazil and is adjacent to an existing sugar and ethanol mill, Paraíso Bioenergia. Amyris Brasil leases approximately 800,000 square feet of space for this plant, which has six 200,000 liter production fermenters and was designed to process sugarcane juice, or its equivalent, from up to one million tons of raw sugarcane annually; this lease expires in March 2026.  Amyris Brasil also leases approximately 500,000 square feet of space for a future manufacturing site; this lease expires in January 2031.

We have also secured the use of a Biofene storage tank with an aggregate capacity of 10,000 barrels in Illinois. This facility provides temporary storage of our renewable farnesene prior to further processing into one of our finished products. Our current agreement expires in September 2013. In addition, we have secured a second location for the same purpose in Texas for the use of a Biofene storage tank with an aggregate capacity of 10,000 barrels. Our current agreement in Texas expires in January 2014.

We believe that our current facilities are suitable and adequate to meet our needs and that suitable additional space will be available to accommodate the foreseeable expansion of our operations.

ITEM 3. LEGAL PROCEEDINGS

We are not involved in any legal proceedings that we believe will have a material adverse effect on our business, results of operations, financial position or cash flows. We may, however, be involved, from time to time, in legal proceedings and claims arising in the ordinary course of our business. Such matters are subject to many uncertainties and there can be no assurance that legal proceedings arising in the ordinary course of business or otherwise will not have a material adverse effect on our business, results of operations, financial position or cash flows.

ITEM 4. MINE SAFETY DISCLOSURES

Not applicable.

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PART II

ITEM 5. MARKET FOR REGISTRANT’S COMMON EQUITY, RELATED STOCKHOLDER MATTERS AND ISSUER PURCHASES OF EQUITY SECURITIES

Market Information for Common Stock

Our common stock commenced trading on the NASDAQ Global Market on September 28, 2010 under the symbol “AMRS” and currently trades on the NASDAQ Global Select Market under the same symbol. The following table sets forth the high and low per share sale prices of our common stock as reported on the NASDAQ Global Select Market during each of the previous eight quarters.

	Price Range Per Share
	High		Low
Fiscal 2012
Fourth quarter	$	3.48	$	2.16
Third quarter	$	4.56	$	2.74
Second quarter	$	5.16	$	1.57
First quarter	$	12.29	$	4.45
Fiscal 2011
Fourth quarter	$	20.86	$	9.90
Third quarter	$	28.75	$	17.57
Second quarter	$	30.78	$	24.01
First quarter	$	33.99	$	26.57

Holders

As of March 1, 2013, there were approximately 121 holders of record (not including beneficial holders of stock held in street names) of our common stock.

Dividend Policy

We have never declared or paid cash dividends on our capital stock. We currently intend to retain any future earnings and do not expect to declare or pay any dividends in the foreseeable future. Any further determination to pay dividends on our capital stock will be at the discretion of our Board of Directors and will depend on our financial condition, results of operations, capital requirements and other factors that our Board of Directors considers relevant. In addition, our equipment lease with TriplePoint Capital LLC currently restricts our ability to pay dividends.

Securities Authorized for Issuance Under Equity Compensation Plans

See Item 12 of Part III of this Report regarding information about securities authorized for issuance under our equity compensation plans.

Performance Graph⁽¹⁾ 

The following graph shows a comparison from September 28, 2010 through December 31, 2012 of cumulative total return on an assumed investment of $100.00 in cash in our common stock, the S&P SmallCap 600 Index and the NASDAQ Clean Edge Green Energy Index. Such returns are based on historical results and are not intended to suggest future performance. Data for the S&P SmallCap 600 Index and the NASDAQ Clean Edge Green Energy Index assume reinvestment of dividends.

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COMPARISON OF 27 MONTH CUMULATIVE TOTAL RETURN

Among Amyris, Inc., the S&P SmallCap 600 Index, and the NASDAQ Clean Edge Green Energy Index

	9/28/2010		12/31/2010		3/31/2011		6/30/2011		9/30/2011		12/31/2011		3/31/2012		6/30/2012		9/30/2012		12/31/2012
Amyris, Inc.	$	100	$	162	$	173	$	170	$	123	$	70	$	31	$	27	$	21	$	19
S&P SmallCap 600 Index	$	100	$	116	$	124	$	124	$	99	$	116	$	129	$	124	$	130	$	133
NASDAQ Clean Edge Green Energy Index	$	100	$	109	$	112	$	102	$	66	$	64	$	72	$	62	$	59	$	63

(1) This performance graph shall not be deemed “soliciting material” or to be “filed” with the SEC for purposes of Section 18 of the Securities Exchange Act of 1934, as amended, or otherwise subject to the liabilities under that Section, and shall not be deemed incorporated by reference into any filing of Amyris, Inc. under the Securities Act of 1933, as amended.

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Recent Sales of Unregistered Securities

On February 23, 2012, we sold 10,160,325 shares of our common stock at a price of $5.78 per share for aggregate cash proceeds of approximately $58.7 million.

On February 24, 2012, we sold senior unsecured convertible promissory notes in an aggregate principal amount of $25.0 million for aggregate cash proceeds of $25.0 million. Such notes were 3% senior unsecured convertible promissory notes with a March 1, 2017 maturity date and a conversion price equal to $7.0682 per share of common stock. As of December 31, 2012, the notes were convertible into an aggregate of up to 3,536,968 shares of common stock. The conversion price of the notes is subject to adjustment for proportional adjustments to outstanding common stock and under anti-dilution provisions in case of certain dividends and distributions. The note holders have a right to require repayment of 101% of the principal amount of the notes in the event of a change of control of Amyris. In addition, if the note holders do not require such repayment upon a change of control, then upon conversion of the notes following such change of control, we are required to pay the interest that would have otherwise accrued through maturity.

On May 18, 2012, we sold 1,736,100 shares of our common stock at a price of $2.36 per share for aggregate cash proceeds of approximately $4.1 million.

In July and September 2012, we completed the sale of senior unsecured convertible promissory notes in an aggregate principal amount of $53.3 million pursuant to a purchase agreement with Total ("Total Notes"). Under the purchase agreement: (i) on July 30, 2012, we sold a 1.5% senior unsecured convertible note due 2017 to Total in the face amount of $38.3 million, including $15.0 million in new funds and repayment by Amyris of $23.3 million in previously-provided diesel research and development funding by Total, and (ii) on September 14, 2012, we sold another note (in the same form) for $15.0 million in new funds from Total. The purchase agreement provides that additional notes may be sold in subsequent closings in July 2013 (for cash proceeds to Amyris of $30.0 million) and July 2014 (for cash proceeds to Amyris of $21.7 million, which would be settled in an initial installment of $10.85 million payable at such closing and a second installment of $10.85 million payable in January 2015).

The Total Notes each have a March 1, 2017 maturity date and a conversion price equal to $7.0682 per share of our common stock. The Total Notes bear interest of 1.5% per year (with a default rate of 2.5%), accruing from date of funding and payable at maturity or on conversion or a change of control where Total exercises a right to require us to repay the notes. Accrued interest is canceled if the notes are canceled based on a decision by Total to proceed with the underlying program and joint venture (a "Go" decision as discussed in "Note 9 - Significant Agreements" in Part I, Item 1 of this report). The notes become convertible into our common stock (i) within 10 trading days prior to maturity (if they are not canceled as described above prior to their maturity date), (ii) on a change of control of Amyris, (iii) if Total is no longer the largest stockholder of Amyris following a “No-Go” decision (subject to a six-month lock-up with respect to any shares of common stock issued upon conversion), and (iv) on a default by Amyris. If Total makes a final “Go” decision, then the notes will be exchanged by Total for equity interests in the Fuels JV, after which the notes will not be convertible and any obligation to pay principal or interest on the notes will be extinguished. If Total makes a “No-Go” decision, outstanding notes will remain outstanding and become payable at maturity.

As of September 30, 2012, the Total Notes were convertible into an aggregate of approximately 7,540,817 shares of our common stock. The conversion price of the notes is subject to adjustment for proportional adjustments to outstanding common stock and under anti-dilution provisions in case of certain dividends and distributions. Total has a right to require repayment of 101% of the principal amount of the notes in the event of a change of control of Amyris and the notes provide for payment of unpaid interest on conversion following such a change of control if Total does not require such repayment.

On December 24, 2012, we sold 14,177,849 shares common stock at a price of $2.98 per share for aggregate cash proceeds of $37.2 million and cancellation of $5.0 million of an outstanding senior unsecured convertible promissory notes we previously issued to Total. The cash settlement with respect to 5,033,557 of such shares occurred on January 14, 2013.

No underwriters were involved in the foregoing sales of securities. These securities were issued in private transactions pursuant to Section 4(2) of the Securities Act. The recipients of these securities acquired the securities for investment purposes only and without intent to resell, were able to fend for themselves in these transactions, and were accredited investors as defined in Rule 501 of Regulation D promulgated under Section 3(b) of the Securities Act, and appropriate restrictions were set out in the agreements for, and stock certificates and notes issued in, these transactions. These security holders had adequate access, through their relationships with us, to information about us.

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ITEM 6. SELECTED FINANCIAL DATA

The selected consolidated statements of operations data for the years ended December 31, 2012, 2011 and 2010 and the selected consolidated balance sheets data as of December 31, 2012 and 2011 are derived from our audited Consolidated Financial Statements, appearing elsewhere in this report. The historical results presented below are not necessarily indicative of financial results to be achieved in future periods. You should read the following selected financial data in conjunction with “Management’s Discussion Analysis of Financial Condition and Results of Operations” and our Consolidated Financial Statements and related Notes included in Item 8 of this report.

	Years Ended December 31,
	2012			2011			2010			2009			2008
	(In Thousands, Except Share and Per Share Amounts)
Consolidated Statements of Operations Data:
Revenues
Product sales	$	49,638		$	129,837		$	68,664		$	61,689		$	10,680
Grants and collaborations revenue	24,056			17,154			11,647			2,919			3,212
Total revenues	73,694			146,991			80,311			64,608			13,892
Cost and operating expenses
Cost of products sold	77,314			155,615			70,515			60,428			10,364
Loss on purchase commitments and write off of production assets	45,854			—			—			—			—
Research and development(1)	73,630			87,317			55,249			38,263			30,306
Sales, general and administrative(1)	78,718			83,231			40,393			23,558			16,622
Restructuring and asset impairment (income) charges	—			—			(2,061		)	5,768			—
Total cost and operating expenses	275,516			326,163			164,096			128,017			57,292
Net loss from operations	(201,822		)	(179,172		)	(83,785		)	(63,409		)	(43,400		)
Other income (expense):
Interest income	1,472			1,542			1,540			448			1,378
Interest expense	(4,926		)	(1,543		)	(1,443		)	(1,218		)	(377		)
Other income (expense), net	224			214			898			(621		)	(144		)
Total other income (expense)	(3,230		)	213			995			(1,391		)	857
Loss before income taxes	(205,052		)	(178,959		)	(82,790		)	(64,800		)	(42,543		)
Income tax benefit (provision)	(981		)	(552		)	—			—			207
Net loss	$	(206,033	)	$	(179,511	)	$	(82,790	)	$	(64,800	)	$	(42,336	)
Loss attributable to noncontrolling interest	894			641			920			341			472
Net loss attributable to Amyris, Inc.	$	(205,139	)	$	(178,870	)	$	(81,870	)	$	(64,459	)	$	(41,864	)
Deemed dividend related to a beneficial conversion feature	—			—			(42,009		)	—			—
Net loss attributable to Amyris, Inc. common stockholders	$	(205,139	)	$	(178,870	)	$	(123,879	)	$	(64,459	)	$	(41,864	)
Net loss per share attributable to common stockholders, basic and diluted	$	(3.62	)	$	(3.99	)	$	(8.35	)	$	(13.56	)	$	(9.91	)
Weighted-average shares of common stock outstanding used in computing net loss per share of common stock, basic and diluted	56,717,869			44,799,056			14,840,253			4,753,085			4,223,533

⁽¹⁾  Includes stock-based compensation expense.

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	As of December 31,
	2012		2011		2010		2009			2008
	(In Thousands)
Consolidated Balance Sheets Data:
Cash, cash equivalents, investments and restricted cash	$	31,644	$	103,592	$	257,933	$	71,716		$	52,888
Working capital	3,668		47,205		242,818		51,062			32,356
Property, plant and equipment, net	163,121		128,101		54,847		42,560			41,565
Total assets	242,834		320,111		357,453		122,159			98,823
Total indebtedness(1)	106,774		47,660		12,590		20,608			6,747
Convertible preferred stock warrant liability	—		—		—		2,740			2,132
Convertible preferred stock	—		—		—		179,651			121,436
Redeemable noncontrolling interest	—		—		—		5,506			—
Total equity (deficit)	66,229		160,812		307,548		(113,745		)	(52,143		)

⁽¹⁾  Total indebtedness as of December 31, 2012, 2011, 2010, 2009 and 2008 includes $2.6 million, $6.3 million, $5.9 million, $7.2 million and $3.6 million, respectively, in capital lease obligations, $1.6 million, $3.1 million, $5.7 million, $4.0 million and zero, respectively, in notes payable, $26.2 million, $19.4 million, $1.0 million, $1.0 million and $3.1 million, respectively, in loan payable, $12.4 million, $18.9 million, zero, $8.3 million and zero respectively, in credit facility. Total indebtedness as of December 31, 2012 also included $25.0 million in convertible notes and $39.0 million in related party convertible notes. There was no convertible notes balance outstanding as of December 31, 2011, 2010, 2009 and 2008 (see Note 5 and Note 6 to our Consolidated Financial Statements).

ITEM 7. MANAGEMENT’S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS OF OPERATIONS

Overview

Amyris is a renewable products company focused on providing sustainable alternatives to a broad range of petroleum-sourced products. We developed innovative microbial engineering and screening technologies that modify the way microorganisms process sugars. We are using our proprietary synthetic biology platform to design microbes, primarily yeast, and use them as living factories in established fermentation processes to convert plant-sourced sugars into renewable hydrocarbons. We are developing, and, in some cases, already commercializing, products from these hydrocarbons in several target markets, including cosmetics, lubricants, flavors and fragrances, polymers and plastic additives, home and personal care products, and transportation fuels. We call these No Compromise products because we design them to perform comparably to or better than currently available products.

We have been applying our industrial synthetic biology platform to provide alternatives to a broad range of petroleum-sourced products. We have focused our development efforts on the production of Biofene, our brand of renewable farnesene, a long-chain, branched liquid hydrocarbon molecule. Using Biofene as a first commercial building block molecule, we are developing a wide range of renewable products for our target markets.

While our platform is able to utilize a wide variety of feedstocks, we are focusing our large-scale production plans primarily on the use of Brazilian sugarcane as our feedstock because of its abundance, low cost and relative price stability. We have also produced Biofene from other feedstocks such as sugar beets, corn dextrose, sweet sorghum and cellulosic sugars.

Our first purpose-built, large-scale Biofene production plant commenced operations in southeastern Brazil in December 2012. This plant in Brotas, in the state of São Paulo, is adjacent to an existing sugar and ethanol mill, Paraíso Bioenergia. We have also advanced initial construction of a second large-scale production plant in Brazil, located at the Usina São Martinho sugar and ethanol mill also in the state of São Paulo, which we intend to complete when production economics support start-up of that plant. To satisfy initial commercial demand for our products until our own facilities are operating, we have leveraged contract-manufacturing capabilities of established companies.

Our business strategy is to focus our direct commercialization efforts on higher-value, lower-volume markets while moving lower-margin, higher-volume commodity products, including our fuels and base oil lubricants products, into joint venture arrangements with established industry leaders. We believe this approach will permit access to the capital and resources necessary

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to support large-scale production and global distribution for our large-market commodity products. Our initial renewable products efforts have been focused on cosmetics, niche fuel opportunities, fragrance oils, and farnesene for liquid polymers.

Total Relationship

In June 2010, we entered into a collaboration agreement with Total. This agreement provided for joint collaboration on the development of products through the use of our synthetic biology platform. In connection with this agreement, Total invested $133.2 million in our equity. In November 2011, we entered into an amendment of the collaboration agreement with Total with respect to development and commercialization of Biofene for diesel. This represented an expansion of the initial collaboration with Total, and established a global, exclusive collaboration for the development of Biofene for diesel and a framework for the creation of a joint venture to manufacture and commercialize Biofene for diesel. In addition, a limited number of other potential products were subject to development for the joint venture on a non-exclusive basis. In July 2012, we entered into a further amendment of the collaboration agreement with Total that expanded Total's investment in the Biofene collaboration, incorporated the development of certain joint venture products for use in diesel and jet fuel into the scope of the collaboration, and changed the structure of the funding from Total to include a convertible debt mechanism. Under the new agreements, we issued senior unsecured convertible notes to Total for an aggregate of $30.0 million in new cash in the third quarter of 2012. Total may decide to provide further funding at annual decision points in mid-2013 and 2014. Upon completion of the research and development program, we and Total would form a joint venture company that would have exclusive rights to produce and market renewable diesel and/or jet fuel. Should Total decide not to pursue commercialization, under certain conditions, it is eligible to recover up to $100 million, payable in March 2017, in the form of cash or in the form of common stock at a conversion price of $7.0682 per share (or, for notes issued in 2013, a lower price as determined under the March 2013 letter agreement as described below).

In connection with a private placement of our common stock that occurred in December 2012, Total elected to participate by exchanging approximately $5.0 million of its $53.3 million in senior unsecured convertible debt outstanding for 1,677,852 shares at the purchase price in this private placement of $2.98 per share. As such, $5.0 million of the outstanding $53.3 million in senior unsecured convertible debt was cancelled.

In March 2013, we entered into a letter agreement with Total under which Total agreed to waive its right to cease its participation in our fuels collaboration at the July 2013 decision point referenced above and committed to proceed with the July 2013 funding tranche of $30.0 million (subject to our satisfaction of the relevant closing conditions for such funding in the securities purchase agreement). As consideration for this waiver and commitment, we agreed to:

• Reduce the conversion price for the senior unsecured convertible promissory notes to be issued in connection with such funding from $7.0682 per share to a price per share equal to the greater of (i) the consolidated closing bid price of our common stock on the date of the letter agreement, plus $0.01, and (ii) $3.08 per share, provided that the conversion price will not be reduced by more than the maximum possible amount permitted under the NASDAQ rules such that the new conversion price would require us to obtain stockholder consent; and

• Grant Total a senior security interest in our intellectual property, subject to certain exclusions and subject to release by Total when we and Total enter into final documentation regarding the establishment of the Fuels JV.

In addition to the waiver by Total described above, Total also agreed that, at our request and contingent upon us meeting our obligations described above, it would pay advance installments of the amounts otherwise payable at the July 2013 closing.  Specifically, if we request such advance installments, subject to certain closing conditions and delivery of certifications regarding our cash levels, Total is obligated to fund $10.0 million no later than May 15, 2013, and an additional $10.0 million no later than June 15, 2013 , with the remainder funding on the original July 2013 closing date.

Contract Manufacturing

In 2010 and 2011, to support our initial commercial production of Biofene, we entered into contract manufacturing agreements with various contract manufacturing partners. We also established contract manufacturing relationships to support conversion of Biofene into finished chemical products. Under the terms of the associated contract manufacturing agreements, we provided necessary equipment for the manufacturing of products, over which we retained ownership. During 2012 and 2011, we reimbursed contract manufacturers for an aggregate of $13.8 million in expenditures related to the modification of their facilities. We recorded these costs as facility modification costs in other assets and amortized them as an offset against purchases of inventory. Certain of our contract manufacturing agreements have also imposed fixed purchase commitments on us, regardless of production volumes.

In January 2011, we entered into a production service agreement with Glycotech under which Glycotech performs finishing steps to convert Biofene into squalane, diesel, base oils for industrial lubricants, and other products. In addition, in July 2011, we

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entered into a contract manufacturing agreement with Albemarle under which Albemarle is to provide toll manufacturing services at its facility in South Carolina and we are obligated to reimburse Albemarle for capital expenditures related to facility modifications required for the services. In February 2012, we entered into an amended and restated agreement with Albemarle, which superseded the original contract manufacturing agreement with Albemarle. The term of the new agreement continues through December 31, 2019.  The agreement includes certain obligations for us to pay fixed costs totaling $7.5 million, of which $3.5 million and $4.0 million are payable in 2012 and 2014, respectively. In addition, fixed costs of $2.0 million per quarter are payable in 2013 if we exercise our option to have product manufactured in the facility in 2013.  The agreement also includes variable pricing during the contract term. We may seek to enter into additional contract manufacturing arrangements. We expect to work with third parties specializing in particular industries to convert Biofene by simple chemical processes and initially to sell it primarily in the forms of squalane, diesel, base oils for industrial lubricants, and other products.

Beginning in March 2012, we initiated a plan to shift production capacity from the contract manufacturing facilities to Amyris-owned plants that were then under construction. As a result, we evaluated our contract manufacturing agreements and recorded a loss of $31.2 million related to $10.0 million in facility modification costs and $21.2 million of fixed purchase commitments in the first quarter of 2012. We recognized additional charges of $1.4 million and $7.8 million, respectively, in the third and fourth quarter of 2012 associated with losses on fixed purchase commitments. We computed the loss on facility modification costs and fixed purchase commitments using the same lower of cost or market approach that is used to value inventory. The computation of the loss on firm purchase commitments is subject to several estimates, including cost to complete and the ultimate selling price of any of our products manufactured at the relevant production facilities, and is therefore inherently uncertain. We also recorded a loss on write-off of production assets of $5.5 million related to Amyris-owned production equipment at contract manufacturing facilities in the three months ended March 31, 2012.We will continue to evaluate the potential for losses in future periods based on updated production and sales price assumptions.

During the year endedDecember 31, 2012, we incurred $38.7 million of scale-up costs to support our production of Biofene-derived products that are included within cost of products sold. These scale-up costs include the contract manufacturing cost related to production of Biofene-derived products and the finishing of Biofene into finished products. We continue to commit significant resources to our production process in advance of our achieving full commercial production volume. As only a portion of our production costs varies with our revenue, our production costs will be greater than our revenue until we achieve significant product volume. We anticipate that our production costs will decrease as we continue to improve our processes and increase throughput.

Sales and Revenue

To commercialize our initial Biofene-derived product, squalane, for sale to cosmetics companies for use as a moisturizing ingredient in cosmetics and other personal care products, we have entered into marketing and distribution agreements with a number of distributors since June 2010. As an initial step towards commercialization of Biofene-based diesel, we have entered into agreements with several bus operators in São Paulo, Brazil. Our diesel fuel is supplied to BR Distribudora, a division of Petrobras, which in turn blends our product with petroleum diesel and sells to a number of bus operators including Santa Brigida, the largest bus fleet operator in São Paulo. For the industrial lubricants market, in June 2011 we established a joint venture with Cosan for the worldwide development, production and commercialization of renewable base oils.

We have also entered into agreements to sell Biofene and its derivatives directly to various potential customers, including with M&G for use in plastics, with Kuraray for use in production of polymers, with Michelin for use in tires, with Firmenich and Givaudan for ingredients for the flavors and fragrances market, and with Method for use in home and personal care products. Production and sale of our products pursuant to any of these relationships will depend on the achievement of contract-specific technical, development and commercial milestones.

Since inception through December 31, 2012, we have recognized $392.5 million in revenue, primarily from the sale of ethanol and reformulated ethanol-blended gasoline. We transitioned out of the ethanol and ethanol-blended business during the third quarter ended September 30, 2012. We do not expect to be able to replace much of the revenues lost in the near term as a result of this transition, particularly in 2013 while we continue our efforts to establish our renewable products business.

Financing

In 2012, we completed multiple financings involving loans and convertible debt and equity offerings. In February 2012, we completed a private placement of 10.2 million shares of common stock for aggregate proceeds of $58.7 million and raised $25.0 million from an offering of senior unsecured convertible promissory notes. In May 2012, we completed a private placement of 1.7 million shares of common stock for aggregate proceeds of $4.1 million. In July 2012, we completed a sale of $38.3 million in a senior unsecured convertible promissory note for cash proceeds of $15.0 million and our repayment of $23.3 million in

41

previously-provided research and development funds and, in September 2012, we completed a sale of an additional senior unsecured convertible promissory note for additional cash proceeds of $15.0 million. In December 2012, we completed a private placement of 14.2 million shares of common stock for aggregate proceeds of $37.2 million and the cancellation of $5.0 million worth of outstanding senior unsecured convertible promissory notes we previously issued to Total in exchange for approximately 1.7 million shares of common stock. Under the December 2012 purchase agreement and related documents, the purchase of a portion of the shares, representing $15.0 million of the proceeds from that transaction, was not settled until January 2013. Cash received as of December 31, 2012 in the December 2012 financing, net of the note conversion and the January 2013 settlement, was $22.2 million.

Liquidity

We have incurred significant losses in each year since our inception and believe that we will continue to incur losses and negative cash flow from operations into at least 2014. As of December 31, 2012, we had an accumulated deficit of $586.3 million and had cash, cash equivalents and short term investments of $30.7 million. We have significant outstanding debt and contractual obligations related to purchase commitments, as well as capital and operating leases. As of December 31, 2012, our debt totaled $104.2 million, of which $3.3 million matures within the next twelve months. In addition, our debt agreements contain various covenants, including restrictions on business that could cause us to be at risk of defaults. In March 2013, we signed a collaboration agreement that included a funding component, and obtained a commitment letter from Total with respect to additional convertible note funding (as described above), and we expect to use amounts received under these arrangements to fund our operations. Furthermore, we are expecting additional funding in 2013 from collaborations, equity or debt offerings, or combinations of these sources. Our operating plan contemplates securing a portion of this additional funding in the second quarter of 2013. However, as of the date of this filing, we have not yet secured this additional funding. There can be no assurance that financing will be available on commercially acceptable terms or at all. If we are unable to raise additional financing, or if other expected sources of funding are delayed or not received, we would take actions to support our liquidity needs that could have a material negative impact on our ability to continue our business as currently contemplated. See “Liquidity and Capital Resources” below in this section for additional detail regarding these contingency plans and their potential effects on our business.

Critical Accounting Policies and Estimates

Our discussion and analysis of our financial condition and results of operations is based upon our consolidated financial statements, which have been prepared in accordance with accounting principles generally accepted in the United States. The preparation of these consolidated financial statements requires us to make estimates and assumptions that affect the reported amounts of assets, liabilities, revenues, expenses and related disclosures. We base our estimates and assumptions on historical experience and on various other factors that we believe to be reasonable under the circumstances. We evaluate our estimates and assumptions on an ongoing basis. The results of our analysis form the basis for making assumptions about the carrying values of assets and liabilities that are not readily apparent from other sources. Our actual results may differ from these estimates under different assumptions or conditions.

We believe the following critical accounting policies involve significant areas of management’s judgments and estimates in the preparation of our financial statements.

Revenue Recognition

We currently recognize revenues from the sale of farnesene-derived products, from the delivery of collaborative research services and from government grants. Through the third quarter of 2012, we also sold ethanol and reformulated ethanol-blended gasoline under short-term agreements and in spot transactions at prevailing market prices. Revenues are recognized when all of the following criteria are met: persuasive evidence of an arrangement exists, delivery has occurred or services have been rendered, the fee is fixed or determinable and collectibility is reasonably assured.

If sales arrangements contain multiple elements, we evaluate whether the components of each arrangement represent separate units of accounting. Application of revenue recognition standards requires subjective determination and requires management to make judgments about the fair values of each individual element and whether it is separable from other aspects of the contractual relationship.

For each source of revenues, we apply the above revenue recognition criteria in the following manner:

Product Sales

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Starting in the second quarter of 2011, we commenced sales of farnesene-derived products. Through the third quarter of 2012, we also sold ethanol and reformulated ethanol-blended gasoline under short-term agreements and in spot transactions at prevailing market prices. Revenues are recognized, net of discounts and allowances, once passage of title and risk of loss have occurred, provided all other revenue recognition criteria have also been met.

Shipping and handling costs charged to customers are recorded as revenues. Shipping costs are included in cost of products sold. Such charges were not significant in any of the periods presented.

Grants and Collaborative Research Services

Revenues from collaborative research services are recognized as the services are performed consistent with the performance requirements of the contract. In cases where the planned levels of research services fluctuate over the research term, we recognize revenues using the proportionate performance method based upon actual efforts to date relative to the amount of expected effort to be incurred by us. When up-front payments are received and the planned levels of research services do not fluctuate over the research term, revenues are recorded on a ratable basis over the arrangement term, up to the amount of cash received. When up-front payments are received and the planned levels of research services fluctuate over the research term, revenues are recorded using the proportionate performance method, up to the amount of cash received. Where arrangements include milestones that are determined to be substantive and at risk at the inception of the arrangement, revenues are recognized upon achievement of the milestone and is limited to those amounts whereby collectibility is reasonably assured.

Government grants are made pursuant to agreements that generally provide cost reimbursement for certain types of expenditures in return for research and development activities over a contractually defined period. Revenues from government grants are recognized in the period during which the related costs are incurred, provided that the conditions under which the government grants were provided have been met and only perfunctory obligations are outstanding. Under a government contract signed in June 2012, we will receive funding based on achievement of program milestones and accordingly revenues are recognized using the proportionate performance method based upon actual efforts to date relative to the amount of expected effort to be incurred, up to the amount of verified payable milestones.

Consolidations

We have interests in certain joint venture entities that are variable interest entities or VIEs. Determining whether to consolidate a variable interest entity may require judgment in assessing (i) whether an entity is a variable interest entity and (ii) if we are the entity’s primary beneficiary and thus required to consolidate the entity. To determine if we are the primary beneficiary of a VIE, we evaluate whether we have (i) the power to direct the activities that most significantly impact the VIE’s economic performance and (ii) the obligation to absorb losses or the right to receive benefits of the VIE that could potentially be significant to the VIE. Our evaluation includes identification of significant activities and an assessment of our ability to direct those activities based on governance provisions and arrangements to provide or receive product and process technology, product supply, operations services, equity funding and financing and other applicable agreements and circumstances. Our assessment of whether we are the primary beneficiary of our VIEs requires significant assumptions and judgment.

Impairment of Long-Lived Assets

We assess impairment of long-lived assets, which include property, plant and equipment and test long-lived assets for recoverability when events or changes in circumstances indicate that their carrying amount may not be recoverable. Circumstances which could trigger a review include, but are not limited to, significant decreases in the market price of the asset; significant adverse changes in the business climate or legal factors; accumulation of costs significantly in excess of the amount originally expected for the acquisition or construction of the asset; current period cash flow or operating losses combined with a history of losses or a forecast of continuing losses associated with the use of the asset; or expectations that the asset will more likely than not be sold or disposed of significantly before the end of its estimated useful life.

Recoverability is assessed based on the fair value of the asset, which is calculated as the sum of the undiscounted cash flows expected to result from the use and the eventual disposal of the asset. An impairment loss is recognized in the consolidated statements of operations when the carrying amount is determined not to be recoverable and exceeds fair value, which is determined on a discounted cash flow basis.

We make estimates and judgments about future undiscounted cash flows and fair values. Although our cash flow forecasts are based on assumptions that are consistent with our plans, there is significant exercise of judgment involved in determining the cash flow attributable to a long-lived asset over its estimated remaining useful life. Our estimates of anticipated cash flows could be reduced significantly in the future. As a result, the carrying amounts of our long-lived assets could be reduced through impairment

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charges in the future. We recorded losses on write-off of production assets of $6.4 million during the year ended December 31, 2012. There were no such losses on write off of production assets recorded in the years ended December 31, 2011 and 2010.

Inventories

Inventories, which consist of farnesene-derived products, ethanol and reformulated ethanol-blended gasoline, are stated at the lower of cost or market. In the quarter ended September 30, 2012, we sold our remaining inventory of ethanol and reformulated ethanol-blended gasoline as we transitioned out of this business. We evaluate the recoverability of our inventories based on assumptions about expected demand and net realizable value. If we determine that the cost of inventory exceeds its estimated net realizable value, we record a write-down equal to the difference between the cost of inventory and the estimated net realizable value. If actual net realizable values are lower than those projected by management, additional inventory write-downs may be required that could negatively impact our operating results. If actual net realizable values are more than those projected by management, we may have favorable operating results when products that have been previously written down are sold in the normal course of business. We also evaluate the terms of our agreements with our suppliers and establish accruals for estimated losses on adverse purchase commitments as necessary, applying the same lower of cost or market approach that is used to value inventory.

Goodwill and Intangible Assets 

Goodwill represents the excess of the cost over the fair value of net assets acquired from our business combinations. Intangible assets are comprised primarily of in-process research and development ('IPR&D"). We make significant judgments in relation to the valuation of goodwill and intangible assets resulting from business combinations and asset acquisitions.

There are several methods that can be used to determine the estimated fair value of the IPR&D acquired in a business combination. We have used the "income method," which applies a probability weighting that considers the risk of development and commercialization, to the estimated future net cash flows that are derived from projected sales revenues and estimated costs. These projections are based on factors such as relevant market size, pricing of similar products, and expected industry trends. The estimated future net cash flows are then discounted to the present value using an appropriate discount rate. These assets are treated as indefinite-lived intangible assets until completion or abandonment of the projects, at which time the assets will be amortized over the remaining useful life or written off, as appropriate.

Goodwill and intangible assets with indefinite lives are assessed for impairment using fair value measurement techniques on an annual basis or more frequently if facts and circumstance warrant such a review. When required, a comparison of fair value to the carrying amount of assets is performed to determine the amount of any impairment.

We evaluate our intangible assets with finite lives for indications of impairment whenever events or changes in circumstances indicate that the carrying value may not be recoverable. Intangible assets consist of purchased licenses and permits and are amortized on a straight-line basis over their estimated useful lives. Factors that could trigger an impairment review include significant under-performance relative to historical or projected future operating results, significant changes in the manner of our use of the acquired assets or the strategy for our overall business or significant negative industry or economic trends. If this evaluation indicates that the value of the intangible asset may be impaired, we make an assessment of the recoverability of the net carrying value of the asset over its remaining useful life. If this assessment indicates that the intangible asset is not recoverable, based on the estimated undiscounted future cash flows of the technology over the remaining amortization period, we will reduce the net carrying value of the related intangible asset to fair value and may adjust the remaining amortization period. Any such impairment charge could be significant and could have a material adverse effect on our reported financial results. We have not recognized any impairment charges on our intangible assets through December 31, 2012.

Stock-Based Compensation

Stock-based compensation cost for RSUs is measured based on the closing fair market value of our common stock on the date of grant. Stock-based compensation cost for stock options and employee stock purchase plan rights is estimated at the grant date and offering date, respectively, based on the fair-value of our common stock using the Black-Scholes option pricing model. We amortize the fair value of the employee stock options on a straight-line basis over the requisite service period of the award, which is generally the vesting period. The measurement of nonemployee stock-based compensation is subject to periodic adjustments as the underlying equity instruments vest, and the resulting change in value, if any, is recognized in our consolidated statements of operations during the period the related services are rendered. There is inherent uncertainty in these estimates and if different assumptions had been used, the fair value of the equity instruments issued to nonemployee consultants could have been significantly different.

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In future periods, our stock-based compensation expense is expected to change as a result of our existing unrecognized stock-based compensation still to be recognized and as we issue additional stock-based awards in order to attract and retain employees and nonemployee consultants.

Significant Factors, Assumptions and Methodologies Used In Determining Fair Value

We utilize the Black-Scholes option pricing model to estimate the fair value of our equity awards. The Black-Scholes option pricing model requires inputs such as the expected term of the grant, expected volatility and risk-free interest rate. Further, the forfeiture rate also affects the amount of aggregate compensation that we are required to record as an expense. These inputs are subjective and generally require significant judgment.

The fair value of employee stock options was estimated using the following weighted-average assumptions:

	Years Ended December 31,
	2012	2011	2010
Expected dividend yield	—%	—%	—%
Risk-free interest rate	1.1%	2.3%	2.5%
Expected term (in years)	6.0	5.8	6.0
Expected volatility	77%	86%	96%

Expected term is derived from a comparable group of publicly listed companies that has a similar industry, life cycle, revenue, and market capitalization and the historical data on employee exercises.

Expected volatility is derived from a combination of historical volatility for our stock and the historical volatilities of a comparable group of publicly listed companies within our industry over a period equal to the expected term of our options because we do not yet have a long trading history.

Risk-free interest rate is the market yield currently available on United States Treasury securities with maturities approximately equal to the option’s expected term.

Expected dividend yield was assumed to be zero as we have not paid, and do not anticipate, declaring any cash dividends to holders of our common stock in the foreseeable future.

We estimate our forfeiture rate based on an analysis of our actual forfeitures and will continue to evaluate the appropriateness of the forfeiture rate based on actual forfeiture experience, analysis of employee turnover and other factors. Quarterly changes in the estimated forfeiture rate can have a significant effect on reported stock-based compensation expense, as the cumulative effect of adjusting the rate for all expense amortization is recognized in the period the forfeiture estimate is changed. If a revised forfeiture rate is higher than the previously estimated forfeiture rate, an adjustment is made that will result in a decrease to the stock-based compensation expense recognized in the consolidated financial statements. If a revised forfeiture rate is lower than the previously estimated forfeiture rate, an adjustment is made that will result in an increase to the stock-based compensation expense recognized in the consolidated financial statements.

We will continue to use judgment in evaluating the expected term, volatility and forfeiture rate related to our own stock-based compensation on a prospective basis and incorporating these factors into the Black-Scholes option pricing model.

Each of these inputs is subjective and generally requires significant management judgment to determine. If, in the future, we determine that another method for calculating the fair value of our stock options is more reasonable, or if another method for calculating these input assumptions is prescribed by authoritative guidance, and, therefore, should be used to estimate expected volatility or expected term, the fair value calculated for our employee stock options could change significantly. Higher volatility and longer expected terms generally result in an increase to stock-based compensation expense determined at the date of grant.

Income Taxes

We are subject to income taxes in both the U.S. and foreign jurisdictions, and we use estimates in determining our provisions for income taxes. We use the liability method of accounting for income taxes, whereby deferred tax assets or liability account

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balances are calculated at the balance sheet date using current tax laws and rates in effect for the year in which the differences are expected to affect taxable income.

Recognition of deferred tax assets is appropriate when realization of such assets is more likely than not. We recognize a valuation allowance against our net deferred tax assets if it is more likely than not that some portion of the deferred tax assets will not be fully realizable. This assessment requires judgment as to the likelihood and amounts of future taxable income by tax jurisdiction. At December 31, 2012, we had a full valuation allowance against all of our deferred tax assets.

We apply the provisions of FASB's guidance on accounting for uncertainty in income taxes. We assess all material positions taken in any income tax return, including all significant uncertain positions, in all tax years that are still subject to assessment or challenge by relevant taxing authorities. Assessing an uncertain tax position begins with the initial determination of the position’s sustainability and the tax benefit to be recognized is measured at the largest amount of benefit that is greater than 50 percent likely of being realized upon ultimate settlement. As of each balance sheet date, unresolved uncertain tax positions must be reassessed, and we will determine whether (i) the factors underlying the sustainability assertion have changed and (ii) the amount of the recognized tax benefit is still appropriate. The recognition and measurement of tax benefits requires significant judgment. Judgments concerning the recognition and measurement of a tax benefit might change as new information becomes available.

Embedded Derivatives Related to Convertible Notes

Embedded derivatives that are required to be bifurcated from the underlying debt instrument (i.e. host) are accounted for and valued as a separate financial instrument. We evaluated the terms and features of our convertible notes payable and identified a compound embedded derivative (a conversion option that contains a “make-whole interest” provision) requiring bifurcation and accounting at fair value because the economic and contractual characteristics of the embedded derivative met the criteria for bifurcation and separate accounting due to the conversion option containing a “make-whole interest” provision, that requires cash payment for forgone interest upon a change of control. We estimate the fair value of the compound embedded derivative using a Black-Scholes valuation model that combines expected cash outflows with market-based assumptions regarding risk-adjusted yields, stock price volatility, probability of a change of control and the trading information of our common stock into which the notes are convertible. The change in the fair value of the bifurcated compound derivative is primarily related to the change in price of the underlying common stock and is reflected in our consolidated statements of operations as “other income (expense).”

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Results of Operations

Comparison of Year Ended December 31, 2012 to Year Ended December 31, 2011

Revenues

	Years Ended December 31,				Year-to  Year Change			Percentage Change
	2012		2011
	(Dollars in thousands)
Revenues
Product sales	$	49,638	$	129,837	$	(80,199	)	(62	)%
Grants and collaborations revenue	24,056		17,154		6,902			40	%
Total revenues	$	73,694	$	146,991	$	(73,297	)	(50	)%

Our total revenues decreased by $73.3 million to $73.7 million in 2012 with such reduction resulting primarily from decreases in product sales. Revenue from product sales decreased by $80.2 million to $49.6 million primarily from lower sales of ethanol and reformulated ethanol-blended gasoline purchased from third parties which accounted for $90.2 million of the reduction, with a decrease in gallons sold and an increase in average selling price per gallon compared to 2011. We sold 2.3 million gallons of ethanol and11.2 million gallons of reformulated ethanol-blended gasoline in the 2012 compared to 10.1 million gallons of ethanol and 36.4 million gallons of reformulated ethanol-blended gasoline sales in the prior year. Product sales of our farnesene-derived products increased $10.0 million in 2012 compared to the prior year. Grants and collaborations revenue in 2012 increased by $6.9 million compared to the prior year primarily due to the revenue recognized upon the amendment of our collaboration agreement with Total as described in more detail in "Financial Statements and Supplementary Data-Note 4-Balance Sheet Components," which resulted in the recognition of approximately $9.8 million in collaboration revenue, partially offset by a decline in other collaboration revenue of $2.9 million.

Nearly all of our revenues to date have come from the sale of ethanol and reformulated ethanol-blended gasoline with the remainder coming from renewable products as well as from collaborations and government grants. We transitioned out of the ethanol and ethanol-blended gasoline business during the third quarter of 2012. We do not expect to be able to replace much of the revenue lost in the near term as a result of this transition, particularly in 2013 while we continue our efforts to establish a renewable products business.

Cost and Operating Expenses

	Years Ended December 31,				Year-to  Year Change			Percentage Change
	2012		2011
	(Dollars in thousands)
Cost of products sold	$	77,314	$	155,615	$	(78,301	)	(50	)%
Loss on purchase commitments and write-off of production assets	45,854		—		45,854			nm
Research and development	73,630		87,317		(13,687		)	(16	)%
Sales, general and administrative	78,718		83,231		(4,513		)	(5	)%
Total cost and operating expenses	$	275,516	$	326,163	$	(50,647	)	(16	)%

______________ 

nm= not meaningful

Cost of Products Sold

Cost of products sold consists primarily of cost of purchased ethanol and reformulated ethanol-blended gasoline, terminal fees paid for storage and handling, transportation costs between terminals and changes in the fair value of derivative commodity instruments. Starting in the second quarter of 2011, our cost of products sold also included production costs of farnesene-derived products, which included cost of raw materials, amounts paid to contract manufacturers and period costs including inventory write-

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downs resulting from applying lower-of-cost-or-market inventory valuations. Cost of farnesene-derived products sold also includes certain costs related to the scale-up in production of such products. Our cost of products sold decreased by $78.3 million to $77.3 million in 2012 compared to the prior year. We had a decrease of $91.5 million in costs of ethanol and reformulated ethanol-blended gasoline purchased from third parties primarily due to a decline in product volume partially offset by an increase in average unit cost. This decrease in cost of products sold for ethanol and reformulated ethanol-blended gasoline was partially offset by an increase in product costs of farnesene-derived products of $13.2 million compared to the prior year as we scale up our renewable operations.

We transitioned out of our ethanol and gasoline business in the quarter ended September 30, 2012, which resulted in a reduction of cost of products sold. As we are now operating our own large-scale Biofene production plant in Brotas, in the state of São Paulo, Brazil as of December 2012, we will have a scale-up of production from this facility and the associated manufacturing costs. As we develop cost efficient manufacturing in our first production facility, we expect to seek to work selectively with other Brazilian sugar and ethanol producers to build additional facilities adjacent to their existing mills, thereby reducing the capital required to establish and scale our production operations.

We expect our cost per unit of products sold associated with farnesene-derived products to decline if and when we achieve full-scale commercial production at our large-scale manufacturing facility. We are not able to predict when or if this will occur.

Cost of Products Sold Associated with Loss on Purchase Commitments and Write-Off of Production Assets

Beginning in March 2012, we initiated a plan to shift a portion of our production capacity from contract manufacturing facilities to Amyris-owned plants that were then under construction. As a result, we evaluated our contract manufacturing agreements and, in the first quarter of 2012, recorded a loss of $31.2 million related to facility modification costs and fixed purchase commitments. We also recorded an impairment charge of $5.5 million in the three months ended March 31, 2012 related to Amyris-owned equipment at contract manufacturing facilities, based on the excess of the carrying value of the assets over their fair value. We recognized additional charges of $1.4 million and $7.8 million, respectively, in the third and fourth quarter of 2012 associated with losses on fixed purchase commitments. We computed the loss on facility modification costs and fixed purchase commitments using the same approach that is used to value inventory-the lower of cost or market value. The computation of the loss on firm purchase commitments is subject to several estimates, including the ultimate selling price of any of our products manufactured at the relevant production facilities, and is therefore inherently uncertain.

Research and Development Expenses

Our research and development expenses decreased by $13.7 million in 2012 over the prior year, primarily as a result of overall lower spending. The decreases were attributable to a $5.7 million reduction in expenses associated with completions of certain outsourced process development projects, a $2.5 million decrease in outsourced services resulting from completion of certain phases of our government grants project, $2.2 million reduction in outside consulting expenses, a $1.9 million decrease in personnel-related expenses associated with lower headcount, and a $0.9 million decrease in travel-related expenses and other overhead expenses. Research and development expenses included stock-based compensation expense of $6.5 million in 2012 compared to $6.3 million in 2011.

Sales, General and Administrative Expenses

Our sales, general and administrative expenses decreased by $4.5 million in 2012 compared to the same period of the prior year. The decrease is attributed primarily to a $7.3 million reduction in spend for consulting and professional service fees and a $0.9 million decrease in travel-related expenses partially offset by a $3.6 million increase in personnel-related expenses associated with severance and transition costs and higher stock-based compensation. Sales, general and administrative expenses included stock-based compensation expense of $21.0 million and $19.1 million during 2012 and 2011, respectively.

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Other Income (Expense)

	Years Ended December 31,						Year-to  Year Change			Percentage Change
	2012			2011
	(Dollars in thousands)
Other income (expense):
Interest income	$	1,472		$	1,542		$	(70	)	(5	)%
Interest expense	(4,926		)	(1,543		)	(3,383		)	219	%
Other income, net	224			214			10			5	%
Total other income (expense)	$	(3,230	)	$	213		$	(3,443	)	(1,616	)%

Total other expense increased by approximately $3.4 million to $3.2 million in 2012 compared to the prior year. The increase in total other expense was related primarily to higher interest expense of $3.4 million associated with increased borrowings to fund our operations including capital expenditures for the coming year. Other income, net for the year ended December 31, 2012 included a gain of $3.1 million attributable to the change in fair value of a compound embedded derivative liability associated with our senior unsecured convertible promissory notes issued to Total which was partially offset by a $1.4 million expense recognized for the fair market value of a currency interest swap derivative liability, a $0.9 million loss on the extinguishment of the $5.0 million debt associated with the December 2012 private placement and a $0.5 million realized loss on foreign currency transactions. No corresponding amounts related to these transactions were recognized during the year ended December 31, 2011.

Comparison of Year Ended December 31, 2011 to Year Ended December 31, 2010

Revenues

	Years Ended December 31,				Year-to  Year Change		Percentage Change
	2011		2010
	(Dollars in thousands)
Revenues
Product sales	$	129,837	$	68,664	$	61,173	89	%
Grants and collaborations revenue	17,154		11,647		5,507		47	%
Total revenues	$	146,991	$	80,311	$	66,680	83	%

Our total revenue increased by $66.7 million to $147.0 million in 2011 from $80.3 million in 2010 primarily as a result of increases in product sales. Revenue from product sales increased by $61.2 million to $129.8 million primarily from sales of ethanol and reformulated ethanol-blended gasoline purchased from third parties in 2011, resulting primarily from an increase in average selling price per gallon and an increase in gallons sold over 2010 due primarily to an increase in demand from existing customers. We sold 10.1 million gallons of ethanol and 36.4 million gallons of reformulated ethanol-blended gasoline in the 2011 compared to 20.6 million gallons of ethanol and 12.4 million gallons of reformulated ethanol-blended gasoline sales in the prior year. We recognized product sales from farnesene-derived products for the first time in the quarter ended June 30, 2011, which have not been significant to date. The increase of $5.5 million in grants and collaborations revenue was primarily the result of higher revenue generated from collaborative research offset in part by lower grant revenue in 2011 compared to the prior year.

Cost and Operating Expenses

	Years Ended December 31,					Year-to  Year Change		Percentage Change
	2011		2010
	(Dollars in thousands)
Cost of products sold	$	155,615	$	70,515		$	85,100	121	%
Research and development	87,317		55,249			32,068		58	%
Sales, general and administrative	83,231		40,393			42,838		106	%
Restructuring and asset impairment (income) charges	—		(2,061		)	2,061		(100	)%
Total cost and operating expenses	$	326,163	$	164,096		$	162,067	99	%

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Cost of Products Sold

Our cost of products sold increased by $85.1 million to $155.6 million in 2011 compared to the prior year. The increase was primarily the result of an increase of $59.6 million in costs of ethanol and reformulated ethanol-blended gasoline purchased from third parties, which was based on an increase in product cost per gallon and higher product volume. We also incurred $25.5 million of cost of renewable products, of which $15.4 million is associated with inventory write downs resulting from applying the lower-of-cost-or-market inventory valuation. Cost of renewable products also included some costs related to the scale-up in production of such products and had no corresponding charge in the prior year.

Research and Development Expenses

Our research and development expenses increased by $32.1 million in 2011 over the prior year, primarily as a result of an $11.3 million increase in personnel-related expenses associated with headcount growth and higher stock-based compensation, a $10.0 million increase in outside consulting expenses associated with increased development activities and $5.8 million in higher overhead costs associated with increased headcount and development activities. Research and development expenses included stock-based compensation expense of $6.3 million in 2011 compared to $2.2 million in 2010.

Sales, General and Administrative Expenses

Our sales, general and administrative expenses increased by $42.8 million in 2011 over the prior year, primarily as a result of increased personnel-related expenses of $24.1 million, higher consulting fees of $8.4 million and higher professional fees of $2.0 million associated with higher legal and auditing fees. The increase in consulting and professional fees was due primarily to a success fee of $5.0 million owed to a chemical conversion contract manufacturer and a termination penalty of $1.0 million owed to terminate a research and development contract related to production development. Sales, general and administrative expenses included stock-based compensation expense of $19.1 million and $8.3 million during 2011 and 2010, respectively.

Restructuring and Asset Impairment Charges (Income)

In June 2009, we initiated a restructuring plan to reduce our cost structure. The restructuring plan resulted in the consolidation of our headquarter facility located in Emeryville, California, which is under an operating lease. We ceased using a certain part of our headquarter facility in August 2009. We recorded approximately $5.4 million of restructuring charges associated with the facility lease costs after the operations ceased. In addition, as a result of the consolidation of the headquarter facility, we recorded approximately $3.1 million related to asset impairments and reversed $2.7 million related to deferred rent associated with the leased facility.

In September 2010, our Board of Directors approved our plan to reoccupy the part of our headquarter facility that previously was the subject of the 2009 restructuring. This reoccupied space was used to meet our expansion requirements. As a result, we reversed approximately $4.6 million of our restructuring liability that had been accrued in connection with the 2009 restructuring and recognized income from restructuring of $2.1 million during the year ended December 31, 2010.

Other Income (Expense)

	Years Ended December 31,						Year-to  Year Change			Percentage Change
	2011			2010
	(Dollars in thousands)
Other income (expense):
Interest income	$	1,542		$	1,540		$	2		—	%
Interest expense	(1,543		)	(1,443		)	(100		)	7	%
Other income, net	214			898			(684		)	(76	)%
Total other income	$	213		$	995		$	(782	)	(79	)%

Total other income decreased by approximately $0.8 million to $0.2 million in 2011 compared to the prior year. The decrease is related primarily to a decline in other income, net of approximately $0.7 million and to higher interest expense of $0.1 million associated with higher debt balances. The $0.7 million decrease in other income, net is primarily the result of our having recorded $0.9 million in income for the change in fair value of our convertible preferred stock warrants in 2010. These warrants converted into warrants to purchase our common stock upon completion of our initial public offering, or IPO, in September 2010.

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Deemed Dividend

We recognized a deemed dividend in 2010 related to the charges incurred with the one-time beneficial conversion feature of the Series D convertible preferred stock of $39.3 million and to the one-time beneficial conversion feature related to the conversion of Amyris Brasil S.A. shares of $2.7 million, each of which converted into Amyris Inc. common stock upon the consummation of our IPO. The deemed dividend was recorded at the closing of the IPO and impacted earnings and earnings per share in 2010.

Liquidity and Capital Resources

	December 31,
	2012			2011
	(Dollars in thousands)
Working capital	$	3,668		$	47,205
Cash and cash equivalents and short-term investments	$	30,689		$	103,592
Debt and capital lease obligations	$	106,774		$	47,660
Accumulated deficit	$	(586,327	)	$	(381,188	)

	Years Ended December 31,
	2012			2011			2010
Net cash used in operating activities	$	(150,872	)	$	(92,496	)	$	(64,577	)
Net cash provided by (used in) investing activities	(49,644		)	5,853			(79,405		)
Net cash provided by financing activities	138,117			41,052			266,687

Working Capital. Working capital was $3.7 million at December 31, 2012, a decrease of $43.5 million from working capital as of December 31, 2011. This decrease was principally attributable to a reduction in net cash and investment balances of $72.9 million due primarily to our investment in large scale production plants, and a decline of $10.9 million in other current assets largely related to the write off of facility modification costs at one of our contract manufacturing facilities. This decrease was offset in part by a reduction of $24.7 million in short term debt balances and a reduction of $17.6 million in accounts payable and accrued and other current liabilities.

To support production of our products in contract manufacturing and dedicated production facilities, we have incurred, and we expect to continue to incur, capital expenditures as we invest in these facilities.We plan to continue to seek external debt financing from U.S. and Brazilian sources to help fund our investment in these contract manufacturing and dedicated production facilities.

We expect to fund our operations for the foreseeable future with cash and investments currently on hand, with cash inflows from collaboration and grant funding, cash contributions from product sales, and with new debt and equity financing. Our planned 2013 working capital needs and our planned operating and capital expenditures for 2013 are dependent on significant inflows of cash from existing collaboration partners, as well as additional funding from new collaborations, equity or debt offerings, credit facilities or loans, or combinations of these sources. We will continue to need to fund our research and development and related activities and to provide working capital to fund production, storage, distribution and other aspects of its business. Our operating plan contemplates capital expenditures of approximately $10.0 million in 2013 and we expect to continue to incur costs in connection with our existing contract manufacturing arrangements.

Liquidity. We have incurred significant losses in each year since our inception and believe that we will continue to incur losses and negative cash flow from operations into at least 2014. As of December 31, 2012, we had an accumulated deficit of $586.3 million and had cash, cash equivalents and short term investments of $30.7 million. We have significant outstanding debt and contractual obligations related to purchase commitments, as well as capital and operating leases. As of December 31, 2012, our debt totaled $104.2 million, of which $3.3 million matures within the next twelve months. In addition, our debt agreements contain various covenants, including restrictions on business that could cause us to be at risk of defaults. In March 2013, we signed

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a collaboration agreement that included a funding component, and obtained a commitment letter from Total with respect to additional convertible note funding (as described above under "Overview-Total Relationship"), and we expect to use amounts received under these arrangements to fund our operations. Furthermore, we are expecting additional funding in 2013 from collaborations, equity or debt offerings, or combinations of these sources. Our operating plan contemplates securing a portion of this additional funding in the second quarter of 2013. However, as of the date of this filing, we have not yet secured this additional funding. There can be no assurance that financing will be available on commercially acceptable terms or at all.

If we are unable to raise additional financing, or if other expected sources of funding are delayed or not received, we would take the following actions as early as the second quarter of 2013 to support our liquidity needs through the remainder of 2013 and into 2014:

• Effect significant headcount reductions in the U.S. and in Brazil, particularly with respect to both general and administrative employees and other employees not connected to critical or contracted activities.

• Shift our focus to existing products and customers with significantly reduced investment in new product and commercial development efforts.

• Reduce our expenditures for third party contractors, including consultants, professional advisors and other vendors.

• Suspend operations at our pilot plants and demonstration facilities.

• Reduce or delay uncommitted capital expenditures, including non-essential lab equipment and information technology projects.

The contingency cash plan contemplating these actions is designed to save us an estimated $35 million to $40 million over the next twelve months. Implementing this plan could have a material negative impact on our ability to continue our business as currently contemplated, including, without limitation, delays or failures in our ability to:

• Achieve planned production levels;

• Develop and commercialize products within planned timelines or at planned scales; and

• Continue other core activities.

Furthermore, any inability to scale-back operations as necessary, and any unexpected liquidity needs, could create pressure to implement more severe measures. Such measures could have a material adverse effect on our ability to meet contractual requirements, including obligations to maintain manufacturing operations, and increase the severity of the consequences described above.

Convertible Note Offering. In February 2012, we sold $25.0 million in principal amount of senior unsecured convertible promissory notes due March 1, 2017. The notes have a 3.0% annual interest rate and are convertible into shares of our common stock at a conversion price of $7.0682 per share, subject to adjustment for proportional adjustments to outstanding common stock and anti-dilution provisions in case of dividends and distributions.  The note holders have a right to require repayment of 101% of the principal amount of the notes in an acquisition of Amyris, and the notes provide for payment of unpaid interest on conversion following such an acquisition if the note holders do not require such repayment.  The securities purchase agreement and notes include covenants regarding payment of interest, maintaining our listing status, limitations on debt, maintenance of corporate existence, and filing of SEC reports. The notes include standard events of default resulting in acceleration of indebtedness, including failure to pay, bankruptcy and insolvency, cross-defaults, and breaches of the covenants in the securities purchase agreement and notes, with default interest rates and associated cure periods applicable to the covenant regarding SEC reporting.

In July and September of 2012, we issued $53.3 million worth of senior unsecured convertible notes to Total for an aggregate of $30.0 million in cash proceeds and our repayment of $23.3 million in previously-provided research and development funds as described in more detail under "Overview - Total Relationship" above. As part of the December 2012 private placement, 1,677,852 shares of the Company's common stock were issued in exchange for the cancellation of $5.0 million worth of an outstanding senior unsecured convertible promissory note held by Total.

Common Stock Offerings. In February 2012, we sold 10,160,325 shares of our common stock in a private placement for aggregate offering proceeds of $58.7 million.

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In May 2012, we completed a private placement of 1,736,100 shares of our common stock for aggregate cash proceeds of $4.1 million.

In December 2012, we completed a private placement of 14,177,849 shares common stock for aggregate proceeds of $37.2 million, of which $22.2 million in cash was received in December 2012 and $15.0 million in cash was received in January 2013. As part of this private placement, 1,677,852 of such shares were issued to Total in exchange for the cancellation of $5.0 million worth of an outstanding senior unsecured convertible promissory note we previously issued to Total.

Banco Pine Loans. In December 2011, we received a loan of R$35.0 million (approximately US$17.1 million based on the exchange rate as of December 31, 2012) from Banco Pine. Such loan was an advance on an anticipated 2012 financing from Nossa Caixa, the Sao Paulo State development bank, and Banco Pine, under which Banco Pine and Nossa Caixa would provide us with loans of up to approximately R$52.0 million (approximately $25.4 million based on the exchange rate at December 31, 2012) as financing for capital expenditures relating to our manufacturing facility in Brotas. The maturity date for this loan was originally February 17, 2012; however, in February 2012, we entered into a supplemental agreement with Banco Pine under which the parties agreed to extend the maturity date for the repayment of the original loan from February 17, 2012 to May 17, 2012, and in May 2012, we entered into an additional supplemental extending the maturity date to August 15, 2012. This loan was repaid in July 2012.

In June 2012, we entered into a separate loan agreement with Banco Pine under which Banco Pine provided a bridge loan of R$52.0 million (approximately US$25.4 million based on the exchange rate as of December 31, 2012). The bridge loan was an additional advance on the anticipated Banco Pine and Nossa Caixa financing described above. The interest rate for the bridge loan was 0.4472% monthly (approximately 5.5% on an annualized basis). The principal and interest of this bridge loan matured and were required to be repaid on September 19, 2012, subject to extension by Banco Pine. This bridge loan was repaid in July 2012.

We secured these loans to allow us to continue construction and process development at our manufacturing facility in Brotas, and we expect to seek additional loans from this bank and others in order to be able to fund the establishment of other plants in Brazil and elsewhere.

Banco Pine/Nossa Caixa Financing. In July 2012, we entered into a Note of Bank Credit and a Fiduciary Conveyance of Movable Goods agreement with each of Nossa Caixa and Banco Pine. Under such instruments, we borrowed an aggregate of

R$52.0 million (approximately US$25.4 million based on the exchange rate as of December 31, 2012) as financing for capital expenditures relating to our manufacturing facility in Brotas. Under the loan agreements, Banco Pine agreed to lend R$22.0 million and Nossa Caixa agreed to lend R$30.0 million. The funds for these loans are provided by Banco Nacional de Desenvolvimento Econômico e Social, or BNDES, a government owned bank headquartered in Brazil, but are guaranteed by the lenders. The loans have a final maturity date of July 15, 2022 and bear a fixed interest rate of 5.5% per year. The loans are secured by certain of our farnesene production assets at the manufacturing facility in Brotas, and we were required to provide parent guarantees to each of the lenders.

BNDES Credit Facility. In December 2011, we entered into a credit facility in the amount of R$22.4 million (approximately US$11.0 million based on the exchange rate as of December 31, 2012) with BNDES. This BNDES facility was extended as project financing for a production site in Brazil. The credit line is divided into an initial tranche for up to approximately R$19.1 million and an additional tranche of approximately R$3.3 million that becomes available upon delivery of additional guarantees. The credit line is available for 12 months from the date of the Credit Agreement, subject to extension by the lender.

The principal of loans under the BNDES credit facility is required to be repaid in 60 monthly installments, with the first installment due in January 2013 and the last due in December 2017. Interest was initially due on a quarterly basis with the first installment due in March 2012. From and after January 2013, interest payments will be due on a monthly basis together with principal payments. The loaned amounts carry interest of 7% per year. Additionally, a credit reserve charge of 0.1% on the unused balance from each credit installment from the day immediately after it is made available through its date of use, when it is paid.

The credit facility is collateralized by first priority security interest in certain of our equipment and other tangible assets with an original purchase price of R$24.9 million. We are a parent guarantor for the payment of the outstanding balance under the BNDES credit facility. Additionally, we are required to provide a bank guarantee equal to 10% of the total approved amount (R$22.4 million in total debt) available under the credit facility. For advances in the second tranche (above R$19.1 million ), we are required to provide additional bank guarantees equal to 90% of each such advance, plus additional Amyris guarantees equal to at least 130% of such advance. The credit agreement contains customary events of default, including payment failures, failure to satisfy other obligations under the credit agreement or related documents, defaults in respect of other indebtedness, bankruptcy, insolvency and inability to pay debts when due, material judgments, and changes in control of Amyris Brasil. If any event of

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default under the credit agreement occurs, the lender may terminate its commitments and declare immediately due all borrowings under the facility. As of December 31, 2012 we had R$19.1 million (approximately US$9.3 million based on the exchange rate as of December 31, 2012) in outstanding advances under the BNDES credit facility.

FINEP Credit Facility. In November 2010, we entered into a credit facility with Financiadora de Estudos e Projetos, or FINEP, a state-owned company subordinated to the Brazilian Ministry of Science and Technology. This FINEP Credit Facility was extended to partially fund expenses related to our research and development project on sugarcane-based biodiesel, or the FINEP Project, and provided for loans of up to an aggregate principal amount of R$6.4 million (approximately US$3.1 million based on the exchange rate at December 31, 2012) which are guaranteed by a chattel mortgage on certain of our equipment as well as bank letters of guarantee. The first disbursement of approximately R$1.8 million(approximately US$0.9 million based on the exchange rate at December 31, 2012) was received in February 2011 and an additional disbursement of approximately R$4.6 million (approximately US$2.2 million based on the exchange rate at December 31, 2012) was received in December 2012.

Interest on loans drawn under this credit facility is fixed at 5.0% per annum. In case of default under, or non-compliance with, the terms of the agreement, the interest on loans will be dependent on the long-term interest rate as published by the Central Bank of Brazil, or TJLP. If the TJLP at the time of default is greater than 6%, then the interest will be 5.0% + a TJLP adjustment factor otherwise the interest will be at 11.0% per annum. In addition, a fine of up to 10.0% will apply to the amount of any obligation in default. Interest on late balances will be 1.0% interest per month, levied on the overdue amount. Payment of the outstanding loan balance will be made in 81 monthly installments, which commenced in July 2012 and extends through March 2019. Interest on loans drawn and other charges are paid on a monthly basis and commenced in March 2011. As of December 31, 2012, total outstanding loan balance under this credit facility was R$6.4 million (approximately US$3.1 million based on the exchange rate as of December 31, 2012).

The FINEP Credit Facility contains the following significant terms and conditions:

• We are required to share with FINEP the costs associated with the FINEP Project. At a minimum, we are required to contribute approximately R$14.5 million (US$7.1 million based on the exchange rate at December 31, 2012) of which R$11.1 million was contributed prior to the release of the second disbursement;

• After the release of the first disbursement, prior to any subsequent drawdown from the FINEP Credit Facility, we were required to provide bank letters of guarantee of up to R$3.3 million in aggregate (approximately US$1.6 million based on the exchange rate at December 31, 2012) before receiving the second installment in December 2012;

• Amounts released from the FINEP Credit Facility must be completely used by us towards the FINEP Project within 30 months after the contract execution.

Revolving Credit Facility. In December 2010, we established a revolving credit facility with a financial institution that provided for loans and standby letters of credit of up to an aggregate principal amount of $10.0 million, with a sublimit of $5.0 million on standby letters of credit. Interest on loans drawn under this revolving credit facility was equal to, at our option, (i) the Eurodollar Rate plus 3.0%; or (ii) the Prime Rate plus 0.5%. In case of default or non-compliance with the terms of the agreement, the interest on loans was Prime Rate plus 2.0%. The credit facility was collateralized by a first priority security interest in certain of our present and future assets. In April 2012, we paid $7.7 million of outstanding loans under this credit facility. In May 2012, we entered into a letter agreement with the bank amending the credit facility agreement to reduce the committed amount under the credit facility from $10.0 million to approximately $2.3 million, and the letters of credit sublimit from $5.0 million to approximately $2.3 million. The amendment also modified the current ratio covenant to require a ratio of current assets to current liabilities of at least 1.3:1 (as compared to 2:1 in the credit facility), and required us to maintain unrestricted cash of at least $15.0 million in its account with the bank. In June 2012, the credit facility was terminated and, as of December 31, 2012, no loans or letters of credit were outstanding.

Amyris Fuels Credit Agreement. We had an uncommitted facility letter with a financial institution to finance the purchase and sale of fuel and for working capital requirements, as needed. We were a parent guarantor for the payment of the outstanding balance under the credit agreement. The agreement was collateralized by a first priority security interest in certain of our present and future assets. The agreement was terminated as of June 30, 2012 and, as of December 31, 2012, we had zero in outstanding letters of credit under the Credit Agreement.

The fair values of the notes payable, loan payable, convertible notes and credit facility are based on the present value of expected future cash flows and assumptions about current interest rates and the creditworthiness of the Company that market participants would use in pricing the debt.

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Joint Venture Agreement. In 2010, we established SMA, a joint venture with Usina São Martinho. Under the terms of the agreement, if the SMA fails to commence operations by the end of 2013, Usina São Martinho has the right to terminate the joint venture and to require us to buy Usina São Martinho's equity in SMA at its acquisition cost and transfer SMA's assets at the Usina São Martinho site to another location. In that event, we would incur significant costs beginning in mid-2014 and be required to find alternative locations for the facility. In March 2013, we met with Usina São Martinho and the parties agreed in principle to a revised business plan for the joint venture with the plant becoming operational in 2016, and, while we are in the process of documenting that revised business plan as an amendment to the agreement, we may not be able to reach final agreement on the revised terms.

As of December 31, 2012, we delayed further construction of and commissioning of the SMA plant and we expect to continue to defer the project in the near term based on economic considerations and to allow us to focus on the successful implementation of our plant in Brotas.

Government Contracts. In 2010, we were awarded a $24.3 million “Integrated Bio-Refinery” grant from the U.S. Department of Energy, or DOE. Under this grant, we are required to fund an additional $10.6 million in cost sharing expenses. According to the terms of the DOE grant, we were required to maintain a cash balance of $8.7 million, calculated as a percentage of the total project costs, to cover potential contingencies and cost overruns. As of December 31, 2012, the cash requirement is approximately $0.4 million. These funds are not legally restricted but they must be available and unrestricted during the term of the project. Our obligation for this cost share is contingent on reimbursement for project costs incurred. Through December 31, 2012, we have recognized $23.4 million in revenue under this grant, of which $6.4 million was received in cash during the year ended December 31, 2012.

In August 2010, we were appointed as a subcontractor to National Renewable Energy Laboratory, or NREL, under a DOE grant awarded to NREL. We have the right to be reimbursed for up to $3.6 million, and are required to fund an additional $1.4 million, in cost sharing expenses. Through December 31, 2012, we had recognized $1.5 million in revenue under this grant, of which $0.8 million was received in cash during the year ended December 31, 2012.

In June 2012, we entered into a Technology Investment Agreement with The Defense Advanced Research Projects Agency (DARPA), under which we will perform certain research and development activities funded in part by DARPA. The work is to be performed on a cost-share basis, where DARPA funds 90% of the work and we fund the remaining 10% (primarily by providing specified labor). Under the agreement, we could receive funding of up to approximately $8.0 million over two years based on achievement of program milestones, and, accordingly, would be responsible for contributions equivalent to approximately $900,000. The agreement has an initial term of one year and, at DARPA's option, may be renewed for an additional year. Through December 31, 2012, we had recognized $0.4 million in revenue under this agreement, of which $0.4 million was received in cash during the year ended December 31, 2012.

Cash Flows during the Years Ended December 31, 2012, 2011, and 2010

Cash Flows from Operating Activities

Our primary uses of cash from operating activities are cost of products sold and personnel related expenditures offset by cash received from product sales. Cash used in operating activities was $150.9 million, $92.5 million and $64.6 million for the years ended December 31, 2012, 2011 and 2010.

Net cash used in operating activities was $150.9 million during the year ended December 31, 2012. The largest component of our cash used in operations during this period related to our net loss of $206.0 million, which included non-cash charges of $45.9 million related to losses from fixed purchase commitments and write-off of production assets at contract manufacturers, $27.5 million of stock-based compensation, and $14.6 million of depreciation and amortization expenses. In addition, significant operating cash outflows were primarily related to a $35.8 million decrease in accrued and other long term liabilities, an $11.8 million decrease in accounts payable, a $1.6 million decrease in deferred revenue and a $1.3 million decrease in deferred rent. Accrued and other long term liabilities decreased primarily due to the release of the contingently repayable advance from related party collaborator (Total) of $31.9 million as a result of the July 2012 amendment of the collaboration agreement with Total. Accounts payable decreased primarily due to payments for production and contract manufacturing costs that were accrued for in the prior year but paid in the current year.

Significant operating cash inflows during the year ended December 31, 2012 were derived primarily from sales of ethanol and reformulated ethanol-blended gasoline purchased from third parties and from collaborative research services. In addition, operating cash inflows were comprised primarily of an $11.2 million decrease in prepaid expenses and other assets, a $2.8 million

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decrease in accounts receivable and a $2.9 million decrease in net inventory. The decrease in prepaid expenses and other assets was primarily related to the reduction of $18.8 million in deferred charge asset related to Total as a result of the July 2012 amendment of the collaboration agreement with Total. The decrease in accounts receivable was primarily due to our transition out of the ethanol and ethanol-blended gasoline business during the third quarter of 2012.

Cash used in operating activities of $92.5 million in 2011 reflected a net loss of $179.5 million partially offset by non-cash charges of $37.5 million and a $49.5 million net change in our operating assets and liabilities. Net change in operating assets and liabilities of $49.5 million primarily consisted of a $53.9 million increase in accrued and other long term liabilities of which $31.9 million was due to the contingently repayable advance from Total, a $15.6 million increase in accounts payable and a $5.5 million increase in deferred revenue partially offset by a $5.3 million increase in inventory, a $17.3 million increase in prepaid expenses and other assets, a $2.0 million increase in accounts receivable and a $1.1 million reduction in deferred rent. Non-cash charges primarily included $25.5 million of stock-based compensation and $11.1 million of depreciation and amortization expenses.

Cash used in operating activities of $64.6 million in 2010 reflected a net loss of $82.8 million partially offset by non-cash charges of $16.6 million and a $1.6 million net change in our operating assets and liabilities. Non-cash charges primarily included $10.4 million of stock-based compensation and $7.3 million of depreciation and amortization.

Cash Flows from Investing Activities

Our investing activities consist primarily of capital expenditures, net investment purchases, maturities and sales.

For the year ended December 31, 2012, cash used in investing activities was $49.6 million as a result of $56.9 million of capital expenditures and deposits on plant, property and equipment due to the construction of our first owned production facility in Brotas and $1.0 million of restricted cash, offset by net sales of short term investments of $8.2 million.

For the year ended December 31, 2011, cash provided by investing activities was $5.9 million$ as a result of $105.0 million in net investment securities maturities and $0.3 million in acquisition of cash in noncontrolling interest offset by a $97.0 million of capital expenditures and deposits on property, plant and equipment and a $2.9 million payment to Draths Corporation in relation to a business acquisition.

For the year ended December 31, 2010, cash used in investing activities was $79.4 million as a result of $68.4 million in net investment purchases and $15.5 million of capital expenditures and deposits on property, plant and equipment, offset by the release of $4.5 million in restricted cash.

Cash Flows from Financing Activities

For the year ended December 31, 2012, cash provided by financing activities was $138.1 million, primarily the result of the net receipt of $108.9 million from debt financing, of which $30.0 million is debt financing from a related party, the receipt of $84.7 million in proceeds from sales of common stock in private placements net of issuance cost, and the receipt of $0.9 million in proceeds from option exercises. These cash inflows were offset in part by principal payments on debt of $52.6 million and principal payments on capital leases of $3.7 million.

For the year ended December 31, 2011, cash provided by financing activities was $41.1 million, as a result of the net receipt of $38.0 million from debt financing, the receipt of $8.4 million in proceeds from option exercises, and the receipt of $3.0 million in equipment financing. These cash receipts were offset in part by principal payments on debt of $5.0 million, principal payments on capital leases of $2.8 million, and $0.5 million in costs related to the initial public offering of our common stock.

For the year ended December 31, 2010, cash provided by financing activities was $266.7 million, primarily the result of the net receipt of $132.9 million from our sale of Series D convertible preferred stock, the receipt of the net proceeds of $86.0 million from the initial public offering of our common stock, the net receipt of $47.8 million from our sale of Series C-1 convertible preferred stock, the net receipt of $3.7 million from our sale of Series C convertible preferred stock, the receipt of $7.1 million from investors in Amyris Brasil and $1.4 million in proceeds from equipment financing. These cash receipts were offset in part by principal payments on debt of $9.7 million and principal payments on capital leases of $2.7 million.

Off-Balance Sheet Arrangements

We did not have during the periods presented, and we do not currently have, any material off-balance sheet arrangements, as defined under SEC rules, such as relationships with unconsolidated entities or financial partnerships, which are often referred

56

to as structured finance or special purpose entities, established for the purpose of facilitating financing transactions that are not required to be reflected on our consolidated financial statements.

Contractual Obligations

The following is a summary of our contractual obligations as of December 31, 2012 (in thousands):

	Total		2013		2014		2015		2016		2017		Thereafter
Principal payments on long-term debt	$	113,432	$	3,325	$	3,962	$	5,846	$	5,875	$	79,131	$	15,293
Interest payments on long-term debt, fixed rate(1)	17,102		2,919		3,073		2,528		2,175		4,508		1,899
Operating leases	38,289		6,624		6,772		6,900		6,891		6,760		4,342
Principal payments on capital leases	2,610		1,366		957		287		—		—		—
Interest payments on capital leases	175		123		50		2		—		—		—
Terminal storage costs	157		148		9		—		—		—		—
Purchase obligations(2)	53,113		16,275		17,706		10,243		8,623		218		48
Total	$	224,878	$	30,780	$	32,529	$	25,806	$	23,564	$	90,617	$	21,582

____________________

⁽¹⁾  The fixed interest rates are more fully described in Note 6 of our consolidated financial statements.

⁽²⁾  Purchase obligations include non-cancelable contractual obligations and construction commitments of $52.7 million, of which $13.9 million have been accrued as loss on purchase commitments.

This table does not reflect non-reimbursable expenses that we expect to incur in 2013 in connection with research activities under the DOE Integrated Bio-Refinery grant and the NREL subcontract discussed above under the caption "Liquidity and Capital Resources - Government Contracts." We have the right to be reimbursed for up to $24.3 million of a total of up to $34.9 million of expenses for research activities that we undertake under the DOE Integrated Bio-Refinery grant. We have the right to be reimbursed for up to $3.6 million of a total of $5.0 million of expenses for research activities that we undertake under the NREL grant.

Additionally, this table does not reflect the expenses that we expect to incur in 2013 and 2014 in connection with research activities under DARPA under which we will perform certain research and development activities funded in part by DARPA. The work is to be performed on a cost-share basis, where DARPA funds 90% of the work and we fund the remaining 10% (primarily by providing specified labor). Under the agreement, we could receive funding of up to approximately $8.0 million over two years based on achievement of program milestones, and, accordingly, we would be responsible for contributions equivalent to approximately $900,000.

Recent Accounting Pronouncements

The information contained in Note 2 to the Consolidated Financial Statements under the heading "Recent Accounting Pronouncements" is hereby incorporated by reference into this Part II, Item 8.

ITEM 7A. QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK

The market risk inherent in our market risk sensitive instruments and positions is the potential loss arising from adverse changes in: commodity market prices, foreign currency exchange rates, and interest rates as described below.

Interest Rate Risk

Our exposure to market risk for changes in interest rates relates primarily to our investment portfolio and our outstanding debt obligations. We generally invest our cash in investments with short maturities or with frequent interest reset terms. Accordingly, our interest income fluctuates with short-term market conditions. As of December 31, 2012, our investment portfolio consisted primarily of money market funds and certificates of deposit, all of which are highly liquid investments. Due to the short-term nature of our investment portfolio, our exposure to interest rate risk is minimal. Additionally, as of December 31, 2012, 100% of our outstanding debt is in fixed rate instruments.

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Foreign Currency Risk

Most of our sales contracts are principally denominated in U.S. dollars and, therefore, our revenues are not currently subject to significant foreign currency risk. The functional currency of our wholly-owned consolidated subsidiary in Brazil is the local currency (Brazilian real) in which recurring business transactions occur. We do not use currency exchange contracts as hedges against amounts permanently invested in our foreign subsidiary. The amount we consider permanently invested in our foreign subsidiary and translated into U.S. dollars using the year end exchange rate is $76.7 million at December 31, 2012 and $62.8 million at December 31, 2011. This increase between 2012 and 2011 is due to additional capital contributions made during 2012, which are partially offset by the depreciation of the Brazilian real versus the U.S. dollar and an increase in accumulated deficit of our wholly-owned consolidated subsidiary in Brazil. The potential loss in fair value, which would principally be recognized in Other Comprehensive Income (Loss), resulting from a hypothetical 10% adverse change in quoted Brazilian real exchange rates is $7.7 million and $6.3 million for 2012 and 2011, respectively. Actual results may differ.

We make limited use of derivative instruments, which includes currency interest swap agreements to manage the Company's exposure to foreign currency exchange rate and interest rate related to the Company's Banco Pine S.A. loan. In June 2012, we entered into a currency interest rate swap arrangement with Banco Pine for R$22.0 million (approximately US$10.8 million based on the exchange rate of December 31, 2012). The swap arrangement exchanges the principal and interest payments under the Banco Pine loan entered into in July 2012 for alternative principal and interest payments that are subject to adjustment based on fluctuations in the foreign exchange rate between the U.S. dollar and Brazilian real. The swap has a fixed interest rate of 3.94%. This arrangement hedges the fluctuations in the foreign exchange rate between the U.S. dollar and Brazilian real.

Commodity Price Risk

Our primary exposure to market risk for changes in commodity prices currently relates to our purchases of sugar feedstocks. When possible, we managed our exposure to this risk primarily through the use of supplier pricing agreements. Through the third quarter of 2012, we also had commodity market risk related to our purchases of ethanol and reformulated ethanol-blended gasoline in which we used standard derivative commodity instruments to hedge the price volatility of ethanol and reformulated ethanol-blended gasoline, principally through futures contracts. However, as of September 30, 2012, we transitioned out of that business and no longer purchase any ethanol and reformulated ethanol-blended gasoline or use standard derivative commodity instruments. The changes in fair value of these contracts are recorded on the balance sheet and recognized immediately in cost of products sold. We recognized a loss of $0.3 million, $2.4 million and $2.2 million, as the change in fair value for the years ended December 31, 2012, 2011 and 2010, respectively (see Note 3 to our Consolidated Financial Statements).

58

ITEM 8. FINANCIAL STATEMENTS AND SUPPLEMENTARY DATA

AMYRIS, INC.

Index to Financial Statements and Financial Statement Schedules

	Page
Consolidated Financial Statements:
Report of Independent Registered Public Accounting Firm	60
Consolidated Balance Sheets as of December 31, 2012 and 2011	61
Consolidated Statements of Operations for the years ended December 31, 2012, 2011 and 2010	62
Consolidated Statements of Comprehensive Loss for the years ended December 31, 2012, 2011 and 2010	63
Consolidated Statements of Convertible Preferred Stock, Redeemable Noncontrolling Interest and Equity (Deficit) for the years ended December 31, 2012, 2011 and 2010	64
Consolidated Statements of Cash Flows for the years ended December 31, 2012, 2011 and 2010	67
Notes to Consolidated Financial Statements	69
Financial Statement Schedules:
Schedule II Valuation and Qualifying Accounts for the years ended December 31, 2012, 2011 and 2010	122

59

Report of Independent Registered Public Accounting Firm

To the Board of Directors and Stockholders of

Amyris, Inc.:

In our opinion, the consolidated financial statements listed in the accompanying indexpresent fairly, in all material respects, the financial position of Amyris, Inc and its subsidiaries at December 31, 2012and December 31, 2011, and the results of their operations and their cash flows for each of the three years in the period endedDecember 31, 2012 in conformity with accounting principles generally accepted in the United States of America. In addition, in our opinion, the financial statement schedulelisted in the accompanying indexpresents fairly, in all material respects, the information set forth therein when read in conjunction with the related consolidatedfinancial statements. Also in our opinion, the Company maintained, in all material respects, effective internal control over financial reporting as ofDecember 31, 2012, based on criteria established in Internal Control - Integrated Framework issued by the Committee of Sponsoring Organizations of the Treadway Commission (COSO). The Company's management is responsible for these financial statements and financial statement schedule, for maintaining effective internal control over financial reporting and for its assessment of the effectiveness of internal control over financial reporting, included inManagement's Annual Report on Internal Control over Financial Reporting appearing under Item 9A. Our responsibility is to express opinions on these financial statements, on the financial statement schedule, and on the Company's internal control over financial reporting based on our audits (which were integrated audits in 2012 and 2011). We conducted our audits in accordance with the standards of the Public Company Accounting Oversight Board (United States). Those standards require that we plan and perform the audits to obtain reasonable assurance about whether the financial statements are free of material misstatement and whether effective internal control over financial reporting was maintained in all material respects. Our audits of the financial statements included examining, on a test basis, evidence supporting the amounts and disclosures in the financial statements, assessing the accounting principles used and significant estimates made by management, and evaluating the overall financial statement presentation. Our audit of internal control over financial reporting included obtaining an understanding of internal control over financial reporting, assessing the risk that a material weakness exists, and testing and evaluating the design and operating effectiveness of internal control based on the assessed risk. Our audits also included performing such other procedures as we considered necessary in the circumstances. We believe that our audits provide a reasonable basis for our opinions.

A company's internal control over financial reporting is a process designed to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles. A company's internal control over financial reporting includes those policies and procedures that (i) pertain to the maintenance of records that, in reasonable detail, accurately and fairly reflect the transactions and dispositions of the assets of the company; (ii) provide reasonable assurance that transactions are recorded as necessary to permit preparation of financial statements in accordance with generally accepted accounting principles, and that receipts and expenditures of the company are being made only in accordance with authorizations of management and directors of the company; and (iii) provide reasonable assurance regarding prevention or timely detection of unauthorized acquisition, use, or disposition of the company's assets that could have a material effect on the financial statements.

Because of its inherent limitations, internal control over financial reporting may not prevent or detect misstatements. Also, projections of any evaluation of effectiveness to future periods are subject to the risk that controls may become inadequate because of changes in conditions, or that the degree of compliance with the policies or procedures may deteriorate.

PricewaterhouseCoopers LLP

San Jose, California

March 28, 2013

60

Amyris, Inc.

Consolidated Balance Sheets

(In Thousands, Except Share and Per Share Amounts)

	December 31,
	2012			2011
Assets
Current assets:
Cash and cash equivalents	$	30,592		$	95,703
Short-term investments	97			7,889
Accounts receivable, net of allowance of $481 and $245, respectively	3,846			6,936
Inventories, net	6,034			9,070
Prepaid expenses and other current assets	8,925			19,873
Total current assets	49,494			139,471
Property, plant and equipment, net	163,121			128,101
Restricted cash	955			—
Other assets	20,112			43,001
Goodwill and intangible assets	9,152			9,538
Total assets	$	242,834		$	320,111
Liabilities and Equity
Current liabilities:
Accounts payable	$	15,392		$	26,379
Deferred revenue	1,333			3,139
Accrued and other current liabilities	24,410			30,982
Capital lease obligation, current portion	1,366			3,717
Debt, current portion	3,325			28,049
Total current liabilities	45,826			92,266
Capital lease obligation, net of current portion	1,244			2,619
Long-term debt, net of current portion	61,806			13,275
Related party debt	39,033			—
Deferred rent, net of current portion	8,508			9,957
Deferred revenue, net of current portion	4,255			4,097
Other liabilities	15,933			37,085
Total liabilities	176,605			159,299
Commitments and contingencies (Note 5)
Stockholders’ equity:
Preferred stock - $0.0001 par value, 5,000,000 shares authorized, none issued and outstanding	—			—
Common stock - $0.0001 par value, 100,000,000 shares authorized as of December 31, 2012 and 2011; 68,709,660 and 45,933,138 shares issued and outstanding as of December 31, 2012 and 2011, respectively	7			5
Additional paid-in capital	666,233			548,159
Accumulated other comprehensive loss	(12,807		)	(5,924		)
Accumulated deficit	(586,327		)	(381,188		)
Total Amyris, Inc. stockholders’ equity	67,106			161,052
Noncontrolling interest	(877		)	(240		)
Total stockholders' equity	66,229			160,812
Total liabilities and stockholders' equity	$	242,834		$	320,111

See the accompanying notes to the consolidated financial statements.

61

Amyris, Inc.

Consolidated Statements of Operations

(In Thousands, Except Share and Per Share Amounts)

	Years Ended December 31,
	2012			2011			2010
Revenues
Product sales	$	49,638		$	129,837		$	68,664
Grants and collaborations revenue	24,056			17,154			11,647
Total revenues	73,694			146,991			80,311
Cost and operating expenses
Cost of products sold	77,314			155,615			70,515
Loss on purchase commitments and write off of production assets	45,854			—			—
Research and development	73,630			87,317			55,249
Sales, general and administrative	78,718			83,231			40,393
Restructuring and asset impairment (income) charges	—			—			(2,061		)
Total cost and operating expenses	275,516			326,163			164,096
Loss from operations	(201,822		)	(179,172		)	(83,785		)
Other income (expense):
Interest income	1,472			1,542			1,540
Interest expense	(4,926		)	(1,543		)	(1,443		)
Other income, net	224			214			898
Total other income (expense)	(3,230		)	213			995
Loss before income taxes	(205,052		)	(178,959		)	(82,790		)
Provision for income taxes	(981		)	(552		)	—
Net loss	$	(206,033	)	$	(179,511	)	$	(82,790	)
Net loss attributable to noncontrolling interest	894			641			920
Net loss attributable to Amyris, Inc.	$	(205,139	)	$	(178,870	)	$	(81,870	)
Deemed dividend related to a beneficial conversion feature	—			—			(42,009		)
Net loss attributable to Amyris, Inc. common stockholders	$	(205,139	)	$	(178,870	)	$	(123,879	)
Net loss per share attributable to common stockholders, basic and diluted	$	(3.62	)	$	(3.99	)	$	(8.35	)
Weighted-average shares of common stock outstanding used in computing net loss per share of common stock, basic and diluted	56,717,869			44,799,056			14,840,253

See the accompanying notes to the consolidated financial statements.

62

Amyris, Inc.

Consolidated Statements of Comprehensive Loss

(In Thousands)

	Years Ended December 31,
	2012			2011			2010
Comprehensive loss:
Net loss	$	(206,033	)	$	(179,511	)	$	(82,790	)
Change in unrealized loss on investments	—			(5		)	2
Foreign currency translation adjustment, net of tax	(6,626		)	(8,761		)	1,751
Total comprehensive loss	(212,659		)	(188,277		)	(81,037		)
Loss attributable to noncontrolling interest	894			641			920
Foreign currency translation adjustment attributable to noncontrolling interest	(257		)	(30		)	(217		)
Comprehensive loss attributable to Amyris, Inc.	$	(212,022	)	$	(187,666	)	$	(80,334	)

See the accompanying notes to the consolidated financial statements.

63

Amyris, Inc.

Consolidated Statements of Convertible Preferred Stock, Redeemable Noncontrolling Interest and Equity (Deficit)

	Convertible Preferred Stock					Redeemable Noncontrolling Interest			Common Stock				Additional Paid-in Capital			Accumulated Deficit			Accumulated Other Comprehensive Income (Loss)		Noncontrolling Interest			Total Equity (Deficit)
(In Thousands, Except Share and Per Share Amounts)	Shares		Amount						Shares		Amount
December 31, 2009	18,365,222		$	179,651		$	5,506		5,114,205		$	1	$	5,366		$	(120,448	)	$	1,336	$	—		$	(113,745	)
Issuance of Series C convertible preferred stock at $12.46 per shares for cash, net of issuance costs of $5	295,981		3,683			—			—		—		—			—			—		—			—
Issuance of Series C-1 convertible preferred stock at $17.56 per shares for cash, net of issuance costs of $68	2,724,766		47,779			—			—		—		—			—			—		—			—
Issuance of Series D convertible preferred stock at $18.75 per shares for cash and deferred charge asset of $27,909, net of issuance costs of $258	7,101,548		160,805			—			—		—		—			—			—		—			—
Issuance of warrants in connection with issuance of Series C convertible preferred stock	—		(507		)	—			—		—		—			—			—		—			—
Issuance of common stock upon exercise of stock options, net of restricted stock	—		—			—			60,883		—		277			—			—		—			277
Repurchase of common stock	—		—			—			(10,367	)	—		—			—			—		—			—
Shares issued from restricted stock unit settlement	—		—			—			176,272				—			—			—		—			—
Stock-based compensation	—		—			—			—		—		10,432			—			—		—			10,432
Proceeds from noncontrolling interest	—		—			7,041			—		—		—			—			—		28			28
Common stock issuance in public offering, net of issuance costs (Note 11)	—		—			—			6,095,000		—		85,534			—			—		—			85,534
Conversion of convertible preferred stock to common stock	(28,487,517	)	(391,411		)	—			31,550,277		3		391,408			—			—		—			391,411
Conversion of convertible preferred stock warrants to common stock warrants	—		—			—			—		—		2,318			—			—		—			2,318
Conversion of shares of Amyris Brasil S.A. shares into common stock	—		—			(11,870		)	861,155		—		11,653			—			—		—			11,653
Beneficial conversion feature on issuance of Series D convertible preferred stock	—		—			—			—		—		39,292			—			—		—			39,292
Deemed dividend related to the beneficial conversion feature of Series D convertible preferred stock	—		—			—			—		—		(39,292		)	—			—		—			(39,292		)
Beneficial conversion feature on conversion of Amyris Brasil S.A. shares	—		—			—			—		—		2,717			—			—		—			2,717
Deemed dividend related to the beneficial conversion feature of Amyris Brasil S.A. shares	—		—			—			—		—		(2,717		)	—			—		—			(2,717		)
Change in unrealized loss on investments	—		—			—			—		—		—			—			2		—			2
Foreign currency translation adjustment, net of tax	—		—			217			—		—		—			—			1,534		—			1,534
Net loss	—		—			(894		)	—		—		—			(81,870		)	—		(26		)	(81,896		)
December 31, 2010	—		$	—		$	—		43,847,425		$	4	$	506,988		$	(202,318	)	$	2,872	$	2		$	307,548

64

Amyris, Inc.

Consolidated Statements of Convertible Preferred Stock, Redeemable Noncontrolling Interest and Equity (Deficit)—(Continued)

	Convertible Preferred Stock			Redeemable Noncontrolling Interest		Common Stock				Additional Paid-in Capital			Accumulated Deficit			Accumulated Other Comprehensive Income (Loss)			Noncontrolling Interest			Total Equity (Deficit)
(In Thousands, Except Share and Per Share Amounts)	Shares	Amount				Shares		Amount
December 31, 2010	—	$	—	$	—	43,847,425		$	4	$	506,988		$	(202,318	)	$	2,872		$	2		$	307,548
Issuance of common stock upon exercise of stock options, net of restricted stock	—	—		—		1,641,439		1		8,491			—			—			—			8,492
Issuance of common stock upon net exercise of warrants	—	—		—		77,087		—		—			—			—			—			—
Issuance of common stock warrants in connection with equipment financing	—	—		—		—		—		193			—			—			—			193
Issuance of common stock in connection with Draths business acquisition	—	—		—		362,319		—		7,000			—			—			—			7,000
Shares issued from restricted stock unit settlement	—	—		—		6,005		—		—			—			—			—			—
Repurchase of common stock	—	—		—		(1,137	)	—		(5		)	—			—			—			(5		)
Stock-based compensation	—	—		—		—		—		25,492			—			—			—			25,492
Fair value of assets and liabilities assigned to noncontrolling interest	—	—		—		—		—		—			—			—			369			369
Change in unrealized loss on investments	—	—		—		—		—		—			—			(5		)	—			(5		)
Foreign currency translation adjustment, net of tax	—	—		—		—		—		—			—			(8,791		)	30			(8,761		)
Net loss	—	—		—		—		—		—			(178,870		)	—			(641		)	(179,511		)
December 31, 2011	—	$	—	$	—	45,933,138		$	5	$	548,159		$	(381,188	)	$	(5,924	)	$	(240	)	$	160,812

65

Amyris, Inc.

Consolidated Statements of Convertible Preferred Stock, Redeemable Noncontrolling Interest and Equity (Deficit)—(Continued)

	Convertible Preferred Stock			Common Stock
(In Thousands, Except Share and Per Share Amounts)	Shares	Amount	Redeemable Noncontrolling Interest	Shares		Amount		Additional Paid-in Capital			Accumulated Deficit			Accumulated Other Comprehensive Income (Loss)			Noncontrolling Interest			Total Equity (Deficit)
December 31, 2011	—	—	—	45,933,138		$	5	$	548,159		$	(381,188	)	$	(5,924	)	$	(240	)	$	160,812
Issuance of common stock upon exercise of stock options, net of restricted stock	—	—	—	1,441,676		—		1,509			—			—			—			1,509
Issuance of common stock in a private placement, net of issuance cost of $392				21,040,717		2		89,680												89,682
Recovery of shares from Draths escrow	—	—	—	(5,402	)	—		—			—			—			—			—
Shares issued from restricted stock unit settlement	—	—	—	299,584		—		(588		)	—			—			—			(588		)
Repurchase of common stock	—	—	—	(53	)	—		—			—			—			—			—
Stock-based compensation	—	—	—	—		—		27,473			—			—			—			27,473
Foreign currency translation adjustment, net of tax	—	—	—	—		—		—			—			(6,883		)	257			(6,626		)
Net loss	—	—	—	—		—		—			(205,139		)	—			(894		)	(206,033		)
December 31, 2012	—	—	—	68,709,660		$	7	$	666,233		$	(586,327	)	$	(12,807	)	$	(877	)	$	66,229

See the accompanying notes to the consolidated financial statements

66

Amyris, Inc.

Consolidated Statements of Cash Flows

(In Thousands)

	Years Ended December 31,
	2012			2011			2010
Operating activities
Net loss	$	(206,033	)	$	(179,511	)	$	(82,790	)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization	14,570			11,077			7,280
Loss on disposal of property, plant and equipment	370			52			205
Stock-based compensation	27,473			25,492			10,432
Amortization of premium on investments	—			630			1,557
Amortization of debt discount	1,758			—			—
Provision for doubtful accounts	236			245			—
Loss on purchase commitments and write-off of production assets	45,854			—			—
Change in fair value of convertible preferred stock warrant liability	—			—			(929		)
Change in fair value of derivative instruments	(1,764		)	—			—
Restructuring and asset impairment (income) charges	—			—			(2,061		)
Other noncash expenses	159			40			116
Changes in assets and liabilities:
Accounts receivable	2,837			(1,975		)	(3,565		)
Inventories, net	2,919			(5,327		)	(1,708		)
Prepaid expenses and other assets	11,239			(17,250		)	1,133
Accounts payable	(11,811		)	15,648			3,478
Accrued and other long-term liabilities and restructuring	(35,754		)	53,894			664
Deferred revenue	(1,648		)	5,542			1,316
Deferred rent	(1,277		)	(1,053		)	295
Net cash used in operating activities	(150,872		)	(92,496		)	(64,577		)
Investing activities
Purchase of short-term investments	(8,334		)	(67,556		)	(189,486		)
Maturities of short-term investments	—			105,000			100,711
Sales of short-term investments	16,503			68,106			28,374
Purchases of long-term investments	—			—			(7,998		)
Change in restricted cash	(955		)	—			4,506
Payments for business acquisitions	—			(2,934		)	—
Acquisition of cash in noncontrolling interest	—			344			—
Investment in unconsolidated joint venture	—			(83		)	—
Purchase of property, plant and equipment, net of disposals	(56,832		)	(81,917		)	(10,906		)
Deposits on property, plant and equipment	(26		)	(15,107		)	(4,606		)
Net cash provided by (used in) investing activities	(49,644		)	5,853			(79,405		)
Financing activities
Proceeds from issuance of convertible preferred stock, net	—			—			184,360
Proceeds from issuance of common stock, net of repurchases	891			8,445			231
Proceeds from issuance of common stock in private placements, net of issuance costs	84,682			—			—
Proceeds from equipment financing	—			3,000			1,445
Principal payments on capital leases	(3,727		)	(2,835		)	(2,728		)
Proceeds from debt issued	78,904			37,957			—
Proceeds from debt issued to related party	30,000			—			—
Principal payments on debt	(52,633		)	(5,018		)	(9,722		)
Proceeds from issuance of common stock in initial public offering, net	—			(497		)	86,032
Proceeds from sale of noncontrolling interest	—			—			7,069
Net cash provided by financing activities	138,117			41,052			266,687
Effect of exchange rate changes on cash and cash equivalents	(2,712		)	(1,766		)	1,167
Net increase (decrease) in cash and cash equivalents	(65,111		)	(47,357		)	123,872
Cash and cash equivalents at beginning of period	95,703			143,060			19,188
Cash and cash equivalents at end of period	$	30,592		$	95,703		$	143,060

67

Amyris, Inc.

Consolidated Statements of Cash Flows—(Continued)

(In Thousands)

	Years Ended December 31,
	2012			2011			2010
Supplemental disclosures of cash flow information:
Cash paid for interest	$	3,399		$	1,412		$	1,378
Cash paid for income taxes, net of refunds	$	—		$	—		$	—
Supplemental disclosures of noncash investing and financing activities:
Acquisitions of property, plant and equipment under accounts payable, accrued liabilities and notes payable	$	2,538		$	3,177		$	8,278
Financing of equipment	$	—		$	3,420		$	—
Warrants issued in connection with equipment financing	$	—		$	193		$	—
Financing of insurance premium under notes payable	$	—		$	—		$	101
Change in unrealized gain (loss) on investments	$	—		$	(5	)	$	3
Change in unrealized gain (loss) on foreign currency	$	(6,366	)	$	(7,905	)	$	(623	)
Asset retirement obligation	$	—		$	174		$	115
Warrants issued in connection with the issuance of convertible preferred stock	$	—		$	—		$	507
Accrued deferred offering costs	$	—		$	—		$	496
Financing of rent payments under notes payable	$	—		$	—		$	239
Deferred charge asset related to the issuance of Series D preferred stock	$	—		$	—		$	27,909
Issuance of common stock upon exercise of warrants	$	—		$	3,554		$	—
Issuance of common stock related to business acquisition	$	—		$	7,000		$	—
Conversion of convertible preferred stock to common stock	$	—		$	—		$	391,411
Conversion of preferred stock warrants to common stock warrants	$	—		$	—		$	2,318
Conversion of shares of Amyris Brasil S.A. held by third parties into Amyris, Inc. common stock	$	—		$	—		$	11,653
Conversion of other liability to related party debt	$	(23,300	)	$	—		$	—
Conversion of related party debt to common stock	$	5,000		$	—		$	—
Deemed dividend related to a beneficial conversion feature	$	—		$	—		$	42,009
Transfer of property, plant and equipment to current assets	$	—		$	886		$	—
Transfer of long term deposits to property, plant and equipment	$	12,218		$	50		$	—
Acquisition of net assets in noncontrolling interest	$	—		$	25		$	—
Reclassification of long-term investments to short-term investments	$	—		$	—		$	7,998

See the accompanying notes to the consolidated financial statements.

68

Amyris, Inc.

Notes to Consolidated Financial Statements

1. The Company

Amyris, Inc. (the “Company”) was incorporated in California on July 17, 2003 and reincorporated in Delaware on June 10, 2010 for the purpose of leveraging breakthroughs in synthetic biology to develop and provide renewable compounds for a variety of markets. The Company is currently building and applying its industrial synthetic biology platform to provide alternatives to select petroleum-sourced products used in specialty chemical and transportation fuel markets worldwide. The Company's first commercialization efforts have been focused on a renewable hydrocarbon molecule called farnesene (Biofene®), which forms the basis for a wide range of products varying from specialty chemical applications to transportation fuels, such as diesel. While the Company's platform is able to use a wide variety of feedstocks, the Company is focused initially on Brazilian sugarcane. In addition, the Company has entered into various contract manufacturing agreements to support commercial production. The Company has established two principal operating subsidiaries, Amyris Brasil Ltda. (formerly Amyris Brasil S.A., “Amyris Brasil”) for production in Brazil, and Amyris Fuels, LLC ("Amyris Fuels"). Nearly all of the Company's revenues to date have come from the sale of ethanol and reformulated ethanol-blended gasoline with substantially all of the remaining revenues coming from collaborations, government grants and sales of renewable products. In the third quarter of 2012, the Company transitioned out of the ethanol and reformulated ethanol-blended gasoline business. The Company does not expect to be able to replace much of the revenue lost in the near term as a result of this transition, particularly in 2013 while it continues its efforts to establish a renewable products business.

Beginning in March 2012, the Company initiated a plan to shift a portion of its production capacity from contract manufacturing facilities to a Company-owned plant that was then under construction. As a result, the Company evaluated its contract manufacturing agreements and recorded a loss of $30.4 million related to adverse purchase commitments, $10.0 million related to the write-off of facility modification costs and $5.5 million related to Company-owned equipment at contract manufacturing facilities in the year ended December 31, 2012. The Company regularly monitors its plan related to production capacity, sales requirements and related cost structure. Changes to this plan may result in additional losses and impairment charges.

The Company's renewable products business strategy is to focus on direct commercialization of higher-value, lower-volume markets while moving lower-margin, higher-volume commodity products into joint venture arrangements with established industry partners. To commercialize its products, the Company must be successful in using its technology to manufacture its products at commercial scale and on an economically viable basis (i.e., low per unit production costs). The Company is building its experience producing renewable products at commercial scale. The Company's prospects are subject to risks, expenses and uncertainties frequently encountered by companies in this stage of development.

The Company expects to fund its operations for the foreseeable future with cash and investments currently on hand, with cash inflows from collaboration and grant funding, cash contributions from product sales, and with new debt and equity financing. The Company's planned 2013 working capital needs and its planned operating and capital expenditures for 2013 are dependent on significant inflows of cash from existing collaboration partners, as well as additional funding from new collaborations, equity or debt offerings, credit facilities or loans, or combinations of these sources. The Company will continue to need to fund its research and development and related activities and to provide working capital to fund production, storage, distribution and other aspects of its business. The Company's operating plan contemplates capital expenditures of approximately $10.0 million in 2013 and the Company expects to continue to incur costs in connection with its existing contract manufacturing arrangements. During 2012, the Company completed multiple debt and equity financings, raising aggregate cash proceeds of $193.6 million. (See Note 6 - “Debt” and Note 11 - “Stockholders' Equity”). The Company's most recent financing of R$5.0 million reais (approximately US$2.5 million) was completed in March 2013. (See Note 18 - “Subsequent Events”).

Liquidity

The Company has incurred significant losses in each year since its inception and believes that it will continue to incur losses and negative cash flow from operations into at least 2014. As of December 31, 2012, the Company had an accumulated deficit of $586.3 million and had cash, cash equivalents and short term investments of $30.7 million. The Company has significant outstanding debt and contractual obligations related to purchase commitments, as well as capital and operating leases. As of December 31, 2012, the Company's debt totaled $104.2 million, of which $3.3 million matures within the next twelve months. In addition, the Company's debt agreements contain various covenants, including restrictions on business that could cause the Company to be at risk of defaults. Please refer to Note 5 “Commitments and Contingencies” and Note 6 “Debt” for further details regarding the Company's obligations and commitments.

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As of December 31, 2012, the Company had cash, cash equivalents and short-term investments of $30.7 million. In March 2013, the Company signed a collaboration agreement that included a funding component, and obtained a commitment letter from an existing stockholder with respect to additional convertible note funding (see Note 18 - “Subsequent Events”), and the Company expects to use amounts received under these arrangements to fund its operations. Furthermore, the Company is expecting additional funding in 2013 from collaborations, equity or debt offerings, or combinations of these sources. The Company's operating plan contemplates securing a portion of this additional funding in the second quarter of 2013. However, as of the date of this filing, the Company has not yet secured this additional funding. There can be no assurance that financing will be available on commercially acceptable terms or at all.

If the Company is unable to raise additional financing, or if other expected sources of funding are delayed or not received, the Company would take the following actions as early as the second quarter of 2013 to support its liquidity needs through the remainder of 2013 and into 2014:

• Effect significant headcount reductions in the U.S. and in Brazil, particularly with respect to both general and administrative employees and other employees not connected to critical or contracted activities.

• Shift its focus to existing products and customers with significantly reduced investment in new product and commercial development efforts.

• Reduce its expenditures for third party contractors, including consultants, professional advisors and other vendors.

• Suspend operations at its pilot plants and demonstration facilities.

• Reduce or delay uncommitted capital expenditures, including non-essential lab equipment and information technology projects.

The contingency cash plan contemplating these actions is designed to save the Company an estimated $35 million to $40 million over the next twelve months. Implementing this plan could have a material negative impact on the Company's ability to continue its business as currently contemplated, including, without limitation, delays or failures in its ability to:

• Achieve planned production levels;

• Develop and commercialize products within planned timelines or at planned scales; and

• Continue other core activities.

Furthermore, any inability to scale-back operations as necessary, and any unexpected liquidity needs, could create pressure to implement more severe measures. Such measures could have a material adverse effect on the Company's ability to meet contractual requirements, including obligations to maintain manufacturing operations, and increase the severity of the consequences described above.

2. Summary of Significant Accounting Policies

Basis of Presentation

The accompanying consolidated financial statements have been prepared in accordance with the accounting principles generally accepted in the United States of America (“GAAP”) and with the instructions for Form 10-K and Regulations S-X statements. The consolidated financial statements include the accounts of the Company and its consolidated subsidiaries. All intercompany accounts and transactions have been eliminated in consolidation.

Principles of Consolidations

The Company has interests in joint venture entities that are variable interest entities (“VIEs”). Determining whether to consolidate a variable interest entity requires judgment in assessing (i) whether an entity is a VIE and (ii) if the Company is the entity’s primary beneficiary and thus required to consolidate the entity. To determine if the Company is the primary beneficiary of a VIE, the Company evaluates whether it has (i) the power to direct the activities that most significantly impact the VIE’s economic performance and (ii) the obligation to absorb losses or the right to receive benefits of the VIE that could potentially be

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significant to the VIE. The Company’s evaluation includes identification of significant activities and an assessment of its ability to direct those activities based on governance provisions and arrangements to provide or receive product and process technology, product supply, operations services, equity funding and financing and other applicable agreements and circumstances. The Company’s assessment of whether it is the primary beneficiary of its VIEs requires significant assumptions and judgment.

The consolidated financial statements of the Company include the accounts of Amyris, Inc., its subsidiaries and two consolidated VIEs with respect to which the Company is considered the primary beneficiary, after elimination of intercompany accounts and transactions. Disclosure regarding the Company’s participation in the VIEs is included in Note 8.

Use of Estimates

In preparing the consolidated financial statements, management must make estimates and assumptions that affect the reported amounts of assets and liabilities and disclosure of contingent assets and liabilities as of the date of the consolidated financial statements and the reported amounts of revenue and expenses during the reporting period. Actual results could differ from those estimates.

Concentration of Credit Risk

Financial instruments that potentially subject the Company to a concentration of credit risk consist primarily of cash and cash equivalents and accounts receivable. The Company places its cash equivalents and investments with high credit quality financial institutions and, by policy, limits the amount of credit exposure with any one financial institution. Deposits held with banks may exceed the amount of insurance provided on such deposits. The Company has not experienced any losses on its deposits of cash and cash equivalents and short-term investments.

The Company performs ongoing credit evaluation of its customers, does not require collateral, and maintains allowances for potential credit losses on customer accounts when deemed necessary.

Customers representing 10% or greater of accounts receivable were as follows:

	December 31,
Customers	2012		2011
Customer A	*		20	%
Customer B	*		10	%
Customer C	44	%	**
Customer D	22	%	**
Customer E	14	%	**

______________ 

 * No outstanding balance

** Less than 10%

Customers representing 10% or greater of revenues were as follows:

	Years Ended December 31,
Customers	2012		2011		2010
Customer A	13	%	11	%	**
Customer D	**		**		12	%
Customer F	**		**		10	%
Customer G	**		14	%	23	%
Customer H	13	%	*		*
Customer I	**		*		10	%

______________

 * Not a customer

** Less than 10%

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Fair Value of Financial Instruments

The Company measures certain financial assets and liabilities at fair value based on the exchange price that would be received for an asset or paid to transfer a liability (an exit price) in the principal or most advantageous market for the asset or liability in an orderly transaction between market participants. Where available, fair value is based on or derived from observable market prices or other observable inputs. Where observable prices or inputs are not available, valuation models are applied. These valuation techniques involve some level of management estimation and judgment, the degree of which is dependent on the price transparency for the instruments or market and the instruments’ complexity.

The carrying amounts of certain financial instruments, such as cash equivalents, accounts receivable, accounts payable and accrued liabilities, approximate fair value due to their relatively short maturities, and low market interest rates if applicable. The fair values of the notes payable, loan payable, convertible notes and credit facility are based on the present value of expected future cash flows and assumptions about current interest rates and the creditworthiness of the Company.

The Company estimates the fair value of its embedded derivative related to Total senior unsecured convertible notes using a Black-Scholes valuation model that combines expected cash outflows with market-based assumptions regarding risk-adjusted yields, stock price volatility, probability of a change of control and the trading information of the Company's common stock into which the notes are convertible. The Company will continue to mark the bifurcated compound derivative to market due to the conversion price not being indexed to the Company's own stock because of the feature requiring the Company to redeem foregone interest upon conversion by the holder. The change in the fair value of the bifurcated compound derivative is primarily related to the change in price of the underlying common stock and is reflected in the Company's consolidated statements of operations as “other income (expense)”.

Cash and Cash Equivalents

All highly liquid investments purchased with an original maturity date of 90 days or less at the date of purchase are considered to be cash equivalents. Cash and cash equivalents consist of money market funds and certificates of deposit.

Accounts Receivable

The Company maintains an allowance for doubtful accounts receivable for estimated losses resulting from the inability of its customers to make required payments. The Company determines this allowance based on specific doubtful account identification and management judgment on estimated exposure. The Company writes off accounts receivable against the allowance when it determines a balance is uncollectible and no longer actively pursues collection of the receivable. 

Investments

Investments with original maturities greater than 90 days that mature less than one year from the consolidated balance sheet date are classified as short-term investments. The Company classifies investments as short-term or long-term based upon whether such assets are reasonably expected to be realized in cash or sold or consumed during the normal cycle of business. The Company invests its excess cash balances primarily in certificates of deposit. Certificates of deposits that have maturities greater than 90 days that mature less than one year from the consolidated balance sheet date are classified as short term investments. The Company classifies all of its investments as available-for-sale and records such assets at estimated fair value in the consolidated balance sheets, with unrealized gains and losses, if any, reported as a component of accumulated other comprehensive income (loss) in stockholders’ equity. Debt securities are adjusted for amortization of premiums and accretion of discounts and such amortization and accretion are reported as a component of interest income. Realized gains and losses and declines in value that are considered to be other-than-temporary are recognized in the statements of operations. The cost of securities sold is determined on the specific identification method. There were no significant realized gains or losses from sales of debt securities during the years ended December 31, 2012, 2011 and 2010. As of December 31, 2012 and 2011, the Company did not have any other-than-temporary declines in the fair value of its debt securities.

Restricted Cash

Cash accounts that are restricted to withdrawal or usage are presented as restricted cash. As ofDecember 31, 2012 and 2011, the Company had $955,000 and zero, respectively, of restricted cash held by a bank in a certificate of deposit as collateral under a facility lease.

Inventories

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Inventories, which consist of farnesene-derived products, as well as ethanol and reformulated ethanol-blended gasoline, are stated at the lower of cost or market and categorized as finished goods, work-in-process or raw material inventories. During the quarter ended September 30, 2012, the Company sold its remaining inventory of ethanol and reformulated ethanol-blended gasoline as it transitioned out of this business. The Company evaluates the recoverability of its inventories based on assumptions about expected demand and net realizable value. If the Company determines that the cost of inventories exceeds its estimated net realizable value, the Company records a write-down equal to the difference between the cost of inventories and the estimated net realizable value. If actual net realizable values are less favorable than those projected by management, additional inventory write-downs may be required that could negatively impact the Company's operating results. If actual net realizable values are more favorable, the Company may have favorable operating results when products that have been previously written down are sold in the normal course of business. The Company also evaluates the terms of its agreements with its suppliers and establishes accruals for estimated losses on adverse purchase commitments as necessary, applying the same lower of cost or market approach that is used to value inventory. Cost is computed on a first-in, first-out basis. Inventory costs include transportation costs incurred in bringing the inventory to its existing location.

Derivative Instruments

The Company makes limited use of derivative instruments, which includes currency interest rate swap agreements to manage the Company's exposure to foreign currency exchange rate fluctuations and interest rate fluctuations related to the Company's Banco Pine S.A. loan (discussed below under Note 6). Through the third quarter of 2012, the Company held futures positions on the New York Mercantile Exchange and the CME/Chicago Board of Trade to mitigate the risks related to the price volatility of ethanol and reformulated ethanol-blended gasoline but, as of September 30, 2012, the Company had transitioned out of that business and no longer held such derivative instruments. The Company does not engage in speculative derivative activities, and the purpose of its activity in derivative commodity instruments is to manage the financial risk posed by physical transactions and inventory. Changes in the fair value of the derivative contracts are recognized currently in the consolidated statements of operations.

Asset Retirement Obligations

The fair value of an asset retirement obligation is recognized in the period in which it is incurred if a reasonable estimate of fair value can be made. In addition, asset retirement cost is added to the carrying amount of the associated asset and this additional carrying amount is amortized over the life of the asset. The Company’s asset retirement obligations were associated with its commitment to return property subject to an operating lease in Brazil to its original condition upon lease termination. In October 2012, this operating lease was amended which included an amendment to the terms of restitution of the property under lease. As a result of this amendment, the Company no longer has asset retirement obligations and therefore reversed the previously accrued liabilities.

As of December 31, 2012 and 2011, the Company had asset retirement obligations of zero and $1.1 million, respectively. The related leasehold improvements are being amortized to depreciation expense over the term of the lease or the useful life of the assets, whichever is shorter. Related amortization expense was $188,000, $193,000 and $229,000 for the years ended December 31, 2012, 2011 and 2010, respectively.

The change in the asset retirement obligation is summarized below (in thousands):

Balance at December 31, 2010	$	984
Additions	166
Foreign currency impacts and other adjustments	(133		)
Accretion expenses recorded during the period	112
Balance at December 31, 2011	$	1,129
Additions	—
Foreign currency impacts and other adjustments	(98		)
Accretion expenses recorded during the period	91
Reversals	(1,122		)
Balance at December 31, 2012	$	—

Property, Plant and Equipment, net

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Property, plant and equipment, net are stated at cost less accumulated depreciation and amortization. Depreciation and amortization is computed using the straight-line method over the estimated useful lives of the related assets. Maintenance and repairs are charged to expense as incurred, and improvements and betterments are capitalized. When assets are retired or otherwise disposed of, the cost and accumulated depreciation are removed from the balance sheet and any resulting gain or loss is reflected in operations in the period realized.

Depreciation and amortization periods for the Company’s property, plant and equipment are as follows:

Machinery and equipment	7-15 years
Buildings	15 years
Computers and software	3-5 years
Furniture and office equipment	5 years
Vehicles	5 years

Buildings and leasehold improvements are amortized on a straight-line basis over the terms of the lease, or the useful life of the assets, whichever is shorter.

Computers and software includes internal-use software that is acquired to meet the Company’s needs. Amortization commences when the software is ready for its intended use and the amortization period is the estimated useful life of the software, generally 3 to 5 years. Capitalized costs primarily include contract labor and payroll costs of the individuals dedicated to the installation of internal-use software. Capitalized software additions totaled approximately $1.4 million, $1.1 million, and $1.3 million for the years ended December 31, 2012, 2011 and 2010, respectively, related to software costs pertaining to the installation of new financial reporting systems. For the years ended December 31, 2012, 2011 and 2010, $0.7 million, $0.4 million and $0.3 million, respectively, of amortization expense was recorded and as of December 31, 2012 the total unamortized cost of capitalized software was $2.6 million. During the year ended December 31, 2012, the Company wrote-off capitalized software with a net book value of $0.9 million.

Impairment of Long-Lived Assets

Long-lived assets to be held and used are reviewed for impairment whenever events or changes in circumstances indicate that the carrying amount of an asset may not be recoverable or the estimated useful life is no longer appropriate. If indicators of impairment exist and the undiscounted projected cash flows associated with such assets are less than the carrying amount of the asset, an impairment loss is recorded to write the asset down to their estimated fair values. Fair value is estimated based on discounted future cash flows. There were $6.4 million, zero and zero, respectively, of impairment charges recorded during the years ended December 31, 2012, 2011 and 2010, respectively. The impairment charges of $6.4 million in 2012 included the write-off of capitalized software with a net book value of $0.9 million.

Goodwill and Intangible Assets

Goodwill represents the excess of the cost over the fair value of net assets acquired from our business combinations. Intangible assets are comprised primarily of in-process research and development ("IPR&D"). The Company makes significant judgments in relation to the valuation of goodwill and intangible assets resulting from business combinations.

There are several methods that can be used to determine the estimated fair value of the IPR&D acquired in a business combination. We used the "income method," which applies a probability weighting that considers the risk of development and commercialization, to the estimated future net cash flows that are derived from projected sales revenues and estimated costs. These projections are based on factors such as relevant market size, pricing of similar products, and expected industry trends. The estimated future net cash flows are then discounted to the present value using an appropriate discount rate. These assets are treated as indefinite-lived intangible assets until completion or abandonment of the projects, at which time the assets will be amortized over the remaining useful life or written off, as appropriate.

Goodwill and intangible assets with indefinite lives are assessed for impairment using fair value measurement techniques on an annual basis or more frequently if facts and circumstance warrant such a review. When required, a comparison of fair value to the carrying amount of assets is performed to determine the amount of any impairment.

The Company evaluates its intangible assets with finite lives for indications of impairment whenever events or changes in circumstances indicate that the carrying value may not be recoverable. Intangible assets consist of purchased licenses and permits

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and are amortized on a straight-line basis over their estimated useful lives. Amortization of intangible assets was $0.4 million, $0.4 million and zero for the years ended December 31, 2012, 2011 and 2010, respectively. Factors that could trigger an impairment review include significant under-performance relative to expected historical or projected future operating results, significant changes in the manner of our use of the acquired assets or the strategy for our overall business or significant negative industry or economic trends. If this evaluation indicates that the value of the intangible asset may be impaired, we make an assessment of the recoverability of the net carrying value of the asset over its remaining useful life. If this assessment indicates that the intangible asset is not recoverable, based on the estimated undiscounted future cash flows of the technology over the remaining amortization period, we reduce the net carrying value of the related intangible asset to fair value and may adjust the remaining amortization period. Any such impairment charge could be significant and could have a material adverse effect on our reported financial results. The Company has not recognized any impairment charges on our intangible assets through December 31, 2012.

In-Process Research and Development

During 2011, the Company recorded IPR&D of $8.6 million related to the acquisition of Draths. Amounts recorded as IPR&D will begin being amortized upon first sales of the product over the estimated useful life of the technology. In accordance with authoritative guidance, as the technology has not yet been proven, the amortization of the acquired IPR&D has not begun. The Company estimates that it could take up to three years before it will have viable products resulting from the acquired technology.

Noncontrolling Interest and Redeemable Noncontrolling Interest

Changes in noncontrolling interest ownership that do not result in a change of control and where there is a difference between fair value and carrying value are accounted for as equity transactions. On April 14, 2010, the Company entered into a joint venture with Usina São Martinho. The carrying value of the noncontrolling interest from this joint venture is recorded in the equity section of the consolidated balance sheets (see Note 8). On January 3, 2011, the Company entered into a production service agreement with Glycotech, Inc. ("Glycotech"). The Company has determined that the arrangement with Glycotech qualifies as a VIE. The Company determined that it is the primary beneficiary. The carrying value of the noncontrolling interest from this VIE is recorded in the equity section of the consolidated balance sheets (see Note 8).

Revenue Recognition

The Company recognizes revenue from the sale of farnesene-derived products, delivery of research and development services, and from governmental grants. Through the third quarter of 2012, the Company also sold ethanol and reformulated ethanol-blended gasoline under short-term agreements at prevailing market prices. As of September 30, 2012, the Company had transitioned out of that business. Revenue is recognized when all of the following criteria are met: persuasive evidence of an arrangement exists, delivery has occurred or services have been rendered, the fee is fixed or determinable, and collectibility is reasonably assured.

If sales arrangements contain multiple elements, the Company evaluates whether the components of each arrangement represent separate units of accounting.

Product Sales

Beginning in the second quarter of 2011, the Company began to sell farnesene-derived products, which were produced by contracted third parties. Through the third quarter of 2012, the Company also sold ethanol and reformulated ethanol-blended gasoline under short-term agreements at prevailing market prices. As of September 30, 2012, the Company had transitioned out of that business.Ethanol and reformulated ethanol-blended gasoline sales consisted of sales to customers through purchases from third-party suppliers in which the Company took physical control of the ethanol and reformulated ethanol-blended gasoline and accepted risk of loss. The Company's renewable product sales do not include rights of return. Returns are only accepted if the product does not meet product specifications and such nonconformity is communicated to the Company within a set number of days of delivery. Commencing April 1, 2012, the Company began offering a two year standard warranty provision for squalane products sold after March 31, 2012, if the products do not meet Company-established criteria as set forth in the Company's trade terms. The Company bases its return reserve on a combination of historical rate of return for the Company's squalane products and historical returns for companies in the cosmetics industry since the Company did not have a full two years of historical return data. Revenues are recognized, net of discounts and allowances, once passage of title and risk of loss has occurred and contractually specified acceptance criteria have been met, provided all other revenue recognition criteria have also been met.

Grants and Collaborative Revenue

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Revenue from collaborative research services is recognized as the services are performed consistent with the performance requirements of the contract. In cases where the planned levels of research services fluctuate over the research term, the Company recognizes revenue using the proportionate performance method based upon actual efforts to date relative to the amount of expected effort to be incurred by the Company. When up-front payments are received and the planned levels of research services do not fluctuate over the research term, revenue is recorded on a ratable basis over the arrangement term, up to the amount of cash received. When up-front payments are received and the planned levels of research services fluctuate over the research term, revenue is recorded using the proportionate performance method, up to the amount of cash received. Where arrangements include milestones that are determined to be substantive and at risk at the inception of the arrangement, revenue is recognized upon achievement of the milestone and is limited to those amounts whereby collectibility is reasonably assured.

Government grants are agreements that generally provide cost reimbursement for certain types of expenditures in return for research and development activities over a contractually defined period. Revenues from government grants are recognized in the period during which the related costs are incurred, provided that the conditions under which the government grants were provided have been met and only perfunctory obligations are outstanding. Under the Defense Advanced Research Projects Agency (DARPA) contract signed in June 2012, the Company will receive funding based on achievement of program milestones. Accordingly, the Company will recognize revenue using the proportionate performance method based upon actual efforts to date relative to the amount of expected effort to be incurred, up to the amount of verified payable milestones.

Cost of Products Sold

Starting in the second quarter of 2011, cost of products sold includes production costs of farnesene-derived products, which include cost of raw materials, amounts paid to contract manufacturers and period costs including inventory write-downs resulting from applying lower-of-cost-or-market inventory valuation. Cost of farnesene-derived products sold also includes certain costs related to the scale-up in production of such products. Through the third quarter of 2012, cost of products sold consisted primarily of cost of purchased ethanol and reformulated ethanol-blended gasoline, terminal fees paid for storage and handling, transportation costs between terminals and changes in the fair value of derivative commodity instruments. The Company transitioned out of its ethanol and gasoline business in the quarter ended September 30, 2012.

Shipping and handling costs charged to customers are recorded as revenues. Shipping costs are included in cost of products sold. Such charges were not significant in any of the periods presented.

Costs of Start-Up Activities

Start-up activities are defined as those one-time activities related to opening a new facility, introducing a new product or service, conducting business in a new territory, conducting business with a new class of customer or beneficiary, initiating a new process in an existing facility, commencing some new operation or activities related to organizing a new entity. All the costs associated with start-up activities related to a potential facility are expensed and recorded within selling, general and administrative expenses until the facility is considered viable by management, at which time costs would be considered for capitalization based on authoritative accounting literature.

Research and Development

Research and development costs are expensed as incurred and include costs associated with research performed pursuant to collaborative agreements and government grants. Research and development costs consist of direct and indirect internal costs related to specific projects as well as fees paid to others that conduct certain research activities on the Company’s behalf.

Income Taxes

The Company accounts for income taxes under the asset and liability method, which requires, among other things, that deferred income taxes be provided for temporary differences between the tax basis of the Company’s assets and liabilities and their financial statement reported amounts. In addition, deferred tax assets are recorded for the future benefit of utilizing net operating losses and research and development credit carryforwards. A valuation allowance is provided against deferred tax assets unless it is more likely than not that they will be realized.

The Company recognizes and measures uncertain tax positions in accordance with Income Taxes subtopic 05-6 of ASC 740, which prescribes a recognition threshold and measurement process for recording uncertain tax positions taken, or expected to be taken in a tax return, in the consolidated financial statements. Additionally, the guidance also prescribes treatment for the derecognition, classification, accounting in interim periods and disclosure requirements for uncertain tax positions. The Company accrues for the estimated amount of taxes for uncertain tax positions if it is more likely than not that the Company would be

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required to pay such additional taxes. An uncertain tax position will not be recognized if it has a less than 50% likelihood of being sustained.

Currency Translation

The Brazilian real is the functional currency of the Company’s wholly-owned subsidiary in Brazil and of the Company’s joint venture with Usina São Martinho. Accordingly, asset and liability accounts of those operations are translated into United States dollars using the current exchange rate in effect at the balance sheet date and equity accounts are translated into United States dollars using historical rates. The revenues and expenses are translated using the exchange rates in effect when the transactions occur. Gains and losses from foreign currency translation adjustments are included as a component of accumulated other comprehensive income (loss) in the consolidated balance sheets.

Stock-Based Compensation

The Company accounts for stock-based compensation arrangements with employees using a fair value method which requires the recognition of compensation expense for costs related to all stock-based payments including stock options. The fair value method requires the Company to estimate the fair value of stock-based payment awards on the date of grant using an option pricing model. The Company uses the Black-Scholes option pricing model to estimate the fair value of options granted, which is expensed on a straight-line basis over the vesting period. The Company accounts for restricted stock unit awards issued to employees based on the fair market value of the Company’s common stock.

The Company accounts for stock options issued to nonemployees based on the estimated fair value of the awards using the Black-Scholes option pricing model. The Company accounts for restricted stock units issued to nonemployees based on the fair market value of the Company’s common stock. The measurement of stock-based compensation is subject to periodic adjustments as the underlying equity instruments vest, and the resulting change in value, if any, is recognized in the Company’s consolidated statements of operations during the period the related services are rendered.

Comprehensive Income (Loss)

Comprehensive income (loss) represents all changes in stockholders’ equity except those resulting from investments or contributions by stockholders. The Company’s foreign currency translation adjustments represent the components of comprehensive income (loss) excluded from the Company’s net loss and have been disclosed in the consolidated statements of comprehensive loss for all periods presented.

The components of accumulated other comprehensive loss are as follows (in thousands):

	December 31,
	2012			2011
Foreign currency translation adjustment, net of tax	$	(12,807	)	$	(5,924	)
Total accumulated other comprehensive loss	$	(12,807	)	$	(5,924	)

Net Loss Attributable to Common Stockholders and Net Loss per Share

The Company computes net loss per share in accordance with ASC 260, “Earnings per Share.” Basic net loss per share of common stock is computed by dividing the Company’s net loss attributable to Amyris, Inc. common stockholders by the weighted-average number of shares of common stock outstanding during the period. Diluted net loss per share of common stock is computed by giving effect to all potentially dilutive securities, including stock options, restricted stock units, common stock warrants, using the treasury stock method or the as converted method, as applicable. For all periods presented, basic net loss per share was the same as diluted net loss per share because the inclusion of all potentially dilutive securities outstanding was anti-dilutive. As such, the numerator and the denominator used in computing both basic and diluted net loss are the same for each period presented.

The following table presents the calculation of basic and diluted net loss per share of common stock attributable to Amyris, Inc. common stockholders (in thousands, except share and per share amounts):

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	Years Ended December 31,
	2012			2011			2010
Numerator:
Net loss attributable to Amyris, Inc. common stockholders	$	(205,139	)	$	(178,870	)	$	(123,879	)
Denominator:
Weighted-average shares of common stock outstanding used in computing net loss per share of common stock, basic and diluted	56,717,869			44,799,056			14,840,253
Net loss per share attributable to common stockholders, basic and diluted	$	(3.62	)	$	(3.99	)	$	(8.35	)

The following outstanding shares of potentially dilutive securities were excluded from the computation of diluted net loss per share of common stock for the periods presented because including them would have been anti-dilutive:

	Years Ended December 31,
	2012	2011	2010
Period-end stock options to purchase common stock	8,946,592	8,377,016	7,274,637
Convertible promissory notes	10,370,391	—	—
Period-end common stock subject to repurchase	51	7,929	33,396
Period-end common stock warrants*	21,087	26,223	195,604
Period-end restricted stock units	2,550,799	375,189	—
Total	21,888,920	8,786,357	7,503,637

______________ 

• The common stock warrants at December 31, 2011 includes 21,087 warrants issued in 2011 and 5,136 common stock warrants converted from preferred stock warrants computed on an as converted basis using the conversion ratios in effect as of September 30, 2010, the date of the IPO Closing. The common stock warrants at December 31, 2010 were converted from preferred stock warrants computed on an as converted basis using the conversion ratios in effect as of September 30, 2010.

Recent Accounting Pronouncements

In December 2011, the International Accounting Standards Board ("IASB") and the FASB issued common disclosure requirements that are intended to enhance comparability between financial statements prepared on the basis of U.S. GAAP and those prepared in accordance with IFRS. In January 2013, the FASB issued an accounting standard update to limit the scope of the new balance sheet offsetting disclosures to derivative instruments, repurchase agreements, and securities lending transactions to the extent that they are offset in the financial statement or subject to an enforceable master netting arrangement or similar arrangement. While this guidance does not change existing offsetting criteria in U.S. GAAP or the permitted balance sheet presentation for items meeting the criteria, it requires an entity to disclose both net and gross information about assets and liabilities that have been offset and the related arrangements. Required disclosures under this new guidance should be provided retrospectively for all comparative periods presented. This new guidance is effective for fiscal years beginning on or after January 1, 2013, and interim periods within those years, which would be the Company's first quarter of fiscal 2013. The adoption of this guidance will require expanded disclosure in the Company's consolidated financial statements but will not impact financial results.

In July 2012, the FASB issued an amended accounting standard update to simplify how entities test indefinite-lived intangible assets for impairment which improve consistency in impairment testing requirements among long-lived asset categories. The amended guidance permits an assessment of qualitative factors to determine whether it is more likely than not that the fair value of an indefinite-lived intangible asset is less than its carrying value. For assets in which this assessment concludes it is more likely than not that the fair value is more than its carrying value, then the amended guidance eliminates the requirement to perform quantitative impairment testing as outlined in the previously issued standards. The amended guidance is effective for fiscal years beginning after September 15, 2012; however, early adoption is permitted. The Company does not expect this amended guidance to have an impact on the Company's financial results.

In February 2013, in connection with the accounting standard related to the presentation of the Statement of Comprehensive Income, the FASB issued an accounting standard update to improve the reporting of reclassifications out of accumulated other comprehensive income of various components. This guidance requires companies to present either parenthetically on the face of the financial statements or in the notes, significant amounts reclassified from each component of accumulated other comprehensive

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income and the income statement line items affected by the reclassification. This standard is effective for interim periods and fiscal years beginning after December 15, 2012, which would be the Company's first quarter of fiscal 2013. The adoption of this guidance will require expanded disclosure in the Company's consolidated financial statements but will not impact financial results.

3. Fair Value of Financial Instruments

The inputs to the valuation techniques used to measure fair value are classified into the following categories:

Level 1: Quoted market prices in active markets for identical assets or liabilities.

Level 2: Observable market-based inputs or unobservable inputs that are corroborated by market data.

Level 3: Unobservable inputs that are not corroborated by market data.

As of December 31, 2012, the Company’s financial assets and financial liabilities are presented below at fair value and were classified within the fair value hierarchy as follows (in thousands):

	Level 1		Level 2		Level 3		Balance as of December 31, 2012
Financial Assets
Money market funds	$	15,847	$	—	$	—	$	15,847
Certificates of deposit	757		—		—		757
Total financial assets	$	16,604	$	—	$	—	$	16,604
Financial Liabilities
Notes payable	$	—	$	1,676	$	—	$	1,676
Loans payable	—		20,707		—		20,707
Credit facilities	—		11,503		—		11,503
Convertible notes	—		—		62,522		62,522
Compound embedded derivative liability	—		—		7,894		7,894
Currency interest rate swap derivative liability	—		1,367		—		1,367
Total financial liabilities	$	—	$	35,253	$	70,416	$	105,669

The Company’s assessment of the significance of a particular input to the fair value measurement in its entirety requires management to make judgments and consider factors specific to the asset or liability. The fair values of money market funds are based on fair values of identical assets. The fair values of the notes payable, loan payable, convertible notes, credit facility and currency interest rate swaps are based on the present value of expected future cash flows and assumptions about current interest rates and the creditworthiness of the Company. Market risk associated with our fixed and variable rate long-term debt relates to the potential reduction in fair value and negative impact to future earnings, respectively, from an increase in interest rates.

The following table provides a reconciliation of the beginning and ending balances for the compound embedded derivative liability measured at fair value using significant unobservable inputs (Level 3) (in thousands):

	Compound Embedded Derivative Liability
Balance at December 31, 2011	$	—
Transfers in to Level 3	11,025
Total (gain) losses included in other income (expense), net	(3,131		)
Balance at December 31, 2012	$	7,894

The compound embedded derivative liability, which is included in other liabilities, represents the value of the equity conversion option and a "make-whole" provision of outstanding senior unsecured convertible promissory notes issued to Total Gas & Power USA SAS (see Note 6). There is no current observable market for this type of derivative and, as such, the Company determined the value of the embedded derivative using a Black-Scholes valuation model that combines expected cash outflows with market-based assumptions regarding risk-adjusted yields, stock price volatility, probability of a change of control and the

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trading information of the Company's common stock into which the notes are convertible. The Company marks the embedded derivative to market due to the conversion price not being indexed to the Company's own stock. Except for the "make-whole interest" provision included in the conversion option, which is only required to be settled in cash upon a change of control at the noteholder's option, the embedded derivative will be settled in either cash or shares. As of December 31, 2012, the Company had enough common shares to settle the conversion option in shares.

The Company’s financial assets and financial liabilities as of December 31, 2011 are presented below at fair value and were classified within the fair value hierarchy as follows (in thousands):

	Quoted Prices in Active Markets for Identical Assets (Level 1)		Other Observable Inputs (Level 2)		Significant Unobservable Inputs (Level 3)		Balance as of December 31, 2011
Financial Assets
Money market funds	$	57,127	$	—	$	—	$	57,127
Certificates of Deposit	27,384		—		—		27,384
Total financial assets	$	84,511	$	—	$	—	$	84,511
Financial Liabilities
Derivative liabilities	$	18	$	—	$	—	$	18
Total financial liabilities	$	18	$	—	$	—	$	18

Derivative Instruments

The Company’s derivative instruments included Chicago Board of Trade (CBOT) ethanol futures and Reformulated Blendstock for Oxygenate Blending (RBOB) gasoline futures. All derivative commodity instruments were recorded at fair value on the consolidated balance sheets. None of the Company’s derivative instruments were designated as a hedging instrument. Changes in the fair value of these non-designated hedging instruments were recognized in cost of products sold in the consolidated statements of operations. As of December 31, 2012, the Company had no outstanding derivative commodity instruments resulting from the Company's transition out of of its ethanol and gasoline business in the quarter ended September 30, 2012.

In June 2012, the Company entered into a loan agreement with Banco Pine S.A. under which the bank provided the Company with a short term loan of R$52.0 million (approximately US$25.4 million based on the exchange rate as of December 31, 2012) (the “Bridge Loan”). At the time of the Bridge Loan, the Company also entered into a currency interest rate swap arrangement with Banco Pine with respect to the repayment of R$22.0 million (approximately US$10.8 million based on the exchange rate of as of December 31, 2012). The swap arrangement exchanges the principal and interest payments under the Banco Pine loan of R$22.0 million entered into in July 2012 for alternative principal and interest payments that are subject to adjustment based on fluctuations in the foreign exchange rate between the U.S. dollar and Brazilian real. The swap has a fixed interest rate of 3.94%. Changes in the fair value of the swap are recognized in other income (expense), net in the consolidated statements of operations.

As of December 31, 2012, the Company recognized compound embedded derivative liability of $7.9 million which was included in other liabilities and represents the value of the equity conversion option and a "make-whole" provision of outstanding senior unsecured convertible promissory notes issued to Total Gas & Power USA SAS (see Note 6).

Derivative instruments measured at fair value as of December 31, 2012 and 2011, and their classification on the consolidated balance sheets and consolidated statements of operations, are presented in the following tables (in thousands except contract amounts):

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	Asset/Liability as of
	December 31, 2012			December 31, 2011
Type of Derivative Contract	Quantity of Short Contracts	Fair Value		Quantity of Short Contracts	Fair Value
Regulated fixed price futures contracts, included as liability in accounts payable	—	$	—	22	$	18
Currency interest rate swap, included as net liability in other long term liability	1	$	1,367	—	$	—

	Income Statement Classification	Years Ended December 31,
Type of Derivative Contract		2012			2011			2010
		Gain (Loss) Recognized
Regulated fixed price futures contracts	Cost of products sold	$	(288	)	$	(2,365	)	$	(2,225	)
Currency interest rate swap	Other income (expense), net	$	(1,367	)	$	—		$	—

4. Balance Sheet Components

Investments

The following table summarizes the Company’s investments as of December 31, 2012 (in thousands):

	December 31, 2012
	Amortized Cost		Unrealized Gain (Loss)		Fair Value
Short-Term Investments
Certificates of Deposit	$	97	$	—	$	97
Total short-term investments	$	97	$	—	$	97

The following table summarizes the Company’s investments as of December 31, 2011 (in thousands):

	December 31, 2011
	Amortized Cost		Unrealized Gain (Loss)		Fair Value
Short-Term Investments
Certificates of Deposit	$	7,889	$	—	$	7,889
Total short-term investments	$	7,889	$	—	$	7,889

Inventories

Inventories, net is comprised of the following (in thousands):

	December 31,
	2012		2011
Raw materials	$	1,574	$	2,191
Work-in-process	1,771		1,237
Finished goods	2,689		5,642
Inventories, net	$	6,034	$	9,070

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Prepaid and Other Current Assets

Prepaid and other current assets is comprised of the following (in thousands):

	December 31,
	2012		2011
Advances to contract manufacturers(1)	$	784	$	10,748
Manufacturing catalysts	1,895		3,929
Recoverable VAT and other taxes	4,167		2,193
Other	2,079		3,003
Prepaid and other current assets	$	8,925	$	19,873

⁽¹⁾  At December 31, 2012 and 2011, the amount of $784,000 and $748,000, respectively, relates to the current unamortized portion of equipment costs funded by the Company to a contract manufacturer. The related amortization is being offset against purchases of inventory.

Property, Plant and Equipment, net

Property, plant and equipment, net is comprised of the following (in thousands):

	December 31,
	2012			2011
Leasehold improvements	$	39,290		$	40,011
Machinery and equipment	105,162			59,657
Computers and software	8,232			6,491
Furniture and office equipment	2,467			2,223
Buildings	5,888			—
Vehicles	575			596
Construction in progress	45,372			45,318
	$	206,986		154,296
Less: accumulated depreciation and amortization	(43,865		)	(26,195		)
Property, plant and equipment, net	$	163,121		$	128,101

Property, plant and equipment, net includes $9.1 million and $13.7 million of machinery and equipment and furniture and office equipment under capital leases as of December 31, 2012 and 2011, respectively. Accumulated amortization of assets under capital leases totaled $4.1 million and $4.7 million as of December 31, 2012 and 2011, respectively.

Depreciation and amortization expense, including amortization of assets under capital leases, was $14.2 million, $10.7 million and $7.3 million for the years ended December 31, 2012, 2011 and 2010, respectively.

The Company capitalizes interest costs incurred to construct plant and equipment. The capitalized interest is recorded as part of the depreciable cost of the asset to which it relates to and is amortized over the asset's estimated useful life. Interest cost capitalized as of December 31, 2012 and 2011was $0.6 million and zero, respectively.

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Other Assets

Other assets are comprised of the following (in thousands):

	December 31,
	2012		2011
Deferred charge asset(1)	$	—	$	18,792
Deposits on property and equipment, including taxes	2,363		17,455
Advances to contract manufacturers, net of current portion(2)	2,222		2,866
Recoverable taxes on purchased property, plant and equipment(3)	13,597		2,075
Other	1,930		1,813
Total other assets	$	20,112	$	43,001

______________ 

⁽¹⁾  The deferred charge asset relates to the collaboration agreement between the Company and Total (see Note 9).

⁽²⁾  At December 31, 2012 and 2011, $2.2 million and $2.9 million, respectively, relates to the non-current unamortized portion of equipment costs funded by the Company to a contract manufacturer. The related amortization is being offset against purchases of inventory.

⁽³⁾  At December 31, 2012 and December 31, 2011, $13.6 million and $2.1 million, respectively, are recoverable taxes from the Brazilian government.

Accrued and Other Current Liabilities

Accrued and other current liabilities are comprised of the following (in thousands):

	December 31,
	2012		2011
Professional services	$	824	$	4,384
Accrued vacation	2,673		2,761
Payroll and related expenses	5,809		6,343
Construction in progress	—		4,992
Tax-related liabilities	851		2,180
Deferred rent, current portion	1,448		1,274
Contractual obligations to contract manufacturers	9,952		—
Customer advances	970		3,667
Other	1,883		5,381
Total accrued and other current liabilities	$	24,410	$	30,982

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Other Liabilities

Other liabilities are comprised of the following (in thousands):

	December 31,
	2012		2011
Contingently repayable advance from related party collaborator(1)	$	—	$	31,922
Bonus payable to contract manufacturer, non-current	—		2,500
Contractual obligations to contract manufacturers, non-current	4,000		—
Fair market value of swap obligations	1,367		—
Asset retirement obligations	—		1,129
Fair value of compound embedded derivative liability(2)	7,894		—
Other	2,672		1,534
Total other liabilities	$	15,933	$	37,085

______________ 

⁽¹⁾  The contingently repayable advance from related party collaborator as of December 31, 2011 relates to the collaboration agreement between the Company and Total.

⁽²⁾  The compound embedded derivative liability represents the fair value of the equity conversion feature and a "make-whole" feature of the outstanding senior unsecured convertible promissory notes issued to Total.

In November 2011, the Company and Total entered into an amendment of their Technology License, Development, Research and Collaboration Agreement (the "Amendment”). The Amendment provided for an exclusive strategic collaboration for the development of renewable diesel products and contemplated that the parties would establish a joint venture (the “JV”) for the production and commercialization of such renewable diesel products on an exclusive, worldwide basis. In addition, the Amendment contemplated providing the JV with the right to produce and commercialize certain other chemical products on a non-exclusive basis. The amendment further provided that definitive agreements to form the JV had to be in place by March 31, 2012 or such other date as agreed to by the parties or the renewable diesel program, including any further collaboration payments by Total related to the renewable diesel program, would terminate. In the second quarter of 2012, the parties extended the deadline to June 30, 2012, and, through June 30, 2012 the parties were engaged in discussions regarding the structure of future payments related to the program, until the amendment was superseded by a further amendment in July 2012 (as discussed in Note 9).

Pursuant to the Amendment, Total agreed to fund the following amounts: (i) the first $30 million in research and development costs related to the renewable diesel program which have been incurred since August 1, 2011, which amount would be in addition to the $50 million in research and development funding contemplated by the Collaboration Agreement, and (ii) for any research and development costs incurred following the JV formation date that were not covered by the initial $30 million, an additional $10 million in 2012 and up to an additional $10 million in 2013, which amounts would be considered part of the $50 million contemplated by the Collaboration Agreement. In addition to these payments, Total further agreed to fund 50% of all remaining research and development costs for the renewable diesel program under the Amendment.

Under the Amendment,Total had an option for a period of 90 days following the completion of the renewable diesel program on December 31, 2013 (or any other date as determined by the management committee to achieve the end-project milestone), to notify the Company that it did not wish to pursue production or commercialization of renewable diesel under the Amendment. If Total exercised this right, all of Total's intellectual property rights that were developed during the renewable diesel program would terminate and would be assigned to the Company, and the Company would be obligated to pay Total specified royalties based on the Company's net income in consideration of the benefits the Company derived from the technology and intellectual property developed during the renewable diesel development project. Such royalty payments would commence on the royalty notification date and end on the date when the Company had paid Total an aggregate amount equal to $150 million. Such royalty payments would be equal to (20%) of the Company and Company-affiliate (i) net income on a yearly basis derived from licenses or sales of intellectual property developed under the collaboration other than to the extent such licenses or sales relate to the use of such intellectual property for the non-exclusive JV products, and (ii) net income of the Company on a consolidated basis other than that derived from the jet fuel development program with Total or from the non-exclusive JV products.

In addition, under the Amendment, if the Company sold all or substantially all of its renewable diesel business prior to the time the aggregate royalty amount has been paid, the Company would be required to pay Total fifty percent (50%) of the net proceeds from such sale up to the then-remaining unpaid amount of the aggregate royalty amount. Net income was to be calculated

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in accordance with generally accepted accounting principles consistently applied by the Company and in the event that the foregoing net income was negative for a given fiscal quarter, the Company would not be required to pay any royalty for such fiscal quarter). Beginning on the sixth year from the royalty notification date, the aforementioned royalty would be additionally derived from the non-exclusive JV products.

The Company concluded that there was a significant amount of risk associated with the development of these products and therefore the arrangement is within the scope of ASC 730-20 Research and Development. The Company also determined that until Total exercised its royalty option under the Amendment, it would be uncertain that financial risk involved with research and development was transferred from the Company to Total. Accordingly, the funds received from Total for the diesel product research and development activities were recorded as a contingently repayable advance from the collaborator as part of other liabilities in the Company's consolidated balance sheets. Depending on the resolution of Total's royalty option contingency, the Company will record this arrangement as a contract to perform research and development services or as an obligation to repay the funds.

In July 2012, the Company entered into a further amendment of the collaboration agreement with Total that expanded Total's investment in the biofene collaboration, incorporated the development of certain joint venture products for use in diesel and jet fuel into the scope of the collaboration, and changed the structure of the funding from Total to include a convertible debt mechanism (see Note 9). As a part of the July 2012 amendment agreements, Total's royalty option contingency related to diesel was removed and the jet fuel collaboration was combined with the expanded biofene collaboration. As a result, $46.5 million of payments received from Total that had been recorded as an advance from the collaborator were no longer contingently repayable. Of this amount, $23.3 million was treated as a repayment by the Company and included as part of the senior unsecured convertible promissory note issued to Total in July 2012 and the remaining $23.2 million was recorded as a contract to perform research and development services, which was offset by the reduction of the capitalized deferred charge asset of $14.4 million resulting in the Company recording revenue from a related party of $8.9 million.

5. Commitments and Contingencies

Capital Leases

In March 2008, the Company executed an equipment financing agreement intended to cover certain qualifying research and laboratory hardware and software. In January 2009, the agreement was amended to increase the financing amount. During the years ended December 31, 2012, 2011 and 2010, the Company financed certain purchases of hardware equipment and software of approximately zero, zero and $1.4 million, respectively. Pursuant to the equipment financing agreement, the Company financed the equipment with the transactions representing capital leases. Accordingly, fixed assets and capital lease liabilities were recorded at the present values of the future lease payments of $0.4 million and $3.1 million at December 31, 2012 and 2011. The incremental borrowing rates used to determine the present values of the future lease payments was 9.5%. The capital lease obligations expire at various dates, with the latest maturity in March 2013. In connection with the agreement entered into in 2008, the Company issued a warrant to purchase shares of the Company's convertible preferred stock (see Note 11).

In December 2011, the Company executed an equipment financing agreement for $3.0 million for certain qualifying manufacturing and laboratory equipment. Pursuant to the equipment financing agreement, the Company financed the equipment with transactions representing capital leases. This sales/leaseback transaction resulted in a $1.3 million unrealized loss which is being amortized over the life of the assets under lease. Accordingly, a capital lease liability was recorded at the present value of the future lease payments of $2.2 million and $3.4 million during the years ended December 31, 2012 and 2011, respectively. The incremental borrowing rate used to determine the present values of the future lease payments was 6.5%. The lease obligations expire on January 1, 2015. In connection with the capital lease entered into in 2011, the Company issued a warrant to purchase shares of the Company's common stock (see Note 11). Future minimum payments under this sales/leaseback agreement as of December 31, 2012 are as follows (in thousands):

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Years ending December 31:	Sales/Leaseback
2013	$	1,098
2014	1,007
2015	289
2016	—
2017	—
Thereafter	—
Total future minimum lease payments	2,394
Less: amount representing interest	(168		)
Present value of minimum lease payments	2,226
Less: current portion	(982		)
Long-term portion	$	1,244

The Company recorded interest expense in connection with its capital leases of $382,000, $559,000 and $821,000 for the years ended December 31, 2012, 2011 and 2010, respectively. Future minimum payments under capital leases, including the sales/leaseback, as of December 31, 2012 are as follows (in thousands):

Years ending December 31:	Capital Leases
2013	$	1,489
2014	1,007
2015	289
2016	—
2017	—
Thereafter	—
Total future minimum lease payments	2,785
Less: amount representing interest	(175		)
Present value of minimum lease payments	2,610
Less: current portion	(1,366		)
Long-term portion	$	1,244

Operating Leases

The Company has noncancelable operating lease agreements for office, research and development, and manufacturing space in the United States that expire at various dates, with the latest expiration in May 2018 with an estimated annual rent payment of approximately $6.2 million. In addition, the Company leases facilities in Brazil pursuant to noncancelable operating leases that expire at various dates, with the latest expiration in November 2016 and with an estimated annual rent payment of approximately $0.6 million.

In 2007, the Company entered into an operating lease for its headquarters in Emeryville, California, with a term of ten years commencing in May 2008. As part of the operating lease agreement, the Company received a tenant improvements allowance of $11.4 million. The Company recorded the allowance as deferred rent and associated expenditures as leasehold improvements that are being amortized over the shorter of their estimated useful life or the term of the lease. In connection with the operating lease, the Company elected to defer a portion of the monthly base rent due under the lease and entered into notes payable agreements with the lessor for the purchase of certain tenant improvements. In October 2010, the Company amended its lease agreement with the lessor of its headquarters, to lease up to approximately 22,000 square feet of research and development and office space. In return for the removal of the early termination clause in its amended lease agreement, the Company received approximately $1.0 million from the lessor in December 2010.

The Company recognizes rent expense on a straight-line basis over the noncancelable lease term and records the difference between cash rent payments and the recognition of rent expense as a deferred rent liability. Where leases contain escalation clauses, rent abatements, and/or concessions, such as rent holidays and landlord or tenant incentives or allowances, the Company applies them in the determination of straight-line rent expense over the lease term. Rent expense was $4.9 million, $4.8 million and $3.3 million, respectively, for the years ended December 31, 2012, 2011 and 2010, respectively.

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In January 2011, the Company entered into a right of first refusal agreement with respect to a facility and site in Leland, North Carolina leased by Glycotech covering a two year period commencing in January 2011. Under the right of first refusal agreement, the lessor agrees not to sell the facility and site leased by Glycotech during the term of the production service agreement. If the lessor is presented with an offer to sell, or decides to sell, an adjacent parcel, the Company has a right of first refusal to acquire the adjacent parcel or leased property.

In February 2011, the Company commenced payment of rent related to an operating lease on real property owned by Usina São Martinho in Brazil. In conjunction with a joint venture agreement (see Note 7) with the same entity, the real property will be used by the joint venture entity, SMA Indústria Química S.A. (“SMA”), for the construction of a production facility. This lease has a term of 20 years commencing in February 2011 with an estimated annual rent payment of approximately $46,000.

In February 2011, the Company entered into an operating lease for certain equipment owned by GEA Engenharia de Processos e Sistemas Industriais Ltda (“GEA”) in Brazil. The equipment under this lease was used by the Company in its production activities in Brazil. This lease had a term of one year commencing in March 2011 and was terminated in June 2012 and the equipment was returned to GEA.

In March 2011, the Company entered into an operating lease on real property owned by Paraíso Bioenergia S.A. (“Paraíso Bioenergia”) in Brazil. In conjunction with a supply agreement (see Note 9) with the same entity, the real property is being used by the Company for its Biofene production plant in Brotas. This lease has a term of 15 years commencing in March 2011 with an estimated annual rent payment of approximately $116,000.

In August 2011, the Company notified the lessor of its leased office facilities in Brazil of the Company's termination of its existing lease effective November 30, 2011. At the same time, the Company entered into an operating lease for new office facilities in Campinas, Brazil. The new lease has a term of 5 years commencing in November 2011 with an estimated annual rent payment of approximately $367,000.

In October 2012, an operating lease associated with the Company's pilot plant in Brazil was amended. As a result of this amendment, the Company's operating lease was extended and the new expiration is October 2015 and included an amendment to the terms of restitution of the property under lease. As a result of this amendment, the Company no longer has asset retirement obligations and therefore reversed the previously accrued liabilities.

Future minimum payments under operating leases as of December 31, 2012, are as follows (in thousands):

Years ending December 31:	Operating Leases - Facilities		Operating Leases - Land		Total Operating Leases
2013	$	6,463	$	161	$	6,624
2014	6,610		162		6,772
2015	6,738		162		6,900
2016	6,729		162		6,891
2017	6,598		162		6,760
Thereafter	2,786		1,556		4,342
Total future minimum lease payments	$	35,924	$	2,365	$	38,289

Guarantor Arrangements

The Company has agreements whereby it indemnifies its officers and directors for certain events or occurrences while the officer or director is, or was, serving at the Company’s request in such capacity. The term of the indemnification period is for the officer or director’s lifetime. The maximum potential amount of future payments the Company could be required to make under these indemnification agreements is unlimited; however, the Company has a director and officer insurance policy that limits its exposure and enables the Company to recover a portion of any future amounts paid. As a result of its insurance policy coverage, the Company believes the estimated fair value of these indemnification agreements is minimal. Accordingly, the Company had no liabilities recorded for these agreements as of December 31, 2012 and 2011.

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The Company has a facility (“FINEP Credit Facility”) with a financial institution to finance a research and development project on sugarcane-based biodiesel (see Note 6). The FINEP Credit Facility provides for loans of up to an aggregate principal amount of R$6.4 million (approximately US$3.1 million based on the exchange rate as of December 31, 2012) which is guaranteed by a chattel mortgage on certain equipment of the Company. The Company's total acquisition cost for the equipment under this guarantee is approximately R$6.0 million (approximately US$2.9 million based on the exchange rate as of December 31, 2012). Through December 31, 2012, the Company received all four disbursements after compliance with certain terms and conditions under the FINEP Credit Facility as described in more detail in Note 6. After the release of the first disbursement and prior to any subsequent drawdown from the FINEP Credit Facility, the Company provided bank letters of guarantee of R$3.3 million (approximately US$1.6 million based on the exchange rate as of December 31, 2012) through Banco ABC Brasil S.A. As of December 31, 2012, all available credit under this facility was fully drawn.

The Company has a credit facility (“BNDES Credit Facility”) with a financial institution to finance a production site in Brazil. This credit facility is collateralized by a first priority security interest in certain of the Company's equipment and other tangible assets totaling R$24.9 million (approximately US$12.2 million based on the exchange rate at December 31, 2012). The Company is a parent guarantor for the payment of the outstanding balance under the BNDES Credit Facility. Additionally, the Company is required to provide a bank guarantee under the BNDES Credit Facility.

The Company has signed loan agreements and a security agreement where the Company pledged certain farnesene production assets as collateral (the fiduciary conveyance of movable goods) with each of Nossa Caixa and Banco Pine. Under the loan agreements, Banco Pine, agreed to lend R$22.0 million and Nossa Caixa agreed to lend R$30.0 million as financing for capital expenditures relating to the Company's production facility in Brotas. The Company's total acquisition cost for the farnesene production assets pledged as collateral under these agreements is approximately R$68.0 million (approximately US$33.3 million based on the exchange rate as of December 31, 2012). The Company is a also a parent guarantor for the payment of the outstanding balance under these loan agreements. 

Under an operating lease agreement for its office facilities in Brazil, which commenced on November 15, 2011, the Company is required to maintain restricted cash or letters of credit equal to 3 months of rent of approximately R$0.2 million (approximately US$0.1 million based on the exchange rate as of December 31, 2012) in the aggregate as a guarantee that the Company will meet its performance obligations under such operating lease agreement.

Purchase Obligations

As of December 31, 2012, the Company had $53.1 million in purchase obligations which included $52.7 million in non-cancelable contractual obligations and construction commitments, of which $13.9 million have been accrued as loss on purchase commitments.

Other Matters

Certain conditions may exist as of the date the financial statements are issued, which may result in a loss to the Company but which will only be resolved when one or more future events occur or fail to occur. The Company's management assesses such contingent liabilities, and such assessment inherently involves an exercise of judgment. In assessing loss contingencies related to legal proceedings that are pending against and by the Company or unasserted claims that may result in such proceedings, the Company's management evaluates the perceived merits of any legal proceedings or unasserted claims as well as the perceived merits of the amount of relief sought or expected to be sought.

If the assessment of a contingency indicates that it is probable that a material loss has been incurred and the amount of the liability can be estimated, then the estimated liability would be accrued in the Company's financial statements. If the assessment indicates that a potential material loss contingency is not probable but is reasonably possible, or is probable but cannot be estimated, then the nature of the contingent liability, together with an estimate of the range of possible loss if determinable and material would be disclosed. Loss contingencies considered to be remote by management are generally not disclosed unless they involve guarantees, in which case the guarantee would be disclosed.

The Company is subject to disputes and claims that arise or have arisen in the ordinary course of business and that have not resulted in legal proceedings or have not been fully adjudicated. For example, as of December 31, 2012, the Company had accrued approximately R$2.5 million (approximately US$1.2 million based on the exchange rate as of December 31, 2012) for losses it deemed to be probable arising from a potential claim relating to a contract manufacturing arrangement. Such matters that may arise in the ordinary course of business are subject to many uncertainties and outcomes are not predictable with assurance. Therefore, if one or more of these legal disputes or claims resulted in settlements or legal proceedings that were resolved against the Company

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for amounts in excess of management’s expectations, the Company’s consolidated financial statements for the relevant reporting period could be materially adversely affected.

6. Debt

Debt is comprised of the following (in thousands):

	December 31,
	2012			2011
Credit facilities	$	12,409		$	18,852
Notes payable	1,572			3,113
Convertible notes	25,000			—
Related party convertible notes	39,033			—
Loans payable	26,150			19,359
Total debt	104,164			41,324
Less: current portion	(3,325		)	(28,049		)
Long-term debt	$	100,839		$	13,275

FINEP Credit Facility

In November 2010, the Company entered into a credit facility with Financiadora de Estudos e Projetos (“FINEP”), a state-owned company subordinated to the Brazilian Ministry of Science and Technology. This FINEP Credit Facility was extended to partially fund expenses related to the Company’s research and development project on sugarcane-based biodiesel (“FINEP Project”) and provides for loans of up to an aggregate principal amount of R$6.4 million (approximately US$3.1 million based on the exchange rate as of December 31, 2012) which is secured by a chattel mortgage on certain equipment of the Company as well as by bank letters of guarantee. Through December 31, 2012, the Company received all four disbursements after compliance with certain terms and conditions under the FINEP Credit Facility. The first disbursement of approximately R$1.8 million (approximately US$0.9 million based on the exchange rate as of December 31, 2012) was received in February 2011. The remaining balance totaling approximately R$4.6 million (approximately US$2.2 million based on exchange rate as December 31, 2012) was received in December 2012 in three equal disbursements of approximately R$1.6 million (approximately US$0.8 million based on exchange rate as of December 31, 2012). As of December 31, 2012, all available credit under this facility was fully drawn.

Interest on loans drawn under this credit facility is fixed at 5% per annum. In case of default under or non-compliance with the terms of the agreement, the interest on loans will be dependent on the long-term interest rate as published by the Central Bank of Brazil (“TJLP”). If the TJLP at the time of default is greater than 6%, then the interest will be 5% plus a TJLP adjustment factor, otherwise the interest will be at 11% per annum. In addition, a fine of up to 10% shall apply to the amount of any obligation in default. Interest on late balances will be 1% interest per month, levied on the overdue amount. Payment of the outstanding loan balance is being made in 81 monthly installments, which commenced in July 2012 and extends through March 2019. Interest on loans drawn and other charges are paid on a monthly basis and commenced in March 2011. As of December 31, 2012, the total outstanding loan balance under this credit facility was R$6.4 million (approximately US$3.1 million based on exchange rate as of December 31, 2012).

The FINEP Credit Facility contains the following significant terms and conditions:

• The Company would share with FINEP the costs associated with the FINEP Project. At a minimum, the Company would contribute from its own funds approximately R$14.5 million (approximately US$7.1 million based on the exchange rate as of December 31, 2012) of which R$11.1 million was to be contributed prior to the release of the second disbursement. As of December 31, 2012, all four disbursements were completed and for its part, the Company has fulfilled all of its cost sharing obligations;

• After the release of the first disbursement, prior to any subsequent drawdown from the FINEP Credit Facility, the Company was required to provide bank letters of guarantee of up to R$3.3 million in aggregate (approximately US$1.6 million based on the exchange rate as of December 31, 2012). On December 17, 2012 and prior to release of the second disbursement on December 26, 2012, the Company obtained the required bank letter of guarantees from Banco ABC Brasil, S.A.

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• Amounts released from the FINEP Credit Facility must be completely used by the Company towards the FINEP Project within 30 months after the contract execution.

Revolving Credit Facility

In December 2010, the Company established a revolving credit facility with a financial institution that provided for loans and standby letters of credit of up to an aggregate principal amount of $10.0 million with a sublimit of $5.0 million on standby letters of credit. Interest on loans drawn under this revolving credit facility was equal to (i) the Eurodollar Rate plus 3.0%; or (ii) the Prime Rate plus 0.5%. In case of default or non-compliance with the terms of the agreement, the interest on loans was Prime Rate plus 2.0%. The credit facility was collateralized by a first priority security interest in certain of the Company's present and future assets. In April 2012, the Company repaid $7.7 million of its outstanding loans under the Credit Facility. In May 2012, the Company entered into a letter agreement with the bank amending the credit facility agreement to reduce the committed amount under the credit facility from $10.0 million to approximately $2.3 million, and the letters of credit sublimit from $5.0 million to approximately $2.3 million. The amendment also modified the current ratio covenant to require a ratio of current assets to current liabilities of at least $1.3:1 (as compared to 2:1 in the Credit Facility), and required the Company to maintain unrestricted cash of at least $15.0 million in its account with the Bank. In June 2012, the credit facility was terminated and, as of December 31, 2012, no loans or letters of credit were outstanding.

BNDES Credit Facility

In December 2011, the Company entered into a credit facility ("BNDES Credit Facility”) in the amount of R$22.4 million (approximately US$11.0 million based on the exchange rate at December 31, 2012) with Banco Nacional de Desenvolvimento Econômico e Social ('BNDES”), a government owned bank headquartered in Brazil. This BNDES facility was extended as project financing for a production site in Brazil. The credit line is divided into an initial tranche for up to approximately R$19.1 million reais and an additional tranche of approximately R$3.3 million that becomes available upon delivery of additional guarantees. The credit line is available for 12 months from the date of the Credit Facility, subject to extension by the lender.

The principal of the loans under the BNDES Credit Facility is required to be repaid in 60 monthly installments, with the first installment due in January 2013 and the last due in December 2017. Interest will be due initially on a quarterly basis with the first installment due in March 2012. From and after January 2013, interest payments will be due on a monthly basis together with principal payments. The loaned amounts carry interest of 7% per annum. Additionally, there is a credit reserve charge of 0.1% on the unused balance from each credit installment from the day immediately after it is made available through its date of use, when it is paid.

The BNDES Credit Facility is denominated in Brazilian reais. The BNDES Credit Facility is collateralized by a first priority security interest in certain of the Company's equipment and other tangible assets totaling R$24.9 million (approximately US$12.2 million based on the exchange rate as of December 31, 2012). The Company is a parent guarantor for the payment of the outstanding balance under the BNDES Credit Facility. Additionally, the Company is required to provide a bank guarantee equal to 10.0% of the total approved amount (R$22.4 million in total debt) available under this Credit Facility. For advances of the second tranche (above R$19.1 million), the Company is required to provide additional bank guarantees equal to 90.0% of each such advance, plus additional Company guarantees equal to at least 130.0% of such advance. The BNDES Credit Facility contains customary events of default, including payment failures, failure to satisfy other obligations under this credit facility or related documents, defaults in respect of other indebtedness, bankruptcy, insolvency and inability to pay debts when due, material judgments, and changes in control of Amyris Brasil. If any event of default occurs, the Lender may terminate its commitments and declare immediately due all borrowings under the facility. As of December 31, 2012 the Company had R$19.1 million (approximately US$9.3 million based on the exchange rate as of December 31, 2012) in outstanding advances under the BNDES Credit Facility.

Notes Payable

During the period between May 2008 and October 2008, the Company entered into notes payable agreements with the lessor of its headquarters under which it borrowed a total of $3.3 million for the purchase of tenant improvements, bearing an interest rate of 9.5% per annum and to be repaid over a period of 55 to 120 months. As of December 31, 2012 and 2011, a principal amount of $1.6 million and $2.0 million, respectively, was outstanding under these notes payable.

In connection with the operating lease for its headquarters (see Note 5) in Emeryville, California, the Company elected to defer a portion of it's monthly base rent due under the lease. In June 2011, a deferred rent obligation of $1.5 million resulting from this election became due and payable in 24 equal monthly installments of approximately $63,000. As such, the Company reclassified this obligation from Other Liabilities to Notes Payable. In June 2012, the Company paid off the outstanding notes payable balance.

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As of December 31, 2012 and 2011, a principal amount of zero and $1.1 million, respectively, was outstanding under this note payable.

Convertible Notes

In February 2012, the Company completed the sale of senior unsecured convertible promissory notes in an aggregate principal amount of $25.0 million pursuant to a Securities Purchase Agreement, between the Company and certain investment funds affiliated with Fidelity Investments Institutional Services Company, Inc. The offering consisted of the sale of 3.0% senior unsecured convertible promissory notes with a March 1, 2017 maturity date and an initial conversion price equal to $7.0682 per share of the Company's common stock, subject to adjustment for proportional adjustments to outstanding common stock and anti-dilution provisions in case of dividends and distributions. As of December 31, 2012, the notes were convertible into an aggregate of up to 3,536,968 shares of common stock. The note holders have a right to require repayment of 101% of the principal amount of the notes in an acquisition of the Company, and the notes provide for payment of unpaid interest on conversion following such an acquisition if the note holders do not require such repayment.  The securities purchase agreement and notes include covenants regarding payment of interest, maintaining the Company's listing status, limitations on debt, maintenance of corporate existence, and filing of SEC reports. The notes include standard events of default resulting in acceleration of indebtedness, including failure to pay, bankruptcy and insolvency, cross-defaults, material adverse effect clauses and breaches of the covenants in the securities purchase agreement and notes, with default interest rates and associated cure periods applicable to the covenant regarding SEC reporting. Furthermore, the senior unsecured convertible notes include restrictions on the amount of debt the Company is permitted to incur. The Company's total outstanding debt at any time can not exceed the greater of $200.0 million or 50% of its consolidated total assets and its secured debt cannot exceed the greater of $125 million or 30% of its consolidated total assets.

Related Party Convertible Notes

In July 30, 2012, the Company entered into a further amendment of the collaboration agreement with Total that expanded Total's investment in the biofene collaboration, incorporated the development of certain joint venture products for use in diesel and jet fuel into the scope of the collaboration, and changed the structure of the funding from Total to include a convertible debt mechanism (see Note 9).

The purchase agreement for the notes related to the funding from Total provides for the sale of an aggregate of $105.0 million in notes as follows:

• As part of an initial closing under the purchase agreement (which initial closing was completed in two installments), (i) on July 30, 2012, the Company sold a 1.5% Senior Unsecured Convertible Note Due 2017 to Total in the face amount of $38.3 million, including $15.0 million in new funds and $23.3 million in previously-provided diesel research and development funding by Total, and (ii) on September 14, 2012, the Company sold another note (in the same form) for $15.0 million in new funds from Total.

• The purchase agreement provides that additional notes may be sold in subsequent closings in July 2013 (for cash proceeds to the Company of $30.0 million) and July 2014 (for cash proceeds to the Company of $21.7 million, which would be settled in an initial installment of $10.85 million payable at such closing and a second installment of $10.85 million payable in January 2015).

The notes each have a March 1, 2017 maturity date and an initial conversion price equal to $7.0682 per share of the Company's common stock. The notes bear interest of 1.5% per annum (with a default rate of 2.5%), accruing from the date of funding and payable at maturity or on conversion or a change of control where Total exercises the right to require the Company to repay the notes. Accrued interest is canceled if the notes are canceled based on a “Go” decision.

The notes become convertible into the Company's common stock (i) within 10 trading days prior to maturity (if they are not canceled as described above prior to their maturity date), (ii) on a change of control of the Company, (iii) if Total is no longer the largest stockholder of the Company following a “No-Go” decision (subject to a six-month lock-up with respect to any shares of common stock issued upon conversion), and (iv) on a default by the Company. If Total makes a final “Go” decision, then the notes will be exchanged by Total for equity interests in the Fuels JV, after which the notes will not be convertible and any obligation to pay principal or interest on the notes will be extinguished. If Total makes a “No-Go” decision, outstanding notes will remain outstanding and become payable at maturity.

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In connection with the Private Placement that occurred on December 24, 2012, Total elected to participate in the Private Placement by exchanging approximately $5.0 million of its $53.3 million in senior unsecured convertible promissory notes into 1,677,852 of the Company's common stock at $2.98 per share. As such, $5.0 million of the outstanding $53.3 million in senior unsecured convertible promissory notes was cancelled. The cancellation of the debt was treated as an extinguishment of debt in accordance with the guidance outlined in AS 470-50.

The conversion price of the notes is subject to adjustment for proportional adjustments to outstanding common stock and under anti-dilution provisions in case of certain dividends and distributions. Total has a right to require repayment of 101% of the principal amount of the notes in the event of a change of control of the Company and the notes provide for payment of unpaid interest on conversion following such a change of control if Total does not require such repayment. The purchase agreement and notes include covenants regarding payment of interest, maintenance of the Company's listing status, limitations on debt, maintenance of corporate existence, and filing of SEC reports. The notes include standard events of default resulting in acceleration of indebtedness, including failure to pay, bankruptcy and insolvency, cross-defaults, and breaches of the covenants in the purchase agreement and notes, with added default interest rates and associated cure periods applicable to the covenant regarding SEC reporting. Furthermore, the senior unsecured convertible notes include restrictions on the amount of debt the Company is permitted to incur. The Company's total outstanding debt at any time can not exceed the greater of $200.0 million or 50% of its consolidated total assets and its secured debt cannot exceed the greater of $125.0 million or 30% of its consolidated total assets.

Loans Payable

In December 2009, the Company entered into a loans payable agreement with the lessor of its Emeryville pilot plant under which it borrowed a total of $250,000, bearing an interest rate of 10.0% per annum and to be repaid over a period of 96 months. As of December 31, 2012 and 2011, a principal amount of $177,000 and $204,000, respectively, was outstanding under the loan.

In December 2011, the Company entered into a loan agreement with Banco Pine under which Banco Pine provided the Company with a short term loan of R$35.0 million (approximately US$17.1 million based on the exchange rate as of December 31, 2012). Such loan was an advance on an anticipated July 2012 financing from Nossa Caixa Desenvolvimento, ("Nossa Caixa"), the Sao Paulo State development bank, and Banco Pine, under which Banco Pine and Nossa Caxia would provide the Company with loans of up to approximately R$52.0 million (approximately US$25.4 million based on the exchange rate as of December 31, 2012) as financing for capital expenditures relating to the Company's manufacturing facility in Brotas. The interest rate for the loan was 119.2% of the Brazilian interbank lending rate (approximately 12.3% on an annualized basis). The principal and interest due on the principal under the loan agreement, as amended, matured and was repaid on August 15, 2012.

In June 2012, the Company entered into a separate loan agreement with Banco Pine under which Banco Pine provided the Company with a short-term bridge loan of R$52.0 million (approximately US$25.4 million based on the exchange rate as of December 31, 2012). The bridge loan was an additional advance on the anticipated Banco Pine and Nossa Caixa financing described above. The interest rate for the bridge loan was 0.4472% monthly (approximately 5.5% on an annualized basis). The principal and interest due under the bridge loan matured and were required to be repaid on September 19, 2012, subject to extension by Banco Pine. The bridge loan was in addition to the R$35.0 million short term loan to the Company described above. At the time of this bridge loan, the Company entered into a currency interest rate swap arrangement with the lender for R$22.0 million (approximately US$10.8 million based on the exchange rate as of December 31, 2012). The interest rate swap arrangement exchanged the principal and interest payments under the Banco Pine loan of R$22.0 million entered into in July 2012 for alternative principal and interest payments that were subject to adjustment based on fluctuations in the foreign exchange rate between the U.S. dollar and Brazilian real. The swap had a fixed interest rate of 3.94%.

In July 2012, the Company entered into a Note of Bank Credit and a Fiduciary Conveyance of Movable Goods agreements with each of Nossa Caixa and Banco Pine. Under these agreements, the Company's total acquisition cost for the farnesene production assets pledged as collateral is approximately R$68.0 million (approximately US$33.3 million based on the exchange rate as of December 31, 2012). The Company is a also a parent guarantor for the payment of the outstanding balance under these loan agreements.

Under such instruments, the Company could borrow an aggregate of R$52.0 million (approximately US$25.4 million based on the exchange rate as of December 31, 2012) as financing for capital expenditures relating to the Company's manufacturing facility in Brotas.  Under the loan agreements, Banco Pine, agreed to lend R$22.0 million and Nossa Caixa agreed to lend R$30.0 million.  The funds for the loans are provided by Banco Nacional de Desenvolvimento Econômico e Social ("BNDES"), but are guaranteed by the lenders. The loans have a final maturity date of July 15, 2022 and bear a fixed interest rate of 5.5% per year.  For the first two years that the loans are outstanding, the Company is required to pay interest only on a quarterly basis.  After August 15, 2014, the Company is required to pay equal monthly installments of both principal and interest for the remainder of the term of the loans. In July 2012, the Company repaid the outstanding bridge loans of R$52.0 million and R$35.0 million from Banco Pine.

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In October 2012, the Company entered into a loans payable agreement with a lender under which it borrowed $0.6 million to pay the insurance premiums of certain schedule of policies. The loan is payable in nine monthly installments of principal and interest. Interest accrues at a rate of 3.24% per annum. As of December 31, 2012, the outstanding unpaid loan balance was $0.4 million.

Letters of Credit

In November 2008, the Company entered into the Credit Agreement with a financial institution to finance the purchase and sale of fuel and for working capital requirements, as needed. In October 2009, the agreement was amended to decrease the maximum amount that the Company may borrow under such facility. The Credit Agreement, as amended, provided, as of March 31, 2012, for an aggregate maximum availability up to the lower of $20.0 million and the borrowing base as defined in the agreement, and was subject to a sub-limit of $5.7 million for the issuance of letters of credit and a sub-limit of $20.0 million for short-term cash advances for product purchases. The Credit Agreement was collateralized by a first priority security interest in certain of the Company’s present and future assets. The Company was a parent guarantor for the payment of the outstanding balance under the Credit Agreement. Outstanding advances bore an interest rate at the Company’s option of the bank’s prime rate plus 1.0% or the bank’s cost of funds plus 3.5%. In April 2012, the Company, entered into an Amendment to the credit agreement, effective as of April 14, 2012 to extend the maturity date pending the Company's transition out of its ethanol and reformulated ethanol-blended gasoline business, and its plan to repay all amounts remaining outstanding under the Credit Agreement, and terminate the Credit Agreement as of the new maturity date. As of December 31, 2012, the Credit Agreement was terminated. As of December 31, 2012 and 2011, the Company had no outstanding advances and had zero and $5.0 million, respectively, in outstanding letters of credit under the Credit Agreement.

In June 2012, the Company entered into a letter of credit agreement for $1.0 million under which it provided a letter of credit to the landlord for its headquarters in Emeryville, California in order to cover the security deposit on the lease. The letter of credit is secured by a certificate of deposit. Accordingly, the Company recorded $1.0 million as restricted cash as of December 31, 2012.

Future minimum payments under the debt agreements as of December 31, 2012 are as follows (in thousands):

Years ending December 31:	Related Party Convertible Debt			Convertible Debt			Notes Payable			Loans Payable			Credit Facility
2013	$	—		$	760		$	351		$	1,958		$	3,175
2014	—			760			379			2,970			2,926
2015	—			765			379			4,456			2,774
2016	—			760			381			4,286			2,623
2017	51,627			25,125			384			4,110			2,393
Thereafter	—			—			154			16,426			612
Total future minimum payments	51,627			28,170			2,028			34,206			14,503
Less: amount representing interest	(12,594		)	(3,170		)	(456		)	(8,056		)	(2,094		)
Present value of minimum debt payments	39,033			25,000			1,572			26,150			12,409
Less: current portion	—			—			(311		)	(556		)	(2,458		)
Noncurrent portion of debt	$	39,033		$	25,000		$	1,261		$	25,594		$	9,951

7. Joint Ventures

SMA Indústria Química S.A.

On April 14, 2010, the Company established SMA, a joint venture with Usina São Martinho, to build the first facility in Brazil fully dedicated to the production of Amyris renewable products. The new company is located at the Usina São Martinho mill in Pradópolis, São Paulo state. SMA has a 20 year initial term.

 SMA is managed by a three member executive committee, of which the Company appoints two members, one of whom is the plant manager who is the most senior executive responsible for managing the construction and operation of the facility. SMA is governed by a four member board of directors, of which the Company and Usina São Martinho each appoint two members. The

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board of directors has certain protective rights which include final approval of the engineering designs and project work plan developed and recommended by the executive committee.

The joint venture agreements require the Company to fund the construction costs of the new facility and Usina São Martinho would reimburse the Company up to RS$61.8 million (approximately US$30.2 million based on the exchange rate as of December 31, 2012) of the construction costs after SMA commences production. Post commercialization, the Company would market and distribute Amyris renewable products and Usina São Martinho would sell feedstock and provide certain other services to SMA. The cost of the feedstock to SMA would be a price that is based on the average return that Usina São Martinho could receive from the production of its current products, sugar and ethanol. The Company would be required to purchase the output of SMA for the first four years at a price that guarantees the return of Usina São Martinho’s investment plus a fixed interest rate. After this four year period, the price would be set to guarantee a break-even price to SMA plus an agreed upon return.

Under the terms of the joint venture agreements, if the Company becomes controlled, directly or indirectly, by a competitor of Usina São Martinho, then Usina São Martinho has the right to acquire the Company’s interest in SMA. If Usina São Martinho becomes controlled, directly or indirectly, by a competitor of the Company, then the Company has the right to sell its interest in SMA to Usina São Martinho. In either case, the purchase price shall be determined in accordance with the joint venture agreements, and the Company would continue to have the obligation to acquire products produced by SMA for the remainder of the term of the supply agreement then in effect even though the Company would no longer be involved in SMA’s management.

Amyris has a 50% ownership interest in SMA. The Company has identified SMA as a VIE. The Company is the primary beneficiary and consequently consolidates SMA’s operations in its financial statements.

Joint Venture with Cosan

In June 2011, the Company entered into joint venture agreements with Cosan Combustíveis e Lubrificantes S.A. and Cosan S.A. Industria e Comércio (such Cosan entities, collectively or individually, “Cosan”), related to the formation of a joint venture (the “Novvi JV”), to focus on the worldwide development, production and commercialization of base oils made from Biofene for the automotive, commercial and industrial lubricants markets (the "Original JV Agreement"). The parties originally envisioned operating their joint venture through Novvi S.A., a Brazilian entity jointly owned by Cosan and Amyris Brasil.

Under the Original JV Agreement and related agreements (including a Shareholders' Agreement and Joint Venture Implementation Agreement), the Company and Cosan each owned 50% of the Novvi JV and each party would share equally in any costs and any profits ultimately realized by the JV. The joint venture agreement had an initial term of 20 years from the date of the Original JV Agreement, subject to earlier termination by mutual written consent or by a non-defaulting party in the event of specified defaults by the other party (including breach by a party of any material obligations under the joint venture agreements). The Shareholders' Agreement had an initial term of 10 years from the date of the agreement, subject to earlier termination if either the Company or Cosan ceases to own at least 10% of the voting stock of the Novvi JV.

The Company identified Novvi S.A. as a VIE. The power to direct activities, which most significantly impact the economic success of the joint venture, is equally shared between the Company and Cosan who are not related parties. Accordingly, the Company is not the primary beneficiary and therefore accounts for its investment in the JV entity using the equity method. The Company periodically reviews its consolidation analysis on an ongoing basis. As of December 31, 2012, the carrying amounts of the unconsolidated JV entity's assets and liabilities were not material to the Company's consolidated financial statements.

In September 2011, a U.S. JV entity, Novvi LLC, was formed. Novvi LLC is jointly owned by the Company and Cosan US, Inc. ("Cosan US"). For the years ended December 31, 2012, 2011 and 2010, the Company recorded $0.9 million, $3.6 million and zero, respectively, of revenue from the research and development activities that it has performed on behalf of the joint venture.

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8. Noncontrolling Interest

Redeemable Noncontrolling Interest

In December 2009, Amyris Brasil sold 1,111,111 of its shares representing a 4.8% interest in Amyris Brasil for R$10.0 million. The redeemable noncontrolling interest was reported in the mezzanine equity section of the consolidated balance sheet because the Company was then subject to a contingent put option under which it could have been required to repurchase an interest in Amyris Brasil from the noncontrolling interest holder.

In March 2010, Amyris Brasil sold an additional 853,333 shares of its stock, an incremental 3.4% interest, for R$3.0 million. In May 2010, Amyris Brasil sold an additional 1,111,111 shares of its stock, an incremental 4.07% interest, for R$10.0 million.

Under the terms of the agreements with these Amyris Brasil investors, the Company had the right to require the investors to convert their shares of Amyris Brasil into shares of the Company's common stock at a 1:0.28 conversion ratio. On September 30, 2010, in connection with the Company’s IPO, shares of Amyris Brasil held by these investors were converted into 861,155 shares of the Company’s common stock. The remaining noncontrolling interest as of September 30, 2010 was converted to common stock and additional paid-in capital.

At the closing of the IPO, the Company recorded a one-time beneficial conversion feature charge of $2.7 million associated with the conversion of the shares of Amyris Brasil held by investors into shares of Amyris, Inc. common stock, which impacted earnings per share for the year ended December 31, 2010.

The following table provides a roll forward of the redeemable noncontrolling interest (in thousands):

Balance as of December 31, 2009	$	5,506
Proceeds from redeemable noncontrolling interest	7,041
Conversion of shares of Amyris Brasil S.A. subsidiary held by third parties into common stock	(11,870		)
Foreign currency translation adjustment	217
Net loss	(894		)
Balance as of December 31, 2010	$	—

Noncontrolling Interest

SMA Indústria Química

The joint venture, SMA (see Note 7), is a VIE pursuant to the accounting guidance for consolidating VIEs because the amount of total equity investment at risk is not sufficient to permit SMA to finance its activities without additional subordinated financial support, as well as because the related commercialization agreement provides a substantive minimum price guarantee. Under the terms of the joint venture agreement, Amyris directs the design and construction activities, as well as production and distribution. In addition, Amyris has the obligation to fund the design and construction activities until commercialization is achieved. Subsequent to the construction phase, both parties equally fund SMA for the term of the joint venture. Based on those factors, the Company was determined to have the power to direct the activities that most significantly impact SMA’s economic performance and the obligation to absorb losses and the right to receive benefits. Accordingly, the financial results of SMA are included in the Company’s consolidated financial statements and amounts pertaining to Usina São Martinho’s interest in SMA are reported as noncontrolling interests in subsidiaries.

Glycotech

In January 2011, the Company entered into a production service agreement with Glycotech, whereby Glycotech is to provide process development and production services for the manufacturing of various Company products at its leased facility in Leland, North Carolina. The Company products to be manufactured by Glycotech will be owned and distributed by the Company. Pursuant to the terms of the agreement, the Company is required to pay the manufacturing and operating costs of the Glycotech facility which is dedicated solely to the manufacture of Amyris products. The initial term of the agreement is for a two year period commencing on February 1, 2011 and will renew automatically for successive one-year terms, unless terminated by the Company. On the same date as the production service agreement, the Company also entered into a right of first refusal agreement with the lessor of the facility and site leased by Glycotech covering a two year period commencing in January 2011. Per the terms of the

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right of first refusal agreement, the lessor agreed not to sell the facility and site leased by Glycotech during the term of the production service agreement. In the event that the lessor is presented with an offer to sell or decides to sell an adjacent parcel, the Company has the right of first refusal to acquire it.

The Company has determined that the arrangement with Glycotech qualifies as a VIE. The Company determined that it is the primary beneficiary of this arrangement since it has the power through the management committee over which it has majority control to direct the activities that most significantly impact Glycotech's economic performance. In addition, the Company is required to fund 100% of Glycotech's actual operating costs for providing services each month while the facility is in operation under the production service agreement. Accordingly, the Company consolidates the financial results of Glycotech. As of December 31, 2012, the carrying amounts of the consolidated VIE's assets and liabilities were not material to the Company's consolidated financial statements.

The table below reflects the carrying amount of the assets and liabilities of the two consolidated VIEs for which the Company is the primary beneficiary. The assets include $24.7 million in property, plant and equipment and $4.5 million in other assets, and $0.4 million in current assets. The liabilities include $0.3 million in accounts payable and accrued current liabilities and $0.1 million in loan obligations by Glycotech to its shareholders that are non-recourse to the Company. The creditors of each consolidated VIE have recourse only to the assets of that VIE.

	December 31,
(In thousands)	2012		2011
Assets	$	29,564	$	22,094
Liabilities	$	355	$	2,873

The change in noncontrolling interest for the years ended December 31, 2012 and 2011 is summarized below (in thousands):

	2012			2011
Balance at January 1	$	(240	)	$	2
Addition to noncontrolling interest	—			369
Foreign currency translation adjustment	257			30
Loss attributable to noncontrolling interest	(894		)	(641		)
Balance at December 31	$	(877	)	$	(240	)

9. Significant Agreements

Research and Development Activities

Total Collaboration Agreement

In June 2010, the Company entered into a technology license, development, research and collaboration agreement (“collaboration agreement”) with Total Gas & Power USA Biotech, Inc., an affiliate of Total S.A. (Total S.A. and its relevant affiliates, collectively, “Total”). The collaboration agreement sets forth the terms for the research, development, production and commercialization of certain to-be-determined chemical and/or fuel products made through the use of the Company’s synthetic biology platform. The collaboration agreement establishes a multiphased process through which projects are identified, screened, studied for feasibility, and ultimately selected as a project for development of an identified lead compound using an identified microbial strain. Under the terms of the collaboration agreement, Total will fund up to the first $50.0 million in research and development costs for the selected projects; thereafter the parties will share such costs equally. Amyris has agreed to dedicate the laboratory resources needed for collaboration projects. Total also plans to second employees at Amyris to work on the projects. Once a development project has commenced, the parties are obligated to work together exclusively to develop the lead compound during the project development phase. After a development project is completed, the Company and Total expect to form one or more joint ventures to commercialize any products that are developed, with costs and profits to be shared on an equal basis, provided that if Total has not achieved profits from sales of a joint venture product equal to the amount of funding it provided for development plus an agreed upon rate of return within three years of commencing sales, then Total will be entitled to receive all profits from sales until this rate of return has been achieved. Each party has certain rights to independently produce commercial quantities of these products under certain circumstances, subject to paying royalties to the other party. Total has the right of first

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negotiation with respect to exclusive commercialization arrangements that the Company would propose to enter into with certain third parties, as well as the right to purchase any of the Company’s products on terms no less favorable than those offered to or received by the Company from third parties in any market where Total or its affiliates have a significant market position.

The collaboration agreement has an initial term of twelve years and is renewable by mutual agreement by the parties for additional three year periods. Neither the Company nor Total has the right to terminate the agreement voluntarily. The Company and Total each have the right to terminate the agreement in the event the other party commits a material breach, is the subject of certain bankruptcy proceedings or challenges a patent licensed to it under the collaboration agreement. Total also has the right to terminate the collaboration agreement in the event the Company undergoes a sale or change of control to certain entities. If the Company terminates the collaboration agreement due to a breach, bankruptcy or patent challenge by Total, all licenses the Company has granted to Total terminate except licenses related to products for which Total has made a material investment and licenses related to products with respect to which binding commercialization arrangements have been approved, which will survive subject, in most cases, to the payment of certain royalties by Total to the Company. Similarly, if Total terminates the collaboration agreement due to a breach, bankruptcy or patent challenge by the Company, all licenses Total has granted to the Company terminate except licenses related to products for which the Company has made a material investment, certain grant-back licenses and licenses related to products with respect to which binding commercialization arrangements have been approved, which will survive subject, in most cases, to the payment of certain royalties to Total by the Company. On expiration of the collaboration agreement, or in the event the collaboration agreement is terminated for a reason other than a breach, bankruptcy or patent challenge by one party, licenses applicable to activities outside the collaboration generally continue with respect to intellectual property existing at the time of expiration or termination subject, in most cases, to royalty payments. There are circumstances under which certain of the licenses granted to Total will survive on a perpetual, royalty-free basis after expiration or termination of the collaboration agreement. Generally these involve licenses to use the Company’s synthetic biology technology and core metabolic pathway for purposes of either independently developing further improvements to marketed collaboration technologies or products or the processes for producing them within a specified scope agreed to by the Company and Total prior to the time of expiration or termination, or independently developing early stage commercializing products developed from collaboration compounds that met certain performance criteria prior to the time the agreement expired or was terminated and commercializing products related to such compounds. After the collaboration agreement expires, the Company may be obligated to provide Total with ongoing access to Amyris laboratory facilities to enable Total to complete research and development activities that commenced prior to termination.

In June 2010, concurrent with the collaboration agreement, the Company issued 7,101,548 shares of Series D preferred stock to Total for aggregate proceeds of approximately $133.0 million at a per share price of $18.75, which was lower than the per share fair value of common stock as determined by management and the Board of Directors. Due to the fact the collaboration agreement and the issuance of shares to Total occurred concurrently, the terms of both the collaboration agreement and the issuance of preferred stock were evaluated to determine whether their separately stated pricing was equal to the fair value of services and preferred stock. The Company determined that the fair value of Series D preferred stock was $22.68 at the time of issuance, and therefore, the Company measured the preferred stock initially at its fair value with a corresponding reduction in the consideration for the services under the collaboration agreement. As revenue from the collaboration agreement will be generated over a period of time based on the performance requirements, the Company recorded the difference between the fair value and consideration received for the Series D preferred stock of $27.9 million as a Deferred Charge Asset within Other Assets on the balance sheet at the time of issuance which will be recognized as a reduction to revenue in proportion to the total estimated revenue under the collaboration agreement. As of December 31, 2012 and 2011, the Company has recognized a cumulative reduction of $27.9 million and $9.1 million, respectively, against the deferred charge asset.

As a result of recording the Series D preferred stock at its fair value, the effective conversion price was greater than the fair value of common stock as determined by management and the Board of Directors. Therefore, no beneficial conversion feature was recorded at the time of issuance. The Company further determined that the conversion option with a contingent reduction in the conversion price upon a qualified IPO was a potential contingent beneficial feature and, as a result, the Company calculated the intrinsic value of such conversion option upon occurrence of the qualified IPO. The Company determined that a contingent beneficial conversion feature existed and the Company recorded a charge within the equity section of its balance sheet, which impacted earnings per share for the year ended December 31, 2010, based upon the price at which shares were offered to the public in the IPO in relation to the adjustment provisions provided for the Series D preferred stock. Based on the IPO price of $16.00 per share, the charge to net loss attributable to Amyris’ common stockholders was $39.3 million.

In connection with Total’s equity investment, the Company agreed to appoint a person designated by Total to serve as a member of the Company’s Board of Directors in the class subject to the latest reelection date, and to use reasonable efforts, consistent with the Board of Directors’ fiduciary duties, to cause the director designated by Total to be re-nominated by the Board of Directors in the future. These membership rights terminate upon the earlier of Total holding less than half of the shares of common stock originally issuable upon conversion of the Series D preferred stock or a sale of the Company.

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The Company also agreed with Total that, so long as Total holds at least 10% of the Company’s voting securities, the Company will notify Total if the Company’s Board of Directors seeks to cause the sale of the Company or if the Company receives an offer to be acquired. In the event of such decision or offer, the Company must provide Total with all information given to an offering party and certain other information, and Total will have an exclusive negotiating period of fifteen business days in the event the Board of Directors authorizes the Company to solicit offers to buy the Company, or five business days in the event that the Company receives an unsolicited offer to be acquired. This exclusive negotiation period will be followed by an additional restricted negotiation period of ten business days, during which the Company will be obligated to negotiate with Total and will be prohibited from entering into an agreement with any other potential acquirer. Total has also entered into a standstill agreement pursuant to which it agreed for a period of three years not to acquire in excess of the greater of 20% of the number of shares of Series D preferred stock purchased by Total (during the initial two years) or 30% (during the third year) of the Company’s common stock without the prior consent of our Board of Directors, except that, among other things, if another person acquires more than Total’s then current holdings of the Company’s common stock, then Total may acquire up to that amount plus one share.

In November 2011, the Company and Total entered into an amendment of the collaboration agreement as described above in Note 4 under "Other Liabilities".

In July 2012, the Company entered into an amendment of its collaboration agreement with Total and related agreements. Under such July agreements, the scope of the collaboration initially contemplated by the parties under the November 2011 amendment described in Note 4, was expanded to encompass certain joint venture products for use in diesel and jet fuel on a worldwide basis and to provide a new structure for the research and development program and formation of the joint venture (the “Fuels JV”) to commercialize the products encompassed by the diesel and jet fuel research and development program (the “Program”).

Under the new agreements, the Company controls operations and execution of the Program subject to strategic and ultimate decision-making authority by a management committee composed of Company and Total representatives, and Total participates in the ultimate Fuels JV, or receives rights to recover its investment if, at a series of decision points, it decides not to proceed with the project. The agreements contemplate that the parties would grant exclusive manufacturing and commercial licenses to the Fuels JV for the Fuels JV products when the Fuels JV is formed (subject to requirements for the Company to grant the license to Total in the event the Fuels JV is not formed because of a deadlock, followed by an election by the Company to sell to Total the assets it otherwise would have contributed to the Fuels JV, or earlier under certain circumstances), and that the Company would retain the right to make and sell products other than the Fuels JV products. Under the agreements, the Fuels JV licenses would be consistent with the principle that development, production and commercialization of the Fuels JV products in Brazil will remain with the Company unless Total elects, after formation of the Fuels JV, to have such business contributed to the Fuels JV. The agreements also provide that certain Fuels JV non-exclusive products that were contemplated by the November 2011 amendment to the collaboration agreement are no longer to be included in the Fuels JV, but that the parties will explore potential development and commercialization of such products at a later date.

The agreements contemplate that the research and development efforts under the Program may extend through 2016, with a series of “Go/No Go” decisions by Total through such date tied to funding by Total. Each funding tranche involves the issuance of senior unsecured convertible promissory notes by the Company to Total (see Note 6). The agreements provided for cash funding by Total of $15.0 million in July 2012 and an additional $15.0 million in September 2012. (Such funding occurred in July and September as contemplated by the agreements.) Further, Total will fund $30.0 million by July 2013, and, if it chooses to proceed with the Program, fund an additional $10.85 million in July 2014 and $10.85 million in January 2015. Thirty days following the earlier of the completion of the research and development program or December 31, 2016, Total has a final opportunity to decide whether or not to proceed with the Program.

At either of the decision points tied to the funding described above (in July 2013 or July 2014), if Total decides not to continue to fund the Program (or, at any funding date does not provide funding based on (i) the Company's failure to satisfy a closing condition under the purchase agreement for the notes, or (ii) Total's breach of the purchase agreement), the notes previously issued under the purchase agreement would remain outstanding and become payable by the Company at the maturity date in March 2017, the Program and associated agreements would terminate, all Company rights granted for use in farnesene-based diesel and farnesene-based jet fuel would revert to the Company, and no Fuels JV would be formed to commercialize the Fuels JV products.

In the final “Go/No Go” decision described above, Total may elect to (i) go forward with the full Program (diesel and jet fuel) (a “Go” decision), (ii) not continue its participation in the full Program, or (iii) go forward only with the jet fuel component of the Program, with the following outcomes:

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• For a “Go” decision by Total with respect to the whole Program, the parties would form the Fuels JV and the notes would be canceled.

• For a “No-Go” decision by Total with respect to the whole Program, the consequences would be as described in the paragraph above regarding a decision by Total not to continue to fund the Program.

• For a decision by Total to proceed with the jet fuel component of the Program and not the diesel component of the Program, 70% of the principal amount outstanding under the notes would remain outstanding and become payable by the Company and 30% of the outstanding principal of such notes would be canceled, the diesel product would no longer be included in the collaboration, the Fuels JV would not receive rights to products for use in diesel fuels, and the Fuels JV would be formed by the parties to commercialize products for use in jet fuels.

The agreements contemplate that the parties will finalize the structure for the Fuels JV in the future as set forth in the agreements and that the Fuels JV, if and when it is formed, would, subject to the conditions described below and absent other agreement, be owned equally (50%/50%) by the Company and Total. Under the agreements, the parties will, prior to the projected completion date, enter into a shareholders' agreement governing the Fuels JV, agree on the budget and business plan for the Fuels JV, and form the Fuels JV. In addition, following a final “Go” decision, the parties would enter into the Fuels JV license agreements, contribution agreements and other agreements required to establish the Fuels JV and enable it to operate.

Within thirty days prior to the final “Go” decision, Total may declare a “deadlock” if the parties fail to come to agreement on various matters relating to the formation of the Fuels JV, at which point Total may (i) elect to declare a “No-Go” decision, which has the consequences described above, or (ii) initiate a process whereby the fair value of the proposed Fuels JV would be determined and the Company would then have the option to: (i) elect to sell to Total the assets that the Company would have been required to contribute to the Fuels JV for an amount equal to 50% of such fair value; (ii) proceed with the formation of the Fuels JV (accepting Total's position with respect to the funding requirement of the Fuels JV) and becoming a 50% owner of the Fuels JV; or (iii) proceed with the formation of the Fuels JV (accepting Total's position with respect to the funding requirements of the Fuels JV), and then sell all or a portion of its 50% interest in the Fuels JV to Total for a price equal to the fair value multiplied by the percentage ownership of the Fuels JV sold to Total.

The agreements provide that the Company would initially retain its ability to develop its diesel and jet fuel business in Brazil, and that Total has an option to require the Company to contribute its Brazil diesel and jet fuel business to the Fuels JV at a price determined pursuant to the agreements. Such option terminates if the Fuels JV is not formed or if Total subsequently buys out the Company's Fuels JV contribution. Furthermore, the option is limited to the jet fuel business if Total opts out of the diesel component of the Program as described above.

Under the agreements, Total has a right to participate in future equity or convertible debt financings of the Company through December 31, 2013 to preserve its pro rata ownership of the Company and thereafter in limited circumstances. The purchase price for the first $30 million of purchases under this pro rata right would be paid by cancellation of outstanding notes held by Total.

In connection with the purchase agreement and sale of the Notes, the Company entered into a registration rights agreement. Under such agreement, the Company is obligated to file a registration statement on Form S-3 with the SEC registering the resale of all of the shares of the Company's common stock issuable upon conversion of the notes within twenty days prior to the maturity date of the notes or within 30 days following optional conversion. In addition, the Company is obligated to have the registration statement declared effective within 70-100 days following the filing depending on whether the Company receives comments from the SEC. If the registration statement filing is delayed or the registration statement is not declared effective within the foregoing time frames, the Company is required to make certain monthly payments to the Total.

As a result, $46.5 million of payments received from Total that had been recorded as an advance from the collaborator were no longer contingently repayable. Of this amount, $23.3 million was treated as a repayment by the Company and included as part of the senior unsecured convertible promissory note issued to Total in July 2012 and the remaining $23.2 million was recorded as a contract to perform research and development services, which was offset by the reduction of the capitalized deferred charge asset of $14.4 million resulting in the Company recording revenue from a related party of $8.9 million.

In December 2012, Total elected to participate in a private placement of the Company's common stock by exchanging approximately $5.0 million of its $53.3 million in senior unsecured convertible promissory notes into 1,677,852 shares of the Company's common stock at $2.98 per share. As such, $5.0 million of the outstanding $53.3 million in senior unsecured convertible debt was cancelled.

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M&G Finanziaria Collaboration Agreement

In June 2010, the Company entered into a collaboration agreement with M&G Finanziaria S.R.L. (“M&G”) to incorporate Biofene as an ingredient in M&G's polyethylene terephthalate, or PET, resins to be incorporated into containers for food, beverages and other products. In April 2011, Amyris and M&G entered into an Amended and Restated Collaboration Agreement to amend certain portions of the original agreement entered into in June 2010 and adding Chemtex Italia S.R.L. and Chemtex International Inc. (both wholly owned subsidiaries of M&G) to the collaboration agreement. Under the terms of the amended agreement, the Company and Chemtex International Inc. will share the costs incurred associated with the PET collaboration on a 50/50 basis. In addition, the amended agreement expanded the collaboration arrangement between the Company and M&G to include a Cellulosic feasibility study with each party bearing its own costs associated with such feasibility study. The collaboration agreement also establishes the terms under which M&G may purchase Biofene from the Company upon successful completion of product integration.

Firmenich Collaboration and Joint Development Agreements

In November 2010, the Company entered into collaboration and joint development agreements with Firmenich SA (“Firmenich”), a flavors and fragrances company based in Geneva, Switzerland. Under the agreements, Firmenich will fund technical development at the Company to produce an ingredient for the flavors and fragrances market. The Company will manufacture the ingredient and Firmenich will market it, and the parties will share in any resulting economic value. The agreement also grants exclusive worldwide flavors and fragrances commercialization rights to Firmenich for the ingredient. In addition, Firmenich has an option to collaborate with the Company to develop a second ingredient. In July 2011, the Company and Firmenich expanded their collaboration agreement to include a third ingredient. The collaboration and joint development agreements will continue in effect unit the later of the expiration or termination of the development agreements or the supply agreements. The Company is also eligible to receive potential total payments of $6.0 million upon the achievement of certain performance milestones towards which the Company will be required to make a contributory performance. These milestones are accounted for under the guidance in the FASB accounting standard update related to revenue recognition under the milestone method. The Company concluded that these milestone payments are substantive.

For the years ended December 31, 2012 and 2011, the Company recorded $4.8 million and $5.2 million, respectively, of revenue from the collaboration agreement with Firmenich. Included in these collaboration revenues were the first milestone payment of $2.0 million which was recognized as revenue during the year ended December 31, 2011 and the second milestone payment of $2.0 million which was recognized as revenue during the year ended December 31, 2012.

In March 2013, the Company and Firmenich entered into a collaboration agreement as described in Note 18-"Subsequent Events."

Michelin Collaboration Agreement

In September 2011, the Company entered into a collaboration agreement with Manufacture Francaise des Pneumatiques Michelin (“Michelin”). Under the terms of the collaboration agreement, the Company and Michelin will collaborate on the development, production and worldwide commercialization of isoprene or isoprenol, generally for tire applications, using the Company's technology. Under the agreement, Michelin has agreed to pay an upfront payment to the Company of $5.0 million, subject to a reimbursement provision under which the Company would have to repay $1.0 million if it fails to achieve specified future technical milestones. The agreement provides that, subject to achievement of technical milestones, Michelin can notify the Company of its desired date for initial delivery, and the parties will either collaborate to establish a production facility or use an existing Company facility for production. The agreement also includes a term sheet for a supply agreement that would be negotiated at the time the decision regarding production facilities is made. The agreement has an initial term that will expire upon the earlier of 42 months from the effective date and the completion of a development work plan. As of December 31, 2012, the Company recorded the upfront payment of $5.0 million from Michelin as deferred revenue.

Manufacturing Agreements

In 2010 and 2011, the Company entered into contract manufacturing agreements with various contract manufacturing partners to utilize their manufacturing facilities to produce Amyris products.

Under the terms of these contract manufacturing agreements, the Company provided necessary equipment for the manufacturing of its products, over which the Company retained ownership. The Company also reimbursed the contract manufacturers for an aggregate of $13.8 million in expenditures related to the modification of their facilities. The Company

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recorded facility modification costs as Other Assets on the balance sheet and amortized them as an offset against purchases of inventory. Certain of these contract manufacturing agreements also impose fixed purchase commitments on the Company, regardless of the production volumes.

Beginning in March 2012, the Company initiated a plan to shift a portion of its production capacity from contract manufacturing facilities to a Company-owned plant that was then under construction. As a result, the Company evaluated its contract manufacturing agreements and recorded a loss of $31.2 million related to the write-off of $10.0 million in facility modification costs and the recognition of $21.2 million of fixed purchase commitments in the three months ended March 31, 2012. The Company recognized an additional charge of $1.4 million and $7.8 million, respectively, in the third and fourth quarters of 2012 associated with loss on fixed purchase commitments. The Company computed the loss on facility modification costs and fixed purchase commitments using the same lower of cost or market approach that is used to value inventory. The computation of the loss on fixed purchase commitments is subject to several estimates, including cost to complete and the ultimate selling price of any Company products manufactured at the relevant production facilities, and is therefore inherently uncertain. The Company also recorded a loss on write-off of production assets of $5.5 million related to Amyris-owned production equipment at contract manufacturing facilities in the quarter ended March 31, 2012. Total loss on purchase commitments and write-off of production assets for the year ended December 31, 2012 was $45.9 million. The Company will continue to evaluate the potential for losses in future periods based on updated production and sales price assumptions.

Tate & Lyle

In November 2010, the Company entered into a contract manufacturing agreement with Tate & Lyle Ingredients Americas, Inc. (“Tate & Lyle”), an affiliate of Tate & Lyle PLC. Tate & Lyle commenced production operations in the fourth quarter of 2011. At December 31, 2012 and 2011, the Company has recorded $0.8 million and $0.7 million, respectively, in prepaid and other current assets and $2.2 million and $2.9 million, respectively, in other noncurrent assets pertaining to the unamortized portion of equipment costs funded by the Company to Tate & Lyle (see Note 4). The related amortization is being offset against purchases of inventory from this contract manufacturer.

Paraíso Bioenergia

In March 2011, the Company entered into a supply agreement with Paraíso Bioenergia, a renewable energy company producing sugar, ethanol and electricity headquartered in São Paulo State, Brazil. Under the agreement, the Company will construct fermentation and separation capacity to produce its products and Paraíso Bioenergia will supply sugar cane juice and other utilities. The Company will retain the full economic benefits enabled by the sale of Amyris renewable products over the lower of sugar or ethanol alternatives. In conjunction with the supply agreement, the Company also entered into an operating lease on a real property owned by Paraíso Bioenergia. The real property is being used by the Company for its production site in Brotas (see Note 5).

Per the terms of the supply agreement, in the event that Paraíso is presented with an offer to sell or decides to sell the real property, the Company has the right of first refusal to acquire it. If the Company fails to exercise its right of first refusal the purchaser of the real property will need to comply with the specific obligations of Paraíso Bioenergia to the Company under the lease agreement.

Albemarle

In July 2011, the Company entered into a contract manufacturing agreement with Albemarle Corporation ("Albemarle"), which will provide toll manufacturing services at its facility in Orangeburg, South Carolina. Under this agreement, Albemarle will manufacture lubricant base oils from Biofene, which will be owned and distributed by the Company or a Company-designated commercial partner. The initial term of this agreement is from July 31, 2011 through December 31, 2012. Albemarle is required to modify its facility, including installation and qualification of equipment and instruments necessary to perform the toll manufacturing services under the agreement. The Company reimbursed Albemarle $10.0 million for all capital expenditures related to the facility modification, which was accounted for as a prepaid asset. All equipment or facility modifications acquired or made by Albemarle will be owned by Albemarle, subject to Albemarle's obligation to transfer title to, and ownership of, certain assets to the Company within 30 days after termination of the agreement, at the Company's discretion and sole expense. In March 2012, the Company recorded a loss of $10.0 million related to the write-off of the facility modification costs, described above.

In addition, the Company will pay a one-time, non-refundable performance bonus of $5.0 million if Albemarle delivers to the Company certain quantity of the lubricant base stock by December 31, 2011 or $2.0 million if Albemarle delivers the same quantity by January 31, 2012. Based on Albermarle's performance as of December 31, 2011, the Company concluded that Albermarle had earned the bonus which is payable in two payments. The Company paid Albemarle $2.5 million during the year

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ended December 31, 2012 and recorded a liability of $2.5 million as of December 31, 2012 for the second payment which is payable on March 31, 2013.

In February 2012, the Company entered into an amended and restated agreement with Albemarle, which superseded the original contract manufacturing agreement with Albemarle.  The term of the new agreement continues through December 31, 2019.  The agreement includes certain obligations for the Company to pay fixed costs totaling $7.5 million, of which $3.5 million and $4.0 million are payable in 2012 and 2014, respectively. In the three months ended March 31, 2012, the Company recorded a corresponding loss related to these fixed purchase commitments, as described above. In addition, fixed costs of $2.0 million per quarter are payable in 2013 if the Company exercises its option to have product manufactured in the facility in 2013.  The agreement also includes variable pricing during the contract term.

Supply Agreements

The Company has also entered into agreements to sell Biofene and its derivatives directly to various potential customers, including M&G for use in plastics, Kuraray Co., Ltd. ("Kuraray") for use in the production of polymers, Firmenich and Givaudan SA. ("Givaudan") for ingredients for the flavors and fragrances market, and Method Products, Inc. ("Method") for use in home and personal care products.

Soliance Agreements

In June 2010, the Company entered into an agreement with Soliance for the development and commercialization of Biofene-based squalane for use as an ingredient in cosmetics products. In December 2011, the Company and Soliance entered into an agreement and release to terminate the collaboration agreement and any other obligations with respect to the proposed joint venture. As part of the termination agreement the parties agreed that for a period commencing October 1, 2011 and ending on December 31, 2013, Soliance will be paid a commission of 10.0% of amounts received by the Company from Nikko Chemicals Co., Ltd. (“Nikko") on quantities of squalane sold by the Company to Nikko with respect to Nikko's committed minimum purchase obligation pursuant to a distribution agreement with Nikko. Concurrently with the execution of such termination agreement, the parties executed a distribution agreement, pursuant to which the Company appointed Soliance as its exclusive distributor to distribute the Company's squalane in the cosmetic market in the approved territory.

Nikko Chemicals

In August 2011, the Company entered into an agreement with Nikko, a private limited company in Japan, for the sales of renewable squalane to Nikko (commencing in September 2011 and continuing for two years through the end of December 2013).

10. Draths Corporation Acquisition

On October 6, 2011 (the Closing Date), the Company completed an acquisition of certain assets from Draths related to production of renewable chemicals. The acquisition was accounted for as a business combination. In connection with the acquisition, the Company issued 362,319 shares of common stock, of which 41,408 shares were held in escrow and paid $2.9 million in cash. In the quarter ended June 30, 2012, the Company recovered 5,402 shares of common stock from the escrow in connection with certain Draths indemnification obligations under the purchase agreement.

The components of the purchase price allocation for Draths are as follows:

Purchase Consideration:
(in thousands)
Fair value of common stock issued to Draths	$	7,000
Cash paid to Draths	2,934
Total purchase consideration	$	9,934

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Allocation of Purchase Price:
(in thousands)
Property and Equipment	$	713
Other	101
In-process research and development	8,560
Goodwill	560
Total purchase consideration	$	9,934

The Company has allocated $8.6 million of the purchase price of Draths to acquired IPR&D. This amount represents management's valuation of the fair value of assets acquired at the date of the acquisition. Management used the income approach to determine the estimated fair values of acquired IPR&D, applying a risk adjusted discount rate of 30% to the development project's cash flows. The discounted cash flow model applies probability weighting factors, based on estimates of successful product development and commercialization, to estimated future net cash flows resulting from projected revenues and related costs. These success rates take into account the stages of completion and the risks surrounding successful development and commercialization of the underlying products such as estimates of revenues and operating profits related to the IPR&D considering its stage of development; the time and resources needed to complete the development; the life of the potential commercialized product and associated risks, including the inherent difficulties and uncertainties in developing a product.

Goodwill totaling $0.6 million represents the excess of the purchase price over the fair value of tangible and identifiable intangible assets acquired and is due primarily to synergies expected from combining the new genetic pathway with the Company's existing platform to accelerate development to get the technology to market sooner leading to increased market penetration from future products and customers.

The Draths business acquisition is a taxable transaction. For federal and state tax purposes, the above in-process research and development and goodwill is amortized over a 15-year period. The Company has determined that there are no significant differences in the tax basis of assets and the basis for financial reporting purposes. In addition, the business combination did not have any impact on the Company's deferred tax balance, net of the full valuation allowance, or to uncertain tax positions, at the acquisition date.

The Company applies the applicable accounting principles set forth in the U.S. Financial Accounting Standards Board's Accounting Standards Codification to its intangible assets (including goodwill), which prohibits the amortization of intangible assets with indefinite useful lives and requires that these assets be reviewed for impairment at least annually. There are several methods that can be used to determine the estimated fair value of the IPR&D acquired in a business combination. The Company utilized the "income method," which applies a probability weighting that considers the risk of development and commercialization, to the estimated future net cash flows that are derived from projected sales revenues and estimated costs. These projections are based on factors such as relevant market size, pricing of similar products, and expected industry trends. The estimated future net cash flows are then discounted to the present value using an appropriate discount rate. These assets are treated as indefinite-lived intangible assets until completion or abandonment of the projects, at which time the assets will be amortized over the remaining useful life or written off, as appropriate.If the carrying amount of the assets is greater than the measures of fair value, impairment is considered to have occurred and a write-down of the asset is recorded. Any finding that the value of its intangible assets has been impaired would require the Company to write-down the impaired portion, which could reduce the value of its assets and reduce its net income for the year in which the related impairment charges occur.  

11. Stockholders’ Equity

Private Placement

In February 2012, the Company completed a private placement of its common stock of 10,160,325 shares of it's common stock at a price of $5.78 per share for aggregate proceeds of $58.7 million. In connection with this private placement, the Company entered into an agreement with an investor to purchase additional shares of the Company's Common Stock for an additional $15.0 million by March 2013 upon satisfaction by the Company of criteria associated with the commissioning of the Company's production plant in Brotas. This was partially satisfied by the investor through its $10.0 million investment under the private placement in December 2012. Additionally, such agreement granted certain investors Board designation rights and certain rights of first investment with respect to future issuances of the Company's securities.

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In May 2012, the Company also completed a private placement of its common stock for the issuance of 1,736,100 shares of it's common stock at a price of $2.36 per share for aggregate proceeds of $4.1 million.

In December 2012, the Company completed a private placement of its common stock for the issuance of 14,177,849 shares of its common stock at a price of $2.98 per share for aggregate proceeds of $37.2 million and the cancellation of $5.0 million worth of outstanding senior unsecured convertible promissory notes previously issued by the Company. Shares totaling 1,677,852 were issued to Total in exchange for this cancellation. Net cash received as of December 31, 2012 was $22.2 million and the remaining $15.0 million of proceeds was settled in January 2013. In connection with this private placement, the Company entered into a Letter of Agreement, dated December 24, 2012 with an investor under which the Company acknowledged that the investor's initial investment of $10.0 million in December 2012 represented partial satisfaction of the investor's preexisting contractual obligation to fund $15.0 million by March 31, 2013 upon satisfaction by the Company of criteria associated with the commissioning of the Company's production plant in Brotas.

Initial Public Offering

On September 30, 2010, the Company closed its initial public offering (“IPO”) of 5,300,000 shares of common stock at an offering price of $16.00 per share, resulting in net proceeds to the Company of approximately $73.7 million, after deducting underwriting discounts of $5.9 million and offering costs of $5.2 million. Upon the closing of the IPO, the Company’s outstanding shares of convertible preferred stock were automatically converted into 31,550,277 shares of common stock and the outstanding convertible preferred stock warrants were automatically converted into common stock warrants to purchase a total of 195,604 shares of common stock and shares of Amyris Brasil held by third party investors were automatically converted into 861,155 shares of common stock.

In connection with the IPO, the Company granted the underwriters the right to purchase up to an additional 795,000 shares of common stock to cover over-allotments. In October 2010, the underwriters exercised such right to purchase 795,000 shares and the Company received approximately $11.8 million of proceeds, net of underwriter’s discount.

Common Stock

Pursuant to the Company’s amended and restated certificate of incorporation, the Company is authorized to issue 100,000,000 shares of common stock. Holders of the Company’s common stock are entitled to dividends as and when declared by the Board of Directors, subject to the rights of holders of all classes of stock outstanding having priority rights as to dividends. There have been no dividends declared to date. The holder of each share of common stock is entitled to one vote.

Preferred Stock

Pursuant to the Company’s amended and restated certificate of incorporation, the Company is authorized to issue 5,000,000 shares of preferred stock. The Board of Directors has the authority, without action by its stockholders, to designate and issue shares of preferred stock in one or more series and to fix the rights, preferences, privileges and restrictions thereof. Prior to the closing of the Company’s IPO, the Company had four series of convertible preferred stock outstanding, including Series D preferred stock issued to Total (see Note 9). As of December 31, 2012 and December 31, 2011, the Company had zero convertible preferred stock outstanding.

Common Stock Warrants

During the period from January 1, 2008 to September 30, 2010, the Company issued 182,405 warrants in connection with placement agent fees associated with its preferred stock issuance, capital and operating lease agreements and consulting services. Upon the closing of the Company’s IPO on September 30, 2010, these outstanding convertible preferred stock warrants were automatically converted into common stock warrants to purchase 195,604 shares of common stock. In addition, the fair value of the convertible preferred stock warrants as of September 30, 2010, estimated to be $2.3 million using the Black-Scholes option pricing model, was reclassified to additional paid in capital.

In December 2011, in connection with a capital lease agreement, the Company issued warrants to purchase 21,087 shares of the Company's common stock at an exercise price of $10.67 per share. The Company estimated the fair value of these warrants as of the issuance date to be $193,000 and recorded these warrants as other assets and were amortized subsequently over the term of the lease. The fair value was based on the contractual term of the warrants of 10 years, risk free interest rate of 2.0%, expected volatility of 86% and zero expected dividend yield. The warrants remain unexercised and outstanding as of December 31, 2012.

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Each of these warrants includes a cashless exercise provision which permits the holder of the warrant to elect to exercise the warrant without paying the cash exercise price, and receive a number of shares determined by multiplying (i) the number of shares for which the warrant is being exercised by (ii) the difference between the fair market value of the stock on the date of exercise and the warrant exercise price, and dividing such by (iii) the fair market value of the stock on the date of exercise. During the years ended December 31, 2012 and 2011, warrants were exercised with respect to zero and 190,468 shares, respectively through the cashless exercise provision and zero and 77,087 shares of common stock were issued after deducting the shares to cover the cashless exercises.

As of December 31, 2012 and 2011, the Company had the following unexercised common stock warrants:

		Exercise Price per Share		Shares as of
Underlying Stock	Expiration Date			December 31, 2012	December 31, 2011
Common Stock	1/31/2018	$	24.88	—	2,884
Common Stock	9/23/2018	$	25.26	—	2,252
Common Stock	12/23/2021	$	10.67	21,087	21,087
Total				21,087	26,223

12. Stock-Based Compensation Plans

2010 Equity Incentive Plan

The Company's 2010 Equity Incentive Plan (“2010 Equity Plan”) became effective on September 28, 2010 and will terminate in 2020. Pursuant to the 2010 Equity Plan, any shares of the Company’s common stock (i) issued upon exercise of stock options granted under the Company's 2005 Stock Option/Stock Issuance Plan (the "2005 Plan") that cease to be subject to such option and (ii) issued under the 2005 Plan that are forfeited or repurchased by the Company at the original purchase price will become part of the 2010 Equity Plan. Subsequent to the effective date of the 2010 Equity Plan, an additional 803,944 shares that were forfeited under the 2005 Plan were added to the shares reserved for issuance under the 2010 Equity Plan.

The number of shares reserved for issuance under the 2010 Equity Plan increase automatically on January 1^st of each year starting with January 1, 2011, by a number of shares equal to 5.0% percent of the Company’s total outstanding shares as of the immediately preceding December 31^st. The Company’s Board of Directors or the Leadership Development and Compensation Committee of the Board of Directors is able to reduce the amount of the increase in any particular year. The 2010 Equity Plan provides for the granting of common stock options, restricted stock awards, stock bonuses, stock appreciation rights, restricted stock units and performance awards. It allows for time-based or performance-based vesting for the awards. Options granted under the 2010 Equity Plan may be either incentive stock options ("ISOs") or non-statutory stock options ("NSOs"). ISOs may be granted only to Company employees (including officers and directors who are also employees). NSOs may be granted to Company employees, non-employee directors and consultants. The Company will be able to issue no more than 30,000,000 shares pursuant to the grant of ISOs under the 2010 Equity Plan. Options under the 2010 Equity Plan may be granted for periods of up to ten years. All options issued to date have had a ten year life. Under the plan, the exercise price of any ISOs and NSOs may not be less than 100% of the fair market value of the shares on the date of grant. The exercise price of any ISOs and NSOs granted to a 10% stockholder may not be less than 110% of the fair value of the underlying stock on the date of grant. The options granted to date generally vest over four to five years.

As of December 31, 2012, options to purchase 5,708,475 shares of the Company's common stock granted from the 2010 Equity Plan were outstanding and 1,059,715 shares of the Company’s common stock remained available for future awards that may be granted from the 2010 Equity Plan. The options outstanding as of December 31, 2012 had a weighted-average exercise price of approximately $9.84 per share.

2005 Stock Option/Stock Issuance Plan

In 2005, the Company established its 2005 Plan which provided for the granting of common stock options, restricted stock units, restricted stock and stock purchase rights awards to employees and consultants of the Company. The 2005 Plan allowed for time-based or performance-based vesting for the awards. Options granted under the 2005 Plan were ISOs or NSOs. ISOs were granted only to Company employees (including officers and directors who are also employees). NSOs were granted to Company employees, non-employee directors, and consultants.

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All options issued under the 2005 Plan have had a ten year life. The exercise prices of ISOs and NSOs granted under the 2005 Plan were not less than 100% of the estimated fair value of the shares on the date of grant, as determined by the Board of Directors. The exercise price of an ISO and NSO granted to a 10% stockholder could not be less than 110% of the estimated fair value of the underlying stock on the date of grant as determined by the Board of Directors. The options generally vested over 5 years.

As of December 31, 2012, options to purchase 3,178,117 shares of the Company’s common stock granted from the 2005 Stock Option/Stock Issuance Plan remained outstanding and, as a result of the adoption of the 2010 Equity Incentive Plan discussed above, zero shares of the Company’s common stock remained available for issuance under the 2005 Plan. The options outstanding under the 2005 Plan as of December 31, 2012 had a weighted-average exercise price of approximately $7.79 per share.

No income tax benefit has been recognized relating to stock-based compensation expense and no tax benefits have been realized from exercised stock options or release of restricted stock units.

2010 Employee Stock Purchase Plan

The 2010 Employee Stock Purchase Plan (the “2010 ESPP”) became effective on September 28, 2010. The 2010 ESPP is designed to enable eligible employees to purchase shares of the Company’s common stock at a discount. Each offering period is for one year and consists of two six-month purchase periods. Each twelve-month offering period generally commences on May 16^th and November 16^th, each consisting of two six-month purchase periods. The purchase price for shares of common stock under the 2010 ESPP is the lesser of 85% of the fair market value of the Company’s common stock on the first day of the applicable offering period or the last day of each purchase period. A total of 168,627 shares of common stock were initially reserved for future issuance under the 2010 Employee Stock Purchase Plan. During the first eight years of the life of the 2010 ESPP, the number of shares reserved for issuance increases automatically on January 1^st of each year, starting with January 1, 2011, by a number of shares equal to 1% of the Company’s total outstanding shares as of the immediately preceding December 31^st. Pursuant to the automatic increase provision, an additional 459,325 shares were reserved for issuance during the year ended December 31, 2012 for a cumulative total of 897,799 additional shares reserved for issuance under the automatic increase provision. The Company’s Board of Directors or the Leadership Development and Compensation Committee of the Board of Directors is able to reduce the amount of the increase in any particular year. No more than 10,000,000 shares of the Company’s common stock may be issued under the 2010 ESPP and no other shares may be added to this plan without the approval of the Company’s stockholders.

During the year ended December 31, 2012, 579,167 shares of the Company's common stock were purchased under the 2010 ESPP. At December 31, 2012, 186,700 shares of the Company’s common stock remained available for issuance under the 2010 ESPP.

Stock Option Activity

The Company’s stock option activity and related information for the year ended December 31, 2012 was as follows:

		Number Outstanding		Weighted - Average Exercise Price		Weighted - Average Remaining Contractual Life (Years)	Aggregate Intrinsic Value
							(in thousands)
Outstanding - December 31, 2011		8,377,016		$	14.05	7.9	$	29,127
	Options granted	3,592,593		$	3.49
	Options exercised	(866,203	)	$	0.72
	Options cancelled	(2,156,814	)	$	15.78
Outstanding - December 31, 2012		8,946,592		$	9.07	7.5	$	954
Vested and expected to vest after December 31, 2012		8,281,330		$	9.18	7.3	$	893
Exercisable at December 31, 2012		4,134,023		$	9.94	5.8	$	575

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The aggregate intrinsic value of options exercised under all option plans was $2.7 million, $28.7 million and $934,000 for the years ended December 31, 2012, 2011 and 2010, respectively, determined as of the date of option exercise.

The Company’s restricted stock units and restricted stock activity and related information for the year ended December 31, 2012 was as follows:

	RSUs		Weighted Average Grant-Date Fair Value		Weighted Average Remaining Contractual Life (Years)
Outstanding - December 31, 2011	375,189		$	29.84	1.4
Awarded	2,966,900		$	3.45	—
Vested	(415,792	)	$	13.47	—
Forfeited	(375,498	)	$	10.28	—
Outstanding - December 31, 2012	2,550,799		$	7.92	1.3
Expected to vest after December 31, 2012	2,237,365		$	7.92	1.2

The following table summarizes information about stock options outstanding as of December 31, 2012:

	Options Outstanding				Options Exercisable
Exercise Price	Number of Options	Weighted - Average Remaining Contractual Life (Years)	Weighted Average Exercise Price		Number of Options	Weighted Average Exercise Price
$0.10—$2.76	1,129,158	8.1	$	2.31	279,345	$	1.06
$3.04—$3.55	768,990	9.7	$	3.12	10,936	$	3.13
$3.86—$3.86	1,424,649	8.9	$	3.86	296,482	$	3.86
$3.93—$3.93	1,198,288	3.9	$	3.93	1,152,673	$	3.93
$4.06—$9.32	1,351,331	6.8	$	6.37	799,576	$	6.38
$10.44—$14.28	326,936	7.2	$	12.61	190,964	$	13.51
$16.00—$16.00	1,174,667	8.0	$	16.00	531,966	$	16.00
$16.50—$20.41	959,303	7.0	$	18.72	552,878	$	18.77
$24.20—$27.13	533,270	7.5	$	26.32	272,539	$	26.15
$30.17—$30.17	80,000	8.2	$	30.17	46,664	$	30.17
$0.10—$30.17	8,946,592	7.5	$	9.07	4,134,023	$	9.94

Common Stock Subject to Repurchase

Historically under the 2005 Plan, the Company allowed employees to exercise options prior to vesting. The Company has the right to repurchase at the original purchase price any unvested (but issued) common shares upon termination of service of an employee. The consideration received for an early exercise of an option is considered to be a deposit of the exercise price and the related dollar amount is recorded as a liability. The shares and liability are reclassified into equity on a ratable basis as the award vests. The Company recorded a liability in accrued expenses of $197 and $30,000, respectively, relating to options for 51 and 7,929 shares of common stock that were exercised and unvested as of December 31, 2012 and 2011, respectively. These shares were subject to a repurchase right held by the Company and are included in issued and outstanding shares as of December 31, 2012 and 2011, respectively.

Stock-Based Compensation Expense

Stock-based compensation expense related to options and restricted stock units granted to employees and nonemployees was allocated to research and development expense and sales, general and administrative expense as follows (in thousands):

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	Years Ended December 31,
	2012		2011		2010
Research and development	$	6,451	$	6,345	$	2,161
Sales, general and administrative	21,022		19,147		8,271
Total stock-based compensation expense	$	27,473	$	25,492	$	10,432

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Employee Stock–Based Compensation

During the years ended December 31, 2012, 2011 and 2010, the Company granted options to purchase 3,589,593 shares, 2,677,249 shares, and 2,918,440 shares of its common stock, respectively, to employees with weighted average grant date fair values of $2.28, $18.41, and $11.84 per share, respectively. As of December 31, 2012 and 2011, there were unrecognized compensation costs of $51.2 million, and $54.7 million, respectively, related to these stock options. The Company expects to recognize those costs over a weighted average period of 2.9 years as of December 31, 2012. Future option grants will increase the amount of compensation expense to be recorded in these periods.

In August 2012, the Company's CEO exercised outstanding options to purchase 668,730 shares of the Company's common stock and sold the shares to certain members of the Company's Board of Directors or their affiliates through a private sale at a price of $3.70, which was greater than the fair market value of the stock at the date of sale. The Company recorded $388,000 in stock-based compensation expense as an excess of the sale price over the fair market value of shares in this transaction during the year ended December 31, 2012.

During the years ended December 31, 2012 and 2011, 2,956,900 and 352,301 of restricted stock units, respectively, were granted to employees with a weighted average service-inception date fair value of $3.46 and $29.85 per unit, respectively . The Company recognized a total of $6.3 million and $3.6 million, respectively, in December 31, 2012 and 2011 in stock-based compensation expense for restricted stock units granted to employees. No restricted stock units was granted to employees in 2010. As of December 31, 2012 and 2011, there were unrecognized compensation costs of $7.8 million and $6.0 million, respectively, related to these restricted stock units.

During the years ended December 31, 2012, 2011 and 2010, the Company also recognized stock-based compensation expense related to its 2010 ESPP of $0.8 million, $1.9 million, and $0.5 million, respectively.

Compensation expense was recorded for stock-based awards granted to employees based on the grant date estimated fair value (in thousands):

	Years Ended December 31,
	2012		2011		2010
Research and development	$	6,442	$	6,306	$	2,086
Sales, general and administrative	20,887		18,288		5,696
Total stock-based compensation expense	$	27,329	$	24,594	$	7,782

Employee stock-based compensation expense recognized for the year ended December 31, 2012 included $907,000, related to option modifications. As part of separation agreements with certain former senior employees, the Company agreed to accelerate the vesting of options for 825,523 shares of common stock and extend the exercise period for certain grants. The stock-based compensation expense above includes the impact of a repricing of stock options in June 2012 under which certain non-executive employees received a one-time reduction in the exercise price for such options with per share exercise prices per share higher than $24.00 held by U.S. employees of Amyris and the new exercise price for such options was $16.00, our initial public offering price. The total amount of the stock-based compensation associated with repricing was immaterial to the consolidated financial statements.

In the quarter ended June 30, 2011, the Company commenced sales of farnesene-derived products which were produced by contracted third parties. Accordingly, the Company did not have any dedicated production headcount so there is no stock-based compensation expense recorded in cost of products sold.

Stock-based compensation cost for RSUs is measured based on the closing fair market value of the Company's common stock on the date of grant. Stock-based compensation cost for stock options and employee stock purchase plan rights is estimated at the grant date and offering date, respectively, based on the fair-value using the Black-Scholes option pricing model. The fair value of employee stock options is being amortized on a straight-line basis over the requisite service period of the awards. The fair value of employee stock options was estimated using the following weighted-average assumptions:

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	Years Ended December 31,
	2012		2011		2010
Expected dividend yield	—	%	—	%	—	%
Risk-free interest rate	1.1	%	2.3	%	2.5	%
Expected term (in years)	6.0		5.8		6.0
Expected volatility	77	%	86	%	96	%

Expected Dividend Yield—The Company has never paid dividends and does not expect to pay dividends.

Risk-Free Interest Rate—The risk-free interest rate was based on the market yield currently available on United States Treasury securities with maturities approximately equal to the option’s expected term.

Expected Term—Expected term represents the period that the Company’s stock-based awards are expected to be outstanding. The Company’s assumptions about the expected term have been based on that of companies that have similar industry, life cycle, revenue, and market capitalization and the historical data on employee exercises.

Expected Volatility—The expected volatility is based on a combination of historical volatility for the Company's stock and the historical stock volatilities of several of the Company’s publicly listed comparable companies over a period equal to the expected terms of the options, as the Company does not have a long trading history.

Fair Value of Common Stock— Prior to the IPO, the fair value of the shares of common stock underlying the stock options was determined by the Board of Directors. Because there was no public market for the Company’s common stock, the Board of Directors determined the fair value of the common stock at the time of grant of the option by considering a number of objective and subjective factors including valuation of comparable companies, sales of convertible preferred stock to unrelated third parties, operating and financial performance, the lack of liquidity of capital stock and general and industry specific economic outlook, amongst other factors. The Company’s common stock started trading in the NASDAQ Global Market under ticker symbol AMRS on September 28, 2010. Consequently, after the IPO, the fair value of the shares of common stock underlying the stock options is the closing price on the option grant date.

Forfeiture Rate—The Company estimates its forfeiture rate based on an analysis of its actual forfeitures and will continue to evaluate the adequacy of the forfeiture rate based on actual forfeiture experience, analysis of employee turnover behavior, and other factors. The impact from a forfeiture rate adjustment will be recognized in full in the period of adjustment, and if the actual number of future forfeitures differs from that estimated by the Company, the Company may be required to record adjustments to stock-based compensation expense in future periods.

Each of the inputs discussed above is subjective and generally requires significant management and director judgment to determine.

Nonemployee Stock–Based Compensation

During the years ended December 31, 2012, 2011 and 2010, the Company granted nonemployee options to purchase 3,000, 15,000 and 101,000 shares of its common stock, respectively, to nonemployees in exchange for services. Compensation expense of $86,000, $797,000 and $834,000 was recorded for the years ended December 31, 2012, 2011 and 2010, respectively, for stock-based awards granted to nonemployees. The nonemployee options were valued using the Black-Scholes option pricing model.

During the years ended December 31, 2012, 2011 and 2010, 10,000, 32,855 and 126,272 restricted stock units, respectively, were granted to nonemployees and a total of $58,000, $101,000 and $1.8 million, respectively, in stock-based compensation expense was recognized by the Company for the years ended December 31, 2012, 2011 and 2010. The 126,272 restricted stock units that were granted in 2010 were awarded to a related party as compensation for advisory services rendered. These restricted stock units vested quarterly and became fully vested as of September 30, 2010.

The fair value of nonemployee stock options was estimated using the following weighted-average assumptions:

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	Years Ended December 31,
	2012		2011		2010
Expected dividend yield	—	%	—	%	—	%
Risk-free interest rate	1.4	%	2.1	%	3.2	%
Expected term (in years)	7.0		7.8		8.6
Expected volatility	77	%	86	%	95	%

13. Employee Benefit Plan

The Company established a 401(k) Plan to provide tax deferred salary deductions for all eligible employees. Participants may make voluntary contributions to the 401(k) Plan up to 90% of their eligible compensation, limited by certain Internal Revenue Service restrictions. The Company does not match employee contributions.

14. Related Party Transactions

The Company has entered into a license agreement with University of California, Berkeley. A co-founder and advisor to the Company is a professor at the University of California, Berkeley. The Company paid the advisor zero, $2,500 and $23,000, during the years ended December 31, 2012, 2011 and 2010, respectively.

During 2008, the Company entered into an agreement with a venture capital group to provide strategic advisory services to Amyris and its then majority owned subsidiary, Amyris Brasil. One of the venture capital group's former directors is also a member of the Company’s Board of Directors. Under the agreement, the Company issued options to the venture capital group, which vest and become exercisable based on the service of the former director of the group on the Company's Board of Directors.

In June 2010, the Company entered into agreements with Total relating to the Company’s Series D preferred stock and collaboration for the research, development, production and commercialization of chemical and/or fuel products (see Note 9).

In October 2011, the Company completed a business combination with Draths. In connection with the acquisition, the Company issued 362,319 shares of the Company's common stock, of which 41,408 shares were held in escrow and paid $2.9 million in cash. In the quarter ended June 30, 2012, the Company recovered 5,402 shares of common stock from the escrow in connection with certain Draths indemnification obligations under the purchase agreement. One of the Company's Board of Directors was also on the board of Draths.

In November 2011, the Company and Total entered into an amendment to their Technology License, Development, Research and Collaboration Agreement (see Note 4).

In February 2012, the Company completed a private placement of 10,160,325 shares of its common stock at a price of $5.78 per share for aggregate proceeds of $58.7 million pursuant to a securities purchase agreement, among the Company and existing certain investors, including Total and Maxwell (Mauritius) Pte Ltd, each a beneficial owner of more than 5% of the Company's existing common stock at the time of the transaction. In addition, members of the Company's Board of Directors and certain parties related to such directors participated in the offering.

In May 2012, the Company completed a private placement of 1,736,100 shares of it's common stock at a price of $2.36 per share for aggregate proceeds of $4.1 million pursuant to a series of Common Stock Purchase Agreements, among the Company and members of the Company's Board of Directors and certain parties related to such directors.

In July 2012, the Company entered into various agreements with Total relating to the Program (see Note 9).

In December 2012, the Company completed a private placement of its common stock for the issuance of 14,177,849 shares it's common stock at a price of $2.98 per share for aggregate proceeds of $37.2 million and the cancellation of $5.0 million worth of outstanding senior unsecured convertible promissory notes previously issued by the Company (see Note 6). Shares totaling 1,677,852 were issued to Total in exchange for this cancellation. Net cash received as of December 31, 2012 was $22.2 million and the remaining $15.0 million of proceeds were settled in January 2013.

In connection with the December 2012 private placement, the Company entered into a Letter of Agreement, dated December 24, 2012 with Biolding, an existing investor. Under the letter agreement, the Company acknowledged that Biolding's initial investment of $10.0 million under the Purchase Agreement represented partial satisfaction of Biolding's preexisting contractual obligation to fund $15.0 million by March 31, 2013 upon satisfaction by the Company of criteria associated with the commissioning

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of the Company's production plant in Brotas. Pursuant to the letter agreement, Biolding would invest the remaining $5.0 million no later than March 31, 2013 following satisfaction of the criteria. A member of the Company's Board of Directors is affiliated with Biolding.

In connection with the February 2012 and December 2012 private placement, Naxyris SA and TPG Biotechnology Partners II, L.P., each a beneficial owner of more than 5% of the Company's outstanding common stock at the time of the December 2012 offering, purchased shares in the December 2012 offering; in addition, Naxyris SA's Board designee (pursuant to the February 2012 agreement), was serving on the Company's Board of Directors at the time of both the February 2012 and the December 2012 offerings, and a partner of TPG Biotech, an affiliate of TPG Biotechnology Partners II, L.P., was serving on the Company's Board of Directors at the time of the December 2012 offering.

Foris Ventures LLC and Sualk Capital Ltd, entities affiliated with two of the Company's existing Board of Directors, purchased shares of the Company's common stock in both the February 2012 and December 2012 offerings; in addition, Sualk Capital Ltd's Board designee (pursuant to the February 2012 agreement), was serving on the Company's Board of Directors at the time of the December 2012 offering.

Please refer to Note 18 "Subsequent Events" for additional related party transactions.

15. Restructuring

In June 2009, the Company initiated a restructuring plan to reduce its cost structure. The restructuring plan resulted in the consolidation of the Company’s headquarter facility located in Emeryville, California, which is under an operating lease. The Company ceased using a certain part of this headquarter facility in August 2009. The Company recorded approximately $5.4 million of restructuring charges associated with the facility lease costs after the operations ceased. In addition, as a result of the consolidation of the headquarter facility, the Company recorded approximately $3.1 million related to asset impairments and reversed $2.7 million related to deferred rent associated with the leased facility. In September 2010, the Company’s Board of Directors approved the Company’s plan to reoccupy the part of its headquarter facility which was previously the subject of the 2009 restructuring. This reoccupied space was used to meet the Company’s expansion requirements. As a result, the Company reversed approximately $4.6 million of its restructuring liability and recognized an income from restructuring of $2.1 million during the year ended December 31, 2010.

The following table summarizes the liability and utilization by cost type associated with the restructuring (in thousands):

	Exit Costs			Deferred Rent			Total
Accrued restructuring as of December 31, 2009	$	5,078		$	—		$	5,078
Cash payments	(906		)	—			(906		)
Accretion expense	395			—			395
Reversal of restructuring liability	(2,061		)	(2,506		)	(4,567		)
Accrued restructuring as of December 31, 2010	$	2,506		$	(2,506	)	$	—

16. Income Taxes

For the years ended December 31, 2012, 2011 and 2010, the Company recorded a provision for income taxes of $981,000, $552,000 and zero, respectively. The provision for income taxes for the year ended December 31, 2012 consisted of an accrual of Brazilian withholding tax on an intercompany interest liability. The provision for incomes taxes for the year ended December 31, 2011 consisted of $727,000 for the accrual of Brazilian withholding tax on an intercompany interest liability, partially offset by a $175,000 benefit from income taxes resulting from valuation allowance adjustments due to an increase in currency translation adjustments classified as other comprehensive losses. Other than the above mentioned provision for income tax, no additional provision for income taxes has been made, net of the valuation allowance, due to cumulative losses since the commencement of operations.

The components of loss before income taxes and minority interests are as follows for the years ended December 31, 2012, 2011 and 2010 (in thousands):

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	Years Ended December 31,
	2012			2011			2010
United States	$	(146,028	)	$	(140,153	)	$	(67,525	)
Foreign	(59,024		)	(38,806		)	(15,265		)
Loss before income taxes	$	(205,052	)	$	(178,959	)	$	(82,790	)

The components of the provision for income taxes are as follows for the years ended December 31, 2012, 2011 and 2010 (in thousands):

	Years Ended December 31,
	2012		2011			2010
Current:
Federal	$	—	$	—		$	—
State	—		—			—
Foreign	981		727			—
Total current provision (benefit)	981		727			—
Deferred:
Federal	—		(150		)	—
State	—		(25		)	—
Foreign	—		—			—
Total deferred provision (benefit)	—		(175		)	—
Total provision for income taxes	$	981	$	552		$	—

A reconciliation between the statutory federal income tax and the Company’s effective tax rates as a percentage of loss before income taxes is as follows:

	Years Ended December 31,
	2012		2011		2010
Statutory tax rate	(34.0	)%	(34.0	)%	(34.0	)%
State tax rate, net of federal benefit	(0.4	)%	(4.4	)%	(1.6	)%
Stock-based compensation	0.2	%	0.6	%	0.3	%
Federal R&D credit	—	%	(0.8	)%	(0.8	)%
Other	1.6	%	(0.7	)%	1.6	%
Foreign losses	(5.8	)%	(5.4	)%	—	%
Change in valuation allowance	38.8	%	45.0	%	34.5	%
Effective income tax rate	0.4	%	0.3	%	—	%

Temporary differences and carryforwards that gave rise to significant portions of deferred taxes are as follows (in thousands):

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	December 31,
	2012			2011			2010
Net operating loss carryforwards	$	145,324		$	103,390		$	56,615
Fixed assets	—			—			340
Research and development credits	7,259			5,937			3,325
Foreign Tax Credit	1,782			801			—
Accruals and reserves	15,997			12,150			2,257
Stock-based compensation	15,882			11,351			4,316
Capitalized start-up costs	16,070			22,974			8,993
Capitalized research and development costs	26,850			—			—
Other	7,649			2,904			225
Total deferred tax assets	236,813			159,507			76,071
Fixed assets	(525		)	(2,742		)	—
Other	—			—			—
Total deferred tax liabilities	(525		)	(2,742		)	—
Net deferred tax asset prior to valuation allowance	236,288			156,765			76,071
Less: Valuation allowance	(236,288		)	(156,765		)	(76,071		)
Net deferred tax assets (liabilities)	$	—		$	—		$	—

Recognition of deferred tax assets is appropriate when realization of such assets is more likely than not. Based upon the weight of available evidence, especially the uncertainties surrounding the realization of deferred tax assets through future taxable income, the Company believes it is not yet more likely than not that the net deferred tax assets will be fully realizable. Accordingly, the Company has provided a full valuation allowance against its net deferred tax assets as of December 31, 2012. The valuation allowance increased $79.5 million, $80.7 million, and $28.3 million, during the years ended December 31, 2012, 2011 and 2010, respectively.

As of December 31, 2012, the Company had federal and state net operating loss carryforwards of approximately $373.7 million and $202.4 million , respectively, available to reduce future taxable income, if any. Approximately $25.7 million and $12.7 million of the federal and state net operating loss carryforwards, respectively, resulted from exercises of employee stock options and vesting of restricted stock units and have not been included in the Company’s gross deferred tax assets. In accordance with ASC 718, such unrealized tax benefits of approximately $9.5 million will be accounted for as a credit to additional paid-in capital if and when realized through a reduction in income taxes payable.

The Company also has federal research and development credits of $5.1 million and foreign tax credit carryforwards of $1.8 million, and California research and development credit carryforwards of $7.9 million, respectively, at December 31, 2012. The American Taxpayer Relief Act of 2012 (the "Act") was enacted on January 2, 2013. The Act retroactively reinstates the federal research and development credit from January 1, 2012, through December 31, 2013. The benefit of the reinstated credit is not expected to impact the income statement in the period of enactment, which is the first quarter of 2013 as the research and development credit carryforwards are offset by a full valuation allowance.

The Tax Reform Act of 1986 and similar state provisions limit the use of net operating loss and credit carryforwards in certain situations where equity transactions result in a change of ownership as defined by Internal Revenue Code Section 382. In the event the Company has experienced an ownership change, as defined, utilization of its federal and state net operating loss and credit carryforwards could be limited. If not utilized, the federal net operating loss carryforward begins expiring in 2025, and the California net operating loss carryforward begins expiring in 2015. The federal foreign tax credits and research and development credit carryforwards will expire starting in 2020 and in 2024; respectively, if not utilized. The California tax credits can be carried forward indefinitely.

Effective January 1, 2007, the Company adopted the accounting guidance on uncertainties in income taxes. A reconciliation of the beginning and ending amounts of unrecognized tax benefits since the adoption of accounting guidance on uncertainty in income taxes is as follows:

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Balance at December 31, 2010	1,734
Increases in tax positions for prior period	—
Increases in tax positions during current period	1,369
Balance at December 31, 2011	$	3,103
Increases in tax positions for prior period	82
Increases in tax positions during current period	733
Balance at December 31, 2012	$	3,918

The Company’s policy is to include interest and penalties related to unrecognized tax benefits within the provision for taxes. The Company determined that no accrual for interest and penalties was required as of December 31, 2012.

As of December 31, 2012, the Company’s total unrecognized tax benefits were $3.9 million, of which none of the tax benefits, if recognized, would affect the effective income tax rate due to the valuation allowance that currently offsets deferred tax assets. The Company does not anticipate the total amount of unrecognized income tax benefits will significantly increase or decrease in the next 12 months.

The Company’s primary tax jurisdiction is the United States. For United States federal and state tax purposes, tax years 2003 and forward remain open and subject to tax examination by the appropriate federal or state taxing authorities. Brazil tax years 2008 through the current remain open and subject to examination.

The Company is currently under audit by the US Internal Revenue Service for tax year 2008. As of December 31, 2012, the Company has received a Form 4549-A, Income Tax Discrepancy Adjustments (Examination No Change Report) which concluded that there were no adjustments resulting from the audit by the US Internal Revenue Service for the tax year 2008.  As of December 31, 2012, the Company has not yet received the Area Director's final approval of the report.

17. Reporting Segments

The chief operating decision maker for the Company is the chief executive officer. The chief executive officer reviews financial information presented on a consolidated basis, accompanied by information about revenue by geographic region, for purposes of allocating resources and evaluating financial performance. The Company has one business activity comprised of research and development and sales of fuels and farnesene-derived products and there are no segment managers who are held accountable for operations, operating results or plans for levels or components below the consolidated unit level. Accordingly, the Company has determined that it has a single reportable segment and operating unit structure.

Revenues by geography are based on the location of the customer. The following tables set forth revenue and long-lived assets by geographic area (in thousands):

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Revenues

	Years Ended December 31,
	2012		2011		2010
United States	$	49,111	$	141,098	$	80,311
Brazil	3,786		141		—
Europe	16,461		5,695		—
Asia	4,336		57		—
Total	$	73,694	$	146,991	$	80,311

Long-Lived Assets

	December 31,
	2012		2011
United States	$	70,273	$	76,108
Brazil	90,982		48,240
Europe	1,866		3,753
Total	$	163,121	$	128,101

18. Subsequent Events

Evergreen Shares for 2010 Equity Plan and 2010 ESPP

On January 23, 2013, the Company's Board of Directors approved the additional shares which will be available for issuance under the 2010 Equity Plan and the 2010 ESPP. These shares represent an automatic increase in the number of shares available for issuance under the 2010 Equity Plan and the 2010 ESPP of 3,435,483 and 687,096, respectively, equal to 5% and 1%, respectively of 68,709,660 shares, the total outstanding shares of the Company’s common stock as of December 31, 2012. This automatic increase was effective as of January 1, 2013. Shares available for issuance under the 2010 Equity Plan and 2010 ESPP were initially registered on a registration statement on Form S-8 filed with the Securities and Exchange Commission on October 1, 2010 (Registration No. 333-169715). The Company intends to file a registration statement on Form S-8 with respect to a portion of the shares added by the automatic increase on January 1, 2013 following the filing of its annual report on Form 10-K.

Proceeds from December 2012 Private Placement

On January 11, 2013, the Company received the remaining $15.0 million of proceeds from the private placement offering that closed in December 2012. Consequently, the Company issued 5,033,557 shares of the Company's common stock to an investor on that date.

Firmenich Agreement

On March 13, 2013, the Company entered into a Master Collaboration Agreement (the “Agreement”) with Firmenich to establish a collaboration for the development and commercialization of multiple renewable flavors and fragrances ("F&F") compounds. Under this Agreement, except for rights granted under preexisting collaboration relationships, the Company is granting Firmenich exclusive access for such compounds to specified Company intellectual property for the development and commercialization of F&F products in exchange for research and development funding and a profit sharing arrangement. The Agreement supersedes and expands a prior collaboration agreement between the Company and Firmenich as described in Note 9.

The Agreement provides annual, up-front funding to the Company by Firmenich of $10.0 million for each of the first three years of the collaboration. The initial payment of $10.0 million was received by the Company on March 27, 2013. The Agreement contemplates additional funding by Firmenich on a discretionary basis and up to $5.0 million in milestone payments from Firmenich to the Company. In addition, the Agreement contemplates that the parties will mutually agree on a supply price for each compound and share product margins from sales of each compound on a 70/30 basis (70% for Firmenich) until Firmenich receives $15.0 million more than the Company in the aggregate, after which the parties will share 50/50 in the product margins on all compounds. The Company also agreed to pay a one-time success bonus of up to $2.5 million to Firmenich for outperforming certain commercialization targets.

The Agreement does not impose any specific research and development commitments on either party after year six, but if the parties mutually agree to perform development after year six, the Agreement provides that the parties will fund it equally.

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Under the Agreement, the parties jointly select target compounds, subject to final approval of compound specifications by Firmenich. During the development phase, the Company is required to provide labor, intellectual property and technology infrastructure and Firmenich is required to contribute downstream polishing expertise and market access. The Agreement provides that the Company will own research and development and strain engineering intellectual property, and Firmenich will own blending and, if applicable, chemical conversion intellectual property. Under certain circumstances such as the Company's insolvency, Firmenich gains expanded access to the Company's intellectual property. Following development of F&F compounds under the Agreement, the Agreement contemplates that Company will manufacture the initial target molecules for the compounds and Firmenich will perform any required downstream polishing and distribution, sales and marketing.

Export Financing with ABC Brasil

On March 18, 2013, the Company entered into an export financing agreement with Banco ABC Brasil S.A. (ABC Bank) for approximately US$2.5 million (approximately R$5.0 million based on exchange rate as of March 18, 2013) for a 1 year-term to fund exports through March 2014.

Letter Agreement with Total

As of March 24, 2013, the Company entered into a letter agreement with Total under which Total agreed to waive its right to cease its participation in our fuels collaboration at the July 2013 decision point referenced above under Note 9 - “Significant Agreements,” and committed to proceed with the July 2013 funding tranche of $30.0 million (subject to the Company's satisfaction of the relevant closing conditions for such funding in the securities purchase agreement).  As consideration for this waiver and commitment, the Company agreed to:

• Reduce the conversion price for the senior unsecured convertible promissory notes to be issued in connection with such funding from $7.0682 per share to a price per share equal to the greater of (i) the consolidated closing bid price of the Company's common stock on the date of the letter agreement, plus $0.01, and (ii) $3.08 per share, provided that the conversion price will not be reduced by more than the maximum possible amount permitted under the NASDAQ rules such that the new conversion price would require the Company to obtain stockholder consent; and

• Grant Total a senior security interest in the Company's intellectual property, subject to certain exclusions and subject to release by Total when the Company and Total enter into final documentation regarding the establishment of the Fuels JV.

In addition to the waiver by Total described above, Total also agreed that, at the Company's request and contingent upon the Company meeting its obligations described above, it would pay advance installments of the amounts otherwise payable at the July 2013 closing.  Specifically, if the Company requests such advance installments, subject to certain closing conditions and delivery of certifications regarding the Company's cash levels, Total is obligated to fund $10.0 million no later than May 15, 2013, and an additional $10.0 million no later than June 15, 2013, with the remainder funding on the original July 2013 closing date.

Biolding Follow-on Investment

On March 27, 2013, the Company completed a private placement of its common stock to Biolding for the issuance of 1,533,742 of its common stock at a price of $3.26 per share aggregate proceeds of approximately $5.0 million. This private placement represented the final tranche of Biolding's preexisting contractual obligation to fund $15.0 million upon satisfaction by the Company of certain criteria associated with the commissioning of a production plant in Brazil.

Joint Venture with Cosan

As of March 26, 2013, the Company and Cosan US, Inc. (“Cosan US”) entered into agreements to (i) expand their base oils joint venture to also include additives and lubricants and (ii) operate their joint venture exclusively through Novvi LLC. Specifically, the parties entered into an Amended and Restated Operating Agreement for Novvi LLC, which sets forth the governance procedures for Novvi LLC and the joint venture and the parties initial contribution, which for the Company are the licenses granted under the IP License Agreement. The Company also entered into an IP License Agreement with Novvi LLC under which the Company granted Novvi LLC (i) an exclusive (subject to certain limited exceptions for the Company), worldwide, royalty-free license to develop, produce and commercialize base oils, additives, and lubricants derived from Biofene for use in the automotive, commercial and industrial lubricants markets and (ii) a non-exclusive, royalty-free license, subject to certain conditions, to manufacture Biofene solely for its own products. In addition, both the Company and Cosan US granted Novvi LLC certain rights of first refusal with respect to alternative base oil and additive technologies that may be acquired by the Company or Cosan US during the term of the IP License Agreement. Under these agreements, the Company and Cosan US will each own 50% of Novvi LLC, and each party

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will share equally in any costs and any profits ultimately realized by the joint venture. The IP License Agreement has an initial term of 20 years from the date of the agreement, subject to standard early termination provisions such as uncured material breach or a party's insolvency.

In conjunction with the execution of the documents above, the Company, Amyris Brasil and Cosan are also entering into a termination of the Original JV Agreement.  In addition, Amyris Brasil agreed to sell, for a nominal amount, its 50% interest in the Novvi S.A. entity, a now-dormant company, to Cosan.  Following consummation of such sale, the Shareholders' Agreement between Amyris Brasil and Cosan with regard to Novvi S.A. will automatically terminate pursuant to its terms.

SUPPLEMENTARY FINANCIAL DATA

Selected Quarterly Financial Data (unaudited)

The following table presents selected unaudited consolidated financial data for each of the eight quarters in the two-year periods ended December 31, 2012. In the Company’s opinion, this unaudited information has been prepared on the same basis as the audited information and includes all adjustments (consisting of only normal recurring adjustments) necessary for a fair statement of the financial information for the periods presented. Net loss per share—basic and diluted, for the four quarters of each fiscal year may not sum to the total for the fiscal year because of the different number of shares outstanding during each period.

	Quarter
	First			Second			Third			Fourth
	(In thousands, except share and per share amounts)
Year Ended December 31, 2012
Total revenues	$	29,469		$	19,263		$	19,108		$	5,854
Product sales	$	26,307		$	15,580		$	4,728		$	3,023
Gross profit (loss) from product sales	$	(17,504	)	$	(8,056	)	$	284		$	(2,400	)
Net loss attributable to common stockholders	$	(94,548	)	$	(46,806	)	$	(20,293	)	$	(43,492	)
Net loss per share—basic and diluted	$	(1.88	)	$	(0.81	)	$	(0.34	)	$	(0.72	)
Shares used in calculation—basic and diluted	50,214,192			57,442,834			58,964,226			60,187,256
Year Ended December 31, 2011
Total revenues	$	37,174		$	32,002		$	36,276		$	41,539
Product sales	$	34,020		$	27,816		$	31,162		$	36,839
Gross profit (loss) from product sales	$	(362	)	$	(1,320	)	$	(4,567	)	$	(19,529	)
Net loss attributable to common stockholders	$	(33,137	)	$	(42,615	)	$	(43,690	)	$	(59,428	)
Net loss per share—basic and diluted	$	(0.76	)	$	(0.95	)	$	(0.97	)	$	(1.30	)
Shares used in calculation—basic and diluted	43,851,142			44,626,721			45,031,613			45,663,667

ITEM 9. CHANGES IN AND DISAGREEMENTS WITH ACCOUNTANTS ON ACCOUNTING AND FINANCIAL DISCLOSURE

Not applicable.

ITEM 9A. CONTROLS AND PROCEDURES

Disclosure Controls and Procedures

Our management, with the participation of our chief executive officer and chief financial officer, evaluated the effectiveness of our disclosure controls and procedures pursuant to Rule 13a-15 under the Securities Exchange Act of 1934, as amended (Exchange Act), as of the end of the period covered by this Annual Report on Form 10-K.  Based on this evaluation, our chief executive

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officer (CEO) and chief financial officer (CFO) concluded that, as of December 31, 2012, our disclosure controls and procedures are designed and are effective to provide reasonable assurance that information we are required to disclose in reports that we file or submit under the Exchange Act is recorded, processed, summarized, and reported within the time periods specified in the SEC's rules and forms, and that such information is accumulated and communicated to our management, including our CEO and CFO, as appropriate, to allow timely decisions regarding required disclosure.

Our management recognizes that any controls and procedures, no matter how well designed and operated, can provide only reasonable assurance of achieving their objectives and management necessarily applies its judgment in evaluating the cost-benefit relationship of possible controls and procedures.

Management’s Annual Report on Internal Control over Financial Reporting

Our management is responsible for establishing and maintaining adequate internal control over financial reporting. Internal control over financial reporting is a process designed by, or under the supervision of, our CEO and CFO, and effected by our Board of Directors, management and other personnel, to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles and includes those policies and procedures that:

• Pertain to the maintenance of records that accurately and fairly reflect in reasonable detail the transactions and dispositions of the assets of our company;

• Provide reasonable assurance that transactions are recorded as necessary to permit preparation of financial statements in accordance with generally accepted accounting principles, and that our receipts and expenditures are being made only in accordance with authorizations of our management and directors; and

• Provide reasonable assurances regarding prevention or timely detection of unauthorized acquisition, use or disposition of our assets that could have a material adverse effect on our financial statements.

Our management assessed our internal control over financial reporting as of December 31, 2012, the end of our fiscal year. Management based its assessment on criteria established in "Internal Control-Integrated Framework" issued by the Committee of Sponsoring Organizations of the Treadway Commission. Based on management's assessment of our internal control over financial reporting, management concluded that, as of December 31, 2012, our internal control over financial reporting was effective. The effectiveness of the Company's internal control over financial reporting as of December 31, 2012 has been audited by PricewaterhouseCoopers LLP, an independent registered public accounting firm, as stated in their report which appears herein.

Internal control over financial reporting has inherent limitations. Internal control over financial reporting is a process that involves human diligence and compliance and is subject to lapses in judgment and breakdowns resulting from human failures. Internal control over financial reporting also can be circumvented by collusion or improper management override. Because of such limitations, there is a risk that material misstatements will not be prevented or detected on a timely basis by internal control over financial reporting. However, these inherent limitations are known features of the financial reporting process. Therefore, it is possible to design into the process safeguards to reduce, though not eliminate, this risk.

Changes in Internal Control over Financial Reporting

There were no changes in our internal control over financial reporting identified in management’s evaluation pursuant to Rules 13a-15(d) or 15d-15(d) of the Exchange Act during our fourth fiscal quarter ended December 31, 2012 that materially affected, or are reasonably likely to materially affect, our internal control over financial reporting.

ITEM 9B. OTHER INFORMATION

Not applicable.

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PART III

Certain information required by Part III is omitted from this Annual Report on Form 10-K and is incorporated herein by reference from our definitive proxy statement, relating to our 2013 annual meeting of stockholders, pursuant to Regulation 14A of the Exchange Act, also referred to in this Form 10-K as our 2013 Proxy Statement, which we expect to file with the SEC no later than April 30, 2013.

ITEM 10. DIRECTORS, EXECUTIVE OFFICERS AND CORPORATE GOVERNANCE

The information appearing in our 2013 Proxy Statement under the following headings is incorporated herein by reference:

• Proposal 1—Election of Directors

• Corporate Governance

• Section 16(a) Beneficial Ownership Reporting Compliance

The information under the heading “Executive Officers of the Registrant” in Item 1 of this Annual Report on Form 10-K is also incorporated by reference in this section.

We have adopted a Code of Business Conduct and Ethics that applies to all directors, officers and employees of Amyris as required by NASDAQ governance rules and as defined by applicable SEC rules. Our Code of Business Conduct and Ethics includes a section entitled “Code of Ethics for Chief Executive Officer and Senior Financial Officers,” providing additional principles for ethical leadership and a requirement that such individuals foster a culture throughout Amyris that helps ensure the fair and timely reporting of our financial results and condition. Our Code of Business Conduct and Ethics is available on the corporate governance section of our website at “http://investors.amyris.com/governance.cfm.” Stockholders may also obtain a print copy of our Code of Business Conduct and Ethics and our Corporate Governance Guidelines by writing to the Secretary of Amyris at 5885 Hollis Street, Suite 100, Emeryville, California 94608. If we make any substantive amendments to our Code of Business Conduct and Ethics or grant any waiver from a provision of the Internal Revenue Code to any executive officer or director, we will promptly disclose the nature of the amendment or waiver on the corporate governance section of our website at “http://investors.amyris.com/governance.cfm.”

ITEM 11. EXECUTIVE COMPENSATION

The information appearing in our 2013 Proxy Statement under the following headings is incorporated herein by reference:

• Executive Compensation

• Director Compensation

• Compensation Committee Interlocks and Insider Participation

ITEM 12. SECURITY OWNERSHIP OF CERTAIN BENEFICIAL OWNERS AND MANAGEMENT AND RELATED STOCKHOLDER MATTERS

The information appearing in our 2013 Proxy Statement under the following headings is incorporated herein by reference:

• Security Ownership of Certain Beneficial Owners and Management

• Equity Compensation Plan Information

ITEM 13. CERTAIN RELATIONSHIPS AND RELATED TRANSACTIONS, AND DIRECTOR INDEPENDENCE

The information appearing in our 2013 Proxy Statement under the following headings is incorporated herein by reference:

• Transactions with Related Persons

• Proposal 1—Election of Directors—Independence of Directors

• Proposal 1—Election of Directors—Committees of the Board

ITEM 14. PRINCIPAL ACCOUNTING FEES AND SERVICES

The information appearing in our 2013 Proxy Statement under the proposal entitled “Ratification of Appointment of Independent Registered Public Accounting Firm” is incorporated herein by reference.

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PART IV

ITEM 15. EXHIBITS, FINANCIAL STATEMENT SCHEDULES

(a) The following documents are filed as part of this report on Form 10-K:

(1) Financial Statements. Reference is made to the Index to the registrant’s Financial Statements under Item 8 in Part II of this Form 10-K.

(2) Financial Statement Schedules. The following consolidated financial statement schedule of the registrant is filed as part of this report on Form 10-K and should be read in conjunction with the Consolidated Financial Statements of Amyris, Inc.

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SCHEDULE II

VALUATION AND QUALIFYING ACCOUNTS

FOR THE YEARS ENDED DECEMBER 31, 2012, 2011 and 2010

(in thousands)

	Balance at Beginning of Period		Additions		Write-off/ Adjustments		Balance at End of Period
Deferred Tax Assets Valuation Allowance:
Year ended December 31, 2012	$	156,765	$	79,523	$	—	$	236,288
Year ended December 31, 2011	$	76,071	$	80,694	$	—	$	156,765
Year ended December 31, 2010	$	47,799	$	28,272	$	—	$	76,071

	Balance at Beginning of Period		Additions		Write-off/ Adjustments		Balance at End of Period
Allowance for Doubtful Accounts:
Year ended December 31, 2012	$	245	$	236	$	—	$	481
Year ended December 31, 2011	$	—	$	245	$	—	$	245
Year ended December 31, 2010	$	—	$	—	$	—	$	—

Schedules not listed above are omitted because they are not required, they are not applicable or the information is already included in the consolidated financial statements or notes thereto.

(3) Exhibits. Reference is made to the exhibits listed in the index to exhibits in Item 15(b) below.

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(b) Exhibits.

The following table lists the exhibits filed as part of this report on Form 10-K. In some cases, these exhibits are incorporated into this report by reference to exhibits to our other filings with the Securities and Exchange Commission. Where an exhibit is incorporated by reference, we have noted the type of form filed with the Securities and Exchange Commission, the file number of that form, the date of the filing, and the number of the exhibit referenced in that filing.

Exhibit		Previously Filed				Filed
No.	Description	Form	File No.	Filing Date	Exhibit	Herewith
3.01	Restated Certificate of Incorporation	10-Q	001-34885	November 10, 2010	3.01
3.02	Restated Bylaws	10-Q	001-34885	November 10, 2010	3.02
4.01	Form of Stock Certificate	S-1	333-166135	July 6, 2010	4.01
4.02	Amended and Restated Investors’ Rights Agreement, dated June 21, 2010, among registrant and its security holders listed therein	S-1	333-166135	June 23, 2010	4.02
4.03	First Amendment to Amended and Restated Investors' Rights Agreement, dated February 23, 2012, among registrant and registrant's security holders listed therein	S-3	333-180005	March 9, 2012	4.06
4.04	Amendment No. 2 to Amended and Restated Investors' Rights Agreement, dated December 24, 2012, among registrant and registrant's security holders listed therein					X
4.05	Warrant to Purchase Stock, dated December 23, 2011, issued to ATEL Ventures, Inc.	10-K	001-34885	February 28, 2012	4.07
4.06	Side Letter, dated June 21, 2010, between registrant and Total Gas & Power USA, SAS	S-1	333-166135	June 23, 2010	4.19
4.07	Securities Purchase Agreement, dated February 22, 2012, among registrant and certain investors listed therein	10-Q	001-34885	May 9, 2012	4.01
4.08	Agreement, dated February 23, 2012, among registrant, Maxwell (Mauritius) Pte Ltd, Naxyris SA, Biolding Investment SA and Sualk Capital Ltd.	10-Q	001-34885	May 9, 2012	4.02
4.09	Securities Purchase Agreement, dated February 24, 2012, among registrant and certain investment funds affiliated with Fidelity Investments Institutional Services Company, Inc. listed therein (each a "Fidelity Purchaser")	S-3	333-180005	March 9, 2012	4.02
4.10	Form of Unsecured Senior Convertible Promissory Note issued by registrant to the Fidelity Purchasers in the amounts set forth next to each Fidelity Purchaser's name on Schedule I of Exhibit 4.09 hereof	S-3	333-180005	March 9, 2012	4.03
4.11	Registration Rights Agreement, dated February 27, 2012, among registrant and the Fidelity Purchasers	S-3	333-180005	March 9, 2012	4.04
4.12a	Form of Common Stock Purchase Agreement among registrant and certain investors	10-Q	001-34885	August 8, 2012	4.01
4.13	Securities Purchase Agreement, dated July 30, 2012, between registrant and Total Gas & Power USA, SAS	10-Q	001-34885	November 9, 2012	4.01
4.14b	1.5% Senior Unsecured Convertible Notes, dated July 30, 2012, September 14, 2012 and December 24, 2012, respectively, issued by registrant to Total Gas & Power USA, SAS	10-Q	001-34885	November 9, 2012	4.02	b
4.15	Registration Rights Agreement, dated July 30, 2012, between registrant and Total Gas & Power USA, SAS	10-Q	001-34885	November 9, 2012	4.03

123

Exhibit		Previously Filed				Filed
No.	Description	Form	File No.	Filing Date	Exhibit	Herewith
4.16d	Securities Purchase Agreement, dated December 24, 2012, between registrant and certain investors listed therein					X
4.17d	Follow-On Investment Agreement, dated December 24, 2012, between registrant and Biolding Investment SA					X
10.01	Form of Indemnity Agreement between registrant and its directors and officers	S-1	333-166135	June 23, 2010	10.01
10.02c	Uncommitted Facility Letter, dated November 25, 2008, between BNP Paribas and Amyris Fuels, Inc.	S-1	333-166135	August 31, 2010	10.02
10.03c	Amendment to Uncommitted Facility Letter, dated October 7, 2009, among registrant, BNP Paribas and Amyris Fuels, LLC	S-1	333-166135	August 31, 2010	10.03
10.04	Amendment No. 2 to Uncommitted Facility Letter, dated March 8, 2010, among registrant, BNP Paribas and Amyris Fuels, LLC	S-1	333-166135	August 31, 2010	10.04
10.05	Amendment No. 3 to Uncommitted Credit Facility Letter, dated February 7, 2011, among registrant, BNP Paribas and Amyris Fuels, LLC	10-Q	001-34885	August 11, 2011	10.03
10.06	Amendment No. 4 to Uncommitted Credit Facility Letter, dated May 24, 2011, among registrant, BNP Paribas and Amyris Fuels, LLC	10-Q	001-34885	August 11, 2011	10.04
10.07	Amendment to Uncommitted Facility Letter, dated April 17, 2012, among registrant, BNP Paribas and Amyris Fuels, LLC	10-Q	001-34885	August 8, 2012	10.05
10.08	Assistance Agreement, dated December 30, 2009, as modified by Assistance Agreement dated March 26, 2010, between registrant and the U.S. Department of Energy, together with schedules and supplements thereto	S-1	333-166135	April 16, 2010	10.09
10.09	Modification No. 2, dated April 19, 2010, to Assistance Agreement between registrant and the U.S. Department of Energy	S-1	333-166135	May 25, 2010	10.13
10.10	Modification Nos. 3-8 to Assistance Agreement between registrant and the U.S. Department of Energy					X
10.11c	Technology Investment Agreement, dated June 11, 2012, between registrant and The Defense Advanced Research Projects Agency (DARPA)	10-Q	001-34885	August 8, 2012	10.08
10.12ce	Agreement for Credit Opening, dated November 16, 2011, between Amyris Brasil Ltda. and Banco Nacional de Desenvolvimento Econȏmico e Social - BNDES	10-K	001-34885	February 28, 2012	10.11
10.13c	Corporate Guarantee, dated November 28, 2011, issued by registrant to Banco Nacional de Desenvolvimento Econȏmico e Social - BNDES	10-K	001-34885	February 28, 2012	10.12
10.14e	Bank Credit Agreement, dated December 21, 2011, between Amyris Brasil Ltda. and Banco Pine S.A.	10-K	001-34885	February 28, 2012	10.13
10.15e	Addendum to the Banking Credit Form, dated February 17, 2012, between Amyris Brasil Ltda. and Banco Pine S.A.	10-Q	001-34885	May 9, 2012	10.02
10.16e	Addendum to the Banking Credit Form, dated May 17, 2012, between Amyris Brasil Ltda. and Banco Pine S.A.	10-Q	001-34885	August 8, 2012	10.02
10.17e	Note of Bank Credit, dated June 21, 2012, between Amyris Brasil Ltda. and Banco Pine S.A.	10-Q	001-34885	August 8, 2012	10.03
10.18ce	Global Derivatives Contract (swap agreement), dated June 15, 2012, between Amyris Brasil Ltda. and Banco Pine S.A.	10-Q	001-34885	August 8, 2012	10.04

124

Exhibit		Previously Filed				Filed
No.	Description	Form	File No.	Filing Date	Exhibit	Herewith
10.19ce	Note of Bank Credit, dated July 13, 2012, between Amyris Brasil Ltda. and Nossa Caixa Desenvolvimento	10-Q	001-34885	November 9, 2012	10.01
10.20ce	Note of Bank Credit, dated July 13, 2012, between Amyris Brasil Ltda. and Banco Pine S.A.	10-Q	001-34885	November 9, 2012	10.02
10.21e	Fiduciary Conveyance of Movable Goods Agreement, dated July 13, 2012, among Amyris Brasil Ltda., Nossa Caixa Desenvolvimento and Banco Pine S.A.	10-Q	001-34885	November 9, 2012	10.03
10.22	Corporate Guarantee, dated July 13, 2012, issued by registrant to Nossa Caixa Desenvolvimento	10-Q	001-34885	November 9, 2012	10.04
10.23	Corporate Guarantee, dated July 13, 2012, issued by registrant to Banco Pine S.A.	10-Q	001-34885	November 9, 2012	10.05
10.24c	Revolving Credit Facility letter agreement, dated December 23, 2010, between registrant and Bank of the West	10-K/A	001-34885	May 2, 2012	10.14
10.25	Letter agreement, dated May 3, 2012, amending Revolving Credit Facility dated December 23, 2010, between registrant and Bank of the West	10-Q	001-34885	August 8, 2012	10.06
10.26	Letter agreement, dated June 20, 2012, terminating Revolving Credit Facility dated December 23, 2010, as amended, between registrant and Bank of the West	10-Q	001-34885	August 8, 2012	10.07
10.27c	Joint Venture Agreement dated April 14, 2010 among registrant, Amyris Brasil S.A. and Usina São Martinho S.A.	S-1	333-166135	August 31, 2010	10.14
10.28c	Shareholders’ Agreement dated April 14, 2010 among registrant, Amyris Brasil S.A. and Usina São Martinho S.A.	S-1	333-166135	May 25, 2010	10.17
10.29c	Technology License, Development, Research and Collaboration Agreement, dated June 21, 2010, between registrant and Total Gas & Power USA Biotech, Inc.	S-1	333-16135	September 20, 2010	10.46
10.30	Letter agreement, dated January 11, 2011, between registrant and Total Gas & Power USA Biotech, Inc.	10-Q	001-34885	May 11, 2011	10.01
10.31c	First Amendment to Technology License, Development, Research and Collaboration Agreement, dated November 23, 2011, between Amyris and Total Gas & Power USA SAS	10-K/A	001-34885	May 2, 2012	10.19
10.32c	Master Framework Agreement, dated July 30, 2012, between registrant and Total Gas & Power USA, SAS	10-Q	001-34885	November 9, 2012	10.06
10.33c	Second Amendment to the Technology License, Development, Research and Collaboration Agreement, dated July 30, 2012, between registrant and Total Gas & Power USA, SAS	10-Q	001-34885	November 9, 2012	10.07
10.34c	Joint Venture Implementation Agreement dated June 3, 2011 among Amyris, Inc., Amyris Brasil S.A., Cosan Combustíveis e Lubrificantes S.A. and Cosan S.A. Indústria e Comércio	10-Q	001-34885	August 11, 2011	10.01
10.35c	Shareholders' Agreement, dated June 3, 2011, among Amyris Brasil S.A., Cosan Combustíveis e Lubrificantes S.A. and Novvi S.A.	10-Q	001-34885	August 11, 2011	10.02
10.36ce	Agreement for the Supply of Sugarcane Juice and Other Utilities, dated March 18, 2011, between Amyris Brasil Ltda. and Paraíso Bioenergia S.A.	10-Q	001-34885	May 9, 2012	10.06
10.37de	Lease Agreement, dated March 18, 2011, between Amyris Brasil Ltda. and Paraíso Bioenergia S.A.					X

125

Exhibit		Previously Filed				Filed
No.	Description	Form	File No.	Filing Date	Exhibit	Herewith
10.38de	Addendum to Lease Agreement, dated April 28, 2011, between Amyris Brasil Ltda. and Paraíso Bioenergia S.A.					X
10.39	Lease, dated August 22, 2007, between registrant and ES East Associates, LLC	S-1	333-166135	April 16, 2010	10.17
10.40	First Amendment, dated March 10, 2008, to Lease between registrant and ES East Associates, LLC	S-1	333-166135	April 16, 2010	10.18
10.41	Second Amendment, dated April 25, 2008, to Lease between registrant and ES East Associates, LLC	S-1	333-166135	April 16, 2010	10.19
10.42	Third Amendment, dated July 31, 2008, to Lease between registrant and ES East Associates, LLC	S-1	333-166135	April 16, 2010	10.20
10.43	Fourth Amendment, dated November 14, 2009, to Lease between registrant and ES East Associates, LLC	S-1	333-166135	April 16, 2010	10.21
10.44	Fifth Amendment, dated October 15, 2010, to Lease between registrant and ES East, LLC	10-K	001-34885	March 14, 2011	10.17
10.45	Lease dated April 25, 2008 between registrant and EmeryStation Triangle, LLC	S-1	333-166135	April 16, 2010	10.22
10.46	Letter, dated April 25, 2008, amending Lease between registrant and EmeryStation Triangle, LLC	S-1	333-166135	April 16, 2010	10.23
10.47	Second Amendment, dated February 5, 2010, to Lease between registrant and EmeryStation Triangle, LLC	S-1	333-166135	April 16, 2010	10.24
10.48	Pilot Plant Expansion Right Letter dated December 22, 2008 between registrant and EmeryStation Triangle, LLC	S-1	333-166135	April 16, 2010	10.25
10.49	Lease Agreement, dated August 10, 2011, between Amyris Brasil Ltda. and Techno Park Empreendimentos e Administração Imobiliária Ltda.	10-K	001-34885	February 28, 2012	10.32
10.50	Private Instrument of Non-Residential Real Estate Lease Agreement, dated March 31, 2008, as amended, between Lucio Tomasiello and Amyris Brasil S.A.	S-1	333-166135	April 16, 2010	10.26
10.51de	Third Amendment to the Private Instrument of Non Residential Real Estate Lease Agreement, dated October 1, 2012, between Lucio Tomasiello and Amyris Brasil Ltda.					X
10.52f	Offer Letter dated September 27, 2006 between registrant and John Melo	S-1	333-16135	April 16, 2010	10.27
10.53f	Amendment, dated December 18, 2008, between registrant and John Melo	S-1	333-16135	April 16, 2010	10.28
10.54f	Offer letter, dated March 23, 2012, between registrant and Steven R. Mills	10-Q	001-34885	May 9, 2012	10.05
10.55f	Offer letter, dated January 17, 2008, between registrant and Jeryl Hilleman	S-1	333-16135	April 16, 2010	10.31
10.56f	Amendment, dated December 18, 2008, between registrant and Jeryl Hilleman	S-1	333-16135	April 16, 2010	10.32
10.57f	Letter Agreement dated August 2, 2011 between Amyris, Inc. and Jeryl Hilleman	10-Q	001-34885	November 9, 2011	10.01
10.58f	Letter agreement extending exercise period for outstanding stock options, dated May 31, 2012, between registrant and Jeryl Hilleman	10-Q	001-34885	August 8, 2012	10.14
10.59f	Offer letter, dated November 9, 2009, between registrant and Peter Boynton	10-Q	001-34885	August 11, 2011	10.05
10.60f	Offer letter, dated February 11, 2011, between registrant and Paulo Diniz	10-Q	001-34885	August 8, 2012	10.10
10.61f	Letter Confirming Amended and Restated Terms of Employment, dated April 18, 2011, between Amyris, Inc. and Mario Portela	10-Q	001-34885	August 11, 2011	10.06
10.62f	Separation agreement, dated May 2, 2012, between registrant and Mario Portela	10-Q	001-34885	August 8, 2012	10.13

126

Exhibit		Previously Filed				Filed
No.	Description	Form	File No.	Filing Date	Exhibit	Herewith
10.63f	Separation agreement, dated June 18, 2012, between registrant and Neil Renninger	10-Q	001-34885	August 8, 2012	10.15
10.64f	Offer letter, dated December 21, 2010, between registrant and James Richardson	10-Q	001-34885	August 8, 2012	10.09
10.65f	Separation agreement, dated April 5, 2012, between registrant and James Richardson	10-Q	001-34885	August 8, 2012	10.11
10.66f	Offer Letter, dated January 24, 2005, between registrant and Tamara Tompkins	S-1	333-16135	April 16, 2010	10.35
10.67f	Amendment, dated January 15, 2009, between registrant and Tamara Tompkins	S-1	333-16135	April 16, 2010	10.36
10.68f	Separation agreement, dated May 1, 2012, between registrant and Tamara Tompkins	10-Q	001-34885	August 8, 2012	10.12
10.69f	2005 Stock Option/Stock Issuance Plan	10-Q	001-34885	November 9, 2011	10.02
10.70f	Form of Notice of Grant of Stock Option under registrant’s 2005 Stock Option/Stock Issuance Plan	S-1	333-16135	April 16, 2010	10.38
10.71f	Form of Notice of Grant of Stock Option (non-Exempt) under registrant’s 2005 Stock Option/Stock Issuance Plan	S-1	333-16135	April 16, 2010	10.39
10.72f	Form of Notice of Grant of Stock Option (non-US) under registrant’s 2005 Stock Option/Stock Issuance Plan	S-1	333-16135	April 16, 2010	10.40
10.73f	Form of Stock Option Agreement under registrant’s 2005 Stock Option/Stock Issuance Plan	S-1	333-16135	April 16, 2010	10.41
10.74f	Form of Stock Option Agreement (non-US) under registrant’s 2005 Stock Option/Stock Issuance Plan	S-1	333-16135	April 16, 2010	10.42
10.75f	Form of Stock Purchase Agreement under registrant’s 2005 Stock Option/Stock Issuance Plan	S-1	333-16135	April 16, 2010	10.43
10.76f	Form of Stock Purchase Agreement (non-US) under registrant’s 2005 Stock Option/Stock Issuance Plan	S-1	333-16135	April 16, 2010	10.44
10.77f	2010 Equity Incentive Plan and forms of award agreements thereunder	S-1	333-16135	June 23, 2010	10.46
10.78f	2010 Employee Stock Purchase Plan and forms of award agreements thereunder	S-1	333-16135	September 20, 2010	10.45
10.79fg	Compensation arrangements between registrant and its non-employee directors					g
10.80fh	Compensation arrangements between registrant and its executive officers					h
21.01	List of subsidiaries					X
23.01	Consent of PricewaterhouseCoopers LLP, independent registered public accounting firm					X
24.01	Power of Attorney (see signature page to this Form 10-K)					X
31.01	Certification of Chief Executive Officer pursuant to Securities Exchange Act Rules 13a-14(c) and 15d-14(a), as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002					X
31.02	Certification of Chief Financial Officer pursuant to Securities Exchange Act Rules 13a-14(c) and 15d-14(a), as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002					X
32.01i	Certification of Chief Executive Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002					X
32.02i	Certification of Chief Financial Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002					X

127

Exhibit		Previously Filed				Filed
No.	Description	Form	File No.	Filing Date	Exhibit	Herewith
101j	The following materials from registrant's Annual Report on Form 10-K for the fiscal year ended December 31, 2012, formatted in XBRL (Extensible Business Reporting Language): (i) the Consolidated Statements of Operations; (ii) the Consolidated Balance Sheets; (iii) the Consolidated Statements of Comprehensive Income; (iv) the Consolidated Statements of Convertible Preferred Stock, Redeemable Noncontrolling Interest and Equity (Deficit); (v) the Consolidated Statements of Cash Flows; and (vi) Notes to Consolidated Financial Statements.					X

a	Substantially identical Common Stock Purchase Agreements, each dated May 18, 2012, were entered into with five separate investors. Registrant has filed the form of such Common Stock Purchase Agreements, which is substantially identical in all material respects to all of such Common Stock Purchase Agreements, except as to the parties thereto and the number of shares.
b	Registrant issued substantially identical 1.5% Senior Unsecured Convertible Notes (the "Notes") to Total Gas & Power USA, SAS on separate dates. Registrant has filed the first of the Notes (number R-1), and has included, with such exhibit, a schedule (updated Schedule A to Exhibit 4.02) identifying each of the Notes and setting forth the material details in which the other Note(s) differ from the filed Note (i.e., the dates of issuance and the amounts of the Notes).
c	Portions of this exhibit, which have been granted confidential treatment by the Securities and Exchange Commission, have been omitted.
d	Portions of this exhibit have been omitted pending a determination by the Securities and Exchange Commission as to whether these portions should be granted confidential treatment.
e	Translation to English from Portuguese in accordance with Rule 12b-12(d) of the regulations promulgated by the Securities and Exchange Commission under the Securities Exchange Act of 1934, as amended (the "Exchange Act").
f	Indicates management contract or compensatory plan or arrangement.
g	Description contained under the heading "Director Compensation" in registrant's definitive proxy materials filed with the Securities and Exchange Commission on April 12, 2012 is incorporated herein by reference.
h	Descriptions contained under the heading "Executive Compensation" in registrant's definitive proxy materials filed with the Securities and Exchange Commission on April 12, 2012.
i	This certification shall not be deemed “filed” for purposes of Section 18 of the Exchange Act or otherwise subject to the liability of that Section, nor shall it be deemed incorporated by reference into any filing under the Securities Act or the Exchange Act.
j	Pursuant to applicable securities laws and regulations, registrant is deemed to have complied with the reporting obligation relating to the submission of interactive data files in such exhibits and is not subject to liability under any anti-fraud provisions of the federal securities laws as long as registrant has made a good faith attempt to comply with the submission requirements and promptly amends the interactive data files after becoming aware that the interactive data files fails to comply with the submission requirements. These interactive data files are deemed not filed or part of a registration statement or prospectus for purposes of sections 11 or 12 of the Securities Act, are deemed not filed for purposes of section 18 of the Exchange Act and otherwise are not subject to liability under these sections.

(c) Financial statements and schedules.

Reference is made to Item 15(a) above.

128

SIGNATURES

Pursuant to the requirements of Section 13 or 15(d) of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned, thereunto duly authorized.

Dated: March 28, 2013	Amyris, Inc.
	/s/    JOHN G. MELO
	John G. Melo
	President and Chief Executive Officer

POWER OF ATTORNEY

KNOW ALL MEN BY THESE PRESENTS, that each person whose signature appears below constitutes and appoints John Melo and Steven Mills as his or her true and lawful attorneys-in-fact and agents, with full power of substitution and resubstitution, for him or her and in his or her name, place and stead, in any and all capacities, to sign any and all amendments to this Report on Form 10-K, and to file the same, with all exhibits thereto, and other documents in connection therewith, with the Securities and Exchange Commission, granting unto said attorneys-in-fact and agents full power and authority to do and perform each and every act and thing requisite and necessary to be done in connection therewith, as fully to all intents and purposes as he might or could do in person, hereby ratifying and confirming all that said attorneys-in-fact and agents, or their substitute or substitutes, may lawfully do or cause to be done by virtue hereof.

Pursuant to the requirements of the Securities Exchange Act of 1934, this report has been signed below by the following persons on behalf of the Registrant and in the capacities and on the dates indicated.

129

Signature	Title	Date
/s/ JOHN MELO John Melo	Director, President and Chief Executive Officer (Principal Executive Officer)	March 28, 2013
/s/    STEVEN MILLS Steven Mills	Chief Financial Officer (Principal Accounting and Financial Officer)	March 28, 2013
/s/   RALPH ALEXANDER Ralph Alexander	Director	March 28, 2013
/s/   PHILIPPE BOISSEAU  Philippe Boisseau	Director	March 28, 2013
/S/    NAM-HAI CHUA Nam-Hai Chua	Director	March 28, 2013
/S/    JOHN DOERR John Doerr	Director	March 28, 2013
/s/    GEOFFREY DUYK Geoffrey Duyk	Director	March 28, 2013
/s/   ARTHUR LEVINSON Arthur Levinson	Director	March 28, 2013
/s/    PATRICK PICHETTE Patrick Pichette	Director	March 28, 2013
/s/    CAROLE PIWNICA Carole Piwnica	Director	March 28, 2013
/s/    FERNANDO REINACH Fernando Reinach	Director	March 28, 2013
/s/   HH SHEIKH ABDULLAH BIN KHALIFA AL THANI HH Sheikh Abdullah bin Khalifa Al Thani	Director	March 28, 2013

130

EXHIBIT INDEX

Exhibit		Previously Filed				Filed
No.	Description	Form	File No.	Filing Date	Exhibit	Herewith
3.01	Restated Certificate of Incorporation	10-Q	001-34885	November 10, 2010	3.01
3.02	Restated Bylaws	10-Q	001-34885	November 10, 2010	3.02
4.01	Form of Stock Certificate	S-1	333-166135	July 6, 2010	4.01
4.02	Amended and Restated Investors’ Rights Agreement, dated June 21, 2010, among registrant and its security holders listed therein	S-1	333-166135	June 23, 2010	4.02
4.03	First Amendment to Amended and Restated Investors' Rights Agreement, dated February 23, 2012, among registrant and registrant's security holders listed therein	S-3	333-180005	March 9, 2012	4.06
4.04	Amendment No. 2 to Amended and Restated Investors' Rights Agreement, dated December 24, 2012, among registrant and registrant's security holders listed therein					X
4.05	Warrant to Purchase Stock, dated December 23, 2011, issued to ATEL Ventures, Inc.	10-K	001-34885	February 28, 2012	4.07
4.06	Side Letter, dated June 21, 2010, between registrant and Total Gas & Power USA, SAS	S-1	333-166135	June 23, 2010	4.19
4.07	Securities Purchase Agreement, dated February 22, 2012, among registrant and certain investors listed therein	10-Q	001-34885	May 9, 2012	4.01
4.08	Agreement, dated February 23, 2012, among registrant, Maxwell (Mauritius) Pte Ltd, Naxyris SA, Biolding Investment SA and Sualk Capital Ltd.	10-Q	001-34885	May 9, 2012	4.02
4.09	Securities Purchase Agreement, dated February 24, 2012, among registrant and certain investment funds affiliated with Fidelity Investments Institutional Services Company, Inc. listed therein (each a "Fidelity Purchaser")	S-3	333-180005	March 9, 2012	4.02
4.10	Form of Unsecured Senior Convertible Promissory Note issued by registrant to the Fidelity Purchasers in the amounts set forth next to each Fidelity Purchaser's name on Schedule I of Exhibit 4.09 hereof	S-3	333-180005	March 9, 2012	4.03
4.11	Registration Rights Agreement, dated February 27, 2012, among registrant and the Fidelity Purchasers	S-3	333-180005	March 9, 2012	4.04
4.12a	Form of Common Stock Purchase Agreement among registrant and certain investors	10-Q	001-34885	August 8, 2012	4.01
4.13	Securities Purchase Agreement, dated July 30, 2012, between registrant and Total Gas & Power USA, SAS	10-Q	001-34885	November 9, 2012	4.01
4.14b	1.5% Senior Unsecured Convertible Notes, dated July 30, 2012, September 14, 2012 and December 24, 2012, respectively, issued by registrant to Total Gas & Power USA, SAS	10-Q	001-34885	November 9, 2012	4.02	b
4.15	Registration Rights Agreement, dated July 30, 2012, between registrant and Total Gas & Power USA, SAS	10-Q	001-34885	November 9, 2012	4.03

131

Exhibit		Previously Filed				Filed
No.	Description	Form	File No.	Filing Date	Exhibit	Herewith
4.16d	Securities Purchase Agreement, dated December 24, 2012, between registrant and certain investors listed therein					X
4.17d	Follow-On Investment Agreement, dated December 24, 2012, between registrant and Biolding Investment SA					X
10.01	Form of Indemnity Agreement between registrant and its directors and officers	S-1	333-166135	June 23, 2010	10.01
10.02c	Uncommitted Facility Letter, dated November 25, 2008, between BNP Paribas and Amyris Fuels, Inc.	S-1	333-166135	August 31, 2010	10.02
10.03c	Amendment to Uncommitted Facility Letter, dated October 7, 2009, among registrant, BNP Paribas and Amyris Fuels, LLC	S-1	333-166135	August 31, 2010	10.03
10.04	Amendment No. 2 to Uncommitted Facility Letter, dated March 8, 2010, among registrant, BNP Paribas and Amyris Fuels, LLC	S-1	333-166135	August 31, 2010	10.04
10.05	Amendment No. 3 to Uncommitted Credit Facility Letter, dated February 7, 2011, among registrant, BNP Paribas and Amyris Fuels, LLC	10-Q	001-34885	August 11, 2011	10.03
10.06	Amendment No. 4 to Uncommitted Credit Facility Letter, dated May 24, 2011, among registrant, BNP Paribas and Amyris Fuels, LLC	10-Q	001-34885	August 11, 2011	10.04
10.07	Amendment to Uncommitted Facility Letter, dated April 17, 2012, among registrant, BNP Paribas and Amyris Fuels, LLC	10-Q	001-34885	August 8, 2012	10.05
10.08	Assistance Agreement, dated December 30, 2009, as modified by Assistance Agreement dated March 26, 2010, between registrant and the U.S. Department of Energy, together with schedules and supplements thereto	S-1	333-166135	April 16, 2010	10.09
10.09	Modification No. 2, dated April 19, 2010, to Assistance Agreement between registrant and the U.S. Department of Energy	S-1	333-166135	May 25, 2010	10.13
10.10	Modification Nos. 3-8 to Assistance Agreement between registrant and the U.S. Department of Energy					X
10.11c	Technology Investment Agreement, dated June 11, 2012, between registrant and The Defense Advanced Research Projects Agency (DARPA)	10-Q	001-34885	August 8, 2012	10.08
10.12ce	Agreement for Credit Opening, dated November 16, 2011, between Amyris Brasil Ltda. and Banco Nacional de Desenvolvimento Econȏmico e Social - BNDES	10-K	001-34885	February 28, 2012	10.11
10.13c	Corporate Guarantee, dated November 28, 2011, issued by registrant to Banco Nacional de Desenvolvimento Econȏmico e Social - BNDES	10-K	001-34885	February 28, 2012	10.12
10.14e	Bank Credit Agreement, dated December 21, 2011, between Amyris Brasil Ltda. and Banco Pine S.A.	10-K	001-34885	February 28, 2012	10.13
10.15e	Addendum to the Banking Credit Form, dated February 17, 2012, between Amyris Brasil Ltda. and Banco Pine S.A.	10-Q	001-34885	May 9, 2012	10.02
10.16e	Addendum to the Banking Credit Form, dated May 17, 2012, between Amyris Brasil Ltda. and Banco Pine S.A.	10-Q	001-34885	August 8, 2012	10.02
10.17e	Note of Bank Credit, dated June 21, 2012, between Amyris Brasil Ltda. and Banco Pine S.A.	10-Q	001-34885	August 8, 2012	10.03
10.18ce	Global Derivatives Contract (swap agreement), dated June 15, 2012, between Amyris Brasil Ltda. and Banco Pine S.A.	10-Q	001-34885	August 8, 2012	10.04

132

Exhibit		Previously Filed				Filed
No.	Description	Form	File No.	Filing Date	Exhibit	Herewith
10.19ce	Note of Bank Credit, dated July 13, 2012, between Amyris Brasil Ltda. and Nossa Caixa Desenvolvimento	10-Q	001-34885	November 9, 2012	10.01
10.20ce	Note of Bank Credit, dated July 13, 2012, between Amyris Brasil Ltda. and Banco Pine S.A.	10-Q	001-34885	November 9, 2012	10.02
10.21e	Fiduciary Conveyance of Movable Goods Agreement, dated July 13, 2012, among Amyris Brasil Ltda., Nossa Caixa Desenvolvimento and Banco Pine S.A.	10-Q	001-34885	November 9, 2012	10.03
10.22	Corporate Guarantee, dated July 13, 2012, issued by registrant to Nossa Caixa Desenvolvimento	10-Q	001-34885	November 9, 2012	10.04
10.23	Corporate Guarantee, dated July 13, 2012, issued by registrant to Banco Pine S.A.	10-Q	001-34885	November 9, 2012	10.05
10.24c	Revolving Credit Facility letter agreement, dated December 23, 2010, between registrant and Bank of the West	10-K/A	001-34885	May 2, 2012	10.14
10.25	Letter agreement, dated May 3, 2012, amending Revolving Credit Facility dated December 23, 2010, between registrant and Bank of the West	10-Q	001-34885	August 8, 2012	10.06
10.26	Letter agreement, dated June 20, 2012, terminating Revolving Credit Facility dated December 23, 2010, as amended, between registrant and Bank of the West	10-Q	001-34885	August 8, 2012	10.07
10.27c	Joint Venture Agreement dated April 14, 2010 among registrant, Amyris Brasil S.A. and Usina São Martinho S.A.	S-1	333-166135	August 31, 2010	10.14
10.28c	Shareholders’ Agreement dated April 14, 2010 among registrant, Amyris Brasil S.A. and Usina São Martinho S.A.	S-1	333-166135	May 25, 2010	10.17
10.29c	Technology License, Development, Research and Collaboration Agreement, dated June 21, 2010, between registrant and Total Gas & Power USA Biotech, Inc.	S-1	333-16135	September 20, 2010	10.46
10.30	Letter agreement, dated January 11, 2011, between registrant and Total Gas & Power USA Biotech, Inc.	10-Q	001-34885	May 11, 2011	10.01
10.31c	First Amendment to Technology License, Development, Research and Collaboration Agreement, dated November 23, 2011, between Amyris and Total Gas & Power USA SAS	10-K/A	001-34885	May 2, 2012	10.19
10.32c	Master Framework Agreement, dated July 30, 2012, between registrant and Total Gas & Power USA, SAS	10-Q	001-34885	November 9, 2012	10.06
10.33c	Second Amendment to the Technology License, Development, Research and Collaboration Agreement, dated July 30, 2012, between registrant and Total Gas & Power USA, SAS	10-Q	001-34885	November 9, 2012	10.07
10.34c	Joint Venture Implementation Agreement dated June 3, 2011 among Amyris, Inc., Amyris Brasil S.A., Cosan Combustíveis e Lubrificantes S.A. and Cosan S.A. Indústria e Comércio	10-Q	001-34885	August 11, 2011	10.01
10.35c	Shareholders' Agreement, dated June 3, 2011, among Amyris Brasil S.A., Cosan Combustíveis e Lubrificantes S.A. and Novvi S.A.	10-Q	001-34885	August 11, 2011	10.02
10.36ce	Agreement for the Supply of Sugarcane Juice and Other Utilities, dated March 18, 2011, between Amyris Brasil Ltda. and Paraíso Bioenergia S.A.	10-Q	001-34885	May 9, 2012	10.06
10.37de	Lease Agreement, dated March 18, 2011, between Amyris Brasil Ltda. and Paraíso Bioenergia S.A.					X

133

Exhibit		Previously Filed				Filed
No.	Description	Form	File No.	Filing Date	Exhibit	Herewith
10.38de	Addendum to Lease Agreement, dated April 28, 2011, between Amyris Brasil Ltda. and Paraíso Bioenergia S.A.					X
10.39	Lease, dated August 22, 2007, between registrant and ES East Associates, LLC	S-1	333-166135	April 16, 2010	10.17
10.40	First Amendment, dated March 10, 2008, to Lease between registrant and ES East Associates, LLC	S-1	333-166135	April 16, 2010	10.18
10.41	Second Amendment, dated April 25, 2008, to Lease between registrant and ES East Associates, LLC	S-1	333-166135	April 16, 2010	10.19
10.42	Third Amendment, dated July 31, 2008, to Lease between registrant and ES East Associates, LLC	S-1	333-166135	April 16, 2010	10.20
10.43	Fourth Amendment, dated November 14, 2009, to Lease between registrant and ES East Associates, LLC	S-1	333-166135	April 16, 2010	10.21
10.44	Fifth Amendment, dated October 15, 2010, to Lease between registrant and ES East, LLC	10-K	001-34885	March 14, 2011	10.17
10.45	Lease dated April 25, 2008 between registrant and EmeryStation Triangle, LLC	S-1	333-166135	April 16, 2010	10.22
10.46	Letter, dated April 25, 2008, amending Lease between registrant and EmeryStation Triangle, LLC	S-1	333-166135	April 16, 2010	10.23
10.47	Second Amendment, dated February 5, 2010, to Lease between registrant and EmeryStation Triangle, LLC	S-1	333-166135	April 16, 2010	10.24
10.48	Pilot Plant Expansion Right Letter dated December 22, 2008 between registrant and EmeryStation Triangle, LLC	S-1	333-166135	April 16, 2010	10.25
10.49	Lease Agreement, dated August 10, 2011, between Amyris Brasil Ltda. and Techno Park Empreendimentos e Administração Imobiliária Ltda.	10-K	001-34885	February 28, 2012	10.32
10.50	Private Instrument of Non-Residential Real Estate Lease Agreement, dated March 31, 2008, as amended, between Lucio Tomasiello and Amyris Brasil S.A.	S-1	333-166135	April 16, 2010	10.26
10.51de	Third Amendment to the Private Instrument of Non Residential Real Estate Lease Agreement, dated October 1, 2012, between Lucio Tomasiello and Amyris Brasil Ltda.					X
10.52f	Offer Letter dated September 27, 2006 between registrant and John Melo	S-1	333-16135	April 16, 2010	10.27
10.53f	Amendment, dated December 18, 2008, between registrant and John Melo	S-1	333-16135	April 16, 2010	10.28
10.54f	Offer letter, dated March 23, 2012, between registrant and Steven R. Mills	10-Q	001-34885	May 9, 2012	10.05
10.55f	Offer letter, dated January 17, 2008, between registrant and Jeryl Hilleman	S-1	333-16135	April 16, 2010	10.31
10.56f	Amendment, dated December 18, 2008, between registrant and Jeryl Hilleman	S-1	333-16135	April 16, 2010	10.32
10.57f	Letter Agreement dated August 2, 2011 between Amyris, Inc. and Jeryl Hilleman	10-Q	001-34885	November 9, 2011	10.01
10.58f	Letter agreement extending exercise period for outstanding stock options, dated May 31, 2012, between registrant and Jeryl Hilleman	10-Q	001-34885	August 8, 2012	10.14
10.59f	Offer letter, dated November 9, 2009, between registrant and Peter Boynton	10-Q	001-34885	August 11, 2011	10.05
10.60f	Offer letter, dated February 11, 2011, between registrant and Paulo Diniz	10-Q	001-34885	August 8, 2012	10.10
10.61f	Letter Confirming Amended and Restated Terms of Employment, dated April 18, 2011, between Amyris, Inc. and Mario Portela	10-Q	001-34885	August 11, 2011	10.06
10.62f	Separation agreement, dated May 2, 2012, between registrant and Mario Portela	10-Q	001-34885	August 8, 2012	10.13

134

Exhibit		Previously Filed				Filed
No.	Description	Form	File No.	Filing Date	Exhibit	Herewith
10.63f	Separation agreement, dated June 18, 2012, between registrant and Neil Renninger	10-Q	001-34885	August 8, 2012	10.15
10.64f	Offer letter, dated December 21, 2010, between registrant and James Richardson	10-Q	001-34885	August 8, 2012	10.09
10.65f	Separation agreement, dated April 5, 2012, between registrant and James Richardson	10-Q	001-34885	August 8, 2012	10.11
10.66f	Offer Letter, dated January 24, 2005, between registrant and Tamara Tompkins	S-1	333-16135	April 16, 2010	10.35
10.67f	Amendment, dated January 15, 2009, between registrant and Tamara Tompkins	S-1	333-16135	April 16, 2010	10.36
10.68f	Separation agreement, dated May 1, 2012, between registrant and Tamara Tompkins	10-Q	001-34885	August 8, 2012	10.12
10.69f	2005 Stock Option/Stock Issuance Plan	10-Q	001-34885	November 9, 2011	10.02
10.70f	Form of Notice of Grant of Stock Option under registrant’s 2005 Stock Option/Stock Issuance Plan	S-1	333-16135	April 16, 2010	10.38
10.71f	Form of Notice of Grant of Stock Option (non-Exempt) under registrant’s 2005 Stock Option/Stock Issuance Plan	S-1	333-16135	April 16, 2010	10.39
10.72f	Form of Notice of Grant of Stock Option (non-US) under registrant’s 2005 Stock Option/Stock Issuance Plan	S-1	333-16135	April 16, 2010	10.40
10.73f	Form of Stock Option Agreement under registrant’s 2005 Stock Option/Stock Issuance Plan	S-1	333-16135	April 16, 2010	10.41
10.74f	Form of Stock Option Agreement (non-US) under registrant’s 2005 Stock Option/Stock Issuance Plan	S-1	333-16135	April 16, 2010	10.42
10.75f	Form of Stock Purchase Agreement under registrant’s 2005 Stock Option/Stock Issuance Plan	S-1	333-16135	April 16, 2010	10.43
10.76f	Form of Stock Purchase Agreement (non-US) under registrant’s 2005 Stock Option/Stock Issuance Plan	S-1	333-16135	April 16, 2010	10.44
10.77f	2010 Equity Incentive Plan and forms of award agreements thereunder	S-1	333-16135	June 23, 2010	10.46
10.78f	2010 Employee Stock Purchase Plan and forms of award agreements thereunder	S-1	333-16135	September 20, 2010	10.45
10.79fg	Compensation arrangements between registrant and its non-employee directors					g
10.80fh	Compensation arrangements between registrant and its executive officers					h
21.01	List of subsidiaries					X
23.01	Consent of PricewaterhouseCoopers LLP, independent registered public accounting firm					X
24.01	Power of Attorney (see signature page to this Form 10-K)					X
31.01	Certification of Chief Executive Officer pursuant to Securities Exchange Act Rules 13a-14(c) and 15d-14(a), as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002					X
31.02	Certification of Chief Financial Officer pursuant to Securities Exchange Act Rules 13a-14(c) and 15d-14(a), as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002					X
32.01i	Certification of Chief Executive Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002					X
32.02i	Certification of Chief Financial Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002					X

135

Exhibit		Previously Filed				Filed
No.	Description	Form	File No.	Filing Date	Exhibit	Herewith
101j	The following materials from registrant's Annual Report on Form 10-K for the fiscal year ended December 31, 2012, formatted in XBRL (Extensible Business Reporting Language): (i) the Consolidated Statements of Operations; (ii) the Consolidated Balance Sheets; (iii) the Consolidated Statements of Comprehensive Income; (iv) the Consolidated Statements of Convertible Preferred Stock, Redeemable Noncontrolling Interest and Equity (Deficit); (v) the Consolidated Statements of Cash Flows; and (vi) Notes to Consolidated Financial Statements.					X

a	Substantially identical Common Stock Purchase Agreements, each dated May 18, 2012, were entered into with five separate investors. Registrant has filed the form of such Common Stock Purchase Agreements, which is substantially identical in all material respects to all of such Common Stock Purchase Agreements, except as to the parties thereto and the number of shares.
b	Registrant issued substantially identical 1.5% Senior Unsecured Convertible Notes (the "Notes") to Total Gas & Power USA, SAS on separate dates. Registrant has filed the first of the Notes (number R-1), and has included, with such exhibit, a schedule (updated Schedule A to Exhibit 4.02) identifying each of the Notes and setting forth the material details in which the other Note(s) differ from the filed Note (i.e., the dates of issuance and the amounts of the Notes).
c	Portions of this exhibit, which have been granted confidential treatment by the Securities and Exchange Commission, have been omitted.
d	Portions of this exhibit have been omitted pending a determination by the Securities and Exchange Commission as to whether these portions should be granted confidential treatment.
e	Translation to English from Portuguese in accordance with Rule 12b-12(d) of the regulations promulgated by the Securities and Exchange Commission under the Securities Exchange Act of 1934, as amended (the "Exchange Act").
f	Indicates management contract or compensatory plan or arrangement.
g	Description contained under the heading "Director Compensation" in registrant's definitive proxy materials filed with the Securities and Exchange Commission on April 12, 2012 is incorporated herein by reference.
h	Descriptions contained under the heading "Executive Compensation" in registrant's definitive proxy materials filed with the Securities and Exchange Commission on April 12, 2012.
i	This certification shall not be deemed “filed” for purposes of Section 18 of the Exchange Act or otherwise subject to the liability of that Section, nor shall it be deemed incorporated by reference into any filing under the Securities Act or the Exchange Act.
j	Pursuant to applicable securities laws and regulations, registrant is deemed to have complied with the reporting obligation relating to the submission of interactive data files in such exhibits and is not subject to liability under any anti-fraud provisions of the federal securities laws as long as registrant has made a good faith attempt to comply with the submission requirements and promptly amends the interactive data files after becoming aware that the interactive data files fails to comply with the submission requirements. These interactive data files are deemed not filed or part of a registration statement or prospectus for purposes of sections 11 or 12 of the Securities Act, are deemed not filed for purposes of section 18 of the Exchange Act and otherwise are not subject to liability under these sections.

136

EX-4.04

AMYRIS, INC.

AMENDMENT NO. 2 TO AMENDED AND RESTATED INVESTORS' RIGHTS AGREEMENT

This Amendment No. 2 to the Amended and Restated Investors' Rights Agreement (this “Amendment”) is made and entered into as of December 24, 2012, by and among Amyris, Inc., a Delaware corporation (the “Company”), the Investors and the Common Holders.

RECITALS

WHEREAS, the Company, the Investors and the Common Holders are parties to that certain Amended and Restated Investors' Rights Agreement dated June 21, 2010 (the “Rights Agreement”). Capitalized terms used in this Amendment and not otherwise defined herein have the meanings ascribed to them in the Rights Agreement.

WHEREAS, the Company, certain Investors and certain Common Holders are parties to that certain Amendment No. 1 to Amended and Restated Investors' Rights Agreement, dated as of February 23, 2012 (“Amendment No. 1”), pursuant to which the Rights Agreement was amended and certain parties were added.

WHEREAS, the Company, the Investors and the Common Holders desire to make certain additional amendments to the Rights Agreement.

WHEREAS, pursuant to Section 3.7 of the Rights Agreement, the Rights Agreement may be amended with the written consent of the (i) Company, and (ii) the holders of a majority of the Registrable Securities currently outstanding (together, the “Requisite Majority”).

WHEREAS, the undersigned parties constitute the Requisite Majority.

NOW, THEREFORE,the parties hereby agree as follows:

1.AMENDMENT OF SECTION 1.1(c) OF THE RIGHTS AGREEMENT. Section 1.1(c) of the Rights Agreement shall be deleted in its entirety and replaced with the following:

“The term “Holder” means (i) any Investor having purchased more than 5% of the Preferred Stock sold by the Company, (ii) except with respect to Sections 1.2, 1.12, 1.13 and Section 2 hereof, the Common Holders owning or having the right to acquire Registrable Securities or any assignee thereof in accordance with Section 1.13 hereof, (iii) each “Purchaser” as such term is defined in that certain Securities Purchase Agreement dated February 22, 2012 by and among the Company and the purchasers identified therein (each, a “February Purchaser”), and (iv) each “Purchaser” as such term is defined in that certain Securities Purchase Agreement dated December 24, 2012 by and among the Company and purchasers identified therein (each, a “December Purchaser”).”

2.AMENDMENT OF SECTION 1.1(f) OF THE RIGHTS AGREEMENT. Section 1.1(f) of the Rights Agreement shall be deleted in its entirety and replaced with the following:

“The term “Registrable Securities” means: (i) any Common Stock issued or issuable upon conversion of the Preferred Stock of the Company, (ii) other than with respect to Sections 1.2, 1.12, 1.13 and Section 2 hereof, any Common Stock of the Company held by the Common Holders, (iii) the Common Shares, as defined in that certain Stock Transfer Agreement, dated December 24, 2009, by and among the Company, certain holders of the Company's Preferred Stock and certain holders of the Company's Common Stock, (iv) shares of Common Stock issued pursuant to that certain Securities Purchase Agreement dated February 22, 2012 by and among the Company and the February Purchasers, (v) shares of Common Stock issued pursuant to that certain Securities Purchase Agreement dated December 24, 2012 by and among the Company and the December Purchasers, (vi) any Common Stock of the Company issued as (or issuable upon the conversion or exercise of any warrant, right or other security that is issued as) a dividend or other distribution with respect to, or in exchange for, or in replacement of, the securities set forth in subsection (i), (ii), (iii), (iv) or (v) hereof, excluding, however, any Registrable Securities which (A) have previously been registered or which have been sold to the public either pursuant to a registration statement or Rule 144, (B) which have been sold in a private transaction in which the transferor's rights under this Agreement are not assigned, or (C) held by a Holder (together with its affiliates) if, as reflected on the Company's list of stockholders, such Holder (together with its affiliates) holds less than 1% of the Company's outstanding Common Stock (treating all shares of Preferred Stock on an as converted basis)”

3.FULL FORCE AND EFFECT. Except as expressly modified by this Amendment, the terms of the Rights Agreement shall remain in full force and effect.

4.GOVERNING LAW. This Amendment shall be governed by and construed under the internal laws of the State of California as applied to agreements among California residents entered into and to be performed entirely within California, without reference to principles of conflict of laws or choice of laws.

5.INTEGRATION. This Amendment and the Rights Agreement and the documents referred to herein and therein and the exhibits and schedules thereto, constitute the entire agreement and understanding of the parties with respect to the subject matter hereof, and supersede all prior understandings and agreements, whether oral or written, between or among the parties hereto with respect to the specific subject matter hereof.

6.COUNTERPARTS; FACSIMILE. This Amendment may be executed in two (2) or more counterparts, each of which shall be deemed an original, but all of which together shall constitute one and the same instrument. This Amendment may be executed and delivered by facsimile, or by email in portable document format (.pdf) and delivery of the signature page by such method will be deemed to have the same effect as if the original signature had been delivered to the other parties.

[Remainder of Page Intentionally Left Blank]

IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the date first above written.

COMPANY:

AMYRIS, INC.

By: /s/ John Melo            

John Melo, Chief Executive Officer

[Signature Page to Amendment No. 2 to Amyris, Inc. Amended and Restated Investors' Rights Agreement]

IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the date first above written.

INVESTOR:

By: /s/ Christoph Piel /s/ Jacques Reckinger    

Name: Christoph Piel Jacques Reckinger    

Title: Director                    

[Signature Page to Amendment No. 2 to Amyris, Inc. Amended and Restated Investors' Rights Agreement]

IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the date first above written.

INVESTORS:

TPG BIOTECHNOLOGY PARTNERS II, L.P.

By: TPG Biotechnology GenPar II, L.P., its general partner

By: TPG Biotechnology GenPar II Advisors, LLC, its general partner

By: /s/ Ronald Cami            

Name: Ronald Cami            

Title: Vice President            

[Signature Page to Amendment No. 2 to Amyris, Inc. Amended and Restated Investors' Rights Agreement]

IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the date first above written.

INVESTOR:

MAXWELL (MAURITIUS) PTE LTD

By: /s/ Fidah Alsagoff            

Name: Fidah Alsagoff            

Title: Authorised Signatory        

[Signature Page to Amendment No. 2 to Amyris, Inc. Amended and Restated Investors' Rights Agreement]

IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the date first above written.

INVESTOR:

SUALK CAPITAL LTD

By: /s/ Fernando Reinach        

Name: Fernando Reinach        

Title: Director                

[Signature Page to Amendment No. 2 to Amyris, Inc. Amended and Restated Investors' Rights Agreement]

IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the date first above written.

INVESTOR:

KPCB HOLDINGS, INC., AS NOMINEE

By: /s/ Paul M. Vronsky            

Name: Paul M. Vronsky            

Title: General Counsel            

[Signature Page to Amendment No. 2 to Amyris, Inc. Amended and Restated Investors' Rights Agreement]

IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the date first above written.

INVESTOR:

FORIS VENTURES, LLC

By: /s/ Barbara S. Hager            

Name: Barbara S. Hager        

Title: Manager                

[Signature Page to Amendment No. 2 to Amyris, Inc. Amended and Restated Investors' Rights Agreement]

IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the date first above written.

INVESTOR:

TOTAL GAS & POWER USA, SAS

By: /s/ Arnaud Chaperon        

Name: Arnaud Chaperon        

Title: President                

[Signature Page to Amendment No. 2 to Amyris, Inc. Amended and Restated Investors' Rights Agreement]

IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the date first above written.

INVESTORS:

By: /s/ Sheikh Abdullah bin Khalifa Al Thani    

Name: Biolding Investment SA -        

Sheikh Abdullah bin Khalifa Al Thani    

Title: Director                    

[Signature Page to Amendment No. 2 to Amyris, Inc. Amended and Restated Investors' Rights Agreement]

EX-4.14

Schedule A

(see Exhibit 4.02 Quarterly Report on Form 10-Q as filed on November 9, 2012)

Notes Issued by Registrant

Note Number	Date of Note	Amount	Conversion Price	Comments
R-1	July 30, 2012	$38,300,000	$7.0682	Note No. R-1 was cancelled pursuant to Securities Purchase Agreement dated December 24, 2012 (Exhibit 4.16 Annual Report on Form 10-K for fiscal 2012 as filed on March 2013). The new issued Note is No. R-3.
R-2	September 14, 2012	$15,000,000	$7.0682
R-3	December 24, 2012	$33,300,001.04	$7.0682

EX-4.16

CONFIDENTIAL TREATMENT REQUESTED. CERTAIN PORTIONS OF THIS DOCUMENT HAVE BEEN OMITTED PURSUANT TO A REQUEST FOR CONFIDENTIAL TREATMENT AND, WHERE APPLICABLE, HAVE BEEN MARKED WITH AN ASTERISK TO DENOTE WHERE OMISSIONS HAVE BEEN MADE. THE CONFIDENTIAL MATERIAL HAS BEEN FILED SEPARATELY WITH THE SECURITIES AND EXCHANGE COMMISSION.

SECURITIES PURCHASE AGREEMENT

This SECURITIES PURCHASE AGREEMENT (this “Agreement”) is made and entered into as of December 24, 2012, by and between Amyris, Inc., a Delaware corporation (the “Company”), and the individuals or entities listed on Schedule I hereto (each, a “Purchaser,” and collectively, the “Purchasers”).

Preliminary Statement

The Purchasers desire to purchase, and the Company desires to offer and sell to the Purchasers, shares of the Company's common stock, par value $0.0001 per share (“Common Stock”).

Agreement

The parties, intending to be legally bound, agree as follows:

ARTICLE 1

SALE OF SHARES

Each Purchaser will purchase from the Company the number of shares of Common Stock set forth next to such Purchaser's name on Schedule I hereto (such shares, the “Shares”) at a price of U.S. $2.98 per Share in cash or by cancellation or conversion of indebtedness of the Company to such applicable Purchaser. The total purchase price payable by each Purchaser for the Shares that such Purchaser is hereby agreeing to purchase is set forth next to such Purchaser's name on Schedule I hereto (the “Total Purchase Price”). The sale and purchase of the Shares to each Purchaser shall constitute a separate sale and purchase hereunder.

ARTICLE 2

CLOSING; DELIVERY

2.1.    Closing. The closing (“Closing”) of the transactions contemplated hereby shall be held at the offices of Fenwick & West LLP, 801 California Street, Mountain View, California 94041 within one business day following the date on which the last of the conditions set forth in Articles 6 and 7 have been satisfied or waived in accordance with this Agreement but in no event later than December 26, 2012 (such date, the “Closing Date”), or at such other time and place as the Company and the Purchasers mutually agree upon.

2.2.    Delivery. At the Closing, the Company shall execute and deliver to the Purchasers this Agreement, the Amendment No. 2 to Amended and Restated Investors' Rights Agreement in the form attached hereto as Exhibit A (the “Rights Agreement Amendment”) and the other documents referenced in Article 6. At the Closing, each Purchaser (a) shall pay the Company the applicable Total Purchase Price in immediately available funds or by cancellation or conversion of indebtedness of the Company to Purchaser, (b) if applicable, shall initiate irrevocable payment instructions to its paying bank to make the payment (an “Irrevocable Payment Instruction”) to the Company of the applicable Total Purchase Price in immediately available funds, or (c) if applicable, shall provide to the Company a side letter in the form

1

attached hereto as Schedule 2.2 (a “Payment Commitment Letter”) which shall provide that such applicable Purchaser irrevocably commits to make payment to the Company with respect to the Shares being purchased by such Purchaser hereunder as soon as reasonably practicable but in any event no later than January 14, 2013. At the Closing, or, if applicable, upon receipt of the applicable Total Purchase Price from a Purchaser who makes an Irrevocable Payment Instruction or provides a Payment Commitment Letter at the Closing, the Company shall deliver to each Purchaser a single stock certificate representing the number of Shares purchased by such Purchaser, or deliver irrevocable instructions to the Company's transfer agent to deliver such certificate to a Purchaser who has delivered an Irrevocable Payment Instruction or a Payment Commitment Letter upon the Company's receipt of the Total Purchase Price from such Purchaser, as set forth next to such Purchaser's name on Schedule I hereto, such stock certificate to be registered in the name of such Purchaser, or in such nominee's or nominees' name(s) as designated by such Purchaser in writing in the form of the Purchaser Suitability Questionnaire of the Purchaser attached hereto as (i) for Purchasers who are natural Persons, Exhibit B, or (ii) for Purchasers who are entities, Exhibit C (each, as applicable, the “Purchaser Suitability Questionnaire”), against payment of the purchase price therefor by wire transfer of immediately available funds to such account or accounts as the Company shall designate in writing to Purchaser at least two days prior to the Closing Date or by cancellation or conversion of indebtedness of the Company to such applicable Purchaser. Each Purchaser purchasing Shares through conversion or cancellation of indebtedness agrees that each convertible promissory note held by such Purchaser is cancelled as of the Closing and all principal and interest outstanding thereunder shall be converted as reflected on Schedule I as of the Closing Date; provided that to the extent only a portion of the principal and interest outstanding thereunder shall be converted as reflected on Schedule I as of the Closing Date, then the Company shall issue a new convertible promissory note to such Purchaser reflecting the remaining principal and interest outstanding under such original convertible promissory note after giving effect to the conversion contemplated hereby.

ARTICLE 3

REPRESENTATIONS AND WARRANTIES OF THE COMPANY

The Company represents, warrants and covenants to each Purchaser, except as set forth in the disclosure letter supplied by the Company to the Purchasers dated as of the date hereof, which exceptions shall be deemed to be part of the representations and warranties made hereunder as provided therein, as follows:

3.1.    Organization and Standing. The Company and each of its subsidiaries is duly incorporated, validly existing, and in good standing under the laws of the jurisdiction of its organization. Each of the Company and its subsidiaries has all requisite power and authority to own and operate its respective properties and assets and to carry on its respective business as presently conducted and as proposed to be conducted. The Company and each of its subsidiaries is qualified to do business as a foreign entity in every jurisdiction in which the failure to be so qualified would have, or would reasonably be expected to have, a material adverse effect, individually or in the aggregate, upon the business, properties, tangible and intangible assets, liabilities, operations, prospects, financial condition or results of operation of the Company and its subsidiaries or the ability of the Company or any of its subsidiaries to perform their respective obligations under the Transaction Agreements (as defined below) (a “Material Adverse Effect”).

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3.2.    Subsidiaries. As used in this Agreement, references to any “subsidiary” of a specified Person shall refer to an Affiliate controlled by such Person directly, or indirectly through one or more intermediaries, as such terms are used in and construed under Rule 405 under the Securities Act (which, for the avoidance of doubt, shall include the Company's controlled joint ventures, including shared-controlled joint ventures). The Company's subsidiaries, as of the date hereof, are listed on Exhibit 21.01 to the Company's Annual Report on Form 10-K for the year ended December 31, 2011 and, except as Previously Disclosed (as defined in Section 3.9) are the only subsidiaries, direct or indirect, of the Company as of the date hereof. All the issued and outstanding shares of each subsidiary's capital stock have been duly authorized and validly issued, are fully paid and nonassessable, have been issued in compliance with all federal and state securities laws, were not issued in violation of or subject to any preemptive rights or other rights to subscribe for or purchase securities, and, except as Previously Disclosed, are owned by the Company or a Company subsidiary free and clear of all liens, encumbrances and equities and claims. As used herein, “Person” shall mean any individual, corporation, limited liability company, partnership, joint venture, association, joint-stock company, trust, unincorporated organization or government or any agency or political subdividion thereof, and an “Affiliate” means, with respect to any Person, any other Person that directly or indirectly controls, is controlled by, or is under common control with, such Person.

3.3.    Power. The Company has all requisite power to execute and deliver this Agreement, to sell and issue the Shares hereunder, and to carry out and perform its obligations under the terms of this Agreement, the Rights Agreement Amendment and any ancillary agreements and instruments to be entered into by the Company hereunder (together, the “Transaction Agreements”).

3.4.    Authorization. The execution, delivery, and performance of the Transaction Agreements by the Company has been duly authorized by all requisite action on the part of the Company and its officers, directors and stockholders, and the Transaction Agreements constitute the legal, valid, and binding obligations of the Company enforceable in accordance with their terms, except (a) as limited by applicable bankruptcy, insolvency, reorganization, moratorium, and other laws of general application affecting enforcement of creditors' rights generally, and (b) as limited by laws relating to the availability of specific performance, injunctive relief or other equitable remedies (together, the “Enforceability Exceptions”).

3.5.    Consents and Approvals. Except for any Current Report on Form 8-K or Notice of Exempt Offering of Securities on Form D to be filed by the Company in connection with the transactions contemplated hereby, the Company is not required to give any notice to, make any filing with, or obtain any authorization, consent, or approval of any government or governmental agency in order to consummate the transactions contemplated by the Transaction Agreements. Assuming the accuracy of the representations of each Purchaser in the Purchaser Suitability Questionnaire of such Purchaser, as applicable, no consent, approval, authorization or other order of, or registration, qualification or filing with, any court, regulatory body, administrative agency, self-regulatory organization, stock exchange or market (including The NASDAQ Stock Market), or other governmental body is required for the execution and delivery of these Transaction Agreements, the valid issuance, sale and delivery of the Shares to be sold pursuant to this Agreement other than such as have been made or obtained, or for any securities filings required to be made under federal or state securities laws applicable to the offering of the Shares.

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3.6.    Non-Contravention. The execution and delivery of the Transaction Agreements, the issuance, sale and delivery of the Shares to be sold by the Company under this Agreement, the performance by the Company of its obligations under the Transaction Agreements and/or the consummation of the transactions contemplated thereby will not (a) conflict with, result in the breach or violation of, or constitute (with or without the giving of notice or the passage of time or both) a violation of, or default under, (i) any bond, debenture, note or other evidence of indebtedness, or under any lease, license, franchise, permit, indenture, mortgage, deed of trust, loan agreement, joint venture or other agreement or instrument to which the Company or any subsidiary is a party or by which it or its properties may be bound or affected, (ii) the Company's Restated Certificate of Incorporation, as amended and as in effect on the date hereof (the “Certificate of Incorporation”), the Company's Bylaws, as amended and as in effect on the date hereof (the “Bylaws”), or the equivalent document with respect to any subsidiary, as amended and as in effect on the date hereof, or (iii) any statute or law, judgment, decree, rule, regulation, ordinance or order of any court or governmental or regulatory body (including The NASDAQ Stock Market), governmental agency, arbitration panel or authority applicable to the Company, any of its subsidiaries or their respective properties, except in the case of clauses (i) and (iii) for such conflicts, breaches, violations or defaults that would not be likely to have, individually or in the aggregate, a Material Adverse Effect, or (b) result in the creation or imposition of any lien, encumbrance, claim, security interest or restriction whatsoever upon any of the material properties or assets of the Company or any of its subsidiaries or an acceleration of indebtedness pursuant to any obligation, agreement or condition contained in any material bond, debenture, note or any other evidence of indebtedness or any material indenture, mortgage, deed of trust or any other agreement or instrument to which the Company or any if its subsidiaries is a party or by which the Company or any of its subsidiaries is bound or to which any of the property or assets of the Company is subject. For purposes of this Section 3.6, the term “material” shall apply to agreements, understandings, instruments, contracts or proposed transactions to which the Company is a party or by which it is bound involving obligations (contingent or otherwise) of, or payments to, the Company in excess of $100,000 in a consecutive 12-month period.

3.7.    Shares. The Shares are duly authorized and when issued pursuant to the terms of this Agreement will be validly issued, fully paid, and nonassessable, and will be free of any liens or encumbrances with respect to the issuance thereof; provided, however, that the Shares shall be subject to restrictions on transfer under state or federal securities laws as set forth in this Agreement, or as otherwise may be required under state or federal securities laws as set forth in this Agreement at the time a transfer is proposed. The issuance and delivery of the Shares is not subject to preemptive, co-sale, right of first refusal or any other similar rights of the stockholders of the Company or any other Person, or any liens or encumbrances or result in the triggering of any anti-dilution or other similar rights under any outstanding securities of the Company.

3.8.    No Registration. Assuming the accuracy of each of the representations and warranties of each Purchaser herein and in the Purchaser Suitability Questionnaire, the issuance by the Company of the Shares is exempt from registration under the Securities Act of 1933, as amended (the “Securities Act”).

3.9.    Reporting Status. The Company is subject to the reporting requirements of the Securities Exchange Act of 1934, as amended (the “Exchange Act”), and has, in a timely manner, filed all documents and reports that the Company was required to file pursuant to

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Section I.A.3.b of the General Instructions to Form S-3 promulgated under the Securities Act in order for the Company to be eligible to use Form S-3 for the two years preceding the Closing Date or such shorter time period as the Company has been subject to such reporting requirements (the foregoing materials, together with any materials filed by the Company under the Exchange Act, whether or not required, collectively, the “SEC Documents”). The SEC Documents complied as to form in all material respects with requirements of the Securities Act and Exchange Act and the rules and regulations of the U.S. Securities and Exchange Commission (the “SEC”) promulgated thereunder (collectively, the “SEC Rules”), and none of the SEC Documents and the information contained therein, as of their respective filing dates, contained any untrue statement of a material fact or omitted to state a material fact required to be stated therein or necessary in order to make the statements therein, in light of the circumstances under which they were made, not misleading. As used in this Agreement, “Previously Disclosed” means information set forth in or incorporated by reference into the SEC Documents filed with the SEC on or after February 28, 2012 but prior to the date hereof (except for risks and forward-looking information set forth in the “Risk Factors” section of the applicable SEC Documents or in any forward-looking statement disclaimers or similar statements that are similarly non-specific and are predictive or forward-looking in nature).    

3.10.    Contracts. Each indenture, contract, lease, mortgage, deed of trust, note agreement, loan or other agreement or instrument of a character that is required to be described or summarized in the SEC Documents or to be filed as an exhibit to the SEC Documents under the SEC Rules (collectively, the “Material Contracts”) is so described, summarized or filed. The Material Contracts to which the Company or its subsidiaries are a party have been duly and validly authorized, executed and delivered by the Company and constitute the legal, valid and binding agreements of the Company or its subsidiaries, as applicable, enforceable by and against the Company or its subsidiaries, as applicable, in accordance with their respective terms, subject to the Enforceability Exceptions.

3.11.    Capitalization. Immediately prior to the Closing, the authorized capital stock of the Company consists of (a) 100,000,000 shares of Common Stock, $0.0001 par value per share, 59,555,333 shares of which are issued and outstanding as of the date hereof, and (b) 5,000,000 shares of Preferred Stock, $0.0001 par value per share, of which no shares are issued and outstanding as of the date hereof. All subscriptions, warrants, options, convertible securities, and other rights (contingent or other) to purchase or otherwise acquire equity securities of the Company issued and outstanding as of the date hereof, or material contracts, commitments, understandings, or arrangements by which the Company or any of its subsidiaries is or may be obligated to issue shares of capital stock, or securities or rights convertible or exchangeable for shares of capital stock, are as set forth in the SEC Documents. The issued and outstanding shares of the Company's capital stock have been duly authorized and validly issued, are fully paid and nonassessable, have been issued in compliance with all applicable federal and state securities laws, and were not issued in violation of or subject to any preemptive rights or other rights to subscribe for or purchase securities. Except as Previously Disclosed, no holder of the Company's capital stock is entitled to preemptive or similar rights. There are no bonds, debentures, notes or other indebtedness having general voting rights (or convertible into securities having such rights) of the Company issued and outstanding. Except as Previously Disclosed, there are no agreements or arrangements under which the Company or any of its subsidiaries is obligated to register the sale of any of their securities under the Securities Act. The Company has made available to the

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Purchasers, a true, correct and complete copy of the Company's Certificate of Incorporation and Bylaws.

3.12.    Legal Proceedings. Except as Previously Disclosed, there is no action, suit or proceeding before any court, governmental agency or body, domestic or foreign, now pending or, to the knowledge of the Company, threatened against the Company or its subsidiaries wherein an unfavorable decision, ruling or finding would reasonably be expected to, individually or in the aggregate, (i) materially adversely affect the validity or enforceability of, or the authority or ability of the Company to perform its obligations under, this Agreement or (ii) have a Material Adverse Effect. The Company is not a party to or subject to the provisions of any injunction, judgment, decree or order of any court, regulatory body, administrative agency or other governmental agency or body that might have, individually or in the aggregate, a Material Adverse Effect.

3.13.    No Violations. Neither the Company nor any of its subsidiaries is in violation of its respective certificate of incorporation, bylaws or other organizational documents, or to its knowledge, is in violation of any statute or law, judgment, decree, rule, regulation, ordinance or order of any court or governmental or regulatory body (including The NASDAQ Stock Market), governmental agency, arbitration panel or authority applicable to the Company or any of its subsidiaries, which violation, individually or in the aggregate, would be reasonably likely to have a Material Adverse Effect. Neither the Company nor any of its subsidiaries is in default (and there exists no condition which, with or without the passage of time or giving of notice or both, would constitute a default) in the performance of any bond, debenture, note or any other evidence of indebtedness in any indenture, mortgage, deed of trust or any other material agreement or instrument to which the Company or any of its subsidiaries is a party or by which the Company or any of its subsidiaries is bound or by which the properties of the Company are bound, which would be reasonably likely to have a Material Adverse Effect. There has not been, and to the knowledge of the Company, there is not pending or contemplated, any investigation by the SEC involving the Company or any current or former director or officer of the Company and the Company is not an “ineligible issuer” pursuant to Rules 164, 405 and 433 under the Securities Act. The Company has not received any comment letter from the SEC relating to any SEC Documents which has not been finally resolved. The SEC has not issued any stop order or other order suspending the effectiveness of any registration statement filed by the Company under the Exchange Act or the Securities Act.

3.14.    Governmental Permits; FDA Matters.

(a)    Permits. The Company and its subsidiaries possess all necessary franchises, licenses, certificates and other authorizations from any foreign, federal, state or local government or governmental agency, department or body that are currently necessary for the operation of their respective businesses as currently conducted, except where such failure to possess would not reasonably be expected to have, individually or in the aggregate, a Material Adverse Effect. Neither the Company nor any of its subsidiaries has received any notice of proceedings relating to the revocation or modification of any such permit which, if the subject of an unfavorable decision, ruling or finding, could reasonably be expected to have, individually or in the aggregate, a Material Adverse Effect.

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(b)    EPA and FDA Matters. As to each of the manufacturing processes, intermediate products and research or commercial products of the Company and each of its subsidiaries, including, without limitation, products or compounds currently under research and/or development by the Company, subject to the jurisdiction of the United States Environmental Protection Agency (“EPA”) under the Toxic Substances Control Act and regulations thereunder (“TSCA”) or the Food and Drug Administration (“FDA”) under the Federal Food, Drug and Cosmetic Act and the regulations thereunder (“FDCA”) (each such product, a “Life Science Product”), such Life Science Product is being researched, developed, manufactured, tested, distributed and/or marketed in compliance in all material respects with all applicable requirements under the FDCA and TSCA and similar laws and regulations applicable to such Life Science Product, including those relating to investigational use, premarket approval, good manufacturing practices, labeling, advertising, record keeping, filing of reports and security. The Company has not received any notice or other communication from the FDA, EPA or any other federal, state or foreign governmental entity (i) contesting the premarket approval of, the uses of or the labeling and promotion of any Life Science Product or (ii) otherwise alleging any violation by the Company of any law, regulation or other legal provision applicable to a Life Science Product. Neither the Company, nor any officer, employee or agent of the Company has made an untrue statement of a material fact or fraudulent statement to the FDA or other federal, state or foreign governmental entity performing similar or equivalent functions or failed to disclose a material fact required to be disclosed to the FDA or such other federal, state or foreign governmental entity.

3.15.    Listing Compliance. The Company is in compliance with the requirements of The NASDAQ Stock Market LLC (“The NASDAQ Stock Market”) for continued listing of the Common Stock thereon and has no knowledge of any facts or circumstances that could reasonably lead to delisting of its Common Stock from The NASDAQ Stock Market. The Company has taken no action designed to, or likely to have the effect of, terminating the registration of the Common Stock under the Exchange Act or the listing of the Common Stock on The NASDAQ Stock Market, nor has the Company received any notification that the SEC or The NASDAQ Stock Market is contemplating terminating such registration or listing. The transactions contemplated by the Transaction Agreements will not contravene the rules and regulations of The NASDAQ Stock Market. The Company will comply with all requirements of The NASDAQ Stock Market with respect to the issuance of the Shares, including the filing of any listing notice with respect to the issuance of the Shares.

3.16.    Intellectual Property.

(a)    The Company and/or its subsidiaries owns or possesses, free and clear of all encumbrances, all legal rights to all intellectual property and industrial property rights and rights in confidential information, including all (i) patents, patent applications, invention disclosures, and all related continuations, continuations-in-part, divisional, reissues, re-examinations, substitutions and extensions thereof, (ii) trademarks, trademark rights, service marks, service mark rights, corporate names, trade names, trade name rights, domain names, logos, slogans, trade dress, design rights, and other similar designations of source or origin, together with the goodwill symbolized by and of the foregoing, (iii) trade secrets and all other confidential information, ideas, know-how, inventions, proprietary processes, formulae, models, and other methodologies, (iv) copyrights, (v) computer programs (whether in object code,

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subject code or other form), algorithms, databases, compilations and data, technology supporting the foregoing, and all related documentation, (vi) licenses to any of the foregoing, and (vii) all applications and registrations of the foregoing, and (viii) all other similar proprietary rights (collectively, “Intellectual Property”) used or held for use in, or necessary for the conduct of their businesses as now conducted and as proposed to be conducted, and neither the Company nor any of its subsidiaries (i) has received any communications alleging that either the Company or any of its subsidiaries has violated, infringed or misappropriated or, by conducting their businesses as now conducted and as proposed to be conducted, would violate, infringe or misappropriate any of the Intellectual Property of any other Person, (ii) knows of any basis for any claim that the Company or any of its subsidiaries has violated, infringed or misappropriated, or, by conducting their businesses as now conducted and as proposed to be conducted, would violate, infringe or misappropriate any of the Intellectual Property of any other Person, and (iii) knows of any third-party infringement, misappropriation or violation of any Company or any Company subsidiary's Intellectual Property. The Company has taken and takes reasonable security measures to protect the secrecy, confidentiality and value of its Intellectual Property, including requiring all Persons with access thereto to enter into appropriate non-disclosure agreements. To the knowledge of the Company, there has not been any disclosure of any material trade secret of the Company or a Company subsidiary (including any such information of any other Person disclosed in confidence to the Company) to any other Person in a manner that has resulted or is likely to result in the loss of trade secret in and to such information. Except as Previously Disclosed, and except as would not reasonably be expected to have, individually or in the aggregate, a Material Adverse Effect, there are no outstanding options, licenses or agreements, claims, encumbrances or shared ownership interests of any kind relating to the Company's or its subsidiaries' Intellectual Property, nor is the Company or its subsidiaries bound by or a party to any options, licenses or agreements of any kind with respect to the Intellectual Property of any other Person.

(b)    To the Company's knowledge, none of the employees of the Company or its subsidiaries are obligated under any contract (including, without limitation, licenses, covenants or commitments of any nature or contracts entered into with prior employers), or subject to any judgment, decree or order of any court or administrative agency, that would interfere with the use of his or her best efforts to promote the interests of the Company or its subsidiaries or would conflict with their businesses as now conducted and as proposed to be conducted. Neither the execution nor delivery of the Transaction Agreements will conflict with or result in a breach of the terms, conditions or provisions of, or constitute a default under any contract, covenant or instrument under which the Company or its subsidiaries or any of the employees of the Company or its subsidiaries is now obligated, and neither the Company nor its subsidiaries will need to use any inventions that any of its employees, or Persons it currently intends to employ, have made prior to their employment with the Company or its subsidiaries, except for inventions that have been assigned or licensed to the Company or its subsidiaries as of the date hereof. Each current and former employee or contractor of the Company or its subsidiaries that has developed any Intellectual Property owned or purported to be owned by the Company or its subsidiaries has executed and delivered to the Company a valid and enforceable Invention Assignment and Confidentiality Agreement that (i) assigns to the Company or such subsidiaries all right, title and interest in and to any Intellectual Property rights arising from or developed or delivered to the Company or such subsidiaries in connection with such Person's work for or on behalf of the Company or such subsidiaries, and (ii) provides reasonable

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protection for the trade secrets, know-how and other confidential information (1) of the Company or such subsidiaries and (2) of any third party that has disclosed same to the Company or such subsidiaries. To the knowledge of the Company, no current or former employee, officer, consultant or contractor is in default or breach of any term of any employment, consulting or contractor agreement, non-disclosure agreement, assignment agreement, or similar agreement. Except as Previously Disclosed, to the knowledge of the Company, no present or former employee, officer, consultant or contractor of the Company has any ownership, license or other right, title or interest, directly or indirectly, in whole or in part, in any Intellectual Property that is owned or purported to be owned, in whole or part, by the Company or its subsidiaries.

3.17.    Financial Statements. The consolidated financial statements of the Company and its subsidiaries and the related notes thereto included in the SEC Documents (the “Financial Statements”) comply in all material respects with applicable accounting requirements and the rules and regulations of the SEC with respect thereto as in effect at the time of filing and present fairly, in all material respects, the financial position of the Company and its subsidiaries as of the dates indicated and the results of its operations and cash flows for the periods therein specified subject, in the case of unaudited statements, to normal year-end audit adjustments. Except as set forth in such Financial Statements (or the notes thereto), such Financial Statements (including the related notes) have been prepared in accordance with U.S. generally accepted accounting principles applied on a consistent basis throughout the periods therein specified (“GAAP”). Except as set forth in the Financial Statements, neither the Company nor its subsidiaries has any material liabilities other than liabilities and obligations that have arisen in the ordinary course of business and which would not be required to be reflected in financial statements prepared in accordance with GAAP.

3.18.    Accountants. PricewaterhouseCoopers LLP, which has expressed its opinion with respect to the consolidated financial statements contained in the Company's Annual Report on Form 10-K for the year ended December 31, 2011, are registered independent public accountants as required by the Exchange Act and the rules and regulations promulgated thereunder (and by the rules of the Public Company Accounting Oversight Board). The Company believes based on the Company's current cash plan, as disclosed to the Purchasers and that the Company intends to adopt, that at the time of the filing of the Company's Annual Report on Form 10-K for the year ended December 31, 2012 (the “2012 10-K”), the Company will have sufficient cash on hand to fund the Company's operations for at least twelve months thereafter. The Company shall use its best efforts to ensure that the opinion of PricewaterhouseCoopers LLP with respect to the consolidated financial statements contained in the 2012 10-K do not contain any “going concern” opinions.

3.19.    Internal Accounting Controls. The Company maintains a system of internal accounting controls sufficient to provide reasonable assurances that (i) transactions are executed in accordance with management's general or specific authorizations; (ii) transactions are recorded as necessary to permit preparation of financial statements in conformity with GAAP and to maintain accountability for assets; (iii) access to assets is permitted only in accordance with management's general or specific authorization; and (iv) the recorded accountability for assets is compared with existing assets at reasonable intervals and appropriate action is taken with respect to any differences. The Company has disclosure controls and procedures (as defined in Rules 13a-14 and 15d-14 under the Exchange Act) that are effective and designed to ensure

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that (i) information required to be disclosed in the reports that it files or submits under the Exchange Act is recorded, processed, summarized and reported, within the time periods specified by the SEC Rules, and (ii) such information is accumulated and communicated to the Company's management, including its principal executive officer and principal financial officer, to allow timely decisions regarding required disclosure. The Company is otherwise in compliance in all material respects with all applicable provisions of the Sarbanes-Oxley Act of 2002, as amended and the rules and regulations promulgated thereunder.

3.20.    Off-Balance Sheet Arrangements. There is no transaction, arrangement or other relationship between the Company or its subsidiaries and an unconsolidated or other off-balance sheet entity that is required to be disclosed by the Company in its Exchange Act filings and is not so disclosed or that otherwise would be reasonably likely to have, individually or in the aggregate, a Material Adverse Effect. There are no such transactions, arrangements or other relationships with the Company that may create contingencies or liabilities that are not otherwise disclosed by the Company in its Exchange Act filings.

3.21.    No Material Adverse Change. Except as set forth in (i) the SEC Documents in each case, filed or made through and including the date hereof, since June 30, 2012, or (ii) the written transcript of the Company's webcast conference call held at 5:00 p.m. E.S.T. on November 6, 2012 previously made available to the Purchasers and/or their respective counsel:

(a)     there has not been any event, occurrence or development that, individually or in the aggregate, has had or that could reasonably be expected to result in a Material Adverse Effect,

(b)     the Company has not incurred any liabilities (contingent or otherwise) other than (1) trade payables and accrued expenses incurred in the ordinary course of business consistent with past practice and (2) liabilities not required to be reflected in the Company's financial statements pursuant to GAAP or not required to be disclosed in filings made with the SEC,

(c)     the Company has not declared or made any dividend or distribution of cash or other property to its stockholders or purchased, redeemed or made any agreements to purchase or redeem any shares of its capital stock other than routine withholding in accordance with the Company's existing stock-based plan,

(d)    the Company has not altered its method of accounting or the identity of its auditors, except as Previously Disclosed,

(e)    the Company has not issued any equity securities except pursuant to the Company's existing stock based plans or as otherwise Previously Disclosed; and

(f)    there has not been any loss or damage (whether or not insured) to the physical property of the Company or any of its subsidiaries.

The Company is not as of the date hereof, and after giving effect to the transactions contemplated hereby to occur at the Closing, will not be Insolvent (as defined below). For purposes of this Section, “Insolvent” means, with respect to any Person, (i) the

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present fair saleable value of such Person's assets is less than the amount required to pay such Person's total indebtedness, (ii) such Person is unable to pay its debts and liabilities, subordinated, contingent or otherwise, as such debts and liabilities become absolute and matured, (iii) such Person intends to incur or believes that it will incur debts that would be beyond its ability to pay as such debts mature or (iv) such Person has unreasonably small capital with which to conduct the business in which it is engaged as such business is now conducted and is currently proposed to be conducted.

3.22.    No Manipulation of Stock. Neither the Company nor any of its subsidiaries, nor to the Company's knowledge, any of their respective officers, directors, employees, Affiliates or controlling Persons has taken and will not, in violation of applicable law, take, any action designed to or that might reasonably be expected to, directly or indirectly, cause or result in stabilization or manipulation of the price of the Common Stock.

3.23.    Insurance. The Company and its subsidiaries are insured by insurers of recognized financial responsibility against such losses and risks and in such amounts as are prudent and customary in the businesses in which the Company and its subsidiaries are engaged. The Company and its subsidiaries will continue to maintain such insurance or substantially similar insurance, which covers the same risks at the same levels as the existing insurance with insurers which guarantee the same financial responsibility as the current insurers, and neither the Company nor any subsidiary has any reason to believe that it will not be able to renew its existing insurance coverage as and when such coverage expires or to obtain similar coverage from similar insurers as may be necessary to continue its business without a significant increase in cost.

3.24.    Properties. The Company and its subsidiaries have good and marketable title to all the properties and assets (both tangible and intangible) described as owned by them in the consolidated financial statements included in the SEC Documents, free and clear of all liens, mortgages, pledges, or encumbrances of any kind except (i) those, if any, reflected in such consolidated financial statements (including the notes thereto), or (ii) those that are not material in amount and do not adversely affect the use made and proposed to be made of such property by the Company or its subsidiaries. The Company and each of its subsidiaries hold their leased properties under valid and binding leases. The Company and each of its subsidiaries own or lease all such properties as are necessary to its operations as now conducted.

3.25.    Tax Matters. The Company and its subsidiaries have filed all Tax Returns, and these Tax Returns are true, correct, and complete in all material respects. The Company and each subsidiary (i) have paid all Taxes that are due from the Company or such subsidiary for the periods covered by the Tax Returns or (ii) have duly and fully provided reserves adequate to pay all Taxes in accordance with GAAP. No agreement as to indemnification for, contribution to, or payment of Taxes exists between the Company or any subsidiary, on the one hand, and any other Person, on the other, including pursuant to any Tax sharing agreement, lease agreement, purchase or sale agreement, partnership agreement or any other agreement not entered into in the ordinary course of business. Neither the Company nor any of its subsidiaries has any liability for Taxes of any Person (other than the Company or any of its subsidiaries) under Treasury Regulation Section 1.1502-6 (or any similar provision of any state, local or foreign law), or as a transferee or successor, by contract or otherwise. Since the date of the Company's most recent

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Financial Statements, the Company has not incurred any liability for Taxes other than in the ordinary course of business consistent with past practice. Neither the Company nor its subsidiaries has been advised (a) that any of its Tax Returns have been or are being audited as of the date hereof, or (b) of any deficiency in assessment or proposed judgment to its Taxes. Neither the Company nor any of its subsidiaries has knowledge of any Tax liability to be imposed upon its properties or assets as of the date of this Agreement that is not adequately provided for. The Company has not distributed stock of another corporation, or has had its stock distributed by another corporation, in a transaction that was governed, or purported or intended to be governed, in whole or in part, by Section 355 of the Internal Revenue Code (i) in the two years prior to the date of this Agreement or (ii) in a distribution that could otherwise constitute part of a “plan” or “series of related transactions” (within the meaning of Section 355(e) of the Internal Revenue Code) in conjunction with the purchase of the Shares. “Tax” or “Taxes” means any foreign, federal, state or local income, gross receipts, license, payroll, employment, excise, severance, stamp, occupation, premium, property, windfall, profits, environmental, customs, capital stock, franchise, employees' income withholding, foreign or domestic withholding, social security, unemployment, disability, real property, personal property, sales, use, transfer, value added, alternative or add-on minimum or other similar tax, governmental fee, governmental assessment or governmental charge, including any interest, penalties or additions to Taxes or additional amounts with respect to the foregoing. “Tax Returns” means all returns, reports, or statements required to be filed with respect to any Tax (including any elections, notifications, declarations, schedules or attachments thereto, and any amendment thereof) including any information return, claim for refund, amended return or declaration of estimated Tax.

3.26.    Investment Company Status. The Company is not, and immediately after receipt of payment for the Shares will not be, an “investment company,” an “affiliated person” of, “promoter” for or “principal underwriter” for, or an entity “controlled” by an “investment company,” within the meaning of the Investment Company Act of 1940, as amended, or the rules and regulations promulgated thereunder.

3.27.    Transactions With Affiliates and Employees. Except as Previously Disclosed, none of the officers or directors of the Company or its subsidiaries and, to the knowledge of the Company, none of the employees of the Company or its subsidiaries is presently a party to any transaction with the Company or any subsidiary (other than for services as employees, officers and directors required to be disclosed under Item 404 of Regulation S-K under the Exchange Act).

3.28.    Foreign Corrupt Practices. Neither the Company nor its subsidiaries or Affiliates, any director or officer, nor to the knowledge of the Company, any agent, employee or other Person acting on behalf of the Company or its subsidiaries has, in the course of its actions for, or on behalf of, the Company or any of its subsidiaries (a) used any corporate funds for any unlawful contribution, gift, entertainment or other unlawful expenses relating to political activity, (b) made or promised to make any direct or indirect unlawful payment to any foreign or domestic government official or employee (including any officer or employee of a government or government-owned or controlled entity or of a public international organization, or any Person acting in an official capacity for or on behalf of any of the foregoing, or of any political party or part official or candidate for political office (each such Person, a “Government Official”)) from corporate funds, (c) violated or is in violation of any provision of the U.S. Foreign Corrupt

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Practices Act of 1977, as amended or (d) made or promised to make any unlawful bribe, rebate, payoff, influence payment, kickback or other unlawful payment to any foreign or domestic Government Official.

3.29.    Money Laundering Laws. The operations of the Company and its subsidiaries are and have been conducted at all times in compliance with applicable financial record-keeping and reporting requirements of the Currency and Foreign Transactions Reporting Act of 1970, as amended, and the Bank Secrecy Act, as amended by Title III of the Uniting and Strengthening America by Providing Appropriate Tools Required to Intercept and Obstruct Terrorism Act of 2001 (Title III of Pub. L. 107-56 (signed into law on October 26, 2001)), applicable money laundering statutes and applicable rules and regulations thereunder (collectively, the “Money Laundering Laws”), and no action, suit or proceeding by or before any court or governmental agency, authority or body or any arbitrator involving the Company or any of its subsidiaries with respect to the Money Laundering Laws is pending or, to the Company's knowledge, threatened.

3.30.    OFAC. Neither the Company, any director or officer, nor, to the Company's knowledge, any agent, employee, subsidiary or Affiliate of the Company is currently subject to any U.S. sanctions administered by the Office of Foreign Assets Control of the U.S. Treasury Department (“OFAC”); and the Company will not directly or indirectly use the proceeds of the offering, or lend, contribute or otherwise make available such proceeds to any subsidiary, joint venture partner or other Person, for the purpose of financing the activities of any Person currently subject to any U.S. sanctions administered by OFAC.

3.31.    Environmental Laws. The Company and its subsidiaries (i) are in compliance with any and all applicable foreign, federal, state and local laws and regulations relating to the protection of human health and safety, the environment or hazardous or toxic substances or wastes, pollutants or contaminants (“Environmental Laws”), (ii) have received all permits, licenses or other approvals required of them under applicable Environmental Laws to conduct their respective businesses and (iii) are in compliance with all terms and conditions of any such permit, license or approval, except where such noncompliance with Environmental Laws, failure to receive required permits, licenses or other approvals or failure to comply with the terms and conditions of such permits, licenses or approvals would not, singly or in the aggregate, have a Material Adverse Effect on the Company and its subsidiaries, taken as a whole. There are no costs or liabilities associated with Environmental Laws (including, without limitation, any capital or operating expenditures required for clean-up, closure of properties or compliance with Environmental Laws or any permit, license or approval, any related constraints on operating activities and any potential liabilities to third parties) which would, singly or in the aggregate, have a Material Adverse Effect on the Company and its subsidiaries, taken as a whole.

3.32.    Employee Relations. Neither the Company nor any of its subsidiaries is a party to any collective bargaining agreement or employs any member of a union. Neither the Company nor any of its subsidiaries is engaged in any unfair labor practice. There is (i) (x) no unfair labor practice complaint pending or, to the Company's knowledge, threatened against the Company or any of its subsidiaries before the National Labor Relations Board, and no grievance or arbitration proceeding arising out of or under collective bargaining agreements is pending or threatened, (y) no strike, labor dispute, slowdown or stoppage pending or, to the Company's knowledge, threatened against the Company or any of its subsidiaries and (z) no union representation dispute

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currently existing concerning the employees of the Company or any of its subsidiaries, and (ii) to the Company's knowledge, (x) no union organizing activities are currently taking place concerning the employees of the Company or any of its subsidiaries and (y) there has been no violation of any federal, state, local or foreign law relating to discrimination in the hiring, promotion or pay of employees or any applicable wage or hour laws. No executive officer of the Company (as defined in Rule 501(f) promulgated under the Securities Act) has notified the Company that such officer intends to leave the Company or otherwise terminate such officer's employment with the Company. No executive officer of the Company, to the knowledge of the Company, is, or is now expected to be, in violation of any material term of any employment contract, confidentiality, disclosure or proprietary information agreement, non-competition agreement, or any other agreement or any restrictive covenant, and the continued employment of each such executive officer does not subject the Company or any of its subsidiaries to any liability with respect to any of the foregoing matters.

3.33.    ERISA. The Company and its subsidiaries are in compliance in all material respects with all presently applicable provisions of the Employee Retirement Income Security Act of 1974, as amended, including the regulations and published interpretations thereunder (herein called “ERISA”); no “reportable event” (as defined in ERISA) has occurred with respect to any “pension plan” (as defined in ERISA) for which the Company or any of its subsidiaries would have any liability; the Company has not incurred and does not expect to incur liability under (i) Title IV of ERISA with respect to termination of, or withdrawal from, any “pension plan”; or (ii) Sections 412 or 4971 of the Internal Revenue Code of 1986, as amended, including the regulations and published interpretations thereunder (the “Code”); and each “Pension Plan” for which the Company would have liability that is intended to be qualified under Section 401(a) of the Code is so qualified in all material respects and nothing has occurred, whether by action or by failure to act, which would cause the loss of such qualification.

3.34.    Obligations of Management. To the Company's knowledge, each officer and key employee of the Company or its subsidiaries is currently devoting substantially all of his or her business time to the conduct of the business of the Company or its subsidiaries, respectively. The Company is not aware that any officer or key employee of the Company or its subsidiaries is planning to work less than full time at the Company or its subsidiaries, respectively, in the future. To the Company's knowledge, no officer or key employee is currently working or plans to work for a competitive enterprise, whether or not such officer or key employee is or will be compensated by such enterprise. To the Company's knowledge, no officer or Person currently nominated to become an officer of the Company or its subsidiaries is or has been subject to any judgment or order of, the subject of any pending civil or administrative action by the SEC or any self-regulatory organization.

3.35.    Integration; Other Issuances of Shares. Neither the Company nor its subsidiaries or any Affiliates, nor any Person acting on its or their behalf, has issued any shares of Common Stock or shares of any series of preferred stock or other securities or instruments convertible into, exchangeable for or otherwise entitling the holder thereof to acquire shares of Common Stock which would be integrated with the sale of the Shares to the Purchasers for purposes of the Securities Act or of any applicable stockholder approval provisions, including, without limitation, under the rules and regulations of The NASDAQ Stock Market, nor will the Company or its subsidiaries or Affiliates take any action or steps that would require registration of any of

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the Shares under the Securities Act or cause the offering of the Shares to be integrated with other offerings if any such integration would cause the issuance of the Shares hereunder to fail to be exempt from registration under the Securities Act as provided in Section 3.8 above or cause the transactions contemplated hereby to contravene the rules and regulations of The NASDAQ Stock Market. The Company is eligible to register the Shares for resale by the Purchasers using Form S-3 promulgated under the Securities Act.

3.36.    No General Solicitation. Neither the Company nor its subsidiaries or any Affiliates, nor any Person acting on its or their behalf, has offered or sold any of the Shares by any form of general solicitation or general advertising.

3.37.    No Brokers' Fees. The Company has not incurred any liability for any finder's or broker's fee or agent's commission in connection with the execution and delivery of this Agreement or the consummation of the transactions contemplated hereby.

3.38.    Registration Rights. Except as set forth in (i) the Amended and Restated Investors' Rights Agreement dated June 21, 2010, by and among the Company and the parties listed on Exhibits A through G thereof, as amended by Amendment No. 1 to Amended and Restated Investors' Rights Agreement dated February 23, 2012, and as further amended by the Rights Agreement Amendment (as amended, the “Rights Agreement”); (ii) the Registration Rights Agreement, dated February 27, 2012, by and among the Company and the several purchasers signatory thereto; and (iii) the Registration Rights Agreement, dated July 30, 2012, by and between the Company and Total Gas & Power USA, SAS, the Company has not granted or agreed to grant to any Person any rights (including “piggy-back” registration rights) to have any securities of the Company registered with the SEC or any other governmental authority that have not been satisfied or waived.

3.39.    Application of Takeover Protections. There is no control share acquisition, business combination, poison pill (including any distribution under a rights agreement) or other similar anti-takeover provision under the Company's charter documents or the laws of its state of incorporation that is or could become applicable to any of the Purchasers as a result of the Purchaser and the Company fulfilling their obligations or exercising their rights under the Transaction Agreements, including, without limitation, as a result of the Company's issuance of the Shares and the Purchasers' ownership of the Shares.

3.40.    Disclosure. The Company understands and confirms that the Purchasers will rely on the foregoing representations in effecting transactions in the Shares. All disclosure furnished by or on behalf of the Company to the Purchasers in connection with this Agreement regarding the Company, its business and the transactions contemplated hereby is true and correct in all material respects and does not contain any untrue statement of a material fact or omit to state any material fact necessary in order to make the statements made therein, in light of the circumstances under which they were made, not misleading. The Company acknowledges and agrees that no Purchasers make or have made any representations or warranties with respect to the transactions contemplated hereby other than those set forth in Article 4 hereto. Other than (a) side letters contemplated by Section 6(h) hereof, (b) Payment Commitment Letters contemplated by Section 2.2(c) hereof, (c) that certain letter agreement with Biolding Investment SA in the form attached hereto as Schedule 3.40 (the “Biolding Letter”) and (d) letter agreements regarding

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waivers of rights by any of the Purchasers, the Company has not entered into any letter agreement with a Purchaser hereunder in connection with the transactions contemplated hereby.

ARTICLE 4

REPRESENTATIONS AND WARRANTIES OF THE PURCHASER

Each Purchaser, as to itself only and not with respect to any other Purchaser, represents, warrants and covenants to the Company with respect to this purchase as follows:

4.1    Organization. The Purchaser is duly organized, validly existing, and in good standing under the laws of the jurisdiction of its organization.

4.2.    Power. The Purchaser has all requisite power to execute and deliver this Agreement and to carry out and perform its obligations under the terms of this Agreement.

4.3.    Authorization. The execution, delivery, and performance of this Agreement by the Purchaser has been duly authorized by all requisite action, and this Agreement constitutes the legal, valid, and binding obligation of the Purchaser enforceable in accordance with its terms, except (a) as limited by applicable bankruptcy, insolvency, reorganization, moratorium, and other laws of general application affecting enforcement of creditors' rights generally, and (b) as limited by laws relating to the availability of specific performance, injunctive relief or other equitable remedies.

4.4.    Consents and Approvals. The Purchaser need not give any notice to, make any filing with, or obtain any authorization, consent, or approval of any government or governmental agency in order to consummate the transactions contemplated by this Agreement.

4.5.    Non-Contravention. Neither the execution and the delivery of this Agreement, nor the consummation of the transactions contemplated hereby, will violate in any material respect any constitution, statute, regulation, rule, injunction, judgment, order, decree, ruling, charge, or other restriction of any government, governmental agency, or court to which the Purchaser is subject. No approval, waiver, or consent by the Purchaser under any instrument, contract, or agreement to which the Purchaser or any of its Affiliates is a party is necessary to consummate the transactions contemplated hereby.

4.6.    Purchase for Investment Only. The Purchaser is purchasing the Shares for the Purchaser's own account for investment purposes only and not with a view to, or for resale in connection with, any “distribution” in violation of the Securities Act. By executing this Agreement, the Purchaser further represents that it does not have any contract, undertaking, agreement, or arrangement with any Person to sell, transfer, or grant participation to such Person or to any third Person, with respect to any of the Shares. The Purchaser understands that the Shares have not been registered under the Securities Act or any applicable state securities laws by reason of a specific exemption therefrom that depends upon, among other things, the bona fide nature of the investment intent as expressed herein.

4.7    Disclosure of Information. The Purchaser has had an opportunity to review the Company's filings under the Securities Act and the Exchange Act (including risks factors set forth therein) and the Purchaser represents that it has had an opportunity to ask questions and

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receive answers from the Company to evaluate the financial risk inherent in making an investment in the Shares. The Purchaser has not been offered the opportunity to purchase the Shares by means of any general solicitation or general advertising.

4.8.    Risk of Investment. The Purchaser realizes that the purchase of the Shares will be a highly speculative investment and the Purchaser may suffer a complete loss of its investment. The Purchaser understands all of the risks related to the purchase of the Shares. By virtue of the Purchaser's experience in evaluating and investing in private placement transactions of securities in companies similar to the Company, the Purchaser is capable of evaluating the merits and risks of the Purchaser's investment in the Company and has the capacity to protect the Purchaser's own interests.

4.9.    Advisors. The Purchaser has reviewed with its own tax advisors the federal, state, and local tax consequences of this investment and the transactions contemplated by this Agreement. The Purchaser acknowledges that it has had the opportunity to review the Transaction Agreements and the transactions contemplated thereby with the Purchaser's own legal counsel.

4.10.    Finder. The Purchaser is not obligated and will not be obligated to pay any broker commission, finders' fee, success fee, or commission in connection with the transactions contemplated by this Agreement.

4.11.    Restricted Shares. The Purchaser understands that the Shares must be held indefinitely unless subsequently registered under the Securities Act or unless an exemption from registration is otherwise available. Moreover, the Purchaser understands that, except as set forth in the Rights Agreement, the Company is under no obligation to register the Shares. The Purchaser is aware of Rule 144 promulgated under the Securities Act (“SEC Rule 144”) that permits limited resales of securities purchased in a private placement subject to the satisfaction of certain conditions.

4.12.    Legend. It is understood by the Purchaser that each certificate representing the Shares shall be endorsed with a legend substantially in the following form:

“THE SECURITIES REPRESENTED BY THIS CERTIFICATE HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED, OR APPLICABLE STATE SECURITIES LAWS. THE SECURITIES MAY NOT BE OFFERED FOR SALE, SOLD, TRANSFERRED OR ASSIGNED (I) IN THE ABSENCE OF (A) AN EFFECTIVE REGISTRATION STATEMENT FOR THE SECURITIES UNDER THE SECURITIES ACT OF 1933, AS AMENDED, OR (B) AN OPINION OF COUNSEL (WHICH COUNSEL SHALL BE SELECTED BY THE HOLDER), IN A FORM REASONABLY ACCEPTABLE TO THE COMPANY, THAT REGISTRATION IS NOT REQUIRED UNDER SAID ACT OR (II) UNLESS SOLD PURSUANT TO RULE 144 UNDER SAID ACT. NOTWITHSTANDING THE FOREGOING, THESE SECURITIES MAY BE PLEDGED IN CONNECTION WITH A BONA FIDE MARGIN

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ACCOUNT OR OTHER LOAN OR FINANCING ARRANGEMENT SECURED BY THE SECURITIES.”

Subject to Section 7.3, the Company need not register a transfer of Shares unless the conditions specified in the foregoing legend are satisfied. Subject to Section 7.3, the Company may also instruct its transfer agent not to register the transfer of any of the Shares unless the conditions specified in the foregoing legend are satisfied.

4.13.    Investor Qualification. The Purchaser is an “accredited investor” as defined in Rule 501(a) of Regulation D under the Securities Act. The Purchaser acknowledges that it has completed the Purchaser Suitability Questionnaire. The Purchaser has truthfully set forth in the Purchaser Suitability Questionnaire the factual basis or reason for qualification as an “accredited investor” as defined in Rule 501(a) of Regulation D under the Securities Act and such information remains true and correct as of the date hereof. The Purchaser agrees to furnish any additional information that the Company deems reasonably necessary in order to verify the answers set forth in the Purchaser Suitability Questionnaire.

ARTICLE 5

CONDITIONS TO COMPANY'S OBLIGATIONS AT THE CLOSING.

The Company's obligation to complete the sale and issuance of the Shares and deliver the Shares to each Purchaser, individually, at the Closing shall be subject to the following conditions to the extent not waived by the Company:

(a)     Receipt of Payment. The Company shall have received payment (or confirmation that an Irrevocable Payment Instruction has been made, or a Payment Commitment Letter has been delivered, with respect to such payment), by wire transfer of immediately available funds or by cancellation or conversion of indebtedness of the Company to Purchaser, in the full amount of the Total Purchase Price for the number of Shares being purchased by such Purchaser at the Closing as set forth next to such Purchaser's name on Schedule I hereto.

(b)     Representations and Warranties. The representations and warranties made by such Purchaser in Section 4 hereof shall be true and correct in all material respects as of, and as if made on, the date of this Agreement and as of the Closing.

(c)     Receipt of Executed Documents. Such Purchaser shall have duly executed and delivered to the Company the Rights Agreement Amendment and the Purchaser Suitability Questionnaire.

ARTICLE 6

CONDITIONS TO PURCHASERS' OBLIGATIONS AT THE CLOSING

Each Purchaser's obligation to accept delivery of the Shares and to pay for the Shares shall be subject to the following conditions to the extent not waived by such Purchaser:

(a)     Delivery. The Company shall have complied with its obligations set forth under Section 2.2 to (i) provide, with respect to each Purchaser, a single stock certificate for each Purchaser representing the number of Shares purchased by such Purchaser, (ii) to have instructed

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the transfer agent to deliver such certificate upon the receipt of the Total Purchase Price from a Purchaser that has delivered an Irrevocable Payment Instruction and to have provided such Purchaser a portable document format (pdf) copy of the stock certificate at the time of the Closing; provided that such pdf copy of the stock certificate will be held by such Purchaser in escrow until the Company has been notified by its bank that it has received by wire transfer such Purchaser's applicable Total Purchase Price, or (iii) to have instructed the transfer agent to deliver such certificate upon the receipt of the Total Purchase Price from a Purchaser that has delivered a Payment Commitment Letter; provided that once such Purchaser provides the Company with an Irrevocable Payment Instruction then the Company shall provide such Purchaser a portable document format (pdf) copy of the stock certificate at such time; provided that such pdf copy of the stock certificate will be held by such Purchaser in escrow until the Company has been notified by its bank that it has received by wire transfer such Purchaser's applicable Total Purchase Price.

(b)     Representations and Warranties. The representations and warranties made by the Company in Section 3 hereof shall be true and correct in all respects as of, and as if made on, the date of this Agreement and as of the Closing.

(c)    Receipt of Rights Agreement Amendment. The Company shall have executed and delivered to each Purchaser the Rights Agreement Amendment.

(d)     Legal Opinion. The Purchasers shall have received an opinion of Fenwick & West LLP, counsel to the Company, substantially in the form set forth in Exhibit D hereto.

(e)     Certificate. Each Purchaser shall have received a certificate signed by the Company's Chief Executive Officer and Chief Financial Officer to the effect that the representations and warranties of the Company in Section 3 hereof are true and correct in all respects as of, and as if made on, the date of this Agreement and as of the Closing and that the Company has satisfied in all material respects all of the conditions set forth in this Agreement.

(f)     Good Standing. The Company is validly existing as a corporation in good standing under the laws of Delaware as evidenced by a certificate of the Secretary of State of the State of Delaware, a copy of which was provided to the Purchasers.

(g)     Waiver of Standstill Obligations. To the extent that any Purchaser is prohibited from purchasing Shares hereunder pursuant to the terms of any existing agreement entered into with the Company, the Company shall deliver to such Purchaser a waiver in form reasonably acceptable to Purchaser that permits such Purchaser to purchase Shares pursuant to this Agreement.

(h)    Receipt of Minimum Funds.    The Company shall have received (i) payments from the Purchasers in consideration of the Shares being sold pursuant to this Agreement, and (ii) with respect to any Purchasers who have not made any payment to the Company in consideration of the Shares to be purchased by such Purchaser, confirmation that such Purchaser has (x) made an Irrevocable Payment Instruction, such confirmation to either be in the form of (A) a federal reference number or other similar written evidence that a wire has been initiated, or (B) a side letter in the form attached hereto as Schedule 6(h), or (y) delivered a Payment

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Commitment Letter to the Company; provided that the payments received under clause (i) above and the payments to be received pursuant to any Irrevocable Payment Instruction or Payment Commitment Letter delivered to the Company pursuant to clause (ii) above shall total at least $42,249,991.06 in the aggregate excluding any payments being made by conversion of indebtedness of the Company to Purchaser (the “Minimum Payment Amount”); provided that upon execution of the Biolding Letter by the Company and Biolding Investment SA the Minimum Payment Amount shall be reduced to $37,249,991.06.

(i)    Secretary's Certificate. A certificate, executed by the Secretary of the Company and dated as of the Closing Date, as to (A) the resolutions approving the issuance of the Shares as adopted by an Independent Committee of the Board of Directors and/or the Company's Board of Directors in a form reasonably acceptable to such Purchaser, (B) the certificate of incorporation, and (C) the bylaws, each as in effect as of the Closing Date.

(j)    Board Approval. The terms and conditions of the issuance of the Shares and the Transaction Agreements shall have been approved by an Independent Committee of the Board of Directors and/or a majority of the disinterested directors of the Board of Directors, as applicable.

(k)    Approvals. The Company shall have obtained all governmental, regulatory or third party consents and approvals, if any, necessary for the sale of the Shares, including, without limitation, from The NASDAQ Stock Market.

ARTICLE 7

OTHER AGREEMENTS OF THE PARTIES

7.1    Securities Laws Disclosure; Publicity. Promptly after the Closing Date, the Company shall issue a press release (the “Press Release”) reasonably acceptable to the Purchasers disclosing all material terms of the transactions contemplated hereby. On or before 5:30 p.m., New York City time, on the fourth trading day immediately following the execution of this Agreement, the Company will file a Current Report on Form 8-K with the SEC describing the terms of the Transaction Agreements.

7.2.    Form D. The Company agrees to timely file a Form D with respect to the Shares as required under Regulation D and to provide a copy thereof to the Purchaser (provided that the posting of the Form D on the SEC's EDGAR system shall be deemed delivery of the Form D for purposes of this Agreement).

7.3.    Removal of Legend and Transfer Restrictions. The Company hereby covenants with the Purchasers to, no later than three trading days following the delivery by the Purchaser to the Company of a legended certificate representing Shares (endorsed or with stock powers attached, signatures guaranteed, and otherwise in form necessary to affect the reissuance and/or transfer), in connection with the transfer or sale of all or a portion of the Shares pursuant to (1) an effective registration statement that is effective at the time of such sale or transfer, (2) a transaction exempt from the registration requirements of the Securities Act in which the Company receives an opinion of counsel reasonably satisfactory to the Company that the Shares are freely transferable and that the legend is no longer required on such stock certificate, or (3) an exemption from registration pursuant to SEC Rule 144, deliver or cause the Company's

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transfer agent to deliver to the transferee of the Shares or to the Purchaser, as applicable, a new stock certificate representing such Shares that is free from all restrictive and other legends. The Company acknowledges that the remedy at law for a breach of its obligations under this Section 7.3 may be inadequate and agrees, in the event of a breach or threatened breach by the Company of the provisions of this Section 7.3 with respect to any Purchaser, the Purchaser shall be entitled, in addition to all other available remedies, to an order and/or injunction restraining any breach and requiring immediate issuance and transfer, without the necessity of showing economic loss and without any bond or other security being required.

7.4.    Use of Proceeds. The Company agrees to use the proceeds of the offering for bona fide general corporate purposes and to provide working capital.

7.5.    Subsequent Equity Sales. The Company shall not, and shall use its commercially reasonable efforts to ensure that no Affiliate of the Company shall, sell, offer for sale or solicit offers to buy or otherwise negotiate in respect of any security (as defined in Section 2 of the Securities Act) that will be integrated with the offer or sale of the Shares in a manner that would require the registration under the Securities Act of the sale of the Shares to the Purchasers, or that will be integrated with the offer or sale of the Shares for purposes of the rules and regulations of any trading market such that it would require stockholder approval prior to the closing of such other transaction unless stockholder approval is obtained before the closing of such subsequent transaction.

7.6.    Listing. The Company shall promptly take any action required to maintain the listing of all of the Shares, once they have been issued, upon each national securities exchange and automated quotation system, if any, upon which shares of Common Stock are then listed (subject to official notice of issuance) and shall maintain, so long as any other shares of Common Stock shall be so listed, such listing of all Shares from time to time issuable under the terms of the Transaction Agreements. The Company shall take all actions within its control to comply with the reporting requirements of the Exchange Act and each applicable national securities exchange and automated quotation system on which the Common Stock is listed. The Company shall make and keep public information available, as those terms are understood and defined in SEC Rule 144, for so long as required in order to permit the resale of the Shares pursuant to SEC Rule 144 and to file period reports with the SEC whether or not required to do so. The Company shall not take any action which would be reasonably expected to result in the delisting or suspension of the Common Stock on The NASDAQ Stock Market.

ARTICLE 8

MISCELLANEOUS

8.1.    Survival. The representations, warranties and covenants contained herein shall survive the execution and delivery of this Agreement and the sale of the Shares.

8.2.    Indemnification.

(a)    Indemnification of Purchasers. The Company agrees to indemnify and hold harmless each Purchaser and its Affiliates and their respective directors, officers, trustees,

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members, managers, employees and agents, and their respective successors and assigns, from and against any and all losses, claims, damages, liabilities and expenses (including without limitation reasonable attorney fees and disbursements and other expenses reasonably incurred in connection with investigating, preparing or defending any action, claim or proceeding, pending or threatened and the costs of enforcement thereof) (collectively, “Losses”) to which such Person may become subject as a result of any breach of representation, warranty, covenant or agreement made by or to be performed on the part of the Company under this Agreement, and will reimburse any such Person for all such Losses as they are incurred by such Person.

(b)    Conduct of Indemnification Proceedings. Any Person entitled to indemnification hereunder shall (i) give prompt notice to the Company of any claim with respect to which it seeks indemnification and (ii) permit the Company to assume the defense of such claim with counsel reasonably satisfactory to the indemnified party; provided that any Person entitled to indemnification hereunder shall have the right to employ separate counsel and to participate in the defense of such claim, but the fees and expenses of such counsel shall be at the expense of such Person unless (a) the Company has agreed to pay such fees or expenses, or (b) the Company shall have failed to assume the defense of such claim and employ counsel reasonably satisfactory to such Person or (c) in the reasonable judgment of any such Person, based upon written advice of its counsel, a conflict of interest exists between such Person and the Company with respect to such claims (in which case, if the Person notifies the Company in writing that such Person elects to employ separate counsel at the expense of the Company, the Company shall not have the right to assume the defense of such claim on behalf of such Person); and provided, further, that the failure of any indemnified party to give notice as provided herein shall not relieve the Company of its obligations hereunder, except to the extent that such failure to give notice shall materially adversely affect the Company in the defense of any such claim or litigation. It is understood that the Company shall not, in connection with any proceeding in the same jurisdiction, be liable for fees or expenses of more than one separate firm of attorneys at any time for all such indemnified parties. The Company will not, except with the consent of the indemnified party, which consent shall not be unreasonably withheld, conditioned or delayed, consent to entry of any judgment or enter into any settlement that does not include as an unconditional term thereof the giving by the claimant or plaintiff to such indemnified party of a release from all liability in respect of such claim or litigation. No indemnified party will, except with the consent of the Company, consent to entry of any judgment or enter into any settlement.

8.3.    Assignment; Successors and Assigns. This Agreement may not be assigned by either party without the prior written consent of the other party; provided, that this Agreement may be assigned by any Purchaser to the valid transferee of any security purchased hereunder if such security remains a “restricted security” under the Securities Act. This Agreement and all provisions thereof shall be binding upon, inure to the benefit of, and are enforceable by the parties hereto and their respective successors and permitted assigns.

8.4.    Notices. All notices, requests, and other communications hereunder shall be in writing and will be deemed to have been duly given and received (a) when personally delivered, (b) when sent by facsimile upon confirmation of receipt, (c) one business day after the day on which the same has been delivered prepaid to a nationally recognized courier service, or (d) five business days after the deposit in the United States mail, registered or certified, return receipt requested, postage prepaid, in each case addressed to, as to the Company, Amyris, Inc., 5885

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Hollis Street, Suite 100, Emeryville, CA 94608, Attn: General Counsel, facsimile number: (510) 740-7416, with a copy to Fenwick & West LLP, 801 California Street, Mountain View, CA 94041, Attn: Dan Winnike, Esq., facsimile number: (650) 938-5200, and as to the Purchaser at the address and facsimile number set forth below the Purchaser's signature on the signature pages of this Agreement. Any party hereto from time to time may change its address, facsimile number, or other information for the purpose of notices to that party by giving notice specifying such change to the other parties hereto. Each Purchaser and the Company may each agree in writing to accept notices and other communications to it hereunder by electronic communications pursuant to procedures reasonably approved by it; provided that approval of such procedures may be limited to particular notices or communications.

8.5.    Governing Law. This Agreement, and the provisions, rights, obligations, and conditions set forth herein, and the legal relations between the parties hereto, including all disputes and claims, whether arising in contract, tort, or under statute, shall be governed by and construed in accordance with the laws of the State of Delaware without giving effect to its conflict of law provisions.

8.6.    Dispute Resolution.

8.6.1    Escalation. Prior to commencing any arbitration in connection with any dispute, controversy or claim arising out of relating to this Agreement or the breach, termination or validity thereof (“Dispute”), the parties shall first engage in the procedures set forth in this Section 8.6.1. Such Dispute shall first be referred by written notice of the Dispute (the “Dispute Notice”) from any party to its executive officers and to the executive officers of each party that the party sending the Dispute Notice has the Dispute with (the “Executive Officers”) and the Executive Officers shall attempt to resolve such Dispute within ten (10) days after a party sent the Dispute Notice to the Executive Officers by meeting (either in person or by video teleconference, unless otherwise mutually agreed) at a mutually acceptable time, and thereafter as often as they reasonably deem necessary, to exchange relevant information and to attempt to resolve the Dispute. If the Dispute has not been resolved within thirty (30) days after the Dispute Notice has been sent by a party to its Executive Officers and to the Executive Officers of the other party or parties, then either the party that has sent the Dispute Notice, or the party or parties that have received the Dispute Notice may, by written notice to the other party or parties, elect to submit the Dispute to arbitration pursuant to Section 8.6.2. If a party's Executive Officer intends to be accompanied at a meeting by an attorney, the Executive Officers of the other party shall be given at least seventy-two (72) hours' notice of such intention and may also be accompanied by an attorney. All negotiations conducted pursuant to this Section 8.6.1, and all documents and information exchanged by the parties in furtherance of such negotiations, (i) are the Confidential Information (as defined in Section 8.6.4) of the parties, and (ii) shall be inadmissible in any arbitration conducted pursuant to this Section 8.6 or other proceeding with respect to a Dispute.

8.6.2    Arbitration.

(a) All Disputes arising out of, relating to or in connection with this Agreement, which have not been resolved pursuant to Section 8.6.1, shall be submitted to mandatory, final and binding arbitration before an arbitral tribunal pursuant to the Rules of Arbitration of the International Court of Arbitration of the International Chamber of Commerce (the “ICC Rules”), in effect at the time of filing of the request for arbitration, as modified hereby.

23

The International Court of Arbitration of the International Chamber of Commerce (the “ICC Court”) shall administer the arbitration.

(b)There shall be three (3) arbitrators. If there are two parties to the arbitration, then one arbitrator shall be nominated by the initiating claimant party in the request for arbitration, the second nominated by the respondent party within thirty (30) days of receipt of the request for arbitration, and the third (who shall act as chairperson of the arbitral tribunal) nominated by the two (2) party-appointed arbitrators within thirty (30) days of the selection of the second arbitrator. In the event that either party fails to nominate an arbitrator, or if the two party-appointed arbitrators are unable or fail to agree upon the third arbitrator, within the time periods specified herein, the ICC Court shall appoint the remaining arbitrator(s) required to comprise the arbitral tribunal. If there are more than two parties to the arbitration, the claimant(s) shall jointly nominate one arbitrator and the respondent(s) shall jointly nominate one arbitrator, within thirty (30) days of receipt by respondent(s) of a copy of the request for arbitration. For avoidance of doubt, where there are two or more claimant(s), none of the claimants has to nominate an arbitrator in their request for arbitration. The third arbitrator (who shall act as chairperson of the arbitral tribunal) shall be nominated by the two (2) party-appointed arbitrators within thirty (30) days of the nomination of the second arbitrator. If either the claimant(s) or the respondent(s) fail to timely nominate an arbitrator, or if the two party-appointed arbitrators are unable or fail to agree upon the third arbitrator, within the time periods specified herein, then on the request of any party, the ICC Court shall appoint the remaining arbitrator(s) required to comprise the arbitral tribunal. The claimant in the arbitration shall provide a copy of the request for arbitration to the respondent at the time such request is submitted to the Secretariat of the International Chamber of Commerce.

(c)Each arbitrator chosen under this Section shall speak, read, and write English fluently and shall be either (i) a practicing lawyer who has specialized in business litigation with at least ten (10) years of experience in a law firm, (ii) an arbitrator experienced with commercial disputes, or (iii) a retired judge.

(d)The place of arbitration shall be Paris, France. The language of the arbitral proceedings and of all submissions and written evidence and any award issued by the arbitral tribunal shall be English. Any party may, at its own expense, provide for translation of any documents submitted in the arbitration or translation or interpretation of any testimony taken at any hearing before the arbitral tribunal. For the avoidance of doubt, no party is under any obligation to provide for translation of any documents submitted in the arbitration or translation or interpretation of any testimony taken at any hearing before the arbitral tribunal.

(e)  The award shall be in writing, state the reasons for the award and be final and binding. The arbitral tribunal shall, subject to its discretion, endeavor to issue its award within four (4) months of the end of the hearing, or as soon as possible thereafter. It is expressly understood and agreed by the parties that the rulings and award of the arbitral tribunal shall be binding on the parties, their successors and permitted assigns. Judgment on the award rendered by the arbitral tribunal may be entered in any court having competent jurisdiction.

(f)Each party shall bear its own costs and expenses and attorneys' fees, and the party that does not prevail in the arbitration proceeding, as determined by the arbitral tribunal, shall pay the arbitrator's fees and any administrative fees of arbitration. All proceedings

24

and decisions of the tribunal shall be deemed Confidential Information of each of the Parties, and shall be subject to Section 8.6.4.

8.6.3    Interim Relief.

(a) The arbitral tribunal shall have the power to grant any remedy or relief that it deems appropriate, whether provisional or final, including conservatory relief and injunctive relief, and any such measures ordered by the arbitral tribunal may, to the extent permitted by applicable law, be deemed to be a final award on the subject matter of the measures and shall be enforceable as such.

(b)In addition to the remedies and relief available under Section 8.6.3(a) above and the ICC Rules, and subject to Section 8.6.2 above, each party expressly retains the right at any time to apply to any court of competent jurisdiction for interim, injunctive, provisional or conservatory relief, including pre-arbitral attachments or injunctions, and any such request shall not be deemed incompatible with the agreement to arbitrate or a waiver of the right to arbitrate.

(c)For purposes of Section 8.6.3(b), each party hereby irrevocably and unconditionally consents and agrees that any action for interim, provisional and/or conservatory relief brought against it with respect to its obligations or liabilities under or arising out of or in connection with this Agreement may be brought in the courts located in Paris, France or the state or federal courts located in the Borough of Manhattan, New York City, New York, and each party hereby irrevocably accepts and unconditionally submits to the non-exclusive jurisdiction of the aforesaid courts in personam, with respect to any such action for interim, provisional or conservatory relief. In any such action, each of the parties irrevocably waives, to the fullest extent they may effectively do so, any objection, including any objection to the laying of venue or based on the grounds of forum non conveniens or any right of objection to jurisdiction on account of its place of incorporation or domicile, which it may now or hereafter have to the bringing of any such action or proceeding in the courts located in Paris, France or the state or federal courts located in the Borough of Manhattan, New York City, New York.

(d)Each party hereby irrevocably consents and agrees that the service of any and all legal process, summons, notices and documents which may be served in any action arising under this Agreement may be made by sending a copy thereof by express courier to the party to be served at the address set forth in the notice provision of this Agreement, with such service to be effective upon receipt. Nothing in this Agreement will affect the right of any party to this Agreement to serve process in any other manner permitted by law.

(e) Each party hereto hereby irrevocably waives any and all right to trial by jury in any legal proceeding brought pursuant to this Section 8.6.

8.6.4    Confidentiality. The Company and each of the Purchasers agree to use, and to use its reasonable best efforts to ensure that its authorized representatives use the same degree of care as such party uses to protect its own confidential information (but in no event less than reasonable care) to keep confidential the information provided to it pursuant to this Agreement, and any other information furnished to it which the disclosing party identifies as being confidential or proprietary (so long as such information is not in the public domain) or, under the circumstances surrounding disclosure, such party knows or has reason to know should

25

be treated as confidential (“Confidential Information”), unless otherwise required by law (provided that a party shall, to the extent permitted by law, promptly notify the other party of any required disclosure and take reasonable steps to minimize the extent of any such required disclosure); provided, however, that Confidential Information shall not include information, that (i) was in the public domain prior to the time it was furnished to such recipient, (ii) is at the time of the alleged breach (through no willful or improper action or inaction by such recipient) generally available to the public, (iii) was rightfully disclosed to such recipient by a third party without restriction or (iv) as of the time of the alleged breach, had been independently developed (as evidenced by written records) without any use of Confidential Information.

8.7.    Severability. In the event that any provision of this Agreement or the application of any provision hereof is declared to be illegal, invalid, or otherwise unenforceable by a court of competent jurisdiction, the remainder of this Agreement shall not be affected except to the extent necessary to delete such illegal, invalid, or unenforceable provision unless that provision held invalid shall substantially impair the benefits of the remaining portions of this Agreement.

8.8.    Headings. The headings in this Agreement are for convenience of reference only and shall not constitute a part of this Agreement, nor shall they affect its meaning, construction, or effect.

8.9.    Entire Agreement. This Agreement embodies the entire understanding and agreement between the parties hereto with respect to the subject matter hereof and supersedes all prior agreements and understandings relating to the subject matter hereof.

8.10.    Finder's Fee. The Company agrees that it shall be responsible for the payment of any placement agent's fees, financial advisory fees, or brokers' commissions (other than for Persons engaged by Purchaser) relating to or arising out of the transactions contemplated hereby. The Company shall pay, and hold each Purchaser harmless against, any liability, loss or expense (including, without limitation, attorney's fees and out-of-pocket expenses) arising in connection with any claim for any such fees or commissions.

8.11.    Expenses. Each party will bear its own costs and expenses in connection with this Agreement.

8.12.    Further Assurances. The parties agree to execute and deliver all such further documents, agreements and instruments and take such other and further action as may be necessary or appropriate to carry out the purposes and intent of this Agreement.

8.13.    Counterparts. This Agreement may be executed in two or more counterparts, each of which shall constitute an original, but all of which, when taken together, shall constitute but one instrument, and shall become effective when one or more counterparts have been signed by each party hereto and delivered to the other party. Facsimile signatures shall be deemed originals for all purposes hereunder.

8.14.    Independent Nature of Purchasers' Obligations and Rights. The obligations of each Purchaser under this Agreement are several and not joint with obligations of each other Purchaser, and no Purchaser shall be responsible in any way for the performance of the obligations of any other Purchaser under this Agreement or any other Transaction Agreements. The decision of each Purchaser to purchase Shares pursuant to this Agreement has been made by

26

such Purchaser independently of any other Purchaser and independently of any information, materials, statements or opinions as to the business, affairs, operations, assets, properties, liabilities, results of operations, condition (financial or otherwise) or prospects of the Company or any of its subsidiaries which may have been made or given by any other Purchaser or by any agent or employee of any other Purchaser, and no Purchaser or any of its agents or employees shall have any liability to any other Purchaser (or any other Person) relating to or arising from any such information, materials, statements or opinions. Nothing contained herein or in any ancillary document, and no action taken by any Purchaser pursuant thereto, shall be deemed to constitute the Purchasers as a partnership, an association, a joint venture or any other kind of entity, or create a presumption that the Purchasers are in any way acting in concert or as a group with respect to such obligations or the transactions contemplated by the Agreement. Each Purchaser acknowledges that no other Purchaser has or will be acting as agent of such Purchaser in enforcing its rights under this Agreement or any other Transaction Agreements. Each Purchaser shall be entitled to independently protect and enforce its rights, including without limitation the rights arising out of this Purchaser, and it shall not be necessary for any other Purchaser to be joined as an additional party in any proceeding for such purpose.

8.15.    Waiver of Conflicts; Representation by Counsel. Each Purchaser and the Company is aware that Fenwick & West LLP (“F&W”) may have previously performed and may continue to perform certain legal services for certain of the Purchasers in matters unrelated to F&W's representation of the Company. In connection with its Purchaser representation, F&W may have obtained confidential information of such Purchasers that could be material to F&W's representation of the Company in connection with negotiation, execution and performance of this Agreement. By signing this Agreement, each Purchaser and the Company hereby acknowledges that the terms of this Agreement were negotiated among the Purchasers and the Company and are fair and reasonable and waives any potential conflict of interest arising out of such representation (including any future representation of such parties) or such possession of confidential information. Each Purchaser and the Company further represents that it has had the opportunity to be, or has been, represented by separate independent counsel in connection with the transactions contemplated by this Agreement, including, without limitation, the waivers contained in this Section 8.15.

[Signature pages follows]

27

This Securities Purchase Agreement is hereby confirmed and accepted by the Company as of December 24, 2012.

AMYRIS, INC.

By: /s/ John Melo        

Name: John Melo

Title: President and CEO

PURCHASERS:

U.S. $42,249,990.02

Total Purchase Price

(U.S. $2.98 per Share)

Number of Shares: 14,177,849

By:

(signature)

Name:

(printed name)

Title: Managing Member

Address:

Facsimile No:

E-mail Address:

This Securities Purchase Agreement is hereby confirmed and accepted by the Purchasers as of December 24, 2012.

PURCHASERS:

U.S. $ 4,999,998.96

Total Purchase Price

(U.S. $2.98 per Share)

Number of Shares: 1,677,852

NAXYRIS S.A.

By: /s/ Christoph Piel /s/ Jacques Reckinger    

(signature)

Name:

(printed name)

Title: Director

Address:     40, Boulevard Joseph II        

L-1840 Luxembourg        

Attention: Sam Reckinger and    

Christoph Piel            

Facsimile No: [*]                

E-mail Address: [*]                

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

This Securities Purchase Agreement is hereby confirmed and accepted by the Purchasers as of

December 24, 2012.

PURCHASERS:

U.S. $ 4,999,998.96

Total Purchase Price

(U.S. $2.98 per Share)

Number of Shares: 1,677,852

FORIS VENTURES, LLC

By: /s/ Barbara Hager            

(signature)

Name: Barbara S. Hager        

(printed name)

Title: Manager

Address: c/o JEMA Management        

555 Bryant Street, #722        

Palo Alto, CA 94301        

Attention: Barbara S. Hager    

Facsimile No: [*]

E-mail Address: [*]            

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

This Securities Purchase Agreement is hereby confirmed and accepted by the Purchasers as of

December 24, 2012.

PURCHASERS:

U.S. $ 1,999,997.20

Total Purchase Price

(U.S. $2.98 per Share)

Number of Shares: 671,140

TPG BIOTECHNOLOGY PARTNERS II, L.P.

By: TPG Biotechnology GenPar II, L.P., its

general partner

By: TPG Biotechnology GenPar II Advisors,

LLC, its general partner

By: /s/ Ronald Cami            

(signature)

Name: Ronald Cami            

(printed name)

Title: Vice President

Address: 301 Commerce Street, Suite 3300    

Fort Worth, TX 76102        

Facsimile No: [*]

Telephone No: [*]

E-mail Address: [*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

This Securities Purchase Agreement is hereby confirmed and accepted by the Purchasers as of

December 24, 2012.

PURCHASERS:

U.S. $ 249,998.16

Total Purchase Price

(U.S. $2.98 per Share)

Number of Shares: 83,892

SUALK CAPITAL LTD

By: /s/ Fernando Reinach        

(signature)

Name: Fernando Reinach        

(printed name)

Title: Director

Address: Marcy Building 2nd Floor    

Purcell Estate            

PO Box 2416            

Road Town            

Tortola, British Virgin Island    

Facsimile No:

E-mail Address:

This Securities Purchase Agreement is hereby confirmed and accepted by the Company as of

December 24, 2012.

PURCHASERS:

U.S. $ 9,999,997.92

Total Purchase Price

(U.S. $2.98 per Share)

Number of Shares: 3,355,704

By: /s/ Sheikh Abdullah bin Khalifa Al Thani

(signature)

Name: Biolding Investment            

(printed name)

Title: President

Address: 11 A BD Prince Henri        

1724 Luxembourg            

Facsimile No:

E-mail Address: illegible            

This Securities Purchase Agreement is hereby confirmed and accepted by the Company as of

December 24, 2012.

PURCHASERS:

U.S. $ 9,999,998.96

Total Purchase Price

(U.S. $2.98 per Share)

Number of Shares: 1,677,852

TOTAL GAS & POWER USA, SAS

By: /s/ Arnaud Chaperon            

(signature)

Name: Arnaud Chaperon            

(printed name)

Title: President

Address: 2, Place Jean Millier        

La Defense            

92400 Courbevoie, France        

Facsimile No: [*]                

E-mail Address:[*]            

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

This Securities Purchase Agreement is hereby confirmed and accepted by the Purchasers as of

December 24, 2012.

PURCHASERS:

U.S. $ 14,999,999.86

Total Purchase Price

(U.S. $2.98 per Share)

Number of Shares: 5,033,557

MAXWELL (MAURITIUS) PTE LTD

By: /s/ Fidah Alsagoff            

(signature)

Name: Fidah Alsagoff            

(printed name)

Title: Authorised Signatory

Address: 60B Orchard Road #06-18        

Tower 2, The Atrium @ Orchard    

Singapore 238891            

Facsimile No: [*]                

E-mail Address:

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

Schedule I

Schedule of Purchasers

Purchaser	Shares Purchased	Cancellation of Indebtedness		Cash paid at Closing		Total Purchase Price
Maxwell (Mauritius) Pte Ltd	5,033,557			$	14,999,999.86	$	14,999,999.86
Biolding Investment SA	3,355,704			$	9,999,997.92	$	9,999,997.92
Naxyris SA	1,677,852			$	4,999,998.96	$	4,999,998.96
Foris Ventures, LLC	1,677,852			$	4,999,998.96	$	4,999,998.96
TPG Biotechnology Partners II, L.P.	671,140			$	1,999,997.20	$	1,999,997.20
Sualk Capital Ltd	83,892			$	249,998.16	$	249,998.16
Total Gas & Power USA, SAS	1,677,852	$	4,999,998.96			$	4,999,998.96
TOTAL	14,177,849	$	4,999,998.96	$	37,249,991.06	$	42,249,990.02

Schedule 2.2

Form of Payment Commitment Letter

December 24, 2012

Maxwell (Mauritius) Pte Ltd

Les Cascades, Edith Cavell Street

Port Louis, Mauritius

Dear Investor:

Effective today, Amyris, Inc. (the “Company”) is selling shares of the Company's Common Stock pursuant to that certain Securities Purchase Agreement dated as of December 24, 2012 (the “SPA”) among the Company, Maxwell (Mauritius) Pte Ltd ( “Investor”) and the other Purchasers named therein. In connection therewith, the Company and Investor are entering into this letter agreement (this “Letter Agreement”). Capitalized terms used herein and not otherwise defined shall have the meaning given to such terms in the SPA.

The Company and Investor agree to the following:

1.    Payment Commitment Obligation. Investor hereby acknowledges and irrevocably agrees that by no later than January 14, 2013 Investor will pay to the Company Investor's applicable Total Purchase Price as set forth on Schedule I of the SPA by wire transfer of immediately available funds.

2.    Stock Certificate. The Company hereby acknowledges and agrees that (a) if Investor delivers to Company an Irrevocable Payment Instruction by Investor, then promptly upon receipt of such Irrevocable Payment Instruction, the Company (i) shall instruct its transfer agent to issue to the Investor a single stock certificate representing the number of Shares purchased by Investor pursuant to the SPA (“Investor's Stock Certificate”), (ii) shall instruct its transfer agent to deliver to Investor the Investor's Stock Certificate immediately upon the Company's confirmation to the transfer agent that it has received in its bank account the applicable Total Purchase Price from Investor, (iii) will not revoke the instructions referenced in clause (ii) of this paragraph, and (iv) will immediately notify its transfer agent once the Company has been notified by its bank that it has received by wire transfer Investor's applicable Total Purchase Price, or (b) if Investor does not deliver to Company an Irrevocable Payment Instruction, then immediately upon receipt by the Company in its bank account of the applicable Total Purchase Price from Investor the Company shall instruct its transfer agent to issue to, and deliver to, Investor Investor's Stock Certificate and the Company will not revoke such instructions.

3.    Amendment and Waiver. No amendment, modification, termination or cancellation of this Letter Agreement shall be effective unless it is in writing signed by the Company and Investor. No waiver of any of the provisions of this Letter Agreement shall be deemed or shall constitute a waiver of any other provisions hereof (whether or not similar) nor shall such waiver constitute a continuing waiver.

4.    Entire Agreement. This Letter Agreement, the SPA and the other documents referenced therein, set forth the entire understanding between the parties hereto relating to the subject matter hereof and supersede and merge all previous written and oral negotiations, commitments, understandings and agreements relating to the subject matter hereof between the Company and Investor.

5.    Notices. All notices and other communications hereunder shall be in writing and shall be deemed given when delivered personally or by commercial messenger or courier service to the parties at the following addresses (or at such other address for a party as shall be specified by like notice) or when sent by facsimile transmission or email to the facsimile number or email address specified below (or such other facsimile number or email as shall be specified by like notice), upon machine or electronic

confirmation of receipt:

(a) if to the Company, to:

Amyris, Inc.

5885 Hollis Street, Suite 100

Emeryville, CA 94608

Attention: General Counsel

Facsimile:

Email:

(b) if to Investor, to:

Maxwell (Mauritius) Pte Ltd

Les Cascades, Edith Cavell Street

Port Louis, Mauritius

Attention:

Facsimile:

With a copy to:

60B Orchard Road

#06-18 Tower 2

The Atrium@Orchard

Singapore 238891

6.    Governing Law. This Letter Agreement, and the provisions, rights, obligations and conditions set forth herein, and the legal relations between the parties hereto, including all disputes and claims, whether arising in contract, tort, or under statute, shall be governed by and construed in accordance with the laws of the State of Delaware without giving effect to its conflict of law provisions.

7.    Counterparts. This Letter Agreement may be executed in one or more counterparts, which shall together constitute one agreement.

Please indicate your agreement to the terms of this Letter Agreement by executing the acknowledgment and agreement below and returning a copy to the attention of our General Counsel.

[Remainder of Page Intentionally Left Blank]

Very truly yours,

AMYRIS, INC.

Name: John G. Melo

Title: President and Chief Executive Officer

Acknowledged and Agreed as

of the date first written above:

INVESTOR

MAXWELL (MAURITIUS) PTE LTD

By:

Name:

Title:

[Signature Page to Letter Agreement]

Schedule 3.40

Form of Biolding Letter

(see Exhibit 4.17 Annual Report on Form 10-K for fiscal 2012 as filed on March 2013)

Schedule 6(h)

Form of Side Letter

December 24, 2012

[Insert Investor Name]

[Insert Investor Address]

Dear Investor:

Effective today, Amyris, Inc. (the “Company”) is selling shares of the Company's Common Stock pursuant to that certain Securities Purchase Agreement dated as of December 24, 2012 (the “SPA”) among the Company, [Insert Investor Name] ( “Investor”) and the other Purchasers named therein. In connection therewith, the Company and Investor are entering into this letter agreement (this “Letter Agreement”). Capitalized terms used herein and not otherwise defined shall have the meaning given to such terms in the SPA.

The Company and Investor agree to the following:

1.    Irrevocable Payment Instruction. Investor hereby acknowledges and agrees that the Investor has given its payment instructions to its paying bank to make payment to the Company of the Investor's applicable Total Purchase Price pursuant to the SPA and will not revoke such payment instructions.

2.    Stock Certificate. The Company hereby acknowledges and agrees that (i) the Company has instructed its transfer agent to issue to the Investor a single stock certificate representing the number of Shares purchased by Investor pursuant to the SPA (“Investor's Stock Certificate”) on December 24, 2012, of which a PDF copy will be delivered to the Company on December 26, 2012; (ii) the Company has instructed its transfer agent to deliver to Investor the Investor's Stock Certificate immediately upon the Company's confirmation to the transfer agent that it has received in its bank account the applicable Total Purchase Price from Investor, (iii) the Company will not revoke the instructions referenced in clause (ii) of this paragraph, and (iv) the Company will immediately notify its transfer agent once the Company has been notified by its bank that it has received by wire transfer Investor's applicable Total Purchase Price.

2. Amendment and Waiver. No amendment, modification, termination or cancellation of this Letter Agreement shall be effective unless it is in writing signed by the Company and Investor. No waiver of any of the provisions of this Letter Agreement shall be deemed or shall constitute a waiver of any other provisions hereof (whether or not similar) nor shall such waiver constitute a continuing waiver.

3.    Entire Agreement. This Letter Agreement, the SPA and the other documents referenced therein, set forth the entire understanding between the parties hereto relating to the subject matter hereof and supersede and merge all previous written and oral negotiations, commitments, understandings and agreements relating to the subject matter hereof between the Company and Investor.

4.    Notices. All notices and other communications hereunder shall be in writing and shall be deemed given when delivered personally or by commercial messenger or courier service to the parties at the following addresses (or at such other address for a party as shall be specified by like notice) or when sent by facsimile transmission or email to the facsimile number or email

address specified below (or such other facsimile number or email as shall be specified by like notice), upon machine or electronic confirmation of receipt:

(a) if to the Company, to:

Amyris, Inc.

5885 Hollis Street, Suite 100

Emeryville, CA 94608

Attention:

Facsimile:

Email:

(b) if to Investor, to:

[Insert Investor Address]

[Insert Investor Address]

[Insert Investor Address]

Attention:

Facsimile:

Email:

5.    Governing Law. This Letter Agreement, and the provisions, rights, obligations and conditions set forth herein, and the legal relations between the parties hereto, including all disputes and claims, whether arising in contract, tort, or under statute, shall be governed by and construed in accordance with the laws of the State of Delaware without giving effect to its conflict of law provisions.

6.    Counterparts. This Letter Agreement may be executed in one or more counterparts, which shall together constitute one agreement.

Please indicate your agreement to the terms of this Letter Agreement by executing the acknowledgement and agreement below and returning a copy to the attention of our General Counsel.

[Remainder of Page Intentionally Left Blank]

Very truly yours,

AMYRIS, INC.

Name: John G. Melo

Title: President and Chief Executive Officer

Acknowledged and Agreed as

of the date first written above:

INVESTOR

MAXWELL (MAURITIUS) PTE LTD

By:

Name:

Title:

[Signature Page to Letter Agreement]

Exhibit A

RIGHTS AGREEMENT AMENDMENT

(see Exhibit 4.04 Annual Report on Form 10-K for fiscal 2012 as filed on March 2013)

Exhibit B

PURCHASER SUITABILITY QUESTIONNAIRE

FOR

AMYRIS, INC.

This Questionnaire is to be completed by each INDIVIDUAL purchasing securities of Amyris, Inc., a Delaware corporation (the "Company"). The purpose of this Questionnaire is to assure the Company that each proposed investor will meet certain suitability standards in connection with investment in the Company and the purchase of shares of the Company's Common Stock, $0.0001 par value per share (the "Shares"), including those imposed by applicable state and federal securities laws and the regulations under those laws.

Individuals investing in the name of a trust should not complete this Questionnaire but should instead complete an "Investor Questionnaire for Entities." If the answer to any question is "None" or "Not Applicable," please so state. If more space is needed for any answer, additional sheets may be attached.

Your answers will be kept confidential at all times. However, by signing this Questionnaire, you agree that the Company may present this Questionnaire to such par-ties as it deems appropriate to establish the availability of exemptions from registration or qualification requirements under federal and state securities laws.

1. IDENTIFICATION

1.1    Name(s) in which the Shares are to be registered:

1.2 If the Shares are to be registered in the name of two or more individuals or are to be community property, check one of the following:

___________    Joint Tenants with Right of Survivorship*

___________    Tenants in Common*

___________    Community Property*

*Each joint tenant and tenant-in-common other than your spouse must complete a separate Questionnaire. Your spouse, if any, must execute this Questionnaire.

1.3    Social Security Number:

1.4 Principal Residence Address:

1.5 Telephone Number:

1.6    Principal Occupation (if retired, previous occupation):

Position or Title:

1.7.    Education:

2. ACCREDITATION

2.1 Amount of the proposed investment: $________________________________________

Is your cash flow from all sources sufficient to satisfy your current needs, including possible contingencies, such that you have no need for liquidity in this proposed investment?

Yes_____        No_____

Do you have the ability to bear the economic risk of the investment, i.e., can you afford to lose your entire investment?

Yes_____        No_____

Do you, by reason of your business and financial experience or the     business and financial experience of a professional advisor, have the capacity to evaluate the merits and risks of your proposed investment and to protect your own interests in connection with the investment?

Yes_____        No_____

IF YES, please describe your business and financial experience, indicating the factual basis for your conclusion that you have such capacity:

Are you relying on the business or financial experience of an accountant, attorney or other professional advisor in evaluating the merits and risks of this investment in order to protect your own interest?

Yes_____        No_____

IF YES, please (a) have your advisor complete the Company's form of Advisor's Questionnaire and submit it with this Questionnaire, and (b) identify the advisor.

Name of professional advisor:

Is the proposed investment less than 10% of your net worth, or joint net worth with your spouse?

Yes_____        No_____

Have you previously invested in private placements of securities of recently formed, non-public companies or of companies without a history of significant earnings or profits?

Never _____        Rarely_____        On Several Occasions_____

2.2 Please initial which, if any, of the following statements are applicable to you:

_____ My individual net worth, or my joint net worth with my spouse, exceeds $1,000,000. (NOTE:  In computing the amount of net worth, please exclude both the value of your primary residence and the amount of indebtedness that is secured by your primary residence from the computation.  However, if the amount of such indebtedness exceeds the value of your primary residence, include the excess (and only the excess) indebtedness amount in the computation of net worth, but still do not include the value of your primary residence in the computation.  In addition, include in the computation any amount of such indebtedness, but not the value of your primary residence, that was incurred within 60 days preceding the proposed investment other than in connection with the acquisition of your primary residence.)

_____ My proposed total investment in the Company is at least $150,000 and does not exceed 10% of my net worth or joint net worth with my spouse.

_____ I personally have had an individual income in excess of $200,000 in each of the two (2) most recent years and I reasonably expect an income in excess of $200,000 in the current year.

_____ My joint income with my spouse is in excess of $300,000 in each of the two (2) most recent years and I reasonably expect a joint income in excess of $300,000 in the current year.

2.3 If you have not initialed one of the responses in Question 2.2 above, please answer the following questions:

My net worth or joint net worth with my spouse exceeds: $________________________.

(NOTE:  In computing the amount of net worth, please exclude both the value of your primary residence and the amount of indebtedness that is secured by your primary residence from the computation.  However, if the amount of such indebtedness exceeds the value of your primary residence, include the excess (and only the excess) indebtedness amount in the computation of net worth, but still do not include the value of your primary residence in the computation.  In addition, include in the computation any amount of such indebtedness, but not the value of your primary residence, that was incurred within 60 days preceding the proposed investment other than in connection with the acquisition of your primary residence.)

My estimated gross income together with my spouse for this calendar year is: (check one)

_____ under $75,000            _____ $75,000 - $99,999

_____ $100,000 - $199,999        _____ $200,000 and over

2.4 Are you related in any way to any other person who also intends to purchase Shares in this offering? If so, please state the name and nature of the relationship of each such person:

2.5 If you have used the services of a securities broker or dealer or a finder in submitting subscription documentation for the Shares, please identify the broker, dealer or finder:

3. EXECUTION

The information provided in this Questionnaire is true and complete as of the date provided below in all material respects and the undersigned recognizes that the Company is relying on the truth and accuracy of such information. The undersigned agrees to notify the Company promptly of any changes in the foregoing information that may occur prior to the closing of the sale of Shares of the Company.

_________________________________        ___________________________________

(Signature of Purchaser)                    (Signature of Spouse, if any)

Name:____________________________        Name:______________________________

(Please Print or Type)                    (Please Print or Type)

Date:_____________________________        Date:______________________________

Exhibit C

PURCHASER SUITABILITY QUESTIONNAIRE

FOR

AMYRIS, INC.

This Questionnaire is to be completed by each ENTITY (trust, corporation, partnership or other organization) purchasing securities of Amyris, Inc., a Delaware corporation (the "Company"). The purpose of this Questionnaire is to assure the Company that each proposed investor will meet certain suitability standards in connection with investment in the Company and the purchase of shares of the Company's Common Stock, $0.0001 par value per share (the "Shares"), including those imposed by applicable state and federal securities laws and the regulations under those laws.

If the answer to any question is "None" or "Not Applicable," please so state. If more space is needed for any answer, additional sheets may be attached.

Your answers will be kept confidential at all times. However, by signing this Questionnaire, you agree that the Company may present this Questionnaire to such parties as it deems appropriate to establish the availability of exemptions from registration or qualification requirements under federal and state securities laws.

1. IDENTIFICATION

1.1    Name(s) in which the Shares are to be registered:

1.2    Tax Identification Number:

1.3    Address of principal place of business:

1.4    Telephone number:___________________________________________

1.5    Jurisdiction of formation or of incorporation (Name the State or Country):

1.6    Form of entity (e.g., corporation, general partnership, limited partnership, trust, etc.):

1.7    Nature of business (e.g., investment, banking, manufacturing, venture capital investment

fund, etc.):

2. ACCREDITATION

2.1    Amount of the proposed investment: $

2.2 Is the entity's cash flow from all sources sufficient to satisfy its current needs, including possible contingencies, such that the entity has no need for liquidity in this proposed investment?

Yes_____        No_____

2.3 Was the entity specifically formed for the purpose of investing in the Company?

Yes_____        No_____

2.4 Does the entity have the ability to bear the economic risk of the investment, i.e., can the entity afford to lose its entire investment?

Yes_____        No_____

2.5 Is the entity an employee benefit plan governed by the Employee Retirement Income Security Act of 1974 (a 401(k) Plan, Keogh Plan, pension plan, etc., maintained by an employer for its employees)?

Yes_____        No_____

IF YES, please indicate which, if any, of the following categories accurately describes the entity:

_____    the employee benefit plan has total assets in excess of $5,000,000.

_____ the plan is a self-directed plan with investment decisions made solely by persons listed in Section 2.6 below or who are individuals, and each such individual has a net worth in excess $1,000,000 or had an individual income in excess of $200,000 in each of the two most recent years and has a reasonable expectation of reaching the same income level in the current year.

_____ investment decisions are made by a plan fiduciary which is either a bank, savings and loan association, insurance company or registered investment advisor.

2.6    Please indicate which, if any, of the following categories accurately describes the entity:

_____    A bank.

_____    A savings and loan association.

_____ A broker-dealer registered under Section 15 of the Securities Exchange Act of 1934.

_____    An insurance company.

_____ An investment company registered under the Investment Company Act of 1940 or a business development company as defined in Section 2(a)(48) of that Act.

_____ A Small Business Investment Company licensed by the U.S. Small Business Administration under Section 301(c) or (d) of the Small Business Investment Act of 1958.

_____ A private business development company defined in Section 202(a)(22) of the Investment Advisors Act of 1940.

_____ An organization described in Section 501(c)(3) of the Internal Revenue Code with total assets in excess of $5,000,000 not formed for the purpose of investing in the Company.

_____ A corporation with total assets in excess of $5,000,000, not formed for the purpose of investing in the Company.

_____ A partnership with total assets in excess of $5,000,000, not formed for the purpose of investing in the Company.

_____ A Massachusetts or similar business trust with total assets in excess of $5,000,000, not formed for the purpose of investing in the Company.

_____ Any other trust with total assets in excess of $5,000,000, not formed for the purpose of investing in the Company.

2.7    Please indicate if one of the following describes the equity owners of the entity:

_____ Each equity owner of the entity (i.e., all shareholders, all general and/or limited partners or all beneficiaries, as applicable) is an individual whose net worth or joint net worth with his or her spouse exceeds $1,000,000.

_____ Each equity owner of the entity is an individual who had a personal income in excess of $200,000 in each of the two (2) most recent years or joint income with that person's spouse in excess of $300,000 in each of those years and reasonably expects to reach the same income level in the current year.

_____ Each equity owner of the entity is an entity described in at least one category of Question 2.6 above.

_____ Although not all equity owners are described in the same category above in this Question 2.7, each equity owner is described in at least one such category.

2.8    Please indicate which of the following also describes the equity owners of the entity:

_____ Each equity owner of the entity has, by reason of his, her or its business and financial experience, the capacity to evaluate the merits and risks of the entity's proposed investment and to protect his, her or its own interests in connection with the investment.

_____ Each of the equity owners of the entity is able to bear the economic risk of the entity's investment, i.e., can afford loss of the entity's entire investment.

_____ The beneficial interest of each equity owner in the entity's proposed investment is less than 10% of such equity owner's net worth, or joint net worth with his or her spouse.

_____ Although not all equity owners are described in the same category above in this Question 2.8, each equity owner is described in at least one such category.

3. ADDITIONAL INFORMATION

3.1 Has your entity previously invested in private placements of securities of newly-formed, non-public companies or companies without a history of significant profits or earnings?

Never _______    Rarely _______    On Several Occasions _______

3.2 Does your entity, by reason of its business and financial knowledge and experience, have the capacity to evaluate the merits and risks of the entity's proposed investment and to protect the entity's own interests in connection with its investment in the Company?

Yes _____    No _____

IF YES, please describe the business and financial knowledge and experience, indicating factual basis for your conclusion that the entity has such capacity.

3.3 Do the persons responsible for making the investment decision for the entity, by reason of their business and financial knowledge and experience, have the capacity to evaluate the merits and risks of the entity's proposed investment?

Yes _____    No _____

IF YES, please describe the business and financial knowledge and experience, indicating factual basis for your conclusion that those persons have such capacity.

3.4 If you have used the services of a securities broker or dealer or a finder in submitting subscription documentation for the Shares, please identify the broker, dealer or finder:

3.5 Are you relying on the business or financial experience of an accountant, attorney or other professional advisor in evaluating the merits and risks of this investment in order to protect your own interest?

Yes_____        No_____

IF YES, please (a) have your advisor complete the Company's form of Advisor's Questionnaire and submit it with this Questionnaire, and (b) identify the advisor.

Name of professional advisor:    

4. EXECUTION

The information provided in this Questionnaire is true and complete as of the date provided below in all material respects and the undersigned recognizes that the Company is relying on the truth and accuracy of such information. The undersigned agrees to notify the Company promptly of any changes in the foregoing information that may occur prior to the closing of the sale of Shares of the Company.

Name of Entity:

___________________________________________________________

(Please Print or Type)

By:________________________________________________________

(Signature)

Name:______________________________________________________

(Please Print or Type)

Title:_______________________________________________________

(Please Print or Type)

Date:_______________________________________________________

Exhibit D

OPINION OF COMPANY COUNSEL

December 24, 2012

To the Purchasers of Common Stock of

Amyris, Inc. Who are Listed as Investing

on the Date Hereof on the Signature Pages to the Purchase Agreement

Ladies and Gentlemen:

We have acted as counsel for Amyris, Inc., a Delaware corporation (the "Company"), in connection with the sale on the date hereof by the Company to you of 14,177,849 shares of the Company's Common Stock (the "Shares") pursuant to the Stock Purchase Agreement, dated as of December 24, 2012 (the "Purchase Agreement"), among the Company and the parties whose names appear on the signature pages thereto (the "Purchasers"), and the execution and delivery by the Company of the Amendment No. 2 to Amended and Restated Investors' Rights Agreement (the "Rights Agreement"), dated as of December 24, 2012. This opinion is given to you pursuant to Article 6(d) of the Purchase Agreement in connection with the Closing of the sale of the Shares. The Purchase Agreement and the Rights Agreement are referred to herein together as the "Transaction Documents." Unless defined herein, capitalized terms used herein have the meaning given to them in the Purchase Agreement.

We have examined such matters of law as we reasonably considered necessary for the purpose of rendering this opinion. As to matters of fact material to the opinions expressed herein, we have relied upon the representations and warranties as to factual matters contained in, and made by the Company pursuant to, the Purchase Agreement and upon certificates and statements of government officials and of officers of the Company, including but not limited to a certificate of the Company to us (the "Opinion Certificate"). In addition, we have examined originals or copies of documents, corporate records and other writings that are listed in Exhibit A attached hereto (the “Reviewed Agreements”) and have not conducted any other factual examination except as listed on Exhibit A. In such examination, we have assumed that the signatures on documents and instruments examined by us are authentic, that each is what it purports to be, and that all documents and instruments submitted to us as copies or facsimiles conform with the originals, which facts we have not independently verified.

In making our examination of documents (including the Transaction Documents) and rendering our opinions, we have further assumed that, except for the Company with respect to the Transaction Documents, (a) each party to such documents had the entity power and entity authority to enter into and perform all of such party's obligations thereunder, (b) each party to such documents has duly authorized, executed and delivered such documents and (c) each of such documents is enforceable against and binding upon the parties thereto. We have also assumed that (i) the representations and warranties of the Purchasers set forth in the Transaction Documents are accurate and complete, (ii) there is no fact or circumstance relating to you or your business that might prevent you from enforcing any of your rights provided for in the Transaction Documents and (iii) there are no extrinsic agreements or understandings among the parties to the Transaction Documents or among the parties to the Reviewed Agreements expressly identified on Exhibit A hereto, that would modify or interpret the terms of the

To the Purchasers of Common

Stock of Amyris, Inc. on the Date Hereof

December 24, 2012

Page 2

Transaction Documents or Reviewed Agreements or the respective rights or obligations of the parties thereto.

Notwithstanding the examination described above, the expressions "to our knowledge," "known to us," "our actual knowledge" or words of similar import when used in this opinion letter, refer to the current actual knowledge of attorneys within the firm who have rendered legal services to the Company in connection with the Transaction Documents and means that, while such attorneys have not been informed by the Company that a matter stated is factually incorrect, we have made no independent factual investigation with respect to such matter. No inference as to our knowledge of any matters bearing on the accuracy of any such statement should be drawn from the fact of our representation of the Company or the rendering of the opinions set forth below.

Where statements in this opinion concerning the Company, or an effect on the Company, are qualified by the term "material" or "materially," those statements involve judgments and opinions as to the materiality or lack of materiality of any matter to the Company's business, assets, results of operations or financial condition that are entirely those of the Company and its officers.

We express no opinion as to matters governed by any laws other than the laws of the State of California, the Delaware General Corporation Law (the "DGCL") and the federal law of the United States of America, including the rules and regulations promulgated by governmental authorities thereunder, as such laws, rules and regulations exist on the date hereof (collectively, "Applicable Laws"). We express no opinion as to whether the laws of any particular jurisdiction apply, or to the extent that the laws of any jurisdiction other than those identified above are applicable to the Transaction Documents or the transactions contemplated thereby.

In rendering the opinion set forth in paragraph (1) (Qualification to Do Business) below as to the

valid existence and good standing of the Company under the laws of the State of Delaware and as to its qualification to do business as a foreign corporation in good standing under the laws of the State of California, we have relied exclusively on certificates of public officials and the Opinion Certificate.

In rendering the opinion set forth in paragraph (2) (Authority and Power to Do Business) below concerning the Company's corporate power and corporate authority to conduct its business as it is presently conducted and as to the types of businesses the Company presently conducts, we have relied exclusively upon representations made to us in the Opinion Certificate. We note that the parties to the Purchase Agreement have designated the laws of the State of Delaware as the laws governing the Purchase Agreement. Notwithstanding the designation therein of the laws of the State of Delaware, our opinion in paragraph (4) (Enforceability) below as to the validity, binding effect and enforceability of the Purchase Agreement is premised upon the results that would be obtained if a California court were to apply the internal laws of the State of California to contracts made between California residents present in California when the Purchase Agreement is entered into and, where applicable, the currently effective DGCL, without regard to laws regarding choice of law or conflict of laws.

To the Purchasers of Common

Stock of Amyris, Inc. on the Date Hereof

December 24, 2012

Page 3

In rendering the opinion in paragraph (6) (No Violations) below relating to violations of Applicable Laws, and paragraph (7) (No Consents) below relating to consents, approvals, authorizations and filings under, or pursuant to, Applicable Laws, such opinions are limited to Applicable Laws that in our experience are typically applicable to transactions of the nature provided for in the Transaction Documents. Moreover, we render no opinion in such paragraphs, or in paragraph (4) (Enforceability), regarding the Company's compliance with applicable securities laws, including but not limited to laws regarding the registration or qualification of the offer and sale of securities, or the registration by the Company under any such securities laws, and no such opinion should be inferred from the language of those paragraphs. Any opinion rendered in connection with applicable securities laws is rendered solely and expressly in paragraphs (8) (Securities Law Compliance) and (9) (Not an Investment Company) below.

In rendering the opinion in paragraph (6) (No Violations) below regarding breach of, or default under, any Reviewed Agreements set forth in Exhibit A, we have not reviewed, and express no opinion on, (a) financial covenants or similar provisions requiring financial calculations or determinations to ascertain whether there is any breach or default nor (b) provisions relating to the occurrence of a "material adverse event" or words of similar import. We also do not express any opinion on parol evidence bearing on interpretation or construction of such Reviewed Agreements, or on any oral modifications to such Reviewed Agreements made by the parties thereto. Moreover, to the extent that any of the Reviewed Agreements are governed by the laws of any jurisdiction other than the State of California our opinion relating to those agreements is based solely upon the plain meaning of their language as though California law applied, without regard to interpretation or construction that might be indicated by the laws stated as governing those agreements.

In rendering the opinion expressed in paragraph (8) (Securities Law Compliance) below, we have assumed the accuracy of, and have relied upon, the Company's representations to us that the Company has made no offer to sell the Shares by means of any general solicitation or publication of any advertisement therefor, and we have assumed that the offer and sale of the Shares is not integrated with any future securities offering of the Company.

This opinion is qualified by, and we render no opinion with respect to, or as to the effect of, the following:

(a)    bankruptcy, insolvency, reorganization, moratorium and other similar laws relating to or affecting the relief of debtors or the rights and remedies of creditors generally, including without limitation the effect of statutory or other law regarding fraudulent transfers, preferential transfers and equitable subordination;

(b)    general principles of equity, including but not limited to judicial decisions holding that certain provisions are unenforceable when their enforcement would violate the implied covenant of good faith and fair dealing, would be commercially unreasonable or involve undue delay, whether or not such principles or decisions have been codified by statute, or that result from the exercise of the court's discretion;

To the Purchasers of Common

Stock of Amyris, Inc. on the Date Hereof

December 24, 2012

Page 4

(c)    Section 1670.5 of the California Civil Code or any other California or United States federal law or provision of the DGCL or equitable principle which provides that a court may refuse to enforce, or may limit the application of, a contract or any clause thereof that the court finds to have been unconscionable at the time it was made, unconscionable in performance or contrary to public policy;

(d)    any provision purporting to (i) exclude conflict of law principles under any law or (ii) select certain courts as the venue, or establish a particular jurisdiction as the forum, for the adjudication of any controversy;

(e)    judicial decisions, that may permit the introduction of extrinsic evidence to modify the terms or the interpretation of any agreement;

(f)    the tax or accounting consequences of any transaction contemplated in connection with the sale of the Shares under applicable tax laws and regulations and under applicable accounting rules, regulations, releases, statements, interpretations or technical bulletins;

(g)    applicable antifraud statutes, rules or regulations of United States federal or applicable state laws concerning the issuance or sale of securities, including, without limitation, (i) the accuracy and completeness of the information provided by the Company to the Purchasers in connection with the offer and sale of the Shares, and (ii) the accuracy or fairness of the past, present or future fair market value of any securities;

(h)    the effect any breach of the fiduciary duties of the members of the Company's Board of Directors, officers or principal stockholders would have on the enforceability authorization and performance of any agreement;

(i)    whether or not any Transaction Document, and the transactions provided for therein, were fair and reasonable to the Company at the time of their authorization by the Company's Board of Directors and stockholders within the meaning of Section 144 of the DGCL;

(j)    any provisions stating that (i) rights or remedies are not exclusive, (ii) rights or remedies may be exercised without notice, (iii) every right or remedy is cumulative and may be exercised in addition to or with any other right or remedy or (iv) the failure to exercise, or any delay in exercising, rights or remedies available under an agreement will not operate as a waiver of any such right or remedy;

(k)    provisions stating that rights set forth in the agreement in which such provision appears may only be waived in writing if an implied agreement by trade practice or course of conduct has given rise to a waiver or that limit the effect of waivers by trade practice or course of conduct;

(l)    any United States federal or other antitrust laws, statutes, rules or regulations, including without limitation the Hart-Scott-Rodino Antitrust Improvements

To the Purchasers of Common

Stock of Amyris, Inc. on the Date Hereof

December 24, 2012

Page 5

Act of 1976, or other laws relating to collusive or unfair trade practices or designed to promote competition in any jurisdiction;

(m)    any provision purporting to (i) waive rights to trial by jury, service of process or objections to the laying of venue or forum in connection with any litigation arising out of or pertaining to the agreement in which such provision appears, (ii) change or waive the rules of evidence, make determinations conclusive or fix the method or quantum of proof or (iii) waive the statute of limitations;

(n)    any choice of law clause, to the extent the provision to be governed by that law could be determined by the court (i) to be contrary to a public or fundamental policy of a state or country whose law would apply in the absence of a choice of law clause, and (ii) to involve an issue in which such state or country, or California State, has a materially greater interest in the determination of the particular issue than does the state whose law is chosen;

(o)    any United States federal laws, statutes, rules or regulations, including without limitation the International Investment and Trade in Services Survey Act (Title 22 of the United States Code, Chapter 46, §§3101-3108), or other state or foreign investment laws, statutes, rules and regulations governing investments in the United States or in U.S. entities by persons that are not citizens of the United States; and

(p)    indemnification and contribution provisions to the extent enforcement of such provisions is contrary to public policy, indemnify a party to a contract against such party's actions taken in bad faith or that constitute a breach of fiduciary duties, or indemnify a party against liability for future conduct or the party's own fraud or wrongful, reckless or negligent acts or omissions.

In accordance with Section 95 of the American Law Institute's Restatement (Third) of the Law Governing Lawyers (2000), this opinion letter is to be interpreted in accordance with customary practices of lawyers rendering opinions to third parties in transactions of the type provided for in the Transaction Documents.

Based upon and subject to the foregoing, and except as set forth in the Purchase Agreement, as of immediately prior to the Closing we are of the following opinion.

(1)    The Company is a corporation duly incorporated, validly existing and in good standing under the laws of the State of Delaware. The Company is qualified to do business as a foreign corporation in good standing under the laws of the State of California.

(2)    The Company has all corporate power and corporate authority required to execute, deliver and perform its obligations under the Transaction Documents.

(3)    All corporate action has been taken on the part of the Company's Board of Directors and

stockholders that (a) is necessary for the execution and delivery of the Transaction Documents by the Company, (b) must be taken by the Company to authorize the sale and

To the Purchasers of Common

Stock of Amyris, Inc. on the Date Hereof

December 24, 2012

Page 6

issuance of the Shares on the date hereof and (c) must be taken by the Company as of the date hereof to authorize performance by the Company of its obligations under the Transaction Documents.

(4)    Each of the Transaction Documents has been duly executed by the Company and has been delivered by the Company to the Purchasers. Each of the Transaction Documents constitutes a valid and binding obligation of the Company, enforceable by you against the Company in accordance with its terms.

(5)    The Shares to be issued to you under the Purchase Agreement are duly authorized, and when issued in compliance with the provisions of the Purchase Agreement, will be validly issued, fully paid and non-assessable, and the issuance of such Shares will not be subject to any preemptive rights, rights of first refusal or rights of first offer set forth in the Restated Certificate or Bylaws or any Reviewed Agreement set forth on Exhibit A (other than the Side Letter for which appropriate waivers have been obtained).

(6)    The execution, delivery and performance of the Transaction Documents by the Company do not, as of the Closing, result in (a) a violation by the Company of the Restated Certificate or Bylaws, (b) a material violation by the Company of any judgment or order of any court or governmental authority, (c) a material violation by the Company of Applicable Law or (d) a breach of, or a default under, any Reviewed Agreements set forth on Exhibit A.

(7)    Other than those that previously may have been obtained or made, no consent, approval or authorization of, or filing with, any governmental authority pursuant to any Applicable Law is required to be made or obtained by the Company or any subsidiary of the Company in connection with the Company's (a) valid execution and delivery of the Transaction Documents, (b) performance of its obligations under the Purchase Agreement on the date hereof and (c) performance of its obligations under the other Transaction Documents as of the date hereof.

(8)    Based in part upon the representations made by you in the Purchase Agreement, and subject to the filings of such securities law notices as may be required to be filed subsequent to the Closing, the offer, sale and issuance of the Shares to be issued to you in conformity with the terms of the Purchase Agreement constitute transactions exempt from the registration requirements of Section 5 of the Securities Act of 1933, as amended, and exempt from the qualification requirements of Section 25110 of the California Corporate Securities Law of 1968, as amended.

(9)    The Company is not and, after giving effect to the offering and sale of the Shares, will not be, required to register as an “investment company” as such term is defined in the Investment Company Act

of 1940, as amended.

In addition to the foregoing opinions, based upon the foregoing and other than as set forth in the Purchase Agreement, we supplementally confirm the following to you as of immediately prior to the Closing.

To the Purchasers of Common

Stock of Amyris, Inc. on the Date Hereof

December 24, 2012

Page 7

Litigation Confirmation. To our knowledge, there is no action, suit, proceeding or investigation by or before any United States federal, California State or Delaware State court or governmental authority that is pending or threatened in writing against the Company and that questions the validity of the Transaction Documents or the right of the Company to enter into and perform its obligations under the Transaction Documents. Please note that we have not conducted a docket search in any jurisdiction with respect to any action, suit, proceeding or investigation that may be pending against the Company and we have not undertaken any search regarding any of its affiliates, officers or directors, nor, other than to request the Opinion Certificate from the Company, have we undertaken any further inquiry whatsoever in connection with the existence any such action, suit, proceeding or investigation.

[Remainder of Page Left Intentionally Blank]

This opinion is rendered as of the date first written above solely for your benefit in connection with the sale and issuance of the Shares pursuant to the Purchase Agreement and may not be relied on by, nor may any copy be delivered to, any other person or entity without our prior written consent. Our opinion is expressly limited to the matters set forth above and we render no opinion, whether by implication or otherwise, as to any other matters. We assume no obligation to inform you of any fact, circumstance, event or change in the law or the facts that may hereafter be brought to our attention that may alter, affect or modify the opinions expressed herein.

Very truly yours,

FENWICK & WEST LLP

By:

Daniel Winnike, a Partner

To the Purchasers of Common

Stock of Amyris, Inc. on the Date Hereof

December 24, 2012

Page 9

Exhibit A

Review of Documents

1) The Purchase Agreement and the Rights Agreement and the Letter Agreement dated February 23, 2012 (the “Side Letter”) by and among the Company and Naxyris S.A., Sualk Capital Ltd, Maxwell (Mauritius) Pte Ltd and Biolding Investment SA.

2) A copy of the Company's Restated Certificate of Incorporation, certified by the Delaware Secretary of State on September 30, 2010 (the "Restated Certificate").

3) A copy of the Company's Bylaws certified by the Company's Secretary on September 30, 2010 (the "Bylaws").

4) The Certificate of Incorporation of the Company filed with the Secretary of State of the State of California upon the Company's incorporation, the Certificate of Merger and Restated Certificate of Incorporation of the Company filed with the Secretary of State of the State of Delaware upon the Company's re-incorporation in Delaware, the California and Delaware bylaws of the Company initially adopted by the Company and minutes of meetings and actions by written consent of the Company's incorporator(s), shareholders and Board of Directors that are contained in the Company's minute books.

5) An Opinion Certificate addressed to us and dated of even date herewith executed by the Company (the "Opinion Certificate").

6) A Certificate of Status regarding the Company issued by the Secretary of State of the Delaware, dated December __, 2012, indicating that the Company is qualified to do business, as a domestic corporation in that state (together with the letter referred to in item (7) below and the certificate referred to in item (8) below, the "Certificate of Good Standing").

7) A letter from the California Franchise Tax Board dated December __, 2012 to the effect that the Company is in good standing with respect to its California franchise tax filings and has no known unpaid franchise tax liability.

8) A Certificate of Good Standing from the Secretary of State of the State of California, indicating that the Company is in good standing and is qualified to do business as a foreign corporation therein.

9) A copy of the Series D Preferred Stock Purchase Agreement dated June 21, 2010.

10) A copy of the Amended and Restated Investors' Rights Agreement dated June 21, 2010, as amended by Amendment No. 1 thereto dated February 23, 2012.

11) A copy of the Stock Purchase Agreement dated February 22, 2012 by and between the Company and the Purchasers listed on the signature pages thereto.

12) A copy of the Securities Purchase Agreement dated February 24, 2012 by and between the Company and the Purchasers listed on the signature pages thereto, the Senior

To the Purchasers of Common

Stock of Amyris, Inc. on the Date Hereof

December 24, 2012

Page 10

Unsecured Convertible Notes issued thereunder and the Registration Rights Agreement by and between the Company and Purchasers listed on the signature pages thereto, dated February 27, 2012.

13)    Copies of those Common Stock Purchase Agreements dated May 18, 2012 by and between the Company and certain Company stockholders.

14)    Securities Purchase Agreement dated July 30, 2012 by and between the Company and Total Gas & Power USA, SAS, the Senior Unsecured Convertible Notes issued thereunder and the Registration Rights Agreement by and between the Company and Total Gas & Power USA, SAS, dated July 30, 2012.

EX-4.17

CONFIDENTIAL TREATMENT REQUESTED. CERTAIN PORTIONS OF THIS DOCUMENT HAVE BEEN OMITTED PURSUANT TO A REQUEST FOR CONFIDENTIAL TREATMENT AND, WHERE APPLICABLE, HAVE BEEN MARKED WITH AN ASTERISK TO DENOTE WHERE OMISSIONS HAVE BEEN MADE. THE CONFIDENTIAL MATERIAL HAS BEEN FILED SEPARATELY WITH THE SECURITIES AND EXCHANGE COMMISSION.

FOLLOW-ON INVESTMENT AGREEMENT

This Follow-On Investment Agreement (this “Agreement”) is entered into between Amyris, Inc., a Delaware corporation (the “Company”) and Biolding Investment SA (“Biolding”) on December 24, 2012.

RECITALS

A.    The Company entered into that certain Letter Agreement, dated February 23, 2012 (the “Letter Agreement”), by and among the Company and the investors named therein, including Biolding. Capitalized terms used herein and not otherwise defined shall have the meaning ascribed to them in the Letter Agreement.

B.    Pursuant to Section 3 of the Letter Agreement, upon completion of the Milestone, Biolding is obligated to purchase $15,000,000 worth of additional shares of the Company's Common Stock in the Follow-On Investment (such obligation, the “Investment Obligation”).

C.    The Company intends to sell, in a private offering exempt from the registration requirements of the Securities Act of 1933, an aggregate of not to exceed 14,177,849 shares of its Common Stock, $0.0001 par value per share (the “Shares”), at a purchase price per share equal to the higher of the book value per Share or the last occurring consolidated closing bid price per Share (as defined by The NASDAQ Stock Market) as of the time of signing of the binding agreement to sell and issue the Shares, to certain existing investors of the Company (the “Financing”) and, Biolding will be purchasing $10,000,000 worth of the Shares (the “Biolding Investment”) in the Financing.

AGREEMENT

Now, therefore, in consideration of the foregoing recitals and the mutual promises hereinafter set forth, the parties hereto hereby agree as follows:

1.Payment Commitment Obligation. Biolding hereby acknowledges and irrevocably agrees that by no later than March 31, 2013, Biolding will purchase from the Company at least $5,000,000 of the Company's Common Stock (the “Additional Shares”) at a purchase price per share equal to the higher of the book value per share of the Company's Common Stock or the last occurring consolidated closing bid price per share of the Company's Common Stock (as defined by The NASDAQ Stock Market) as of the time of signing by the Company of the binding agreement to sell and issue the Additional Shares (such purchase, the “Additional Biolding Investment”); provided that Biolding's obligation hereunder to complete the Additional Biolding Investment shall be contingent upon (i) completion of the Milestone by the Company subject to Biolding's verification to its reasonable satisfaction that the Milestone has been achieved, and (ii) the Company's Leadership Development and Compensation Committee (the “LDCC”) approving minutes from the LDCC meeting held on December 19, 2012, which minutes shall include a resolution that provides that one of the most significant bases in determining the Company's Chief Executive Officer's 2013 bonus will be achieving [*].

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

2.Acknowledgment. The Company hereby acknowledges that upon the closing of the Biolding Investment, Biolding shall have satisfied $10,000,000 of the Investment Obligation under Section 3 of the Letter Agreement and upon completion of the Additional Biolding Investment, Biolding shall have satisfied all of its obligations under Section 3 of the Letter Agreement, and Biolding shall be under no obligation to invest additional funds in the Company pursuant to the Letter Agreement.

3.Rights under Side Letter. Other than as set forth above, this Acknowledgment shall not affect the rights and obligations of the Company and Biolding as set forth in the Letter Agreement.

4.Amendment and Waiver.  No amendment, modification, termination or cancellation of this Agreement shall be effective unless it is in writing signed by the Company and Biolding. No waiver of any of the provisions of this Agreement shall be deemed or shall constitute a waiver of any other provisions hereof (whether or not similar) nor shall such waiver constitute a continuing waiver.

5.Governing Law. This Agreement, and the provisions, rights, obligations and conditions set forth herein, and the legal relations between the parties hereto, including all disputes and claims, whether arising in contract, tort, or under statute, shall be governed by and construed in accordance with the laws of the State of Delaware without giving effect to its conflict of law provisions.

6.Notices.    All notices and other communications hereunder shall be in writing and shall be deemed given when delivered personally or by commercial messenger or courier service to the parties at the following addresses (or at such other address for a party as shall be specified by like notice) or when sent by facsimile transmission or email to the facsimile number or email address specified below (or such other facsimile number or email as shall be specified by like notice), upon machine or electronic confirmation of receipt:

(a)	if to the Company, to:
	Amyris, Inc.
	5885 Hollis Street, Suite 100
	Emeryville, CA 94608
	Attention: Gary Loeb, General Counsel
	Facsimile: [*]
	Email: [*]

(b)	if to Biolding, to
	Biolding Investment SA
	11A  boulevard Prince Henri
	L 1724 Luxembourg.
	Attention: HH Sheikh Abdullah bin Khalifa Al Thani and M. Jean Paul Soulié
	Facsimile: [*]
	Email: [*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

7.Counterparts. This Agreement may be executed in one or more counterparts, which shall together constitute one agreement.

[Remainder of Page Intentionally Left Blank]

IN WITNESS WHEREOF, the undersigned has duly executed this Agreement as of the date first above written.

COMPANY:

AMYRIS, INC.

By: /s/ John G. Melo                

Name: John G. Melo                

Title: President and Chief Executive Officer    

Acknowledged and Accepted by:

BIOLDING INVESTMENT SA

By:

Name:

Title:

[Signature Page to Follow-On Investment Agreement]

IN WITNESS WHEREOF, the undersigned has duly executed this Agreement as of the date first above written.

COMPANY:

AMYRIS, INC.

By:

Name:

Title:

Acknowledged and Accepted by:

BIOLDING INVESTMENT SA

By: /s/ Sheikh Abdullah bin Khalifa Al Thani    

Name: Sheikh Abdullah bin Khalifa Al Thani    

Title: Director                    

[Signature Page to Follow-On Investment Agreement]

EX-10.10

ASSISTANCE AGREEMENT
1. Award No. DE-EE0002869		2. Modification No. 003		3. Effective Date 12/28/2009		4. CFDA No. 81.087
5. Awarded To AMYRIS BIOTECHNOLOGIES, INC. Attn: KINKEAD REILING 5885 HOLLIS STREET SUITE 100 EMERYVILLE CA 946082059			6. Sponsoring Office Golden Field Office U.S. Department of Energy Golden Field Office 1617 Cole Blvd. Golden CO 80401				7. Period of Performance 12/28/2009 through 06/30/2012
8. Type of Agreement _ Grant x Cooperative Agreement _ Other	9. Authority 109-58 Energy Policy Act (2005) 111-5 Recovery Act (2009)				10. Purchase Request or Funding Document No. 10EE005822
11. Remittance Address			12. Total Amount				13. Funds Obligated
AMYRIS BIOTECHNOLOGIES, INC. Attn: KINKEAD REILING 5885 HOLLIS STREET SUITE 100 EMERYVILLE CA 946082059			Govt. Share: $ 24,341,409.00 Cost Share: $ 10,591,590.00 Total: $ 34,932,999.00				This action: $0.00 Total: $24,341,409.00
14. Principal Investigator Neil Renninger Phone: 510-740-7414	15. Program Manager Fred W. Gerdeman Phone: 303-275-4928				16. Administrator Golden Field Office U.S. Department of Energy Golden Field Office 1617 Cole Blvd. Golden CO 80401-3393
17. Submit Payment Requests To OR for Golden U.S. Department of Energy Oak Ridge Financial Service Center P.O. Box 4517 Oak Ridge TN 37831			18. Paying Office OR for Golden U.S. Department of Energy Oak Ridge Financial Service Center P.O. Box 4517 Oak Ridge TN 37831				19. Submit Reports To
20. Accounting and Appropriation Data See Schedule
21. Research Title and/or Description of Project RECOVERY ACT: SCALE-UP & MOBILIZATION OF RENEWABLE DIESEL & CHEMICAL PRODUCTION FROM COMMON INTERMEDIATE USING US-BASED FERMENTABLE SUGAR FEEDSTOCKS
For the Recipient				For the United States of America
22. Signature of Person Authorized to Sign				25. Signature of Grants/Agreements Officer Signature on File
23. Name and Title	24. Date Signed			26. Name of Officer Jon F. Olsen				27. Date Signed 07/02/2010

CONTINUATION SHEET		REFERENCE NO. OF DOCUMENT BEING CONTINUED DE-EE0002869/003			PAGE 2 OF 2
NAME OF OFFEROR OR CONTRACTOR AMYRIS BIOTECHNOLOGIES, INC.
ITEM  NO. (A)	SUPPLIES/SERVICES (B)	QUANTITY (C)	UNIT (D)	UNIT PRICE (E)	AMOUNT (F)
	DUNS Number: 185930182 The purpose of this modification is to: 1) Update the DOE Project Officer, as shown below and in Block 15. All other terms and conditions remain unchanged. In Block 7 of the Assistance Agreement, the Period of Performance reflects the beginning of the Project Period through the end of the current Budget Period, shown as 12/28/2009 through 6/30/2012. DOE Award Administrator: Brenda Dias E-mail: brenda.dias@go.doe.gov Phone: 303-275-6043 DOE Project Officer: Fred Gerdeman E-mail: fred.gerdeman@go.doe.gov Phone: 303-275-4928 Recipient Business Officer: Todd Pray E-mail: pray@amyris.com Phone: 510-740-7441 Recipient Principal Investigator: Neil Renninger E-mail: renninger@amyris.com Phone: 510-740-7414 “Electronic signature or signatures as used in this document means a method of signing an electronic message that-- (A) Identifies and authenticates a particular person as the source of the electronic message; (B) Indicates such person's approval of the information contained in the electronic message; and, (C) Submission via FedConnect constitutes electronically signed documents.” ASAP: NO Extent Competed: COMPETED Davis-Bacon Act: YES
JULY 2004

ASSISTANCE AGREEMENT
1. Award No. DE-EE0002869		2. Modification No. 004		3. Effective Date 12/28/2009		4. CFDA No. 81.087
5. Awarded To AMYRIS BIOTECHNOLOGIES, INC. Attn: KINKEAD REILING 5885 HOLLIS STREET SUITE 100 EMERYVILLE CA 946082059			6. Sponsoring Office Golden Field Office U.S. Department of Energy Golden Field Office 1617 Cole Blvd. Golden CO 80401				7. Period of Performance 12/28/2009 through 06/30/2012
8. Type of Agreement _ Grant x Cooperative Agreement _ Other	9. Authority 109-58 Energy Policy Act (2005) 111-5 Recovery Act (2009)				10. Purchase Request or Funding Document No.
11. Remittance Address			12. Total Amount				13. Funds Obligated
AMYRIS BIOTECHNOLOGIES, INC. Attn: KINKEAD REILING 5885 HOLLIS STREET SUITE 100 EMERYVILLE CA 946082059			Govt. Share: $ 24,341,409.00 Cost Share: $ 10,591,590.00 Total: $ 34,932,999.00				This action: $0.00 Total: $24,341,409.00
14. Principal Investigator Neil Renninger Phone: 510-740-7414	15. Program Manager Fred W. Gerdeman Phone: 303-275-4928				16. Administrator Golden Field Office U.S. Department of Energy Golden Field Office 1617 Cole Blvd. Golden CO 80401-3393
17. Submit Payment Requests To OR for Golden U.S. Department of Energy Oak Ridge Financial Service Center P.O. Box 4517 Oak Ridge TN 37831			18. Paying Office OR for Golden U.S. Department of Energy Oak Ridge Financial Service Center P.O. Box 4517 Oak Ridge TN 37831				19. Submit Reports To
20. Accounting and Appropriation Data See Schedule
21. Research Title and/or Description of Project RECOVERY ACT: SCALE-UP & MOBILIZATION OF RENEWABLE DIESEL & CHEMICAL PRODUCTION FROM COMMON INTERMEDIATE USING US-BASED FERMENTABLE SUGAR FEEDSTOCKS
For the Recipient				For the United States of America
22. Signature of Person Authorized to Sign				25. Signature of Grants/Agreements Officer Signature on File
23. Name and Title	24. Date Signed			26. Name of Officer Lalida Crawford				27. Date Signed 12/27/2010

CONTINUATION SHEET		REFERENCE NO. OF DOCUMENT BEING CONTINUED DE-EE0002869/004			PAGE 2 OF 2
NAME OF OFFEROR OR CONTRACTOR AMYRIS BIOTECHNOLOGIES, INC.
ITEM  NO. (A)	SUPPLIES/SERVICES (B)	QUANTITY (C)	UNIT (D)	UNIT PRICE (E)	AMOUNT (F)
	DUNS Number: 185930182 The purpose of this modification is to: 1) Assign a Technical Project Monitor/Engineer to the award. All other terms and conditions remain unchanged. In Block 7 of the Assistance Agreement, the Period of Performance reflects the beginning of the Project Period through the end of the current Budget Period, shown as 12/28/2009 through 6/30/2012. DOE Award Administrator: Brenda Dias E-mail: brenda.dias@go.doe.gov Phone: 303-275-6043 DOE Project Officer: Fred Gerdeman E-mail: fred.gerdeman@go.doe.gov Phone: 303-275-4928 Recipient Business Officer: Todd Pray E-mail: pray@amyris.com Phone: 510-740-7441 Recipient Principal Investigator: Neil Renninger E-mail: renninger@amyris.com Phone: 510-740-7414 “Electronic signature or signatures as used in this document means a method of signing an electronic message that-- (A) Identifies and authenticates a particular person as the source of the electronic message; (B) Indicates such person's approval of the information contained in the electronic message; and, (C) Submission via FedConnect constitutes electronically signed documents.” ASAP: NO Extent Competed: COMPETED Davis-Bacon Act: YES
JULY 2004

ASSISTANCE AGREEMENT
1. Award No. DE-EE0002869		2. Modification No. 005		3. Effective Date 12/28/2009		4. CFDA No. 81.087
5. Awarded To AMYRIS BIOTECHNOLOGIES, INC. Attn: KINKEAD REILING 5885 HOLLIS STREET SUITE 100 EMERYVILLE CA 946082059			6. Sponsoring Office Golden Field Office U.S. Department of Energy Golden Field Office 1617 Cole Blvd. Golden CO 80401				7. Period of Performance 12/28/2009 through 06/30/2012
8. Type of Agreement _ Grant x Cooperative Agreement _ Other	9. Authority 109-58 Energy Policy Act (2005) 111-5 Recovery Act (2009)				10. Purchase Request or Funding Document No. 11EE002648
11. Remittance Address			12. Total Amount				13. Funds Obligated
AMYRIS BIOTECHNOLOGIES, INC. Attn: KINKEAD REILING 5885 HOLLIS STREET SUITE 100 EMERYVILLE CA 946082059			Govt. Share: $ 24,341,409.00 Cost Share: $ 10,591,590.00 Total: $ 34,932,999.00				This action: $0.00 Total: $24,341,409.00
14. Principal Investigator Neil Renninger Phone: 510-740-7414	15. Program Manager Fred W. Gerdeman Phone: 303-275-4928				16. Administrator Golden Field Office U.S. Department of Energy Golden Field Office 1617 Cole Blvd. Golden CO 80401-3393
17. Submit Payment Requests To OR for Golden U.S. Department of Energy Oak Ridge Financial Service Center P.O. Box 4517 Oak Ridge TN 37831			18. Paying Office OR for Golden U.S. Department of Energy Oak Ridge Financial Service Center P.O. Box 4517 Oak Ridge TN 37831				19. Submit Reports To
20. Accounting and Appropriation Data See Schedule
21. Research Title and/or Description of Project RECOVERY ACT: SCALE-UP & MOBILIZATION OF RENEWABLE DIESEL & CHEMICAL PRODUCTION FROM COMMON INTERMEDIATE USING US-BASED FERMENTABLE SUGAR FEEDSTOCKS
For the Recipient				For the United States of America
22. Signature of Person Authorized to Sign				25. Signature of Grants/Agreements Officer Signature on File
23. Name and Title	24. Date Signed			26. Name of Officer Lalida Crawford				27. Date Signed 03/22/2011

CONTINUATION SHEET		REFERENCE NO. OF DOCUMENT BEING CONTINUED DE-EE0002869/005			PAGE 2 OF 2
NAME OF OFFEROR OR CONTRACTOR AMYRIS BIOTECHNOLOGIES, INC.
ITEM  NO. (A)	SUPPLIES/SERVICES (B)	QUANTITY (C)	UNIT (D)	UNIT PRICE (E)	AMOUNT (F)
	DUNS Number: 185930182 The purpose of this modification is to delete and replace the Special Terms and Conditions to incorporate Provision 31, "National Environmental Policy Act (NEPA) Requirements." All other terms and conditions remain unchanged. In Block 7 of the Assistance Agreement, the Period of Performance reflects the beginning of the Project Period through the end of the current Budget Period, shown as 12/28/2009 through 6/30/2012. For multiple Budget Periods, see Special Terms and Conditions, Provision 4, Award Project Period and Budget Periods. DOE Award Administrator: Brenda Dias E-mail: brenda.dias@go.doe.gov Phone: 303-275-6043 DOE Project Officer: Fred Gerdeman E-mail: fred.gerdeman@go.doe.gov Phone: 303-275-4928 Recipient Business Officer: Todd Pray E-mail: pray@amyris.com Phone: 510-740-7441 Recipient Principal Investigator: Neil Renninger E-mail: renninger@amyris.com Phone: 510-740-7414 “Electronic signature or signatures as used in this document means a method of signing an electronic message that-- (A) Identifies and authenticates a particular person as the source of the electronic message; (B) Indicates such person's approval of the information contained in the electronic message; and, (C) Submission via FedConnect constitutes electronically signed documents.” ASAP: NO Extent Competed: COMPETED Davis-Bacon Act: YES
JULY 2004

SPECIAL TERMS AND CONDITIONS

Table of Contents

Number SubjectPage

1. RESOLUTION OF CONFLICTING CONDITIONS2

2. AWARD AGREEMENT TERMS AND CONDITIONS2

3. ELECTRONIC AUTHORIZATION OF AWARD DOCUMENTS2

4. AWARD PROJECT PERIOD AND BUDGET PERIODS2

5. PAYMENT PROCEDURES3

6. COST SHARING4

7. REBUDGETING AND RECOVERY OF INDIRECT COSTS4

8. FINAL INCURRED COST AUDIT5

9. STATEMENT OF FEDERAL STEWARDSHIP5

10. STATEMENT OF SUBSTANTIAL INVOLVEMENT5

11. SITE VISITS6

12. REPORTING REQUIREMENTS6

13. PUBLICATIONS7

14. FEDERAL, STATE, AND MUNICIPAL REQUIREMENTS8

15. INTELLECTUAL PROPERTY PROVISIONS AND CONTACT INFORMATION8

16. NATIONAL SECURITY: CLASSIFIABLE RESULTS ORIGINATING UNDER AN AWARD8

17. LOBBYING RESTRICTIONS9

18. NOTICE REGARDING THE PURCHASE OF AMERICAN-MADE EQUIPMENT

AND PRODUCTS -- SENSE OF CONGRESS9

19. PROPERTY9

20. DECONTAMINATION AND/OR DECOMMISSIONING (D&D) COSTS    10

21. INSOLVENCY, BANKRUPTCY OR RECEIVERSHIP10

22. INDEMNITY11

23. SPECIAL PROVISIONS RELATING TO WORK FUNDED UNDER AMERICAN RECOVERY AND REINVESTMENT ACT OF 2009 (May 2009)11

24. REPORTING AND REGISTRATION REQUIREMENTS UNDER SECTION 1512

OF THE RECOVERY ACT15

25. REQUIRED USE OF AMERICAN IRON, STEEL, AND MANUFACTURED

GOODS - SECTION 1605 OF THE AMERICAN RECOVERY AND REINVESTMENT ACT OF 200916

26. REQUIRED USE OF AMERICAN IRON, STEEL, AND MANUFACTURED

GOODS (COVERED UNDER INTERNATIONAL AGREEMENTS) - SECTION

1605 OF THE AMERICAN RECOVERY AND REINVESTMENT ACT OF 200919

27. RECOVERY ACT TRANSACTIONS LISTED IN SCHEDULE OF EXPENDITURES OF FEDERAL AWARDS AND RECIPIENT RESPONSIBILITIES FOR

INFORMING SUBRECIPIENTS22

28. WAGE RATE REQUIREMENTS UNDER SECTION 1606 OF THE RECOVERY ACT23

29. DAVIS BACON ACT AND CONTRACT WORK HOURS AND SAFETY

STANDARDS ACT24

30. CONTINGENCY34

31. NATIONAL ENVIRONMENTAL POLICY ACT (NEPA) REQUIREMENTS35

1. RESOLUTION OF CONFLICTING CONDITIONS

Any apparent inconsistency between Federal statutes and regulations and the terms and conditions contained in this award must be referred to the DOE Award Administrator for guidance.

2. AWARD AGREEMENT TERMS AND CONDITIONS

This award/agreement consists of the Assistance Agreement, plus the following:

a. Special Terms and Conditions.

b. Attachments:

Attachment Number        Title

1.        Intellectual Property Provisions

2.        Statement of Project Objectives

3.        Federal Assistance Reporting Checklist and Instructions

4.        Budget Pages (SF 424A)     

5.        Requirements for Contingency Funds for Integrated Biorefinery

Projects    

c. Applicable program regulations.

d. DOE Assistance Regulations, 10 CFR Part 600 at http://ecfr.gpoaccess.gov.

e. If the award is for research and the award is for a university or non-profit, the Research Terms & Conditions and the DOE Agency Specific Requirements at http://www.nsf.gov/bfa/dias/policy/rtc/index.jsp apply.

f. Application/proposal as approved by DOE.

g. National Policy Assurances to be incorporated as award terms in effect on date of award at http://management.energy.gov/business_doe/1374.htm.

3. ELECTRONIC AUTHORIZATION OF AWARD DOCUMENTS

Acknowledgement of award documents by the Recipient's authorized representative through electronic systems used by the Department of Energy, specifically FedConnect, constitutes the Recipient's acceptance of the terms and conditions of the award. Acknowledgement via FedConnect by the Recipient's authorized representative constitutes the Recipient's electronic signature.

4. AWARD PROJECT PERIOD AND BUDGET PERIODS

The Project Period for this award is 12/28/2009 through 6/30/2012, consisting of the following Budget Periods:

2

Budget Period	Start Date	End Date
1	12/28/2009	4/21/2010
2	4/22/2010	6/30/2012

5. PAYMENT PROCEDURES

a. Method of Payment. Payment will be made by reimbursement through ACH.

b. Requesting Reimbursement. Requests for reimbursements must be made electronically through Department of Energy's Oak Ridge Financial Service Center (ORFSC) VIPERS. To access and use VIPERS, you must enroll at https://finweb.oro.doe.gov/vipers.htm. Detailed instructions on how to enroll are provided on the web site.

For non-construction awards, you must submit a Standard Form (SF) 270, “Request for Advance or Reimbursement,” at https://finweb.oro.doe.gov/vipers.htm and attach a file containing appropriate supporting documentation. The file attachment must show the total Federal share claimed on the SF 270, the non-Federal share claimed for the billing period if cost sharing is required, and cumulative expenditures to date (both Federal and non-Federal) for each of the following categories: salaries/wages and fringe benefits; equipment; travel; participant/training support costs, if any; other direct costs, including subawards/contracts; and indirect costs. For construction awards, you must submit a SF 271, “Outlay Report and Request for Reimbursement for Construction Programs,” through VIPERS.

c. Timing of submittals. Submittal of the SF 270 or SF 271 should coincide with your normal billing pattern, but not more frequently than every two weeks. Requests for reimbursement must be limited to the amount of disbursements made during the billing period for the Federal share of direct project costs and the proportionate share of any allowable indirect costs incurred during that billing period.

d. Adjusting payment requests for available cash. You must disburse any funds that are available from repayments to and interest earned on a revolving fund, program income, rebates, refunds, contract settlements, audit recoveries, credits, discounts, and interest earned on any of those funds before requesting additional cash payments from DOE.

e. Payments. The DOE approving official will approve the invoice as soon as practical, but not later than 30 days after your request is received, unless the billing is improper. Upon receipt of an invoice payment authorization from the DOE approving official, the ORFSC will disburse payment to you. You may check the status of payments at the VIPER web site. All payments are made by electronic funds transfer to the bank account identified on the ACH Vendor/Miscellaneous Payment Enrollment Form (SF 3881) that you filed.

3

6. COST SHARING

a. Total Estimated Project Cost is the sum of the Federal Government share, including Federally Funded Research and Development Center (FFRDC) contractor costs, and Recipient share of the estimated project costs. The DOE FFRDC contractor cost is not included in the total approved budget for this award, because DOE will pay the DOE FFRDC contractor portion of the effort under an existing DOE contract. The Recipient is not responsible for reporting on that portion of the total estimated cost that is paid directly to the DOE FFRDC contractor.

The Recipient's cost share must come from non-Federal sources unless otherwise allowed by law. By accepting Federal funds under this award, you agree that you are liable for your percentage share of allowable project costs, on a budget period basis, even if the project is terminated early or is not funded to its completion. This cost is shared as follows:

Budget Period	DOE Cost Share, including FFRDC Costs		Recipient Cost Share $ / %	Total Estimated Costs
	DOE $ / %	FFRDC $ / %
1	$4,207,301/70.2%	—	$1,782,480/29.8%	$5,989,781
2	$20,134,108/68.0%	$658,591/2.2%	$8,809,110/29.8%	$29,601,809
Total Project	$24,341,409	$658,591	$10,591,590	$35,591,590

b. If you discover that you may be unable to provide cost sharing of at least the amount identified in paragraph a of this Article, you should immediately provide written notification to the DOE Award Administrator, indicating whether you will continue the project or phase out the project. If you plan to continue the project, the notification must describe how replacement cost sharing will be secured.

c. You must maintain records of all project costs you claim as cost sharing, including in-kind costs, as well as records of costs to be paid by DOE. Such records are subject to audit.

d. Failure to provide the cost share required by this Article may result in the subsequent recovery by DOE of some or all the funds provided under the award.

7. REBUDGETING AND RECOVERY OF INDIRECT COSTS

a. If actual allowable indirect costs are less than those budgeted and funded under the award, you may use the difference to pay additional allowable direct costs during the project period. If at the completion of the award the Government's share of total allowable costs (i.e., direct and indirect), is less than the total costs reimbursed, you must refund the difference.

4

b. Recipients are expected to manage their indirect costs. DOE will not amend an award solely to provide additional funds for changes in indirect cost rates. DOE recognizes that the inability to obtain full reimbursement for indirect costs means the Recipient must absorb the underrecovery. Such underrecovery may be allocated as part of the organization's required cost sharing.

8. FINAL INCURRED COST AUDIT

In accordance with 10 CFR 600, DOE reserves the right to initiate a final incurred cost audit on this award. If the audit has not been performed or completed prior to the closeout of the award, DOE retains the right to recover an appropriate amount after fully considering the recommendations on disallowed costs resulting from the final audit.

9. STATEMENT OF FEDERAL STEWARDSHIP

DOE will exercise normal Federal stewardship in overseeing the project activities performed under this award. Stewardship activities include, but are not limited to, conducting site visits; reviewing performance and financial reports; providing technical assistance and/or temporary intervention in unusual circumstances to correct deficiencies which develop during the project; assuring compliance with terms and conditions; and reviewing technical performance after project completion to ensure that the award objectives have been accomplished.

10. STATEMENT OF SUBSTANTIAL INVOLVEMENT

a.     Government Insight

In order to adequately monitor project progress and provide technical direction and/or redirection to the Recipient, DOE must be provided an adequate level of insight into various Recipient activities. Government Insight activities by DOE include attendance at Recipient meetings, reviews and tests, as well as access for DOE's consultants to perform independent evaluations of Recipient's plans and processes. Recipient shall notify the DOE Project Officer of meetings, reviews, and tests in sufficient time to permit DOE participation, and provide all appropriate documentation for DOE review.

b.        Specific activities to be conducted by DOE

1.        Risk Evaluation -DOE will review the Recipient's initial Risk Mitigation Plan (RMP) for quality and completeness. DOE will also monitor updates to the RMP and actions taken by the Recipient during the performance of its award to mitigate risks and improve the probability of successful execution of the integrated Biorefinery project. At DOE's discretion, additional independent risk analyses of the project by DOE consultants may be requested.

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2.        Independent Engineering Assessments -DOE will engage a private, independent engineering (IE) firm to assist in assessing the progress of the project and provide timely and accurate reports to DOE. The Recipient will ensure that the IE has access to any and all relevant documentation sufficient to allow the IE to provide independent evaluations to DOE on the progress of the project. Such documentation includes but is not limited to the following:

•Drawings and specifications

•Construction and Execution plans

•Resource loaded schedules

•Design functions and requirements for the site final design review

•Risk management plans

•Value management and engineering studies and/or plans

•Acquisition strategies

•Project execution plans

•Project controls including earned value management systems

•Qualifications of the integrated project team.

•Financial strategy for funding the construction project

•Updated marketing and business plan

•Invoices submitted to DOE

DOE will evaluate the quality and completeness of information and documentation provided by the Recipient to DOE and its consultants in order to allow DOE to provide technical direction and/or redirection to the Recipient about how best to achieve the purposes of the award. Consultants to DOE may not provide technical direction and/or redirection to the Recipient.

11. SITE VISITS

DOE's authorized representatives have the right to make site visits at reasonable times to review project accomplishments and management control systems and to provide technical assistance, if required. You must provide, and must require your subawardees to provide, reasonable access to facilities, office space, resources, and assistance for the safety and convenience of the government representatives in the performance of their duties. All site visits and evaluations must be performed in a manner that does not unduly interfere with or delay the work.

12. REPORTING REQUIREMENTS

a. Requirements. The reporting requirements for this award are identified on the Federal Assistance Reporting Checklist, DOE F 4600.2, attached to this award. Failure to comply with these reporting requirements is considered a material noncompliance with the terms of the award. Noncompliance may result in withholding of future payments, suspension or termination of the current award, and withholding of future awards. A willful failure to perform, a history of failure to perform, or unsatisfactory performance of this and/or other financial assistance awards, may also result in a debarment action to preclude future awards by Federal agencies.

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b. Dissemination of scientific/technical reports. Scientific/technical reports submitted under this award will be disseminated on the Internet via the DOE Information Bridge (www.osti.gov/bridge), unless the report contains patentable material, protected data or SBIR/STTR data. Citations for journal articles produced under the award will appear on the DOE Energy Citations Database (www.osti.gov/energycitations).

c. Restrictions. Reports submitted to the DOE Information Bridge must not contain any Protected Personal Identifiable Information (PII), limited rights data (proprietary data), classified information, information subject to export control classification, or other information not subject to release.

13. PUBLICATIONS

a. You are encouraged to publish or otherwise make publicly available the results of the work conducted under the award.

b. An acknowledgment of DOE support and a disclaimer must appear in the publication of any material, whether copyrighted or not, based on or developed under this project, as follows:

Acknowledgment: “This material is based upon work supported by the Department of Energy [National Nuclear Security Administration] [add name(s) of other agencies, if applicable] under Award Number(s) [enter the award number(s)].”

Disclaimer: “This report was prepared as an account of work sponsored by an agency of the United States Government. Neither the United States Government nor any agency thereof, nor any of their employees, makes any warranty, express or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights. Reference herein to any specific commercial product, process, or service by trade name, trademark, manufacturer, or otherwise does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States Government or any agency thereof. The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States Government or any agency thereof.”

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14. FEDERAL, STATE, AND MUNICIPAL REQUIREMENTS

You must obtain any required permits and comply with applicable federal, state, and municipal laws, codes, and regulations for work performed under this award.

15. INTELLECTUAL PROPERTY PROVISIONS AND CONTACT INFORMATION

a. The intellectual property provisions applicable to this award are provided as an attachment to this award or are referenced in the Assistance Agreement.

b. Questions regarding intellectual property matters should be referred to the DOE Award Administrator identified and the Patent Counsel designated as the service provider for the DOE office that issued the award.

Patent Counsel for the Golden Field Office is Julia Moody, who may be reached at julia.moody@go.doe.gov or 303-275-4867.

16. NATIONAL SECURITY: CLASSIFIABLE RESULTS ORIGINATING UNDER AN AWARD

a. This award is intended for unclassified, publicly releasable research. You will not be granted access to classified information. DOE does not expect that the results of the research project will involve classified information. Under certain circumstances, however, a classification review of information originated under the award may be required. The Department may review research work generated under this award at any time to determine if it requires classification.

b. Executive Order 12958 (60 Fed. Reg. 19,825 (1995)) states that basic scientific research information not clearly related to the national security shall not be classified. Nevertheless, some information concerning (among other things) scientific, technological, or economic matters relating to national security or cryptology may require classification. If you originate information during the course of this award that you believe requires classification, you must promptly:

1. Notify the DOE Project Officer and the DOE Award Administrator;

2. Submit the information by registered mail directly to the Director, Office of Classification and Information Control, SO-10.2; U.S. Department of Energy; P.O. Box A; Germantown, MD 20875-0963, for classification review.

3. Restrict access to the information to the maximum extent possible until you are informed that the information is not classified, but no longer than 30 days after receipt by the Director, Office of Classification and Information Control

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c. If you originate information concerning the production or utilization of special nuclear material (i.e., plutonium, uranium enriched in the isotope 233 or 235, and any other material so determined under section 51 of the Atomic Energy Act) or nuclear energy, you must:

1. Notify the DOE Project Officer and the DOE Award Administrator;

2. Submit the information by registered mail directly to the Director, Office of Classification and Information Control, SO-10.2; U.S. Department of Energy; P. O. Box A; Germantown, MD 20875-0963 for classification review within 180 days of the date the Recipient first discovers or first has reason to believe that the information is useful in such production or utilization; and

3. Restrict access to the information to the maximum extent possible until you are informed that the information is not classified, but no longer than 90 days after receipt by the Director, Office of Classification and Information Control.

d. If DOE determines any of the information requires classification, you agree that the Government may terminate the award by mutual agreement in accordance with 10 CFR 600.25(d). All material deemed to be classified must be forwarded to DOE, in a manner specified by DOE.

e. If DOE does not respond within the specified time periods, you are under no further obligation to restrict access to the information.

17. LOBBYING RESTRICTIONS

By accepting funds under this award, you agree that none of the funds obligated on the award shall be expended, directly or indirectly, to influence congressional action on any legislation or appropriation matters pending before Congress, other than to communicate to Members of Congress as described in 18 U.S.C. 1913. This restriction is in addition to those prescribed elsewhere in statute and regulation.

18. NOTICE REGARDING THE PURCHASE OF AMERICAN-MADE EQUIPMENT AND PRODUCTS -- SENSE OF CONGRESS

It is the sense of the Congress that, to the greatest extent practicable, all equipment and products purchased with funds made available under this award should be American-made.

19. PROPERTY

Real property and equipment acquired by the Recipient shall be subject to the rules set forth in 10 CFR 600.130-137, 10 CFR 600.231-233, or 10 CFR 600.320-324, as applicable.

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Consistent with the goals and objectives of this project, the Recipient may continue to use Recipient acquired property beyond the Period of Performance, without obligation, during the period of such use, to extinguish DOE's conditional title to such property as described in 10 CFR 600.132-135, 10 CFR 600.231-233, or 600.321-324, subject to the following: (a) the Recipient continues to utilize such property for the objectives of the project as set forth in the Statement of Project Objectives; (b) DOE retains the right to periodically ask for, and the Recipient agrees to provide, reasonable information concerning the use and condition of the property; and (c) the Recipient follows the property disposition rules set forth in the applicable sections of 10 CFR Part 600, if the property is no longer used by the Recipient for the objectives of the project, and the fair market value of property exceeds $5,000.

Once the per unit fair market value of the property is less than $5,000, pursuant to the applicable sections of 10 CFR Part 600, DOE's residual interest in the property shall be extinguished and the Recipient shall have no further obligation to the DOE with respect to the property.

The regulations as set forth in 10 CFR Part 600 and the requirements of this article shall also apply to property in the possession of any team member, sub-recipient or other entity where such property was acquired in whole or in part with funds provided by DOE under this award or where such property was counted as cost-sharing under the award.

20. DECONTAMINATION AND/OR DECOMMISSIONING (D&D) COSTS

Notwithstanding any other provisions of this Agreement, the Government shall not be responsible for or have any obligation to the Recipient for (i) Decontamination and/or Decommissioning (D&D) of any of the Recipient's facilities, or (ii) any costs which may be incurred by the Recipient in connection with the D&D of any of its facilities due to the performance of the work under this Agreement, whether said work was performed prior to or subsequent to the effective date of the Agreement.

21. INSOLVENCY, BANKRUPTCY OR RECEIVERSHIP

a. You shall immediately notify the DOE of the occurrence of any of the following events: (i) you or your parent's filing of a voluntary case seeking liquidation or reorganization under the Bankruptcy Act; (ii) your consent to the institution of an involuntary case under the Bankruptcy Act against you or your parent; (iii) the filing of any similar proceeding for or against you or your parent, or your consent to the dissolution, winding-up or readjustment of your debts, appointment of a receiver, conservator, trustee, or other officer with similar powers over you, under any other applicable state or federal law; or (iv) your insolvency due to its inability to pay debts generally as they become due.

b. Such notification shall be in writing and shall: (i) specifically set out the details of the occurrence of an event referenced in paragraph (a); (ii) provide the facts surrounding that event; and (iii) provide the impact such event will have on the project being funded by this award.

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c. Upon the occurrence of any of the four events described in paragraph a. of this provision, DOE reserves the right to conduct a review of your award to determine your compliance with the required elements of the award (including such items as cost share, progress towards technical project objectives, and submission of required reports). If the DOE review determines that there are significant deficiencies or concerns with your performance under the award, DOE reserves the right to impose additional requirements, as needed, including (i) change of payment method; or (ii) institute payment controls.

d. Failure of the Recipient to comply with this provision may be considered a material noncompliance of this financial assistance award by the Contracting Officer.

22. INDEMNITY

The Recipient shall indemnify the Government and its officers, agents, or employees for any and all liability, including litigation expenses and attorneys' fees, arising from suits, actions, or claims of any character for death, bodily injury, or loss of or damage to property or to the environment, resulting from the project, except to the extent that such liability results from the direct fault or negligence of Government officers, agents or employees, or to the extent such liability may be covered by applicable allowable costs provisions. 

23. SPECIAL PROVISIONS RELATING TO WORK FUNDED UNDER AMERICAN RECOVERY AND REINVESTMENT ACT OF 2009 (May 2009)

Preamble

The American Recovery and Reinvestment Act of 2009, Pub. L. 111-5, (Recovery Act) was enacted to preserve and create jobs and promote economic recovery, assist those most impacted by the recession, provide investments needed to increase economic efficiency by spurring technological advances in science and health, invest in transportation, environmental protection, and other infrastructure that will provide long-term economic benefits, stabilize State and local government budgets, in order to minimize and avoid reductions in essential services and counterproductive State and local tax increases. Recipients shall use grant funds in a manner that maximizes job creation and economic benefit.

The Recipient shall comply with all terms and conditions in the Recovery Act relating generally to governance, accountability, transparency, data collection and resources as specified in Act itself and as discussed below.

Recipients should begin planning activities for their first tier subrecipients, including obtaining a DUNS number (or updating the existing DUNS record), and registering with the Central Contractor Registration (CCR).

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Be advised that Recovery Act funds can be used in conjunction with other funding as necessary to complete projects, but tracking and reporting must be separate to meet the reporting requirements of the Recovery Act and related guidance. For projects funded by sources other than the Recovery Act, Contractors must keep separate records for Recovery Act funds and to ensure those records comply with the requirements of the Act.

The Government has not fully developed the implementing instructions of the Recovery Act, particularly concerning specific procedural requirements for the new reporting requirements. The Recipient will be provided these details as they become available. The Recipient must comply with all requirements of the Act. If the recipient believes there is any inconsistency between ARRA requirements and current award terms and conditions, the issues will be referred to the Contracting Officer for reconciliation.

Definitions

For purposes of this clause, Covered Funds means funds expended or obligated from appropriations under the American Recovery and Reinvestment Act of 2009, Pub. L. 111-5. Covered Funds will have special accounting codes and will be identified as Recovery Act funds in the grant, cooperative agreement or TIA and/or modification using Recovery Act funds. Covered Funds must be reimbursed by September 30, 2015.

Non-Federal employer means any employer with respect to covered funds -- the contractor, subcontractor, grantee, or recipient, as the case may be, if the contractor, subcontractor, grantee, or recipient is an employer; and any professional membership organization, certification of other professional body, any agent or licensee of the Federal government, or any person acting directly or indirectly in the interest of an employer receiving covered funds; or with respect to covered funds received by a State or local government, the State or local government receiving the funds and any contractor or subcontractor receiving the funds and any contractor or subcontractor of the State or local government; and does not mean any department, agency, or other entity of the federal government.

Recipient means any entity that receives Recovery Act funds directly from the Federal government (including Recovery Act funds received through grant, loan, or contract) other than an individual and includes a State that receives Recovery Act Funds.

Special Provisions

A. Flow Down Requirement

Recipients must include these special terms and conditions in any subaward.

B. Segregation of Costs

Recipients must segregate the obligations and expenditures related to funding under the Recovery Act. Financial and accounting systems should be revised as necessary to segregate, track and maintain these funds apart and separate from other revenue streams. No part of the funds from the Recovery Act shall be commingled with any other funds or used for a purpose other than that of making payments for costs allowable for Recovery Act projects.

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C. Prohibition on Use of Funds

None of the funds provided under this agreement derived from the American Recovery and Reinvestment Act of 2009, Pub. L. 111-5, may be used by any State or local government, or any private entity, for any casino or other gambling establishment, aquarium, zoo, golf course, or swimming pool.

D. Access to Records

With respect to each financial assistance agreement awarded utilizing at least some of the funds appropriated or otherwise made available by the American Recovery and Reinvestment Act of 2009, Pub. L. 111-5, any representative of an appropriate inspector general appointed under section 3 or 8G of the Inspector General Act of 1988 (5 U.S.C. App.) or of the Comptroller General is authorized --

(1) to examine any records of the contractor or grantee, any of its subcontractors or subgrantees, or any State or local agency administering such contract that pertain to, and involve transactions that relate to, the subcontract, subcontract, grant, or subgrant; and

(2) to interview any officer or employee of the contractor, grantee, subgrantee, or agency regarding such transactions.

E. Publication

An application may contain technical data and other data, including trade secrets and/or privileged or confidential information, which the applicant does not want disclosed to the public or used by the Government for any purpose other than the application. To protect such data, the applicant should specifically identify each page including each line or paragraph thereof containing the data to be protected and mark the cover sheet of the application with the following Notice as well as referring to the Notice on each page to which the Notice applies:

Notice of Restriction on Disclosure and Use of Data

The data contained in pages ---- of this application have been submitted in confidence and contain trade secrets or proprietary information, and such data shall be used or disclosed only for evaluation purposes, provided that if this applicant receives an award as a result of or in connection with the submission of this application, DOE shall have the right to use or disclose the data here to the extent provided in the award. This restriction does not limit the Government's right to use or disclose data obtained without restriction from any source, including the applicant.

Information about this agreement will be published on the Internet and linked to the website www.recovery.gov, maintained by the Accountability and Transparency Board. The Board may exclude posting contractual or other information on the website on a case-by-case basis when necessary to protect national security or to protect information that is not subject to disclosure under sections 552 and 552a of title 5, United States Code.

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F. Protecting State and Local Government and Contractor Whistleblowers.

The requirements of Section 1553 of the Act are summarized below. They include, but are not limited to:

Prohibition on Reprisals: An employee of any non-Federal employer receiving covered funds under the American Recovery and Reinvestment Act of 2009, Pub. L. 111-5, may not be discharged, demoted, or otherwise discriminated against as a reprisal for disclosing, including a disclosure made in the ordinary course of an employee's duties, to the Accountability and Transparency Board, an inspector general, the Comptroller General, a member of Congress, a State or Federal regulatory or law enforcement agency, a person with supervisory authority over the employee (or other person working for the employer who has the authority to investigate, discover or terminate misconduct), a court or grant jury, the head of a Federal agency, or their representatives information that the employee believes is evidence of:

- gross management of an agency contract or grant relating to covered funds;

- a gross waste of covered funds;

- a substantial and specific danger to public health or safety related to the implementation or use of covered funds;

- an abuse of authority related to the implementation or use of covered funds; or

- as violation of law, rule, or regulation related to an agency contract (including the competition for or negotiation of a contract) or grant, awarded or issued relating to covered funds.

Agency Action: Not later than 30 days after receiving an inspector general report of an alleged reprisal, the head of the agency shall determine whether there is sufficient basis to conclude that the non-Federal employer has subjected the employee to a prohibited reprisal. The agency shall either issue an order denying relief in whole or in part or shall take one or more of the following actions:

- Order the employer to take affirmative action to abate the reprisal.

- Order the employer to reinstate the person to the position that the person held before the reprisal, together with compensation including back pay, compensatory damages, employment benefits, and other terms and conditions of employment that would apply to the person in that position if the reprisal had not been taken.

- Order the employer to pay the employee an amount equal to the aggregate amount of all costs and expenses (including attorneys' fees and expert witnesses' fees) that were reasonably incurred by the employee for or in connection with, bringing the complaint regarding the reprisal, as determined by the head of a court of competent jurisdiction.

Nonenforceablity of Certain Provisions Waiving Rights and remedies or Requiring Arbitration: Except as provided in a collective bargaining agreement, the rights and remedies provided to aggrieved employees by this section may not be waived by any agreement, policy, form, or condition of employment, including any predispute arbitration agreement. No predispute arbitration agreement shall be valid or enforceable if it requires arbitration of a dispute arising out of this section.

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Requirement to Post Notice of Rights and Remedies: Any employer receiving covered funds under the American Recovery and Reinvestment Act of 2009, Pub. L. 111-5, shall post notice of the rights and remedies as required therein. (Refer to section 1553 of the American Recovery and Reinvestment Act of 2009, Pub. L. 111-5, www.Recovery.gov, for specific requirements of this section and prescribed language for the notices.).

G. RESERVED

H. False Claims Act

Recipient and sub-recipients shall promptly refer to the DOE or other appropriate Inspector General any credible evidence that a principal, employee, agent, contractor, sub-grantee, subcontractor or other person has submitted a false claim under the False Claims Act or has committed a criminal or civil violation of laws pertaining to fraud, conflict of interest, bribery, gratuity or similar misconduct involving those funds.

I. Information in Support of Recovery Act Reporting

Recipient may be required to submit backup documentation for expenditures of funds under the Recovery Act including such items as timecards and invoices. Recipient shall provide copies of backup documentation at the request of the Contracting Officer or designee.

J. Availability of Funds

Funds appropriated under the Recovery Act and obligated to this award are available for reimbursement of costs until September 30, 2015.

24. REPORTING AND REGISTRATION REQUIREMENTS UNDER SECTION 1512 OF THE RECOVERY ACT

(a) This award requires the recipient to complete projects or activities which are funded under the American Recovery and Reinvestment Act of 2009 (Recovery Act) and to report on use of Recovery Act funds provided through this award. Information from these reports will be made available to the public.

(b) The reports are due no later than ten calendar days after each calendar quarter in which the Recipient receives the assistance award funded in whole or in part by the Recovery Act.

(c) Recipients and their first-tier subrecipients must maintain current registrations in the Central Contractor Registration (http://www.ccr.gov) at all times during which they have active federal awards funded with Recovery Act funds. A Dun and Bradstreet Data Universal Numbering System (DUNS) Number (http://www.dnb.com) is one of the requirements for registration in the Central Contractor Registration.

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(d) The recipient shall report the information described in section 1512(c) of the Recovery Act using the reporting instructions and data elements that will be provided online at http://www.FederalReporting.gov and ensure that any information that is pre-filled is corrected or updated as needed.

25. REQUIRED USE OF AMERICAN IRON, STEEL, AND MANUFACTURED GOODS - SECTION 1605 OF THE AMERICAN RECOVERY AND REINVESTMENT ACT OF 2009

If the Recipient determines at any time that any construction, alteration, or repair activity on a public building or public works will be performed during the course of the project, the Recipient shall notify the Contracting Officer prior to commencing such work and the following provisions shall apply.

(a) Definitions. As used in this award term and condition-

(1) Manufactured good means a good brought to the construction site for incorporation into the building or work that has been-

(i) Processed into a specific form and shape; or

(ii) Combined with other raw material to create a material that has different properties than the properties of the individual raw materials.

(2) Public building and public work means a public building of, and a public work of, a governmental entity (the United States; the District of Columbia; commonwealths, territories, and minor outlying islands of the United States; State and local governments; and multi-State, regional, or interstate entities which have governmental functions). These buildings and works may include, without limitation, bridges, dams, plants, highways, parkways, streets, subways, tunnels, sewers, mains, power lines, pumping stations, heavy generators, railways, airports, terminals, docks, piers, wharves, ways, lighthouses, buoys, jetties, breakwaters, levees, and canals, and the construction, alteration, maintenance, or repair of such buildings and works.

(3) Steel means an alloy that includes at least 50 percent iron, between .02 and 2 percent carbon, and may include other elements.

(b) Domestic preference. (1) This award term and condition implements Section 1605 of the American Recovery and Reinvestment Act of 2009 (Recovery Act) (Pub. L. 111-5), by requiring that all iron, steel, and manufactured goods used in the project are produced in the United States except as provided in paragraph (b)(3) of this section and condition.

(2) This requirement does not apply to the material listed by the Federal Government as follows:

none

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(3) The award official may add other iron, steel, and/or manufactured goods to the list in paragraph (b)(2) of this section and condition if the Federal Government determines that-

(i) The cost of the domestic iron, steel, and/or manufactured goods would be unreasonable. The cost of domestic iron, steel, or manufactured goods used in the project is unreasonable when the cumulative cost of such material will increase the cost of the overall project by more than 25 percent;

(ii) The iron, steel, and/or manufactured good is not produced, or manufactured in the United States in sufficient and reasonably available quantities and of a satisfactory quality; or

(iii) The application of the restriction of section 1605 of the Recovery Act would be inconsistent with the public interest.

(c) Request for determination of inapplicability of Section 1605 of the Recovery Act . (1)(i) Any recipient request to use foreign iron, steel, and/or manufactured goods in accordance with paragraph (b)(3) of this section shall include adequate information for Federal Government evaluation of the request, including-

(A) A description of the foreign and domestic iron, steel, and/or manufactured goods;

(B) Unit of measure;

(C) Quantity;

(D) Cost;

(E) Time of delivery or availability;

(F) Location of the project;

(G) Name and address of the proposed supplier; and

(H) A detailed justification of the reason for use of foreign iron, steel, and/or manufactured goods cited in accordance with paragraph (b)(3) of this section.

(ii) A request based on unreasonable cost shall include a reasonable survey of the market and a completed cost comparison table in the format in paragraph (d) of this section.

(iii) The cost of iron, steel, and/or manufactured goods material shall include all delivery costs to the construction site and any applicable duty.

(iv) Any recipient request for a determination submitted after Recovery Act funds have been obligated for a project for construction, alteration, maintenance, or repair shall explain why the recipient could not reasonably foresee the need for such determination and could not have requested the determination before the funds were obligated. If the recipient does not submit a satisfactory explanation, the award official need not make a determination.

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(2) If the Federal Government determines after funds have been obligated for a project for construction, alteration, maintenance, or repair that an exception to section 1605 of the Recovery Act applies, the award official will amend the award to allow use of the foreign iron, steel, and/or relevant manufactured goods. When the basis for the exception is nonavailability or public interest, the amended award shall reflect adjustment of the award amount, redistribution of budgeted funds, and/or other actions taken to cover costs associated with acquiring or using the foreign iron, steel, and/or relevant manufactured goods. When the basis for the exception is the unreasonable cost of the domestic iron, steel, or manufactured goods, the award official shall adjust the award amount or redistribute budgeted funds by at least the differential established in 2 CFR 176.110(a).

(3) Unless the Federal Government determines that an exception to section 1605 of the Recovery Act applies, use of foreign iron, steel, and/or manufactured goods is noncompliant with section 1605 of the American Recovery and Reinvestment Act.

(d) Data. To permit evaluation of requests under paragraph (b) of this section based on unreasonable cost, the Recipient shall include the following information and any applicable supporting data based on the survey of suppliers:

Foreign and Domestic Items Cost Comparison

Description	Unit of measure	Quantity	Cost (dollars)*
Item 1:
Foreign steel, iron, or manufactured good	_________	_________	_________
Domestic steel, iron, or manufactured good	_________	_________	_________
Item 2:
Foreign steel, iron, or manufactured good	_________	_________	_________
Domestic steel, iron, or manufactured good	_________	_________	_________

List name, address, telephone number, email address, and contact for suppliers surveyed. Attach copy of response; if oral, attach summary.

Include other applicable supporting information.

*Include all delivery costs to the construction site.

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26. REQUIRED USE OF AMERICAN IRON, STEEL, AND MANUFACTURED GOODS (COVERED UNDER INTERNATIONAL AGREEMENTS) - SECTION 1605 OF THE AMERICAN RECOVERY AND REINVESTMENT ACT OF 2009

(a) Definitions. As used in this award term and condition-

Designated country - (1) A World Trade Organization Government Procurement Agreement country (Aruba, Austria, Belgium, Bulgaria, Canada, Cyprus, Czech Republic, Denmark, Estonia, Finland, France, Germany, Greece, Hong Kong, Hungary, Iceland, Ireland, Israel, Italy, Japan, Korea (Republic of), Latvia, Liechtenstein, Lithuania, Luxembourg, Malta, Netherlands, Norway, Poland, Portugal, Romania, Singapore, Slovak Republic, Slovenia, Spain, Sweden, Switzerland, and United Kingdom;

(2) A Free Trade Agreement (FTA) country (Australia, Bahrain, Canada, Chile, Costa Rica, Dominican Republic, El Salvador, Guatemala, Honduras, Israel, Mexico, Morocco, Nicaragua, Oman, Peru, or Singapore); or

(3) A United States-European Communities Exchange of Letters (May 15, 1995) country: Austria, Belgium, Bulgaria, Cyprus, Czech Republic, Denmark, Estonia, Finland, France, Germany, Greece, Hungary, Ireland, Italy, Latvia, Lithuania, Luxembourg, Malta, Netherlands, Poland, Portugal, Romania, Slovak Republic, Slovenia, Spain, Sweden, and United Kingdom.

Designated country iron, steel, and/or manufactured goods - (1) Is wholly the growth, product, or manufacture of a designated country; or

(2) In the case of a manufactured good that consist in whole or in part of materials from another country, has been substantially transformed in a designated country into a new and different manufactured good distinct from the materials from which it was transformed.

Domestic iron, steel, and/or manufactured good - (1) Is wholly the growth, product, or manufacture of the United States; or

(2) In the case of a manufactured good that consists in whole or in part of materials from another country, has been substantially transformed in the United States into a new and different manufactured good distinct from the materials from which it was transformed. There is no requirement with regard to the origin of components or subcomponents in manufactured goods or products, as long as the manufacture of the goods occurs in the United States.

Foreign iron, steel, and/or manufactured good means iron, steel and/or manufactured good that is not domestic or designated country iron, steel, and/or manufactured good.

Manufactured good means a good brought to the construction site for incorporation into the building or work that has been-

(1) Processed into a specific form and shape; or

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(2) Combined with other raw material to create a material that has different properties than the properties of the individual raw materials.

Public building and public work means a public building of, and a public work of, a governmental entity (the United States; the District of Columbia; commonwealths, territories, and minor outlying islands of the United States; State and local governments; and multi-State, regional, or interstate entities which have governmental functions). These buildings and works may include, without limitation, bridges, dams, plants, highways, parkways, streets, subways, tunnels, sewers, mains, power lines, pumping stations, heavy generators, railways, airports, terminals, docks, piers, wharves, ways, lighthouses, buoys, jetties, breakwaters, levees, and canals, and the construction, alteration, maintenance, or repair of such buildings and works.

Steel means an alloy that includes at least 50 percent iron, between .02 and 2 percent carbon, and may include other elements.

(b) Iron, steel, and manufactured goods. (1) The award term and condition described in this section implements-

(i) Section 1605(a) of the American Recovery and Reinvestment Act of 2009 (Pub. L. 111-5) (Recovery Act), by requiring that all iron, steel, and manufactured goods used in the project are produced in the United States; and

(ii) Section 1605(d), which requires application of the Buy American requirement in a manner consistent with U.S. obligations under international agreements. The restrictions of section 1605 of the Recovery Act do not apply to designated country iron, steel, and/or manufactured goods. The Buy American requirement in section 1605 shall not be applied where the iron, steel or manufactured goods used in the project are from a Party to an international agreement that obligates the recipient to treat the goods and services of that Party the same as domestic goods and services. This obligation shall only apply to projects with an estimated value of $7,443,000 or more.

(2) The recipient shall use only domestic or designated country iron, steel, and manufactured goods in performing the work funded in whole or part with this award, except as provided in paragraphs (b)(3) and (b)(4) of this section.

(3) The requirement in paragraph (b)(2) of this section does not apply to the iron, steel, and manufactured goods listed by the Federal Government as follows:

none

(4) The award official may add other iron, steel, and manufactured goods to the list in paragraph (b)(3) of this section if the Federal Government determines that-

(i) The cost of domestic iron, steel, and/or manufactured goods would be unreasonable. The cost of domestic iron, steel, and/or manufactured goods used in the project is unreasonable when the cumulative cost of such material will increase the overall cost of the project by more than 25 percent;

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(ii) The iron, steel, and/or manufactured good is not produced, or manufactured in the United States in sufficient and reasonably available commercial quantities of a satisfactory quality; or

(iii) The application of the restriction of section 1605 of the Recovery Act would be inconsistent with the public interest.

(c) Request for determination of inapplicability of section 1605 of the Recovery Act or the Buy American Act. (1)(i) Any recipient request to use foreign iron, steel, and/or manufactured goods in accordance with paragraph (b)(4) of this section shall include adequate information for Federal Government evaluation of the request, including-

(A) A description of the foreign and domestic iron, steel, and/or manufactured goods;

(B) Unit of measure;

(C) Quantity;

(D) Cost;

(E) Time of delivery or availability;

(F) Location of the project;

(G) Name and address of the proposed supplier; and

(H) A detailed justification of the reason for use of foreign iron, steel, and/or manufactured goods cited in accordance with paragraph (b)(4) of this section.

(ii) A request based on unreasonable cost shall include a reasonable survey of the market and a completed cost comparison table in the format in paragraph (d) of this section.

(iii) The cost of iron, steel, or manufactured goods shall include all delivery costs to the construction site and any applicable duty.

(iv) Any recipient request for a determination submitted after Recovery Act funds have been obligated for a project for construction, alteration, maintenance, or repair shall explain why the recipient could not reasonably foresee the need for such determination and could not have requested the determination before the funds were obligated. If the recipient does not submit a satisfactory explanation, the award official need not make a determination.

(2) If the Federal Government determines after funds have been obligated for a project for construction, alteration, maintenance, or repair that an exception to section 1605 of the Recovery Act applies, the award official will amend the award to allow use of the foreign iron, steel, and/or relevant manufactured goods. When the basis for the exception is nonavailability or public interest, the amended award shall reflect adjustment of the award amount, redistribution of budgeted funds, and/or other appropriate actions taken to cover costs associated with acquiring or using the foreign iron, steel, and/or relevant manufactured goods. When the basis for the exception is the unreasonable cost of the domestic iron, steel, or manufactured goods, the award official shall adjust the award amount or redistribute budgeted funds, as appropriate, by at least the differential established in 2 CFR 176.110(a).

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(3) Unless the Federal Government determines that an exception to section 1605 of the Recovery Act applies, use of foreign iron, steel, and/or manufactured goods other than designated country iron, steel, and/or manufactured goods is noncompliant with the applicable Act.

(d) Data. To permit evaluation of requests under paragraph (b) of this section based on unreasonable cost, the applicant shall include the following information and any applicable supporting data based on the survey of suppliers:

Foreign and Domestic Items Cost Comparison

Description	Unit of measure	Quantity	Cost (dollars)*
Item 1:
Foreign steel, iron, or manufactured good	_________	_________	_________
Domestic steel, iron, or manufactured good	_________	_________	_________
Item 2:
Foreign steel, iron, or manufactured good	_________	_________	_________
Domestic steel, iron, or manufactured good	_________	_________	_________

List name, address, telephone number, email address, and contact for suppliers surveyed. Attach copy of response; if oral, attach summary.

Include other applicable supporting information.

*Include all delivery costs to the construction site.

27. RECOVERY ACT TRANSACTIONS LISTED IN SCHEDULE OF EXPENDITURES OF FEDERAL AWARDS AND RECIPIENT RESPONSIBILITIES FOR INFORMING SUBRECIPIENTS

(a) To maximize the transparency and accountability of funds authorized under the American Recovery and Reinvestment Act of 2009 (Pub. L. 111-5) (Recovery Act) as required by Congress and in accordance with 2 CFR 215.21 “Uniform Administrative Requirements for Grants and Agreements” and OMB Circular A-102 Common Rules provisions, recipients agree to maintain records that identify adequately the source and application of Recovery Act funds. OMB Circular A-102 is available at http://www.whitehouse.gov/omb/circulars/a102/a102.html.

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(b) For recipients covered by the Single Audit Act Amendments of 1996 and OMB Circular A-133, “Audits of States, Local Governments, and Non-Profit Organizations,” recipients agree to separately identify the expenditures for Federal awards under the Recovery Act on the Schedule of Expenditures of Federal Awards (SEFA) and the Data Collection Form (SF-SAC) required by OMB Circular A-133. OMB Circular A-133 is available at http://www.whitehouse.gov/omb/circulars/a133/a133.html. This shall be accomplished by identifying expenditures for Federal awards made under the Recovery Act separately on the SEFA, and as separate rows under Item 9 of Part III on the SF-SAC by CFDA number, and inclusion of the prefix “ARRA-” in identifying the name of the Federal program on the SEFA and as the first characters in Item 9d of Part III on the SF-SAC.

(c) Recipients agree to separately identify to each subrecipient, and document at the time of subaward and at the time of disbursement of funds, the Federal award number, CFDA number, and amount of Recovery Act funds. When a recipient awards Recovery Act funds for an existing program, the information furnished to subrecipients shall distinguish the subawards of incremental Recovery Act funds from regular subawards under the existing program.

(d) Recipients agree to require their subrecipients to include on their SEFA information to specifically identify Recovery Act funding similar to the requirements for the recipient SEFA described above. This information is needed to allow the recipient to properly monitor subrecipient expenditure of ARRA funds as well as oversight by the Federal awarding agencies, Offices of Inspector General and the Government Accountability Office.

28. WAGE RATE REQUIREMENTS UNDER SECTION 1606 OF THE RECOVERY ACT

(a) Section 1606 of the Recovery Act requires that all laborers and mechanics employed by contractors and subcontractors on projects funded directly by or assisted in whole or in part by and through the Federal Government pursuant to the Recovery Act shall be paid wages at rates not less than those prevailing on projects of a character similar in the locality as determined by the Secretary of Labor in accordance with subchapter IV of chapter 31 of title 40, United States Code.

Pursuant to Reorganization Plan No. 14 and the Copeland Act, 40 U.S.C. 3145, the Department of Labor has issued regulations at 29 CFR parts 1, 3, and 5 to implement the Davis-Bacon and related Acts. Regulations in 29 CFR 5.5 instruct agencies concerning application of the standard Davis-Bacon contract clauses set forth in that section. Federal agencies providing grants, cooperative agreements, and loans under the Recovery Act shall ensure that the standard Davis-Bacon contract clauses found in 29 CFR 5.5(a) are incorporated in any resultant covered contracts that are in excess of $2,000 for construction, alteration or repair (including painting and decorating).

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(b) For additional guidance on the wage rate requirements of section 1606, contact your awarding agency. Recipients of grants, cooperative agreements and loans should direct their initial inquiries concerning the application of Davis-Bacon requirements to a particular federally assisted project to the Federal agency funding the project. The Secretary of Labor retains final coverage authority under Reorganization Plan Number 14.

29. DAVIS BACON ACT AND CONTRACT WORK HOURS AND SAFETY STANDARDS ACT

If the Recipient determines at any time that any construction, alteration, or repair activity as defined by 29 CFR 5.2(j) (http://cfr.vlex.com/vid/5-2-definitions-19681309) will be performed during the course of the project, the Recipient shall notify the Contracting Officer prior to commencing such work and the following provisions shall apply. A modification to the award which incorporates the appropriate Davis-Bacon wage rate determination(s) will constitute the Contracting Officer's approval to proceed.

Definitions: For purposes of this provision, “Davis Bacon Act and Contract Work Hours and Safety Standards Act,” the following definitions are applicable:

(1) “Award” means any grant, cooperative agreement or technology investment agreement made with Recovery Act funds by the Department of Energy (DOE) to a Recipient. Such Award must require compliance with the labor standards clauses and wage rate requirements of the Davis-Bacon Act (DBA) for work performed by all laborers and mechanics employed by Recipients (other than a unit of State or local government whose own employees perform the construction) Subrecipients, Contractors, and subcontractors.

(2) “Contractor” means an entity that enters into a Contract. For purposes of these clauses, Contractor shall include (as applicable) prime contractors, Recipients, Subrecipients, and Recipients' or Subrecipients' contractors, subcontractors, and lower-tier subcontractors. “Contractor” does not mean a unit of State or local government where construction is performed by its own employees.”

(3) “Contract” means a contract executed by a Recipient, Subrecipient, prime contractor, or any tier subcontractor for construction, alteration, or repair. It may also mean (as applicable) (i) financial assistance instruments such as grants, cooperative agreements, technology investment agreements, and loans; and, (ii) Sub awards, contracts and subcontracts issued under financial assistance agreements. “Contract” does not mean a financial assistance instrument with a unit of State or local government where construction is performed by its own employees.

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(4) “Contracting Officer” means the DOE official authorized to execute an Award on behalf of DOE and who is responsible for the business management and non-program aspects of the financial assistance process.

(5) “Recipient” means any entity other than an individual that receives an Award of Federal funds in the form of a grant, cooperative agreement, or technology investment agreement directly from the Federal Government and is financially accountable for the use of any DOE funds or property, and is legally responsible for carrying out the terms and conditions of the program and Award.

(6) “Subaward” means an award of financial assistance in the form of money, or property in lieu of money, made under an award by a Recipient to an eligible Subrecipient or by a Subrecipient to a lower-tier subrecipient. The term includes financial assistance when provided by any legal agreement, even if the agreement is called a contract, but does not include the Recipient's procurement of goods and services to carry out the program nor does it include any form of assistance which is excluded from the definition of “Award” above.

(7) “Subrecipient” means a non-Federal entity that expends Federal funds received from a Recipient to carry out a Federal program, but does not include an individual that is a beneficiary of such a program.

(a) Davis Bacon Act

(1) Minimum wages.

(i) All laborers and mechanics employed or working upon the site of the work (or under the United States Housing Act of 1937 or under the Housing Act of 1949 in the construction or development of the project), will be paid unconditionally and not less often than once a week, and, without subsequent deduction or rebate on any account (except such payroll deductions as are permitted by regulations issued by the Secretary of Labor under the Copeland Act (29 CFR part 3)), the full amount of wages and bona fide fringe benefits (or cash equivalents thereof) due at time of payment computed at rates not less than those contained in the wage determination of the Secretary of Labor which is attached hereto and made a part hereof, regardless of any contractual relationship which may be alleged to exist between the Contractor and such laborers and mechanics.

Contributions made or costs reasonably anticipated for bona fide fringe benefits under section 1(b)(2) of the Davis-Bacon Act on behalf of laborers or mechanics are considered wages paid to such laborers or mechanics, subject to the provisions of paragraph (a)(1)(iv) of this section; also, regular contributions made or costs incurred for more than a weekly period (but not less often than quarterly) under plans, funds, or programs which cover the particular weekly period, are deemed to be constructively made or incurred during such weekly period. Such laborers and mechanics shall be paid the appropriate wage rate and fringe benefits on the wage

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determination for the classification of work actually performed, without regard to skill, except as provided in § 5.5(a)(4). Laborers or mechanics performing work in more than one classification may be compensated at the rate specified for each classification for the time actually worked therein, provided that the employer's payroll records accurately set forth the time spent in each classification in which work is performed. The wage determination (including any additional classification and wage rates conformed under paragraph (a)(1)(ii) of this section) and the Davis-Bacon poster (WH-1321) shall be posted at all times by the Contractor and its subcontractors at the site of the work in a prominent and accessible place where it can be easily seen by the workers.

(ii)(A) The Contracting Officer shall require that any class of laborers or mechanics, including helpers, which is not listed in the wage determination and which is to be employed under the Contract shall be classified in conformance with the wage determination. The Contracting Officer shall approve an additional classification and wage rate and fringe benefits therefore only when the following criteria have been met:

(1) The work to be performed by the classification requested is not performed by a classification in the wage determination;

(2) The classification is utilized in the area by the construction industry; and

(3) The proposed wage rate, including any bona fide fringe benefits, bears a reasonable relationship to the wage rates contained in the wage determination.

(B) If the Contractor and the laborers and mechanics to be employed in the classification (if known), or their representatives, and the Contracting Officer agree on the classification and wage rate (including the amount designated for fringe benefits where appropriate), a report of the action taken shall be sent by the Contracting Officer to the Administrator of the Wage and Hour Division, U.S. Department of Labor, Washington, DC 20210. The Administrator, or an authorized representative, will approve, modify, or disapprove every additional classification action within 30 days of receipt and so advise the Contracting Officer or will notify the Contracting Officer within the 30-day period that additional time is necessary.

(C) In the event the Contractor, the laborers or mechanics to be employed in the classification or their representatives, and the Contracting Officer do not agree on the proposed classification and wage rate (including the amount designated for fringe benefits, where appropriate), the Contracting Officer shall refer the questions, including the views of all interested parties and the recommendation of the Contracting Officer, to the Administrator for determination. The Administrator, or an authorized representative, will issue a determination within 30 days of receipt and so advise the Contracting Officer or will notify the Contracting Officer within the 30-day period that additional time is necessary.

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(D) The wage rate (including fringe benefits where appropriate) determined pursuant to paragraphs (a)(1)(ii)(B) or (C) of this section, shall be paid to all workers performing work in the classification under this Contract from the first day on which work is performed in the classification.

(iii) Whenever the minimum wage rate prescribed in the Contract for a class of laborers or mechanics includes a fringe benefit which is not expressed as an hourly rate, the Contractor shall either pay the benefit as stated in the wage determination or shall pay another bona fide fringe benefit or an hourly cash equivalent thereof.

(iv) If the Contractor does not make payments to a trustee or other third person, the Contractor may consider as part of the wages of any laborer or mechanic the amount of any costs reasonably anticipated in providing bona fide fringe benefits under a plan or program, provided that the Secretary of Labor has found, upon the written request of the Contractor, that the applicable standards of the Davis-Bacon Act have been met. The Secretary of Labor may require the Contractor to set aside in a separate account assets for the meeting of obligations under the plan or program.

(2) Withholding. The Department of Energy or the Recipient or Subrecipient shall upon its own action or upon written request of an authorized representative of the Department of Labor withhold or cause to be withheld from the Contractor under this Contract or any other Federal contract with the same prime contractor, or any other federally-assisted contract subject to Davis-Bacon prevailing wage requirements, which is held by the same prime contractor, so much of the accrued payments or advances as may be considered necessary to pay laborers and mechanics, including apprentices, trainees, and helpers, employed by the Contractor or any subcontractor the full amount of wages required by the Contract. In the event of failure to pay any laborer or mechanic, including any apprentice, trainee, or helper, employed or working on the site of the work (or under the United States Housing Act of 1937 or under the Housing Act of 1949 in the construction or development of the project), all or part of the wages required by the Contract, the Department of Energy, Recipient, or Subrecipient, may, after written notice to the Contractor, sponsor, applicant, or owner, take such action as may be necessary to cause the suspension of any further payment, advance, or guarantee of funds until such violations have ceased.

(3) Payrolls and basic records.

(i) Payrolls and basic records relating thereto shall be maintained by the Contractor during the course of the work and preserved for a period of three years thereafter for all laborers and mechanics working at the site of the work (or under

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the United States Housing Act of 1937, or under the Housing Act of 1949, in the construction or development of the project). Such records shall contain the name, address, and social security number of each such worker, his or her correct classification, hourly rates of wages paid (including rates of contributions or costs anticipated for bona fide fringe benefits or cash equivalents thereof of the types described in section 1(b)(2)(B) of the Davis-Bacon Act), daily and weekly number of hours worked, deductions made, and actual wages paid. Whenever the Secretary of Labor has found under 29 CFR 5.5(a)(1)(iv) that the wages of any laborer or mechanic include the amount of any costs reasonably anticipated in providing benefits under a plan or program described in section 1(b)(2)(B) of the Davis-Bacon Act, the Contractor shall maintain records which show that the commitment to provide such benefits is enforceable, that the plan or program is financially responsible, and that the plan or program has been communicated in writing to the laborers or mechanics affected, and records which show the costs anticipated or the actual cost incurred in providing such benefits. Contractors employing apprentices or trainees under approved programs shall maintain written evidence of the registration of apprenticeship programs and certification of trainee programs, the registration of the apprentices and trainees, and the ratios and wage rates prescribed in the applicable programs.

(ii) (A) The Contractor shall submit weekly for each week in which any Contract work is performed a copy of all payrolls to the Department of Energy if the agency is a party to the Contract, but if the agency is not such a party, the Contractor will submit the payrolls to the Recipient or Subrecipient (as applicable), applicant, sponsor, or owner, as the case may be, for transmission to the Department of Energy. The payrolls submitted shall set out accurately and completely all of the information required to be maintained under 29 CFR 5.5(a)(3)(i), except that full social security numbers and home addresses shall not be included on weekly transmittals. Instead, the payrolls shall only need to include an individually identifying number for each employee (e.g., the last four digits of the employee's social security number). The required weekly payroll information may be submitted in any form desired. Optional Form WH-347 is available for this purpose from the Wage and Hour Division Web site at http://www.dol.gov/esa/whd/forms/wh347instr.htm or its successor site. The prime Contractor is responsible for the submission of copies of payrolls by all subcontractors. Contractors and subcontractors shall maintain the full social security number and current address of each covered worker, and shall provide them upon request to the Department of Energy if the agency is a party to the Contract, but if the agency is not such a party, the Contractor will submit them to the Recipient or Subrecipient (as applicable), applicant, sponsor, or owner, as the case may be, for transmission to the Department of Energy, the Contractor, or the Wage and Hour Division of the Department of Labor for purposes of an investigation or audit of compliance with prevailing wage requirements. It is not a violation of this section for a prime contractor to require a subcontractor to provide addresses and social security numbers to the prime contractor for its own records, without weekly submission to the sponsoring government agency (or the Recipient or Subrecipient (as applicable), applicant, sponsor, or owner).

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(B) Each payroll submitted shall be accompanied by a “Statement of Compliance,” signed by the Contractor or subcontractor or his or her agent who pays or supervises the payment of the persons employed under the Contract and shall certify the following:

(1) That the payroll for the payroll period contains the information required to be provided under § 5.5 (a)(3)(ii) of Regulations, 29 CFR part 5, the appropriate information is being maintained under § 5.5 (a)(3)(i) of Regulations, 29 CFR part 5, and that such information is correct and complete;

(2) That each laborer or mechanic (including each helper, apprentice, and trainee) employed on the Contract during the payroll period has been paid the full weekly wages earned, without rebate, either directly or indirectly, and that no deductions have been made either directly or indirectly from the full wages earned, other than permissible deductions as set forth in Regulations, 29 CFR part 3;

(3) That each laborer or mechanic has been paid not less than the applicable wage rates and fringe benefits or cash equivalents for the classification of work performed, as specified in the applicable wage determination incorporated into the Contract.

(C) The weekly submission of a properly executed certification set forth on the reverse side of Optional Form WH-347 shall satisfy the requirement for submission of the “Statement of Compliance” required by paragraph (a)(3)(ii)(B) of this section.

(D) The falsification of any of the above certifications may subject the Contractor or subcontractor to civil or criminal prosecution under section 1001 of title 18 and section 3729 of title 31 of the United States Code.

(iii) The Contractor or subcontractor shall make the records required under paragraph (a)(3)(i) of this section available for inspection, copying, or transcription by authorized representatives of the Department of Energy or the Department of Labor, and shall permit such representatives to interview employees during working hours on the job. If the Contractor or subcontractor fails to submit the required records or to make them available, the Federal agency may, after written notice to the Contractor, sponsor, applicant, or owner, take such action as may be necessary to cause the suspension of any further payment, advance, or guarantee of funds. Furthermore, failure to submit the required records upon request or to make such records available may be grounds for debarment action pursuant to 29 CFR 5.12.

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(4) Apprentices and trainees-

(i) Apprentices. Apprentices will be permitted to work at less than the predetermined rate for the work they performed when they are employed pursuant to and individually registered in a bona fide apprenticeship program registered with the U.S. Department of Labor, Employment and Training Administration, Office of Apprenticeship Training, Employer and Labor Services, or with a State Apprenticeship Agency recognized by the Office, or if a person is employed in his or her first 90 days of probationary employment as an apprentice in such an apprenticeship program, who is not individually registered in the program, but who has been certified by the Office of Apprenticeship Training, Employer and Labor Services or a State Apprenticeship Agency (where appropriate) to be eligible for probationary employment as an apprentice. The allowable ratio of apprentices to journeymen on the job site in any craft classification shall not be greater than the ratio permitted to the Contractor as to the entire work force under the registered program. Any worker listed on a payroll at an apprentice wage rate, who is not registered or otherwise employed as stated above, shall be paid not less than the applicable wage rate on the wage determination for the classification of work actually performed. In addition, any apprentice performing work on the job site in excess of the ratio permitted under the registered program shall be paid not less than the applicable wage rate on the wage determination for the work actually performed. Where a Contractor is performing construction on a project in a locality other than that in which its program is registered, the ratios and wage rates (expressed in percentages of the journeyman's hourly rate) specified in the Contractor's or subcontractor's registered program shall be observed. Every apprentice must be paid at not less than the rate specified in the registered program for the apprentice's level of progress, expressed as a percentage of the journeymen hourly rate specified in the applicable wage determination. Apprentices shall be paid fringe benefits in accordance with the provisions of the apprenticeship program. If the apprenticeship program does not specify fringe benefits, apprentices must be paid the full amount of fringe benefits listed on the wage determination for the applicable classification. If the Administrator determines that a different practice prevails for the applicable apprentice classification, fringes shall be paid in accordance with that determination. In the event the Office of Apprenticeship Training, Employer and Labor Services, or a State Apprenticeship Agency recognized by the Office, withdraws approval of an apprenticeship program, the Contractor will no longer be permitted to utilize apprentices at less than the applicable predetermined rate for the work performed until an acceptable program is approved.

(ii) Trainees. Except as provided in 29 CFR 5.16, trainees will not be permitted to work at less than the predetermined rate for the work performed unless they are employed pursuant to and individually registered in a program which has received prior approval, evidenced by formal certification by the U.S. Department of Labor, Employment and Training Administration. The ratio of trainees to

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journeymen on the job site shall not be greater than permitted under the plan approved by the Employment and Training Administration. Every trainee must be paid at not less than the rate specified in the approved program for the trainee's level of progress, expressed as a percentage of the journeyman hourly rate specified in the applicable wage determination. Trainees shall be paid fringe benefits in accordance with the provisions of the trainee program. If the trainee program does not mention fringe benefits, trainees shall be paid the full amount of fringe benefits listed on the wage determination unless the Administrator of the Wage and Hour Division determines that there is an apprenticeship program associated with the corresponding journeyman wage rate on the wage determination which provides for less than full fringe benefits for apprentices. Any employee listed on the payroll at a trainee rate who is not registered and participating in a training plan approved by the Employment and Training Administration shall be paid not less than the applicable wage rate on the wage determination for the classification of work actually performed. In addition, any trainee performing work on the job site in excess of the ratio permitted under the registered program shall be paid not less than the applicable wage rate on the wage determination for the work actually performed. In the event the Employment and Training Administration withdraws approval of a training program, the Contractor will no longer be permitted to utilize trainees at less than the applicable predetermined rate for the work performed until an acceptable program is approved.

(iii) Equal employment opportunity. The utilization of apprentices, trainees, and journeymen under this part shall be in conformity with the equal employment opportunity requirements of Executive Order 11246, as amended and 29 CFR part 30.

(5) Compliance with Copeland Act requirements. The Contractor shall comply with the requirements of 29 CFR part 3, which are incorporated by reference in this Contract.

(6) Contracts and Subcontracts. The Recipient, Subrecipient, the Recipient's, and Subrecipient's contractors and subcontractor shall insert in any Contracts the clauses contained herein in(a)(1) through (10) and such other clauses as the Department of Energy may by appropriate instructions require, and also a clause requiring the subcontractors to include these clauses in any lower tier subcontracts. The Recipient shall be responsible for the compliance by any subcontractor or lower tier subcontractor with all of the paragraphs in this clause.

(7) Contract termination: debarment. A breach of the Contract clauses in 29 CFR 5.5 may be grounds for termination of the Contract, and for debarment as a contractor and a subcontractor as provided in 29 CFR 5.12.

(8) Compliance with Davis-Bacon and Related Act requirements. All rulings and interpretations of the Davis-Bacon and Related Acts contained in 29 CFR parts 1, 3, and 5 are herein incorporated by reference in this Contract.

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(9) Disputes concerning labor standards. Disputes arising out of the labor standards provisions of this Contract shall not be subject to the general disputes clause of this Contract. Such disputes shall be resolved in accordance with the procedures of the Department of Labor set forth in 29 CFR parts 5, 6, and 7. Disputes within the meaning of this clause include disputes between the Recipient, Subrecipient, the Contractor (or any of its subcontractors), and the contracting agency, the U.S. Department of Labor, or the employees or their representatives.

(10) Certification of eligibility.

(i) By entering into this Contract, the Contractor certifies that neither it (nor he or she) nor any person or firm who has an interest in the Contractor's firm is a person or firm ineligible to be awarded Government contracts by virtue of section 3(a) of the Davis-Bacon Act or 29 CFR 5.12(a)(1).

(ii) No part of this Contract shall be subcontracted to any person or firm ineligible for award of a Government contract by virtue of section 3(a) of the Davis-Bacon Act or 29 CFR 5.12(a)(1).

(iii) The penalty for making false statements is prescribed in the U.S. Criminal Code, 18 U.S.C. 1001.

(b) Contract Work Hours and Safety Standards Act. As used in this paragraph, the terms laborers and mechanics include watchmen and guards.

(1) Overtime requirements. No Contractor or subcontractor contracting for any part of the Contract work which may require or involve the employment of laborers or mechanics shall require or permit any such laborer or mechanic in any workweek in which he or she is employed on such work to work in excess of forty hours in such workweek unless such laborer or mechanic receives compensation at a rate not less than one and one-half times the basic rate of pay for all hours worked in excess of forty hours in such workweek.

(2) Violation; liability for unpaid wages; liquidated damages. In the event of any violation of the clause set forth in paragraph (b)(1) of this section, the Contractor and any subcontractor responsible therefor shall be liable for the unpaid wages. In addition, such Contractor and subcontractor shall be liable to the United States (in the case of work done under contract for the District of Columbia or a territory, to such District or to such territory), for liquidated damages. Such liquidated damages shall be computed with respect to each individual laborer or mechanic, including watchmen and guards, employed in violation of the clause set forth in paragraph (b)(1) of this section, in the sum of $10 for each calendar day on which such individual was required or permitted to work in excess of the standard workweek of forty hours without payment of the overtime wages required by the clause set forth in paragraph (b)(1) of this section.

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(3) Withholding for unpaid wages and liquidated damages. The Department of Energy or the Recipient or Subrecipient shall upon its own action or upon written request of an authorized representative of the Department of Labor withhold or cause to be withheld, from any moneys payable on account of work performed by the Contractor or subcontractor under any such contract or any other Federal contract with the same prime Contractor, or any other federally-assisted contract subject to the Contract Work Hours and Safety Standards Act, which is held by the same prime contractor, such sums as may be determined to be necessary to satisfy any liabilities of such Contractor or subcontractor for unpaid wages and liquidated damages as provided in the clause set forth in paragraph (b)(2) of this section.

(4) Contracts and Subcontracts. The Recipient, Subrecipient, and Recipient's and Subrecipient's contractor or subcontractor shall insert in any Contracts, the clauses set forth in paragraph (b)(1) through (4) of this section and also a clause requiring the subcontractors to include these clauses in any lower tier subcontracts. The Recipient shall be responsible for compliance by any subcontractor or lower tier subcontractor with the clauses set forth in paragraphs (b)(1) through (4) of this section.

(5) The Contractor or subcontractor shall maintain payrolls and basic payroll records during the course of the work and shall preserve them for a period of three years from the completion of the Contract for all laborers and mechanics, including guards and watchmen, working on the Contract. Such records shall contain the name and address of each such employee, social security number, correct classifications, hourly rates of wages paid, daily and weekly number of hours worked, deductions made, and actual wages paid. The records to be maintained under this paragraph shall be made available by the Contractor or subcontractor for inspection, copying, or transcription by authorized representatives of the Department of Energy and the Department of Labor, and the Contractor or subcontractor will permit such representatives to interview employees during working hours on the job.

(c) Recipient Responsibilities for Davis Bacon Act

(1) On behalf of the Department of Energy (DOE), Recipient shall perform the following functions:

(i) Obtain, maintain, and monitor all Davis Bacon Act (DBA) certified payroll records submitted by the Subrecipients and Contractors at any tier under this Award;

(ii) Review all DBA certified payroll records for compliance with DBA requirements, including applicable DOL wage determinations;

(iii) Notify DOE of any non-compliance with DBA requirements by Subrecipients or Contractors at any tier, including any non-compliances identified as the result of reviews performed pursuant to paragraph (ii) above;

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(iv) Address any Subrecipient and any Contractor DBA non-compliance issues; if DBA non-compliance issues cannot be resolved in a timely manner, forward complaints, summary of investigations and all relevant information to DOE;

(v) Provide DOE with detailed information regarding the resolution of any DBA non-compliance issues;

(vi) Perform services in support of DOE investigations of complaints filed regarding noncompliance by Subrecipients and Contractors with DBA requirements;

(vii) Perform audit services as necessary to ensure compliance by Subrecipients and Contractors with DBA requirements and as requested by the Contracting Officer; and

(viii) Provide copies of all records upon request by DOE or DOL in a timely manner.

(d) Rates of Wages

The minimum wages to be paid laborers and mechanics under this award involved in performance of work at the project site, as determined by the Secretary of Labor to be prevailing for the corresponding classes of laborers and mechanics employed on projects of a character similar to the contract work in the pertinent locality, are found at http://www.wdol.gov/, by clicking on “Selecting DBA WDs”. The Wage Determination Number(s) and General Decision Number(s) specific to this award are found below. These wage rates are minimum rates and are not intended to represent the actual wage rates that the Contractor may have to pay.

CONSTRUCTION TYPE	WAGE DETERMINATION NUMBER	GENERAL DECISION NUMBER
Building	CA29, CO7, CA25, KS8	CA100029 03/19/2010 CA29 CO100007 03/12/2010 CO7 CA100025 03/12/2010 CA25 KS100008 03/19/2010 KS8
Highway	n/a	n/a
Residential	n/a	n/a

30. CONTINGENCY

(a) Contingency Requirement. A minimum amount of Contingency is required for awards selected under Funding Opportunity Announcement DE-FOA-0000096. “Contingency” is defined in the Appendix as: “a provision in the Project Management Plan to mitigate cost and/or schedule risk.” Contingency funds must be (a) liquid, (b) immediately available, and (c) unrestricted funds dedicated exclusively to the Project for the purpose of mitigating project performance baseline risk. Contingency funds may come from a variety of sources, as approved by the Contracting Officer on a case-by-case basis in accordance with the Appendix to these Special Terms and Conditions (Attachment 5).

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(b) Minimum Amount of Contingency. Initial Contingency funds shall be not less than 25 percent of the Total Project Cost that begins with Budget Period 2, as more specifically described in Section B(2) of the Appendix to these Special Terms and Conditions (Attachment 5).

(c) Contingency Not Counted Toward Cost Share or DOE Reimbursement. Contingency is in addition to the Total Project Cost and cannot count toward cost share or result in reimbursement by DOE above the share approved in the award.

(d) Appendix. All of the terms and conditions set forth in this provision shall be further subject to the requirements and clarifications of Attachment 5.

31. NATIONAL ENVIRONMENTAL POLICY ACT (NEPA) REQUIREMENTS

For this award, DOE has made a final NEPA determination for all activities under this award that are listed in the Statement of Project Objectives (SOPO) formally approved by DOE through incorporation into and attached to the award. You (Recipient) may proceed with the activities as described in the SOPO. This NEPA determination is specific to the project as described in the SOPO formally approved by DOE through incorporation into and attached to the award.

If you later add to or modify the activities in the above-referenced SOPO, you must submit the revised SOPO to the DOE Project Officer. Those additions or modifications are subject to review by the NEPA Compliance Officer and approval by the DOE's Contracting Officer. Recipients are restricted from taking any action using Federal funds, which would have an adverse effect on the environment or limit the choice of reasonable alternatives prior to DOE providing a final NEPA determination. Any new activities or modification of activities is subject to additional NEPA review and is not authorized for federal funding until DOE provides a NEPA determination on those additions or modifications. DOE may require the Recipient to submit additional information to support a revised NEPA determination. Should you move forward with activities that are not authorized for Federal funding by the DOE Contracting Officer in advance of the final NEPA determination, you are doing so at risk of not receiving Federal funding and such costs may not be recognized as allowable cost share.

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ASSISTANCE AGREEMENT
1. Award No. DE-EE0002869		2. Modification No. 006		3. Effective Date 12/28/2009		4. CFDA No. 81.087
5. Awarded To AMYRIS BIOTECHNOLOGIES, INC. Attn: KINKEAD REILING 5885 HOLLIS STREET SUITE 100 EMERYVILLE CA 946082059			6. Sponsoring Office Golden Field Office U.S. Department of Energy Golden Field Office 1617 Cole Blvd. Golden CO 80401				7. Period of Performance 12/28/2009 through 06/30/2012
8. Type of Agreement _ Grant x Cooperative Agreement _ Other	9. Authority 109-58 Energy Policy Act (2005) 111-5 Recovery Act (2009)				10. Purchase Request or Funding Document No. 11EE005464
11. Remittance Address			12. Total Amount				13. Funds Obligated
AMYRIS BIOTECHNOLOGIES, INC. Attn: KINKEAD REILING 5885 HOLLIS STREET SUITE 100 EMERYVILLE CA 946082059			Govt. Share: $ 24,341,409.00 Cost Share: $ 10,591,590.00 Total: $ 34,932,999.00				This action: $0.00 Total: $24,341,409.00
14. Principal Investigator Neil Renninger Phone: 510-740-7414	15. Program Manager Fred W. Gerdeman Phone: 303-275-4928				16. Administrator Golden Field Office U.S. Department of Energy Golden Field Office 1617 Cole Blvd. Golden CO 80401-3393
17. Submit Payment Requests To OR for Golden U.S. Department of Energy Oak Ridge Financial Service Center P.O. Box 4517 Oak Ridge TN 37831			18. Paying Office OR for Golden U.S. Department of Energy Oak Ridge Financial Service Center P.O. Box 4517 Oak Ridge TN 37831				19. Submit Reports To
20. Accounting and Appropriation Data See Schedule
21. Research Title and/or Description of Project RECOVERY ACT: SCALE-UP & MOBILIZATION OF RENEWABLE DIESEL & CHEMICAL PRODUCTION FROM COMMON INTERMEDIATE USING US-BASED FERMENTABLE SUGAR FEEDSTOCKS
For the Recipient				For the United States of America
22. Signature of Person Authorized to Sign				25. Signature of Grants/Agreements Officer Signature on File
23. Name and Title	24. Date Signed			26. Name of Officer Laura Merrick				27. Date Signed 07/26/2011

CONTINUATION SHEET		REFERENCE NO. OF DOCUMENT BEING CONTINUED DE-EE0002869/006			PAGE 2 OF 2
NAME OF OFFEROR OR CONTRACTOR AMYRIS BIOTECHNOLOGIES, INC.
ITEM  NO. (A)	SUPPLIES/SERVICES (B)	QUANTITY (C)	UNIT (D)	UNIT PRICE (E)	AMOUNT (F)
	DUNS Number: 185930182 The purpose of this modification is to delete and replace Attachment 3, Reporting Requirements Checklist and Instructions, DOE F 4600.2, revising the following sections: A. Management Reporting, D. Closeout Reporting, E. Other Reporting, and Instructions attached to the Reporting Checklist. All other terms and conditions remain unchanged. In Block 7 of the Assistance Agreement, the Period of Performance reflects the beginning of the Project Period through the end of the current Budget Period, shown as 12/28/2009 through 6/30/2012. For multiple Budget Periods, see Special Terms and Conditions, Provision 4, Award Project Period and Budget Periods. DOE Award Administrator: Brenda Dias E-mail: brenda.dias@go.doe.gov Phone: 303-275-6043 DOE Project Officer: Fred Gerdeman E-mail: fred.gerdeman@go.doe.gov Phone: 303-275-4928 Recipient Business Officer: Todd Pray E-mail: pray@amyris.com Phone: 510-740-7441 Recipient Principal Investigator: Neil Renninger E-mail: renninger@amyris.com Phone: 510-740-7414 “Electronic signature or signatures as used in this document means a method of signing an electronic message that-- (A) Identifies and authenticates a particular person as the source of the electronic message; (B) Indicates such person's approval of the information contained in the electronic message; and, (C) Submission via FedConnect constitutes electronically signed documents.” ASAP: NO : STD IMMEDIATE Extent Competed: COMPETED Davis-Bacon Act: YES
JULY 2004

1. Identification Number: DE-EE0002869.006	2. Program/Project Title: Recovery Act: Scale-up and Mobilization of Renewable Diesel and Chemical Production from Common Intermediate using US-based Fermentable Sugar Feedstocks
3. Recipient: Amyris Biotechnologies, Inc.
4. Reporting Requirements:	Frequency	Addresses
A. MANAGEMENT REPORTING X Research Performance Progress Report (RPPR) X Special Status Report B. SCIENTIFIC/TECHNICAL REPORTING (Reports/Products must be submitted with appropriate DOE F 241. The 241 forms are available at www.osti.gov/elink)                Report/Product Form X Final Scientific Report DOE F 241.3 X Conference papers/proceedings* DOE F 241.3 __ Software/Manual DOE F 241.4 __ Other (see special instructions) DOE F 241.3 * Scientific and technical conferences only C. FINANCIAL REPORTING X SF-425, Federal Financial Report FQ D. CLOSEOUT REPORTING X Patent Certification X SF-428 & 428B Final Property Report __ Other E. OTHER REPORTING X Annual Indirect Cost Proposal X Audit of For-Profit Recipients __ SF-428 Tangible Personal Property Report Forms Family X Other	Q A F A FQ F F Y180 Y180 AY	https://www.eere-pmc.energy.gov/ https://www.eere-pmc.energy.gov/SubmitReports.aspx http://www.osti.gov/elink-2413 http://www.osti.gov/elink-2413 http://www.osti.gov/estsc/241-4pre.jsp http://www.osti.gov/elink-2413 https://www.eere-pmc.energy.gov/ https://www.eere-pmc.energy.gov/SubmitReports.aspx https://www.eere-pmc.energy.gov/SubmitReports.aspx https://www.eere-pmc.energy.gov/SubmitReports.aspx See block 5 below for instructions. See block 5 below for addresses. https://www.eere-pmc.energy.gov/SubmitReports.aspxhttps://www.eere-pmc.energy.gov/SubmitReports.aspx
FREQUENCY CODES AND DUE DATES:      A - Within 5 calendar days after events or as specified.      F - Final; 90 calendar days after expiration or termination of the award.      Y - Yearly; 90 days after the end of the reporting period.      S - Semiannually; within 30 days after end of the reporting period.      Q - Quarterly; within 30 days after end of the reporting period.      Y180 - Yearly; 180 days after end of the recipient's fiscal year.      O - Other; See instructions for further details.
5. Special Instructions: Annual Indirect Cost Proposal - If DOE is the Cognizant Federal Agency, then the proposal should be sent to https://www.eere-pmc.energy.gov/SubmitReports.aspx. Otherwise, it should be sent to the Cognizant Federal Agency. Audit of For-Profit Recipients must be sent to 2 different addresses in accordance with the final audit guidance. A copy for the Contracting Officer shall be submitted via https://www.eere-pmc.energy.gov/SubmitReports.aspx; a copy must also be e-mailed to the CFO at DOE-Audit-Submissions@hq.doe.gov OTHER REPORTING Special Instructions: 1) A Project Management Plan (PMP) is due to the Project Officer 30 days after award and should be revised on a yearly basis. An electronic template will be provided to the Recipient to complete or update as needed. 2) An Annual Technical and Financial Report must be developed and submitted to the DOE Project Officer after award and must be updated annually throughout the duration of the award. Subject to the availability of project funding, the Report will also be due annually for three (3) years after the facility is substantially completed. The schedule for submission will be established by the DOE Project Officer after award. The format for the report with instructions for completion, the electronic template for reporting data, and the schedule will be forwarded to the Recipient after award. 3) Comprehensive Annual Project Review - The Recipient will be required to present the Annual Technical and Financial Report at a Comprehensive Annual Project Review meeting. The schedule for the Comprehensive Annual Project Review will be established by the DOE Project Officer after the award. AMERICAN RECOVERY AND REINVESTMENT ACT REPORTING: See the Special Terms and Conditions for Recovery Act reporting requirements, along with the following website: http://www.federalreporting.gov. The required reports are due no later than ten calendar days after each calendar quarter in which the Recipient receives the assistance award funded in whole or in part by the Recovery Act. Recipients are to report according to ARRA reporting instructions.

Federal Assistance Reporting Instructions (3/11)

A. MANAGEMENT REPORTING

Research Performance Progress Report (RPPR)

See attached document entitled "Research Performance Progress Report".

Special Status Report

The recipient must report the following events by e-mail as soon as possible after they occur:

1. Developments that have a significant favorable impact on the project.

2. Problems, delays, or adverse conditions which materially impair the recipient's ability to meet the objectives of the award or which may require DOE to respond to questions relating to such events from the public. The recipient must report any of the following incidents and include the anticipated impact and remedial action to be taken to correct or resolve the problem/condition:

a. Any single fatality or injuries requiring hospitalization of five or more individuals.

b. Any significant environmental permit violation.

c. Any verbal or written Notice of Violation of any Environmental, Safety, and Health statutes.

d. Any incident which causes a significant process or hazard control system failure.

e. Any event which is anticipated to cause a significant schedule slippage or cost increase.

f. Any damage to Government-owned equipment in excess of $50,000.

g. Any other incident that has the potential for high visibility in the media.

B. SCIENTIFIC/TECHNICAL REPORTS

Final Scientific/Technical Report

Content. The final scientific/technical report must include the following information and any other information identified under Special Instructions on the Federal Assistance Reporting Checklist:

1. Identify the DOE award number; name of recipient; project title; name of project director/principal investigator; and consortium/teaming members.

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2. Display prominently on the cover of the report any authorized distribution limitation notices, such as patentable material or protected data. Reports delivered without such notices may be deemed to have been furnished with unlimited rights, and the Government assumes no liability for the disclosure, use or reproduction of such reports.

3. Provide an executive summary, which includes a discussion of: (1) how the research adds to the understanding of the area investigated; (2) the technical effectiveness and economic feasibility of the methods or techniques investigated or demonstrated; or (3) how the project is otherwise of benefit to the public. The discussion should be a minimum of one paragraph and written in terms understandable by an educated layman.

4. Provide a comparison of the actual accomplishments with the goals and objectives of the project.

5. Summarize project activities for the entire period of funding, including original hypotheses, approaches used, problems encountered and departure from planned methodology, and an assessment of their impact on the project results. Include, if applicable, facts, figures, analyses, and assumptions used during the life of the project to support the conclusions.

6. Identify products developed under the award and technology transfer activities, such as:

a. Publications (list journal name, volume, issue), conference papers, or other public releases of results. If not provided previously, attach or send copies of any public releases to the DOE Program Manager identified in Block 15 of the Assistance Agreement Cover page;

b. Web site or other Internet sites that reflect the results of this project;

c. Networks or collaborations fostered;

d. Technologies/Techniques;

e. Inventions/Patent Applications, licensing agreements; and

f. Other products, such as data or databases, physical collections, audio or video, software or netware, models, educational aid or curricula, instruments or equipment.

7. For projects involving computer modeling, provide the following information with the final report:

a. Model description, key assumptions, version, source and intended use;

b. Performance criteria for the model related to the intended use;

c. Test results to demonstrate the model performance criteria were met (e.g., code verification/validation, sensitivity analyses, history matching with lab or field data, as appropriate);

d. Theory behind the model, expressed in non-mathematical terms;

e. Mathematics to be used, including formulas and calculation methods;

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f. Whether or not the theory and mathematical algorithms were peer reviewed, and, if so, include a summary of theoretical strengths and weaknesses;

g. Hardware requirements; and

h. Documentation (e.g., users guide, model code).

Electronic Submission. The final scientific/technical report must be submitted electronically via the DOE Energy Link System (E-Link) accessed at http://www.osti.gov/elink-2413.

Electronic Format. Reports must be submitted in the ADOBE PORTABLE DOCUMENT FORMAT (PDF) and be one integrated PDF file that contains all text, tables, diagrams, photographs, schematic, graphs, and charts. Materials, such as prints, videos, and books, that are essential to the report but cannot be submitted electronically, should be sent to the DOE Administrator at the address listed in Block 16 of the Assistance Agreement Cover Page.

Submittal Form. The report must be accompanied by a completed electronic version of DOE Form 241.3, “U.S. Department of Energy (DOE), Announcement of Scientific and Technical Information (STI).” You can complete, upload, and submit the DOE F 241.3 online via ELink. You are encouraged not to submit patentable material or protected data in these reports, but if there is such material or data in the report, you must: (1) clearly identify patentable or protected data on each page of the report; (2) identify such material on the cover of the report; and (3) mark the appropriate block in Section K of the DOE F 241 3. Reports must not contain any limited rights data (proprietary data), classified information, information subject to export control classification, or other information not subject to release. Protected data is specific technical data, first produced in the performance of the award that is protected from public release for a period of time by the terms of the award agreement.

Conference Papers/Proceedings

Content. The recipient must submit a copy of any conference papers/proceedings, with the following information: (1) Name of conference; (2) Location of conference; (3) Date of conference; and (4) Conference sponsor.

Electronic Submission. Scientific/technical conference paper/proceedings must be submitted electronically via the DOE Energy Link System (E-Link) at http://www.osti.gov/elink-2413. Non-scientific/technical conference papers/proceedings must be sent to the URL listed on the Reporting Checklist.

Electronic Format. Conference papers/proceedings must be submitted in the ADOBE PORTABLE DOCUMENT FORMAT (PDF) and be one integrated PDF file that contains all text, tables, diagrams, photographs, schematic, graphs, and charts. If the proceedings cannot be submitted electronically, they should be sent to the DOE

Administrator at the address listed in Block 16 of the Assistance Agreement Cover Page.

Submittal Form. Scientific/technical conference papers/proceedings must be accompanied by a completed DOE Form 241.3. The form and instructions are available on E-Link at

http://www.osti.gov/elink-2413. This form is not required for non-scientific or non-technical conference papers or proceedings.

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Software/Manual

Content. Unless otherwise specified in the award, the following must be delivered: source code, the executable object code and the minimum support documentation needed by a competent user to understand and use the software and to be able to modify the software in subsequent development efforts.

Electronic Submission. Submissions may be submitted electronically via the DOE Energy Link System (E-Link) at http://www.osti.gov/estsc/241-4pre.jsp. They may also be submitted via regular mail to:

Energy Science and Technology Software Center

P.O. Box 1020

Oak Ridge, TN 37831

Submittal Form. Each software deliverable and its manual must be accompanied by a completed DOE Form 241.4, “Announcement of U.S. Department of Energy Computer Software.” The form and instructions are available on E-Link at http://www.osti.gov/estsc/241-4pre.jsp.

Protected Personally Identifiable Information (PII). Management Reports or Scientific/Technical Reports must not contain any Protected PII. PII is any information about an individual which can be used to distinguish or trace an individual's identity. Some information that is considered to be PII is available in public sources such as telephone books, public websites, university listings, etc. This type of information is considered to be Public PII and includes, for example, first and last name, address, work telephone number, e-mail address, home telephone number, and general educational credentials. In contrast, Protected PII is defined as an individual's first name or first initial and last name in combination with any one or more of types of information, including, but not limited to, social security number, passport number, credit card numbers, clearances, bank numbers, biometrics, date and place of birth, mother's maiden name, criminal, medical and financial records, educational transcripts, etc.

C. FINANCIAL REPORTING

Recipients must complete the SF-425 as identified on the Reporting Checklist in accordance with the report instructions. A fillable version of the form is available at

http://www.whitehouse.gov/omb/grants/grants_forms.aspx.

D. CLOSEOUT REPORTS

Final Invention and Patent Report

The recipient must provide a DOE Form 2050.11 , “PATENT CERTIFICATION.” This form

is available at http://management.energy.gov/business_doe/business_forms.htm

Final Property Report

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See instructions under SF-428 Tangible Personal Property Report Forms Family below.

E. OTHER REPORTING

Annual Indirect Cost Proposal and Reconciliation

Requirement. In accordance with the applicable cost principles, the recipient must submit an annual indirect cost proposal, reconciled to its financial statements, within six months after the close of the recipient's fiscal year, unless the award is based on a predetermined or fixed indirect rate(s), or a fixed amount for indirect or facilities and administration (F&A) costs. Cognizant Agency. The recipient must submit its annual indirect cost proposal directly to the cognizant agency for negotiating and approving indirect costs. If the DOE awarding office is the cognizant agency, submit the annual indirect cost proposal to https://www.eerepmc.energy.gov/SubmitReports.aspx.

Audit of For-Profit Recipients

As required by 10 CFR 600.316, as supplemented by For-Profit Audit Guidance Parts I through IV, audits must be performed of For-Profit Recipients of financial assistance awards (prime awards) and sub-awards. For-Profit Audit Guidance Parts I through IV to assist for-profit recipients in complying with the audit requirements of 10 CFR 600.316 are posted on the Financial Assistance Forms page of the MA home page under the 'Coverage of Independent Audits' subheading, http://management.energy.gov/business_doe/business_forms.htm. Submission: For recipients, financial statement and compliance audit submissions are due to DOE within six months of the recipients' fiscal year-end dates. For sub-awardees, financial statement and compliance audit submissions are due to the pass-through entity within six months of the sub-awardees' fiscal year-end dates. For recipients, the compliance audits must be submitted, along with audited financial statements, to the appropriate DOE Contracting Officer at https://www.eere-pmc.energy.gov/SubmitReports.aspx as well as to the DOE Office of the Chief Financial Officer at DOE-Audit-Submission@hq.doe.gov

SF-428 Tangible Personal Property Report Forms Family

Requirement. The SF-428 is a forms family consisting of 5 forms: the SF-428, SF-428-A, SF- 428-B, SF-428-C, and SF-428S. Fillable versions of the SF-428 forms are available at http://management.energy.gov/business_doe/business_forms.htm.

•The SF-428 is the cover page and the submitter attaches the appropriate form or forms as

listed on the SF-428.

•The SF-428-A is the Annual report, due Oct. 30th of each calendar year.

•The SF-428-B is the Final Award Closeout Report, due at award completion.

•The SF-428-C is the Disposition Report/Request.

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•The SF-428S is the supplemental form for the SF-428-A, SF-428-B and SF-428-C.

If at any time during the award the recipient is provided Government-furnished property or acquires property with project funds and the award specifies that the property vests in the Federal Government (i.e. federally owned property), the recipient must submit an annual inventory of this property to the DOE Administrator using the SF-428 and SF-428-A forms at the address on page 1 of this checklist no later than October 30th of each calendar year, to cover an annual reporting period ending on the preceding September 30th. The SF-428 and SF-428-B reports are required during closeout.

Content of Inventory. As required on the SF-428-A form, the inventory must include a description of the property, tag number, acquisition date, and acquisition cost, if purchased with project funds. The location of property should be listed under the Comments section. The report must list all federally owned property, including property located at subcontractor's facilities or other locations.

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Attachment 1

Reporting Requirements Checklist for RD&D awards

RESEARCH PERFORMANCE PROGRESS REPORT

Standard Cover Page Data Elements and Reporting Categories

The standard cover page data elements shown below, as well as mandatory and optional components comprise the complete research performance progress report format.

Each category in the RPPR is a separate reporting component. Each component is marked to indicate if it is optional or mandatory. Mandatory components must be addressed in each report, optional are at your discretion.

If you have nothing significant to report during the reporting period on a question or item, state

"Nothing To Report".

1. COVER PAGE DATA ELEMENTS: Mandatory

• Federal Agency and Organization Element to Which Report is Submitted

• Federal Grant or Other Identifying Number Assigned by Agency

• Project Title

• PD/PI Name, Title and Contact Information (e-mail address and phone number)

• Name of Submitting Official, Title, and Contact Information (e-mail address and phone number), if other than PD/PI

• Submission Date

• DUNS Number

• Recipient Organization (Name and Address)

• Project/Grant Period (Start Date, End Date)

• Reporting Period End Date

• Report Term or Frequency (annual, semi-annual, quarterly, other)

• Signature of Submitting Official (electronic signatures (i.e., Adobe Acrobat) are acceptable)

2. ACCOMPLISHMENTS: Mandatory

What was done? What was learned?

The information provided in this section allows the agency to assess whether satisfactory progress has been made during the reporting period.

INSTRUCTIONS - Accomplishments

The PI is reminded that the grantee is required to obtain prior written approval from the Contracting Officer whenever there are significant changes in the project or its

direction. Requests for prior written approval must be submitted to the Contracting Officer (submission via Fedconnect is acceptable).

• What are the major goals and objectives of the project?

• What was accomplished under these goals?

• What opportunities for training and professional development has the project provided?

• How have the results been disseminated to communities of interest?

• What do you plan to do during the next reporting period to accomplish the goals and

objectives?

What are the major goals of the project?

List the major goals of the project as stated in the approved application or as approved by the agency. If the application lists milestones/target dates for important activities or phases of the project, identify these dates and show actual completion dates or the percentage of completion. Generally, the goals will not change from one reporting period to the next. However, if the awarding agency approved changes to the goals during the reporting period, list the revised goals and objectives. Also explain any significant changes in approach or methods from the agency approved application or plan.

What was accomplished under these goals?

For this reporting period describe: (1) major activities; (2) specific objectives; (3) significant results, including major findings, developments, or conclusions (both positive and negative); and (4) key outcomes or other achievements. Include a discussion of stated goals not met. As the project progresses, the emphasis in reporting in this section should shift from reporting activities to reporting accomplishments.

What opportunities for training and professional development has the project provided?

Describe opportunities for training and professional development provided to anyone who worked on the project or anyone who was involved in the activities supported by the project. “Training” activities are those in which individuals with advanced professional skills and experience assist others in attaining greater proficiency. Training activities may include, for example, courses or one-on-one work with a mentor. “Professional development” activities result in increased knowledge or skill in one's area of expertise and may include workshops, conferences, seminars, study groups, and individual study. Include participation in conferences, workshops, and seminars not listed under major activities.

How have the results been disseminated to communities of interest?

Describe how the results have been disseminated to communities of interest. Include any outreach activities that have been undertaken to reach members of communities who are not

usually aware of these research activities, for the purpose of enhancing public understanding and increasing interest in learning and careers in science, technology, and the humanities.

What do you plan to do during the next reporting period to accomplish the goals?

Describe briefly what you plan to do during the next reporting period to accomplish the goals and objectives.

3. PRODUCTS: [Optional/Mandatory]

What has the project produced?

Publications are the characteristic product of research. Agencies evaluate what the publications demonstrate about the excellence and significance of the research and the efficacy with which the results are being communicated to colleagues, potential users, and the public, not the number of publications. Many projects (though not all) develop significant products other than publications. Agencies assess and report both publications and other products to Congress, communities of interest, and the public.

INSTRUCTIONS - Products

List any products resulting from the project during the reporting period. Examples of products include:

• Publications, conference papers, and presentations;

• Website(s) or other Internet site(s);

• Technologies or techniques;

• Inventions, patent applications, and/or licenses;

• Other products, such as data or databases, physical collections, audio or video products, software or NetWare, models, educational aids or curricula, instruments, or equipment; and Any other public release of information related to the project.

Publications, conference papers, and presentations

Report only the major publication(s) resulting from the work under this award. There is no restriction on the number. However, agencies are interested in only those publications that most reflect the work under this award in the following categories:

• Journal publications. List peer-reviewed articles or papers appearing in scientific, technical, or professional journals. Include any peer-reviewed publication in the periodically published proceedings of a scientific society, a conference, or the like. A publication in the proceedings of a one-time conference, not part of a series, should be reported under "Books or other non-periodical, one-time publications." Identify for each publication: Author(s); title; journal; volume: year; page numbers; status of publication (published; accepted, awaiting publication; submitted, under review; other); acknowledgement of federal support (yes/no).

• Books or other non-periodical, one-time publications. Report any book, monograph, dissertation, abstract, or the like published as or in a separate publication, rather than a periodical or series. Include any significant publication in the proceedings of a one-time conference or in the report of a one-time study, commission, or the like.

Identify for each one-time publication: author(s); title; editor; title of collection, if applicable; bibliographic information; year; type of publication (book, thesis or dissertation, other); status of publication (published; accepted, awaiting publication; submitted, under review; other); acknowledgement of federal support (yes/no).

• Other publications, conference papers and presentations. Identify any other publications, conference papers and/or presentations not reported above. Specify the status of the publication as noted above.

Website(s) or other Internet site(s)

List the URL for any Internet site(s) that disseminates the results of the research activities. A short description of each site should be provided. It is not necessary to include the publications already specified above in this section.

Technologies or techniques

Identify technologies or techniques that have resulted from the research activities. Describe the technologies or techniques and how they are being shared.

Inventions, patent applications, and/or licenses

Identify inventions, patent applications with date, and/or licenses that have resulted from the research. Submission of this information as part of an interim research performance progress report is not a substitute for any other invention reporting required under the terms and conditions of an award.

Other products

Identify any other significant products that were developed under this project. Describe the product and how it is being shared. Examples of other products are:

• Databases;

• Physical collections;

• Audio or video products;

• Software or NetWare;

• Models;

• Educational aids or curricula;

• Instruments or equipment;

• Data & Research Material (e.g., cell lines, DNA probes, animal models); and

• Other.

4. PARTICIPANTS & OTHER COLLABORATING ORGANIZATIONS:

[Optional/Mandatory]

Who has been involved?

Agencies need to know who has worked on the project to gauge and report performance in promoting partnerships and collaborations.

INSTRUCTIONS - Participants & Other Collaborating Organizations

Provide the following information on participants:

• What individuals have worked on the project?

• What other organizations have been involved as partners?

• Have other collaborators or contacts been involved?

What individuals have worked on the project?

Provide the following information for: (1) principal investigator(s)/project director(s) (PIs/PDs); and (2) each person who has worked at least one person month per year on the project during the reporting period, regardless of the source of compensation (a person month equals approximately 160 hours of effort).

• Provide the name and identify the role the person played in the project. Do NOT include any other identifying information on individuals. Indicate the nearest whole person month (Calendar, Academic, Summer) that the individual worked on the project. Show the most senior role in which the person has worked on the project for any significant length of time. For example, if an undergraduate student graduates, enters graduate school, and continues to work on the project, show that person as a graduate student, preferably explaining the change in involvement.

• Describe how this person contributed to the project and with what funding support. If information is unchanged from a previous submission, provide the name only and indicate “no change”.

• Identify whether this person is collaborating internationally. Specifically is the person collaborating with an individual located in a foreign country and whether the person had traveled to the foreign country as part of that collaboration and duration of stay. The foreign country(ies) should be identified.

Example:

Name:     Mary Smith

Project Role:     Graduate Student

Nearest person month worked:     5

Contribution to Project:     Ms. Smith has performed work in the area of

combined error-control and constrained coding.

Funding Support:     The Ford Foundation (Complete only if the

funding provided from other than this award.)

Collaborated with individual in

foreign country:     Yes

Country(ies) of foreign collaborator:     China

Traveled to foreign country:     Yes

If traveled to foreign country(ies),

duration of stay:     5 months

What other organizations have been involved as partners?

Describe partner organizations - academic institutions, other nonprofits, industrial or commercial firms, state or local governments, schools or school systems, or other organizations (foreign or domestic) - that have been involved with the project. Partner organizations may provide financial or in-kind support, supply facilities or equipment, collaborate in the research, exchange personnel, or otherwise contribute.

Provide the following information for each partnership:

Organization Name:

Location of Organization: (if foreign location list country)

Partner's contribution to the project: (identify one or more)

• Financial support;

• In-kind support (e.g., partner makes software, computers, equipment, etc., available to project staff);

• Facilities (e.g., project staff use the partner's facilities for project activities);

• Collaborative research (e.g., partner's staff work with project staff on the project); and

• Personnel exchanges (e.g., project staff and/or partner's staff use each other's facilities, work at each other's site).

•

More detail on partner and contribution (foreign or domestic).

Have other collaborators or contacts been involved?

Some significant collaborators or contacts within the recipient's organization may not be covered by "What people have worked on the project?" Likewise, some significant collaborators or contacts outside the recipient's organization may not be covered under "What other organizations have been involved as partners?" For example, describe any significant:

• collaborations with others within the recipient's organization; especially interdepartmental or interdisciplinary collaborations;

• collaborations or contact with others outside the organization; and

• collaborations or contacts with others outside the United States or with an international organization.

• country(ies) of collaborations or contacts.

It is likely that many recipients will have no other collaborators or contacts to report.

5. IMPACT: [Optional/Mandatory]

What is the impact of the project? How has it contributed?

Over the years, this base of knowledge, techniques, people, and infrastructure is drawn upon again and again for application to commercial technology and the economy, to health and safety, to cost-efficient environmental protection, to the solution of social problems, to numerous other aspects of the public welfare, and to other fields of endeavor.

The taxpaying public and its representatives deserve a periodic assessment to show them how the investments they make benefit the nation. Through this reporting format, and especially this section, recipients provide that assessment and make the case for Federal funding of research and education.

Agencies use this information to assess how their research programs:

• increase the body of knowledge and techniques;

• enlarge the pool of people trained to develop that knowledge and techniques or put it to use;

and

• improve the physical, institutional, and information resources that enable those people to get

their training and perform their functions.

INSTRUCTIONS - Impact

This component will be used to describe ways in which the work, findings, and specific products of the project have had an impact during this reporting period. Describe distinctive contributions, major accomplishments, innovations, successes, or any change in practice or behavior that has come about as a result of the project relative to:

• the development of the principal discipline(s) of the project;

• other disciplines;

• the development of human resources;

• physical, institutional, and information resources that form infrastructure;

• technology transfer (include transfer of results to entities in government or industry,

adoption of new practices, or instances where research has led to the initiation of a startup

company); or

• society beyond science and technology.

What is the impact on the development of the principal discipline(s) of the project?

Describe how findings, results, techniques that were developed or extended, or other products from the project made an impact or are likely to make an impact on the base of knowledge, theory, and research and/or pedagogical methods in the principal disciplinary field(s) of the project. Summarize using language that an intelligent lay audience can understand (Scientific American style).

How the field or discipline is defined is not as important as covering the impact the work has had on knowledge and technique. Make the best distinction possible, for example, by using a "field" or "discipline", if appropriate, that corresponds with a single academic department (i.e., physics rather than nuclear physics).

What is the impact on other disciplines?

Describe how the findings, results, or techniques that were developed or improved, or other products from the project made an impact or are likely to make an impact on other disciplines.

What is the impact on the development of human resources?

Describe how the project made an impact or is likely to make an impact on human resource development in science, engineering, and technology. For example, how has the project:

• provided opportunities for research and teaching in the relevant fields;

• improved the performance, skills, or attitudes of members of underrepresented groups that will improve their access to or retention in research, teaching, or other related professions;

• developed and disseminated new educational materials or provided scholarships; or

• provided exposure to science and technology for practitioners, teachers, young people, or other members of the public?

What is the impact on physical, institutional, and information resources that form

infrastructure?

Describe ways, if any, in which the project made an impact, or is likely to make an impact, on

physical, institutional, and information resources that form infrastructure, including:

• physical resources such as facilities, laboratories, or instruments;

• institutional resources (such as establishment or sustenance of societies or organizations); or

• information resources, electronic means for accessing such resources or for scientific communication, or the like.

What is the impact on technology transfer?

Describe ways in which the project made an impact, or is likely to make an impact, on commercial technology or public use, including:

• transfer of results to entities in government or industry;

• instances where the research has led to the initiation of a start-up company; or

• adoption of new practices.

What is the impact on society beyond science and technology?

Describe how results from the project made an impact, or are likely to make an impact, beyond the bounds of science, engineering, and the academic world on areas such as:

• improving public knowledge, attitudes, skills, and abilities;

• changing behavior, practices, decision making, policies (including regulatory policies), or

social actions; or

• improving social, economic, civic, or environmental conditions.

What dollar amount of the award's budget is being spent in foreign country(ies)?

Describe what percentage of the award's budget is being spent in foreign country(ies). If more than one foreign country, identify the distribution between the foreign countries.

6. CHANGES/PROBLEMS: [Optional/Mandatory]

The PI is reminded that the grantee is required to obtain prior written approval from the Contracting Officer whenever there are significant changes in the project or its direction. Requests for prior written approval must be submitted to the Contracting Officer (submission via Fedconnect is acceptable). If not previously reported in writing, provide the following additional information, if applicable:

• Changes in approach and reasons for change.

• Actual or anticipated problems or delays and actions or plans to resolve them.

• Changes that have a significant impact on expenditures.

• Significant changes in use or care of animals, human subjects, and/or biohazards.

INSTRUCTIONS - Changes/Problems

Changes in approach and reasons for change

Describe any changes in approach during the reporting period and reasons for these changes. Remember that significant changes in objectives and scope require prior approval of the agency.

Actual or anticipated problems or delays and actions or plans to resolve them

Describe problems or delays encountered during the reporting period and actions or plans to resolve them.

Changes that have a significant impact on expenditures

Describe changes during the reporting period that may have a significant impact on expenditures, for example, delays in hiring staff or favorable developments that enable meeting objectives at less cost than anticipated.

Significant changes in use or care of human subjects, vertebrate animals, and/or

Biohazards

Describe significant deviations, unexpected outcomes, or changes in approved protocols for the use or care of human subjects, vertebrate animals, and/or biohazards during the reporting period. If required, were these changes approved by the applicable institution committee and reported to the agency? Also specify the applicable Institutional Review Board/Institutional Animal Care and Use Committee approval dates.

Change of primary performance site location from that originally proposed

Identify any change to the primary performance site location identified in the proposal, as originally submitted.

7. SPECIAL REPORTING REQUIREMENTS: [Optional/Mandatory]

Respond to any special reporting requirements specified in the award terms and conditions, as well as any award specific reporting requirements.

8. BUDGETARY INFORMATION: [Optional/Mandatory]

This component will be used to collect budgetary data from the recipient organization. The information will be used in conducting periodic administrative/budgetary reviews. Budgetary data should be submitted in an Excel spreadsheet format.

ASSISTANCE AGREEMENT
1. Award No. DE-EE0002869		2. Modification No. 007		3. Effective Date 12/28/2009		4. CFDA No. 81.087
5. Awarded To AMYRIS, INC. Attn: NEIL RENNINGER 5885 HOLLIS STREET SUITE 100 EMERYVILLE CA 946082059			6. Sponsoring Office Energy Effcy & Renewable Energy				7. Period of Performance 12/28/2009 through 06/30/2012
8. Type of Agreement _ Grant x Cooperative Agreement _ Other	9. Authority 109-58 Energy Policy Act (2005) 111-5 Recovery Act (2009)				10. Purchase Request or Funding Document No. 12EE001279
11. Remittance Address			12. Total Amount				13. Funds Obligated
AMYRIS, INC. Attn: NEIL RENNINGER 5885 HOLLIS STREET SUITE 100 EMERYVILLE CA 946082059			Govt. Share: $ 24,341,409.00 Cost Share: $ 10,591,590.00 Total: $ 34,932,999.00				This action: $0.00 Total: $24,341,409.00
14. Principal Investigator Neil Renninger Phone: 510-740-7414	15. Program Manager Bryna E. Berendzen Phone: 720-356-1442				16. Administrator Golden Field Office U.S. Department of Energy Golden Field Office 1617 Cole Blvd. Golden CO 80401-3393
17. Submit Payment Requests To OR for Golden U.S. Department of Energy Oak Ridge Financial Service Center P.O. Box 4517 Oak Ridge TN 37831			18. Paying Office OR for Golden U.S. Department of Energy Oak Ridge Financial Service Center P.O. Box 4517 Oak Ridge TN 37831				19. Submit Reports To
20. Accounting and Appropriation Data See Schedule
21. Research Title and/or Description of Project RECOVERY ACT: SCALE-UP & MOBILIZATION OF RENEWABLE DIESEL & CHEMICAL PRODUCTION FROM COMMON INTERMEDIATE USING US-BASED FERMENTABLE SUGAR FEEDSTOCKS
For the Recipient				For the United States of America
22. Signature of Person Authorized to Sign				25. Signature of Grants/Agreements Officer Signature on File
23. Name and Title	24. Date Signed			26. Name of Officer Brenda L. Dias				27. Date Signed 01/20/2012

CONTINUATION SHEET		REFERENCE NO. OF DOCUMENT BEING CONTINUED DE-EE0002869/007			PAGE 2 OF 2
NAME OF OFFEROR OR CONTRACTOR AMYRIS, INC.
ITEM  NO. (A)	SUPPLIES/SERVICES (B)	QUANTITY (C)	UNIT (D)	UNIT PRICE (E)	AMOUNT (F)
	DUNS Number: 185930182 The purpose of this modification are to: 1) Complete a novation/change of name, changing the recipient from Amyris Biotechnologies, Inc. to Amyris, Inc. See attachment for a copy of the signed and executed novation and change of name agreement which by this modification is incorporated by reference into this award; and, 2) Update the DOE Project Officer, as shown below. All others and conditions remain unchanged. In Block 7 of the Assistance Agreement, the Period of Performance reflects the beginning of the Project Period through the end of the current Budget Period, shown as 12/28/2009 through 6/30/2012. For multiple Budget Periods, see Special Terms and Conditions, Provision 4, Award Project Period and Budget Periods. DOE Award Administrator: Brenda Dias E-mail: brenda.dias@go.doe.gov Phone: 720-356-1519 DOE Project Officer: Bryna Berendzen E-mail: bryna.berendzen@go.doe.gov Phone: 720-356-1442 Recipient Business Officer: Todd Pray E-mail: pray@amyris.com Phone: 510-740-7441 Recipient Principal Investigator: Neil Renninger E-mail: renninger@amyris.com Phone: 510-740-7414 “Electronic signature or signatures as used in this document means a method of signing an electronic message that-- (A) Identifies and authenticates a particular person as the source of the electronic message; (B) Indicates such person's approval of the information contained in the electronic message; and, (C) Submission via FedConnect constitutes electronically signed documents.” ASAP: NO: STD IMMEDIATE Extent Competed: COMPETED Davis-Bacon Act: YES
JULY 2004

NOVATION AND CHANGE OF NAME AGREEMENT

Amyris, Inc. (Transferee), a corporation duly organized and existing under the laws of Delaware, with its principal office in Emeryville, CA; and the United States of America (Government), enter into this Novation and Change of Name Agreement (Agreement) in accordance with the terms set forth below.

WHEREAS, on or about December 30, 2009, the Government, represented by Contracting Officer(s) of the Department of Energy, awarded Cooperative Agreement Number DE-EE0002869, entitled "Recovery Act: Scale-up & Mobilization of Renewable Diesel & Chemical Production from Common Intermediate Using US-Based Fermentable Sugar Feedstocks" (hereinafter, including all modifications, referred to as "the Award") to Amyris Biotechnologies, Inc. a California corporation (Predecessor), who was Transferee's predecessor-in-interest; and

WHEREAS, the Transferee has requested that the Award be assigned to the Transferee as a result of a corporate merger by conversion of shares, change of name and reincorporation; and

WHEREAS, the Transferee represents and warrants the following facts to the Government in support of its request to assign the Award:

1.    By virtue of a certain Agreement and Plan of Merger (attached hereto and incorporated herein by reference as Exhibit A), as verified by that certain Certificate of Merger of Amyris Biotechnologies, Inc., a California corporation, With and Into Amyris Biotechnologies, Inc., a Delaware corporation ("Amyris Delaware") (attached hereto and incorporated herein by reference as Exhibit B), both executed as of June 10, 2010, all of Predecessor's personnel, assets (including intellectual property), and liabilities were transferred to Amyris Delaware; and

2.    By virtue of a certain Restated Certificate of Incorporation, executed as of June 21, 2010 (attached hereto and incorporated herein by reference as Exhibit C), Amyris Delaware changed its name from Amyris Biotechnologies, Inc., to Amyris, Inc.; and

3.    The Transferee owns, or has acquired, all the assets necessary to perform the Award by virtue of the foregoing transactions; and

4.    The Transferee has assumed all obligations and liabilities of the Predecessor under the Award by virtue of the above transactions and this Novation; and

5.    The Transferee unconditionally guarantees, inter alia, the Transferee's performance of all obligations required under the Award; and

6.     The Transferee is in a position to fully perform all obligations that may exist under the Award (see also additional representations contained in the Recipient Change Request Questionnaire and the legal opinion letter dated November 8, 2011, both of which are attached hereto and incorporated herein by reference as Exhibits D and E respectively).

NOW, THEREFORE, in consideration of these facts, guarantees and representations and other good and valuable consideration, the parties agree that by this Novation and Change of Name Agreement:

1.    It is consistent with the Government's interest to recognize the Transferee as the successor party to the Award.

2.    The Transferee confirms that as the successor-in-interest to Predecessor, the assignment of the Award, and all of its rights and responsibilities under the Award, were in fact transferred to the Transferee, and that the Predecessor no longer exists as a legal entity and therefore any claims and rights that the Predecessor may have had against the Government or may have had in the future in connection with the Award, including all claims to any unexpended and uncommitted funds, are no longer of any legal force or effect as to the Predecessor.

3.    The Transferee agrees to be bound by, and to perform in accordance with the conditions contained in the Award. The Transferee also assumes all obligations and liabilities of, and all claims against, the Predecessor under the Award as if the Transferee were the original party to the Award.

4.    The Transferee ratifies all previous actions taken by the Predecessor with respect to the Award, with the same force and effect as if the action had been taken by the Transferee.

5.    The Government recognizes the Transferee as the Predecessor's successor-in-interest in and to the Award. The Transferee by this Agreement becomes entitled to all rights, titles, and interests of the Predecessor in and to the Award as if the Transferee were the original party to the Award.

6.    Except as expressly provided in this Agreement, nothing in it shall be construed as a waiver of any rights of the Government against the Predecessor or the Transferee.

7.    All payments and reimbursements previously made by the Government to the Predecessor, and all other previous actions taken by the Government under the Award, shall be considered to have discharged those parts of the Government's obligations under the Award . All payments and reimbursements made by the Government after the date of this Agreement in the name of or to the Predecessor shall have the same force and effect as if made to the Transferee, and shall constitute a complete discharge of the Government's obligations under the Award, to the extent of the amounts paid or reimbursed.

8.    The Transferee agrees that the Government is not obligated to pay or reimburse it for, or otherwise give effect to, any costs, taxes, or other expenses, or any related increases, directly or indirectly arising out of or resulting from the transfer of the Award or this Agreement, other than those that the Government in the absence of this transfer or Agreement would have been obligated to pay or reimburse under the terms of the Award.

9.    The Government's execution of this Agreement does not constitute approval by the Government of the terms or conditions of the documents submitted by the Predecessor and Transferee in support of their request to assign the Award nor does it constitute a determination by the Government regarding the allow ability of costs incurred by the Transferee pursuant to those documents.

10.    If Transferee is not going to perform an aspect of the award itself and chooses to utilize the services or resources of any of its related companies, the related company will be treated as a sub-recipient and will not be allowable as a vendor.

11.    The Award shall remain in full force and effect, except as modified by this Agreement, and nothing contained herein shall limit the Government's ability to modify the terms and conditions of the Award as the Government finds necessary.

12.    The Award will be modified by substituting the name "Amyris, Inc." for the name "Amyris Biotechnologies, Inc" wherever it appears in the Award.

13.    This Agreement will take effect as of the date the Government formally incorporates this Agreement into the Award through an Award modification.

THE UNITED STATES OF AMERICA

By /s/ Jon Olsen                        Date: 11/18/2011    

Title: Contracting Officer for the Department of Energy

AMYRIS, INC.

By /s/ Mario Portela                        Date: 11/16/2011    

Title: President, Global Operations

CERTIFICATE

I, Tamara L. Tompkins, certify that I am the Secretary of Amyris, Inc., a Delaware corporation, and that Mario Portela, who signed this Agreement for this entity, was then the President, Global Operations of this entity; and that this Agreement was duly signed for and on behalf of this entity by authority of its governing body and within the scope of its corporate powers. Witness my hand and the seal of this corporation this day of November 16, 2011.

By /s/ Tamara L. Tompkins        

[Corporate Seal]

EXHIBIT A

AGREEMENT AND PLAN OF MERGER

AGREEMENT AND PLAN OF MERGER

THIS AGREEMENT AND PLAN OF MERGER (this “Merger Agreement”) is entered into as of June 10, 2010, by and between Amyris Biotechnologies, Inc., a California corporation (“Amyris California”), and Amyris Biotechnologies, Inc., a Delaware corporation (“Amyris Delaware”). Amyris California and Amyris Delaware are hereinafter sometimes collectively referred to as the “Constituent Corporations”.

R E C I T A L S

A.    Amyris California was incorporated on July 17, 2003. Its current authorized capital stock consists of: (i) 38,000,000 shares of Common Stock (“Amyris California Common Stock”), of which 5,121,545 shares are issued and outstanding; and (ii) 23,862,355 shares of Preferred Stock (“Amyris California Preferred Stock”), of which 21,385,969 shares are issued and outstanding.

B.    Amyris Delaware was incorporated on April 15, 2010. Its authorized capital stock consists of: (i) 38,000,000 shares of Common Stock, with a par value of $0.0001 per share (“Amyris Delaware Common Stock”), of which one thousand (1,000) shares are issued and outstanding; and (ii) 23,862,355 shares of Preferred Stock, with a par value of $0.0001 per share (“Amyris Delaware Preferred Stock”), none of which shares are issued and outstanding.

C.    The respective Boards of Directors of Amyris California and Amyris Delaware deem it advisable and to the advantage of each of the Constituent Corporations that Amyris California merge with and into Amyris Delaware upon the terms and subject to the conditions set forth in this Merger Agreement for the purpose of effecting a change of the state of incorporation of Amyris California from California to Delaware.

D.    The Boards of Directors of each of the Constituent Corporations have approved this Merger Agreement.

NOW, THEREFORE, the parties do hereby adopt the plan of reorganization set forth in this Merger Agreement and do hereby agree that Amyris California shall merge with and into Amyris Delaware on the following terms, conditions and other provisions:

1.Merger and Effective Time. At the Effective Time (as defined below), Amyris California shall be merged with and into Amyris Delaware (the “Merger”), and Amyris Delaware shall be the surviving corporation of the Merger (the “Surviving Corporation”). The Merger shall become effective upon the close of business on the date when a duly executed copy of this Merger Agreement (or a Certificate of Merger in lieu thereof) is filed with the Secretary of State of the State of Delaware, provided that such Merger Agreement (or the Certificate of Merger in lieu thereof) is filed with the Secretary of State of the State of California within the time period required by law (the “Effective Time”).

2.Effect of Merger. At the Effective Time, the separate corporate existence of Amyris California shall cease; the corporate identity, existence, powers, rights and immunities of Amyris Delaware as the Surviving Corporation shall continue unimpaired by the Merger; and Amyris Delaware shall succeed to and shall possess all the assets, properties, rights, privileges, powers, franchises, immunities and purposes, and be subject to all the debts, liabilities, obligations, restrictions and duties of Amyris California, all without further act or deed.

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3.Name Change; Governing Documents. At the Effective Time, (i) the name of Amyris Delaware shall be Amyris Biotechnologies, Inc. and (ii) the Certificate of Incorporation of Amyris Delaware in effect immediately prior to the Effective Time shall be amended and restated by virtue of the Merger to read as set forth in full in Exhibit “A” hereto (the “Restated Certificate”).

4.Directors and Officers. At the Effective Time, the directors of Amyris Delaware shall be and become the directors of the Surviving Corporation, and the officers of Amyris Delaware shall be and become the officers (holding the same offices) of the Surviving Corporation, and after the Effective Time shall serve in accordance with the Restated Certificate and Bylaws of the Surviving Corporation.

5.Conversion of Shares of Amyris California. At the Effective Time, by virtue of the Merger and without any further action on the part of the Constituent Corporations or their shareholders, (i) each share of Amyris California Common Stock issued and outstanding immediately prior thereto shall be converted into one (1) fully paid and nonassessable share of Amyris Delaware Common Stock, (ii) each share of Amyris California Series A Preferred Stock outstanding immediately prior thereto shall be automatically changed and converted into one (1) fully paid and nonassessable, issued and outstanding share of Amyris Delaware Series A Preferred Stock, (iii) each share of Amyris California Series B Preferred Stock outstanding immediately prior thereto shall be automatically changed and converted into one (1) fully paid and nonassessable, issued and outstanding share of Amyris Delaware Series B Preferred Stock, (iv) each share of Amyris California Series B-1 Preferred Stock outstanding immediately prior thereto shall be automatically changed and converted into one (1) fully paid and nonassessable, issued and outstanding share of Amyris Delaware Series B-1 Preferred Stock, (v) each share of Amyris California Series C Preferred Stock outstanding immediately prior thereto shall be automatically changed and converted into one (1) fully paid and nonassessable, issued and outstanding share of Amyris Delaware Series C Preferred Stock, and (vi) each share of Amyris California Series C-1 Preferred Stock outstanding immediately prior thereto shall be automatically changed and converted into one (1) fully paid and nonassessable, issued and outstanding share of Amyris Delaware Series C-1 Preferred Stock

6.Cancellation of Shares of Amyris Delaware. At the Effective Time, by virtue of the Merger and without any further action on the part of the Constituent Corporations or their shareholders, all of the previously issued and outstanding shares of Amyris Delaware Common Stock that were issued and outstanding immediately prior to the Effective Time shall be automatically canceled without consideration and returned to the status of authorized but unissued shares.

7.Stock Certificates. At and after the Effective Time, all of the outstanding certificates that, prior to that date, represented shares of Amyris California Common Stock shall be deemed for all purposes to evidence ownership of and to represent the number of shares of Amyris Delaware Common Stock into which such shares of Amyris California Common Stock are converted as provided herein. At and after the Effective Time, all of the outstanding certificates that, prior to that date, represented shares of a series of Amyris California Preferred Stock shall be deemed for all purposes to evidence ownership of and to represent the number of shares of the series of shares of Amyris Delaware Preferred Stock, into which such shares of Amyris California Preferred Stock are converted as provided herein. The registered owner on the books and records of Amyris California of any such outstanding stock certificate for Amyris

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California Common Stock or Amyris California Preferred Stock shall, until such certificate is surrendered for transfer or otherwise accounted for to Amyris Delaware or its transfer agent, be entitled to exercise any voting and other rights with respect to, and to receive any dividend and other distributions upon, the shares of Amyris Delaware Common Stock or Amyris Delaware Preferred Stock evidenced by such outstanding certificate as provided above.

8.Assumption of Options. At the Effective Time, all outstanding and unexercised portions of all options to purchase Amyris California Common Stock under Amyris California's 2005 Stock Option/Stock Issuance Plan (the “Existing Plan”), and all other outstanding options to purchase Amyris California Common Stock, shall be assumed by Amyris Delaware and become options to purchase the samenumber of shares of Amyris Delaware Common Stock at the same exercise price per share at which such option was exercisable immediately prior to the Merger, and shall, to the extent permitted by law and otherwise reasonably practicable, have the same term, exercisability, vesting schedule, acceleration provision, if applicable, status as an “incentive stock option” under Section 422 of the Internal Revenue Code of 1986, as amended (the “Code”), if applicable, and all other material terms and conditions (including but not limited to the terms and conditions applicable to such options by virtue of the Existing Plan). Continuous employment with Amyris California will be credited to an optionee for purposes of determining the vesting of the number of shares of Amyris Delaware Common Stock subject to exercise under an assumed Amyris California option at the Effective Time. At the Effective Time, Amyris Delaware shall adopt and assume the Existing Plan, as amended.

10.Assumption of Warrants. At the Effective Time, all outstanding and unexercised portions of all warrants to purchase Amyris California Preferred Stock, shall be assumed by Amyris Delaware and become warrants to purchase the samenumber of shares of the corresponding series of Amyris Delaware Preferred Stock at the same exercise price per share at which such warrant was exercisable immediately prior to the Merger, and shall, to the extent permitted by law and otherwise reasonably practicable, have the same term, exercisability, vesting schedule, acceleration provision, if applicable, and all other material terms and conditions.

11.Employee Benefit Plans. At the Effective Time, the obligations of Amyris California under or with respect to every plan, trust, program and benefit then in effect or administered by Amyris California for the benefit of the directors, officers and employees of Amyris California or any of its subsidiaries shall become the lawful obligations of Amyris Delaware and shall be implemented and administered in the same manner and without interruption until the same are amended or otherwise lawfully altered or terminated. Effective at the Effective Time, Amyris Delaware hereby expressly adopts and assumes all obligations of Amyris California under such employee benefit plans.

12.Further Assurances. From time to time, as and when required by the Surviving Corporation or by its successors or assigns, there shall be executed and delivered on behalf of Amyris California such deeds, assignments and other instruments, and there shall be taken or caused to be taken by it all such further action, as shall be appropriate, advisable or necessary in order to vest, perfect or confirm, of record or otherwise, in the Surviving Corporation the title to and possession of all property, interests, assets, rights, privileges, immunities, powers, franchises and authority of Amyris California, and otherwise to carry out the purposes of this Merger Agreement. The officers and directors of the Surviving Corporation are fully authorized in the name of and on behalf of Amyris California, or otherwise, to take any and all such actions and to

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execute and deliver any and all such deeds and other instruments as may be necessary or appropriate to accomplish the foregoing.

13.Condition. The consummation of the Merger is subject to the approval of this Merger Agreement and the Merger contemplated hereby by the shareholders of Amyris California and by the sole stockholder of Amyris Delaware, prior to or at the Effective Time.

14.Abandonment. At any time before the Effective Time, this Merger Agreement may be terminated and the Merger abandoned by the Board of Directors of Amyris California or Amyris Delaware, notwithstanding approval of this Merger Agreement by the shareholders of Amyris California and the sole stockholder of Amyris Delaware.

15.Amendment. At any time before the Effective Time, this Merger Agreement may be amended, modified or supplemented by the Boards of Directors of the Constituent Corporations, notwithstanding approval of this Merger Agreement by the shareholders of Amyris California and the sole stockholder of Amyris Delaware; provided, however, that any amendment made subsequent to the adoption of this Merger Agreement by the shareholders of Amyris California or the sole stockholder of Amyris Delaware shall not materially: (i) alter or change the amount or kind of shares, securities, cash, property and/or rights to be received in exchange for or upon conversion of any shares of any class or series of Amyris California; (ii) alter or change any of the terms of the Certificate of Incorporation of the Surviving Corporation to be effected by the Merger; or (iii) alter or change any of the terms or conditions of this Merger Agreement if such alteration or change would adversely affect the holders of any shares of any class or series of Amyris California or Amyris Delaware.

16.Tax-Free Reorganization. The Merger is intended to be a tax-free plan of reorganization within the meaning of Section 368(a)(1)(F) of the Code.

17.Governing Law. This Merger Agreement shall be governed by and construed under the internal laws of the State of California as applied to agreements among California residents entered into and to be performed entirely within California, without reference to the principles of conflicts of law or choice of laws, except to the extent that the laws of the State of Delaware would apply in matters relating to the internal affairs of Amyris Delaware and the Merger.

18.Counterparts. In order to facilitate the filing and recording of this Merger Agreement, it may be executed in any number of counterparts, each of which shall be deemed to be an original, but all of which together shall constitute one and the same instrument.

[REMAINDER OF PAGE INTENTIONALLY LEFT BLANK]

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IN WITNESS WHEREOF, the parties hereto have caused this Merger Agreement to be duly executed on the date and year first above written.

Amyris Biotechnologies, Inc., a Delaware

Corporation

By: /s/ John G. Melo            

Name: John G. Melo

Title: Chief Executive Officer

Amyris Biotechnologies, Inc., a California

Corporation

By: /s/ John G. Melo            

Name: John G. Melo

Title: Chief Executive Officer

[Signature Page to Agreement and Plan of Merger]

EXHIBIT “A”

RESTATED CERTIFICATE OF INCORPORATION

AMYRIS BIOTECHNOLOGIES, INC.

RESTATED CERTIFICATE OF INCORPORATION

(Pursuant to Sections 242 and 245 of the

General Corporation Law of the State of Delaware)

Amyris Biotechnologies, Inc., a corporation organized and existing under and by virtue of the provisions of the General Corporation Law of the State of Delaware (the “General Corporation Law”), does hereby certify as follows.

1.The name of this corporation is Amyris Biotechnologies, Inc. and that this corporation was originally incorporated pursuant to the General Corporation Law on April 15, 2010 under the name Amyris Biotechnologies, Inc.

2.The Board of Directors of this corporation duly adopted resolutions proposing to amend and restate the Certificate of Incorporation of this corporation, declaring said amendment and restatement to be advisable and in the best interests of this corporation and its stockholders, and authorizing the appropriate officers of this corporation to solicit the consent of the stockholders therefor, which resolution setting forth the proposed amendment and restatement is as follows.

RESOLVED, that the Certificate of Incorporation of this corporation be amended and restated in its entirety to read as set forth on Exhibit A attached hereto and incorporated herein by this reference.

3.    Exhibit A referred to above is attached hereto as Exhibit A and is hereby incorporated herein by this reference. This Restated Certificate of Incorporation was approved by the holders of the requisite number of shares of this corporation in accordance with Section 228 of the General Corporation Law.

4.    This Restated Certificate of Incorporation, which restates and integrates and further amends the provisions of this corporation's Certificate of Incorporation, has been duly adopted in accordance with Sections 242 and 245 of the General Corporation Law.

IN WITNESS WHEREOF, this Restated Certificate of Incorporation has been executed by a duly authorized officer of this corporation on this 10th day of June, 2010.

By: /s/ John Melo        

John Melo, President

EXHIBIT A

AMYRIS BIOTECHNOLOGIES, INC.

RESTATED CERTIFICATE OF INCORPORATION

ARTICLE I: NAME

The name of the corporation is Amyris Biotechnologies, Inc. (the “Company”).

ARTICLE II: REGISTERED OFFICE

The address of the registered office of the Corporation in the State of Delaware is 3500 South Dupont Highway, in the City of Dover, County of Kent, Delaware 19901. The name of its registered agent at such address is Incorporation Services, Ltd.

ARTICLE III: PURPOSE

The nature of the business or purposes to be conducted or promoted is to engage in any lawful act or activity for which corporations may be organized under the General Corporation Law.

ARTICLE IV: AUTHORIZED SHARES

The total number of shares of all classes of stock which the Corporation shall have authority to issue is (a) 61,862,355 shares of Common Stock, $0.0001 par value per share (“Common Stock”), and (b) 23,862,355 shares of Preferred Stock, $0.0001 par value per share (“Preferred Stock”). The Preferred Stock may be issued from time to time in one or more series, each of such series to consist of such number of shares and to have such terms, rights, powers and preferences, and the qualifications and limitations with respect thereto, as stated or expressed herein. As of the effective date of this Restated Certificate of Incorporation (this “Restated Certificate”), 9,475,000 shares of the authorized Preferred Stock of the Corporation are hereby designated “Series A Preferred Stock”, 1,929,641 shares of the authorized Preferred Stock of the Corporation are hereby designated “Series B Preferred Stock”, 4,700,000 shares of the authorized Preferred Stock of the Corporation are hereby designated “Series B-1 Preferred Stock”, 4,976,000 shares of the authorized Preferred Stock of the Corporation are hereby designated “Series C Preferred Stock”, and 2,781,714 shares of the authorized Preferred Stock of the Corporation are hereby designated “Series C-1 Preferred Stock”. The following is a statement of the designations and the rights, powers and privileges, and the qualifications, limitations or restrictions thereof, in respect of each class of capital stock of the Corporation.

A.    COMMON STOCK

1.General. The voting, dividend and liquidation rights of the holders of the Common Stock are subject to and qualified by the rights, powers and privileges of the holders of the Preferred Stock set forth herein.

2.Voting. The holders of the Common Stock are entitled to one vote for each share of Common Stock held at all meetings of stockholders (and written actions in lieu of meetings).

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Unless required by law, there shall be no cumulative voting. The number of authorized shares of Common Stock may be increased or decreased (but not below the number of shares thereof then outstanding) by (in addition to any vote of the holders of one or more series of Preferred Stock that may be required by the terms of the Certificate of Incorporation) the affirmative vote of the holders of shares of capital stock of the Corporation representing a majority of the votes represented by all outstanding shares of capital stock of the Corporation entitled to vote, irrespective of the provisions of Section 242(b)(2) of the General Corporation Law.

B.    PREFERRED STOCK

The following rights, powers and privileges, and restrictions, qualifications and limitations, shall apply to the Preferred Stock. Unless otherwise indicated, references to “Sections” in this Part B of this Article IV refer to sections of this Part B.

1.Dividends.

a.Preferred Stock Dividends. The holders of Series A Preferred Stock, Series B Preferred Stock, Series B-1 Preferred Stock, Series C Preferred Stock and Series C-1 Preferred Stock shall be entitled to receive non-cumulative dividends, on a pari passu basis, at the rate of 8% of the Series A Issue Price as defined in Section 2.a. (as adjusted for any stock dividends, combinations or splits with respect to such shares) per annum for the Series A Preferred Stock, at the rate of 8% of the Series B Issue Price as defined in Section 2.a (as adjusted for any stock dividends, combinations or splits with respect to such shares) per annum for the Series B Preferred Stock, at the rate of 8% of the Series B-1 Issue Price as defined in Section 2.a. (as adjusted for any stock dividends, combinations or splits with respect to such shares) per annum for the Series B-1 Preferred Stock, at the rate of 8% of the Series C Issue Price as defined in Section 2.a. (as adjusted for any stock dividends, combinations or splits with respect to such shares) per annum for the Series C Preferred Stock, and at the rate of 8% of the Series C-1 Issue Price as defined in Section 2.a. (as adjusted for any stock dividends, combinations or splits with respect to such shares) per annum for the Series C-1 Preferred Stock, payable out of funds legally available therefor. Such dividends shall be payable only when, as, and if declared by the Board of Directors and shall be non-cumulative.

No dividends (other than those payable solely in the Common Stock of the Company) shall be paid or other distribution made on any Common Stock of the Company, or purchase, redemption or other acquisition of Common Stock for value during any fiscal year of the Company until dividends, in the amount of 8% of the Series A Issue Price (as adjusted for any stock dividends, combinations or splits with respect to such shares) on the Series A Preferred Stock, 8% of the Series B Issue Price as defined in Section 2.a (as adjusted for any stock dividends, combinations or splits with respect to such shares) on the Series B Preferred Stock, 8% of the Series B-1 Issue Price as defined in Section 2.a (as adjusted for any stock dividends, combinations or splits with respect to such shares) on the Series B-1 Preferred Stock, 8% of the Series C Issue Price as defined in Section 2.a (as adjusted for any stock dividends, combinations or splits with respect to such shares) on the Series C Preferred Stock, and 8% of the Series C-1 Issue Price as defined in Section 2.a (as adjusted for any stock dividends, combinations or splits with respect to such shares) on the Series C-1 Preferred Stock shall have been paid or declared and set apart during that fiscal year, except for:

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(i)acquisitions of Common Stock by the Company pursuant to agreements which permit the Company to repurchase such shares at cost (or the lesser of cost or fair market value) upon termination of services to the Company;

(ii)acquisitions of Common Stock in exercise of the Company's right of first refusal to repurchase such shares; or

(iii)distributions to holders of Common Stock in accordance with Section 2.

b.Common Stock Dividends. In the event the Company shall declare a distribution or dividend on any Common Stock (other than dividends payable solely in Common Stock of the Company), then, in each such case, the holders of the Preferred Stock shall be entitled to a proportionate share of any such distribution as though the holders of the Preferred Stock were the holders of the number of shares of Common Stock of the Company into which their respective shares of Preferred Stock are convertible as of the record date fixed for the determination of the holders of Common Stock of the Company entitled to receive such distribution.

2.Liquidation Preference.

a.Payments to Holders of Preferred Stock. In the event of any liquidation, dissolution or winding up of the Company (a “Liquidation”), whether voluntary or involuntary, the holders of the Series A Preferred Stock, Series B Preferred Stock, Series B-1 Preferred Stock, Series C Preferred Stock and Series C-1 Preferred Stock shall be entitled to receive, on a pari passu basis but prior and in preference to any distribution of any of the legally available assets or surplus funds of the Company to the holders of the Common Stock by reason of their ownership thereof, (i) in the case of Series A Preferred Stock, the amount of $2.174 per share, as adjusted for any stock dividends, combinations or splits with respect to such shares, (the “Series A Issue Price”), plus all declared but unpaid dividends, on each such share then held by them, (ii) in the case of Series B Preferred Stock, the amount of $24.88 per share, as adjusted for any stock dividends, combinations or splits with respect to such shares (the “Series B Issue Price”), plus all declared but unpaid dividends, on each such share then held by them, (iii) in the case of Series B-1 Preferred Stock, the amount of $25.26 per share, as adjusted for any stock dividends, combinations or splits with respect to such shares (the “Series B-1 Issue Price”), plus all declared but unpaid dividends, on each such share then held by them, (iv) in the case of Series C Preferred Stock, the amount of $12.46 per share, as adjusted for any stock dividends, combinations or splits with respect to such shares (the “Series C Issue Price”), and (v) in the case of Series C-1 Preferred Stock, the amount of $17.56 per share, as adjusted for any stock dividends, combinations or splits with respect to such shares (the “Series C-1 Issue Price”). If upon the occurrence of such event, the assets and funds thus distributed among the holders of the Preferred Stock shall be insufficient to permit the payment to such holders of the full aforesaid preferential amount, then the entire assets and funds of the Company legally available for distribution shall be distributed ratably among the holders of the Preferred Stock in proportion to the preferential amount each such holder is otherwise entitled to receive.

b.Payments to Holders of Common Stock. After payment to the holders of the Preferred Stock of the amounts set forth in Section 2.a above, the entire remaining

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assets and funds of the Company legally available for distribution, if any, shall be distributed ratably among the holders of the Common Stock pro rata based on the number of shares of Common Stock held by each.

c.Conversion for Payments. Notwithstanding paragraphs (a) and (b) above, solely for purposes of determining the amount each holder of shares of Preferred Stock is entitled to receive with respect to a Liquidation, each series of Preferred Stock shall be treated as if all holders of such series had converted such holder's shares of such series into shares of Common Stock immediately prior to the Liquidation if, as a result of an actual conversion of any series of Preferred Stock (including taking into account the operation of this paragraph (c) with respect to all series of Preferred Stock), holders of such series would receive (with respect to such series), in the aggregate, an amount greater than the amount that would be distributed to holders of such series if such holders had not converted such series of Preferred Stock into shares of Common Stock.

d.Deemed Liquidation. For purposes of this Section 2, (i) any acquisition of the Company by means of merger or other form of corporate reorganization in which outstanding shares of the Company are exchanged for securities or other consideration issued, or caused to be issued, by the acquiring company or its subsidiary (other than a transaction effected solely to reincorporate the Company in another jurisdiction) and pursuant to which the holders of the outstanding voting securities of the Company immediately prior to such consolidation, merger or other transaction fail to hold equity securities representing a majority of the voting power of the Company or surviving entity immediately following such consolidation, merger or other transaction (an “Acquisition”) or (ii) a sale of all or substantially all of the assets of the Company (an “Asset Sale”), shall be treated as a Liquidation of the Company and shall entitle the holders of Preferred Stock to receive at the closing of such transaction in cash, securities or other property (valued as provided in Section 2.e below) the amounts as specified in Section 2.a above; provided that an Acquisition shall not include any transaction or series of transactions principally for bona fide equity financing purposes in which cash is received by the Company or any successor or indebtedness of the Company is cancelled or converted or a combination thereof.

e.Amount Deemed Paid or Distributed. Whenever the distribution provided for in this Section 2 shall be payable in securities or property other than cash, the value of such distribution shall be the fair market value of such securities or other property. Any securities shall be valued as follows:

(i)If traded on a securities exchange, the value shall be deemed to be the average of the closing prices of the securities on such exchange or system over the thirty (30) day period ending three (3) days prior to the closing;

(ii)If actively traded over-the-counter, the value shall be deemed to be the average of the closing bid or sale prices (whichever is applicable) over the thirty (30) day period ending three (3) days prior to the closing; and

(iii)If there is no active market, the value shall be the fair market value thereof, as determined in good faith by the Board of Directors of the Company.

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3.Voting Rights. Except as otherwise provided herein or as required by law, the Preferred Stock will be voted equally with the shares of the Common Stock and not as a separate class, at any annual or special meeting of stockholders of the Company, and may act by written consent in the same manner as the Common Stock, in either case upon the following basis: each holder of shares of the Preferred Stock shall be entitled to the number of votes equal to the respective number of shares of Common Stock into which such shares of Preferred Stock could be converted immediately after the close of business on the record date fixed for such meeting or the effective date of such written consent, and shall be entitled to notice of any stockholders' meeting in accordance with the Bylaws of the Company. Fractional votes shall not, however, be permitted and any fractional voting rights resulting from the above formula (after aggregating all shares into which shares of Preferred Stock held by each holder could be converted) shall be rounded to the nearest whole number (with one-half being rounded upward).

4.Conversion. The holders of the Preferred Stock shall have conversion rights as follows:

a.Right to Convert. Each share of Preferred Stock shall be convertible, at the option of the holder thereof, at any time after the date of issuance of such share, at the office of the Company or any transfer agent for such stock, into fully paid and nonassessable shares of Common Stock. The number of shares of Common Stock to which a holder of Preferred Stock shall be entitled upon conversion shall be determined by dividing the Series A Issue Price, Series B Issue Price, Series B-1 Issue Price, Series C Issue Price, or Series C-1 Issue Price, as applicable, by the conversion price for such share in effect at the time that such certificate is surrendered for conversion, and then multiplying by the number of shares of Preferred Stock being converted. The conversion price per share (the “Conversion Price”) as of the Original Issue Date (as defined below) shall be (i) for shares of Series A Preferred Stock $2.174 per share, (ii) for shares of Series B Preferred Stock shall be $21.86 per share, (iii) for shares of Series B-1 Preferred Stock shall be $22.14 per share, (iv) for shares of Series C Preferred Stock shall be $12.46 per share, and (v) for shares of Series C-1 Preferred Stock, $17.56 per share, in each case each subject to adjustment as hereinafter provided.

b.Automatic Conversion.

(i)Each share of Series A Preferred Stock shall automatically be converted into shares of Common Stock at the then applicable Conversion Price upon the earlier to occur of (i) the date specified by written consent or agreement of stockholders holding at least a majority of the then outstanding shares of Series A Preferred Stock, voting together as a single class, or (ii) immediately upon the closing of the sale of the Company's Common Stock in a firm commitment, underwritten public offering registered under the Securities Act of 1933, as amended (the “Securities Act”), which results in aggregate proceeds to the Company (before deduction for underwriters' discounts and expenses relating to the issuance, including without limitation fees of the Company's counsel) equal to at least $30,000,000 (a “Qualified IPO”). Upon such automatic conversion, any declared and unpaid dividends shall be paid in accordance with the provisions of Section 1.

(ii)Each share of Series B Preferred Stock shall automatically be converted into shares of Common Stock at the then applicable Conversion Price upon the earlier to occur of (i) the date specified by written consent or agreement of (A) stockholders

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holding at least a majority of the then outstanding shares of Preferred Stock, voting together as a single class, and (B) stockholders holding at least a majority of the then outstanding shares of Series B Preferred Stock, voting together as a single class, or (ii) immediately upon the closing of a Qualified IPO. Upon such automatic conversion, any declared and unpaid dividends shall be paid in accordance with the provisions of Section 1.

(iii)Each share of Series B-1 Preferred Stock shall automatically be converted into shares of Common Stock at the then applicable Conversion Price upon the earlier to occur of (i) the date specified by written consent or agreement of (A) stockholders holding at least a majority of the then outstanding shares of Preferred Stock, voting together as a single class, and (B) stockholders holding at least a majority of the then outstanding shares of Series B-1 Preferred Stock, voting together as a single class, or (ii) immediately upon the closing of a Qualified IPO. Upon such automatic conversion, any declared and unpaid dividends shall be paid in accordance with the provisions of Section 1.

(iv)Each share of Series C Preferred Stock shall automatically be converted into shares of Common Stock at the then applicable Conversion Price upon the earlier to occur of (i) the date specified by written consent or agreement of (A) stockholders holding at least a majority of the then outstanding shares of Preferred Stock, voting together as a single class, and (B) stockholders holding at least a majority of the then outstanding shares of Series C Preferred Stock, voting together as a single class, or (ii) immediately upon the closing of a Qualified IPO. Upon such automatic conversion, any declared and unpaid dividends shall be paid in accordance with the provisions of Section 1.

(v)Each share of Series C-1 Preferred Stock shall automatically be converted into shares of Common Stock at the then applicable Conversion Price upon the earlier to occur of (i) the date specified by written consent or agreement of (A) stockholders holding at least a majority of the then outstanding shares of Preferred Stock, voting together as a single class, and (B) stockholders holding at least a majority of the then outstanding shares of Series C-1 Preferred Stock, voting together as a single class, or (ii) immediately upon the closing of a Qualified IPO. Upon such automatic conversion, any declared and unpaid dividends shall be paid in accordance with the provisions of Section 1.

c.Mechanics of Conversion.

(i)Except in the case of an automatic conversion pursuant to Section 4.b., before any holder of Preferred Stock shall be entitled to convert the same into shares of Common Stock, such holder shall surrender the certificate or certificates therefor, duly endorsed, at the office of the Company or of any transfer agent for such stock, and shall give written notice to the Company at such office that such holder elects to convert the same and shall state therein the name or names in which such holder wishes the certificate or certificates for shares of Common Stock to be issued. The Company shall, as soon as practicable thereafter, issue and deliver at such office to such holder of Preferred Stock a certificate or certificates for the number of shares of Common Stock to which such holder shall be entitled as aforesaid and shall promptly pay (i) in cash or, to the extent sufficient funds are not then legally available therefor, in Common Stock (at the Common Stock's fair market value determined by the Board as of the date of such conversion), any declared and unpaid dividends on the shares of Preferred Stock being converted and (ii) in cash (at the Common Stock's fair market value determined by

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the Board as of the date of conversion) the value of any fractional share of Common Stock otherwise issuable to any holder of Preferred Stock. Such conversion shall be deemed to have been made immediately prior to the close of business on the date of surrender of the shares of Preferred Stock to be converted, and the person or persons entitled to receive the shares of Common Stock issuable upon such conversion shall be treated for all purposes as the record holder or holders of such shares of Common Stock on such date.

(ii)If the conversion is in connection with an underwritten offering of securities pursuant to the Securities Act, the conversion may, at the option of any holder tendering shares of Preferred Stock for conversion, be conditioned upon the closing with the underwriters of the sale of securities pursuant to such offering, in which event the person(s) entitled to receive the Common Stock upon conversion of the Preferred Stock shall not be deemed to have converted such Preferred Stock until immediately prior to the closing of such sale of securities.

d.Adjustments to Conversion Price for Certain Diluting Issues.

(i)Special Definitions. For purposes of this Section 4, the following definitions apply:

(1)“Options” shall mean rights, options or warrants to subscribe for, purchase or otherwise acquire either Common Stock or Convertible Securities (as defined below).

(2)“Original Issue Date” shall mean the date of the filing with the Delaware Secretary of State of the Certificate of Merger (the “Certificate ofMerger”) of the Company and Amyris Biotechnologies, Inc., a California corporation (“Amyris California”).

(3)“Convertible Securities” shall mean any evidences of indebtedness, shares (other than Common Stock, Series A Preferred Stock, Series B Preferred Stock, Series B-1 Preferred Stock, Series C Preferred Stock or Series C-1 Preferred Stock) or other securities convertible into or exchangeable for Common Stock, including securities described in Section 4.d.(i)(4).

(4)“Additional Shares of Common Stock” shall mean all shares of Common Stock issued (or, pursuant to Section 4.d(iii) deemed to be issued) by the Company after the Original Issue Date, other than shares of Common Stock issued or issuable after the Original Issue Date:

(A)upon conversion of shares of Preferred Stock;

(B)pursuant to or issuable upon exercise of options or warrants to purchase shares of Common stock, issued to employees, officers, directors or consultants of the Company or a subsidiary pursuant to stock option or stock purchase plans or other arrangements in each case on terms approved by at least 76% of the members of the Board of Directors of the Company;

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(C)pursuant to transactions involving research or development funding, technology licensing, joint ventures, strategic alliances, partnering arrangements, bank financings or lease arrangements pursuant to agreements in each case approved by at least 76% of the members of the Board of Directors of the Company;

(D)pursuant to the acquisition of another corporation or entity by the corporation by way of merger, purchase of assets, stock for stock exchange or other reorganization or recapitalization in each case approved by at least 76% of the members of the Board of Directors of the Company;

(E)in a Qualified IPO;

(F)pursuant to a transaction described in Section 4.e or 4.f;

(G)for which adjustment of the applicable Conversion Price is made pursuant to this Section 4;

(H)pursuant to or issuable upon exercise of warrants, options or other rights to acquire securities of the Company outstanding as of the Original Issue Date and any securities issuable upon conversion thereof;

(I)pursuant to or issuable upon conversion, exchange or cancellation of shares of Amyris Brasil S.A., a majority-owned subsidiary of the Company;

(J)in connection with the merger effected by the Certificate of Merger (the “Merger”) or pursuant to or issuable upon conversion, exchange or cancellation of shares of Amyris California in connection with the Merger; or

(K)upon the affirmative vote of at least a majority of the then outstanding shares of Preferred Stock, voting together as a single class on an as-if converted basis.

(ii)No Adjustment of Conversion Price. Any provision herein to the contrary notwithstanding, no adjustment in the applicable Conversion Price shall be made in respect of the issuance of Additional Shares of Common Stock unless the consideration per share (determined pursuant to Section 4.d(v) hereof) for an Additional Share of Common Stock issued or deemed to be issued by the Company is less than the applicable Conversion Price in effect immediately prior to such issue.

(iii)Deemed Issue of Additional Shares of Common Stock. In the event the Company at any time or from time to time after the Original Issue Date shall issue any Options or Convertible Securities (other than shares of Series C-1 Preferred Stock authorized herein) or shall fix a record date for the determination of holders of any class of securities then entitled to receive any such Options or Convertible Securities, then the maximum number of shares (as set forth in the instrument relating thereto without regard to any provisions contained therein designed to protect against dilution) of Common Stock issuable upon the exercise of such Options or, in the case of Convertible Securities and Options therefor, the conversion or

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exchange of such Convertible Securities, shall be deemed to be Additional Shares of Common Stock issued as of the time of such issue or, in case such a record date shall have been fixed, as of the close of business on such record date, provided further that in any such case in which Additional Shares of Common Stock are deemed to be issued:

(1)no further adjustments in the applicable Conversion Price shall be made upon the subsequent issue of Convertible Securities or shares of Common Stock upon the exercise of such Options or conversion or exchange of such Convertible Securities;

(2)if such Options or Convertible Securities by their terms provide, with the passage of time or otherwise, for any increase in the consideration payable to the Company, or decrease in the number of shares of Common Stock issuable, upon the exercise, conversion or exchange thereof, the applicable Conversion Price computed upon the original issue thereof (or upon the occurrence of a record date with respect thereto), and any subsequent adjustments based thereon, shall, upon any such increase or decrease becoming effective, be recomputed to reflect such increase or decrease insofar as it affects such Options or the rights of conversion or exchange under such Convertible Securities (provided, however, that no such adjustment of the Conversion Price shall affect Common Stock previously issued upon conversion of the Preferred Stock);

(3)upon the expiration of any such options or rights, the termination of any such rights to convert or exchange or the expiration of any options or rights related to such convertible or exchangeable securities, the applicable Conversion Price to the extent in any way affected by or computed using such options, rights or securities or options or rights related to such securities, shall be recomputed to reflect the issuance of only the number of shares of Common Stock (and convertible or exchangeable securities which remain in effect) actually issued upon the exercise of such options or rights, upon the conversion or exchange of such securities or upon the exercise of the options or rights related to such securities;

(4)no readjustment pursuant to clause (2) or (3) above shall have the effect of increasing the applicable Conversion Price to an amount which exceeds the lower of (a) the Conversion Price on the original adjustment date or (b) the Conversion Price that would have resulted from any issuance of Additional Shares of Common Stock between the original adjustment date and such readjustment date.

(iv)Adjustment of Conversion Price Upon Issuance of Additional Shares of Common Stock. In the event the Company, at any time after the Original Issue Date shall issue Additional Shares of Common Stock (including Additional Shares of Common Stock deemed to be issued pursuant to Section 4.d(iii)) without consideration or for a consideration per share less than the applicable Conversion Price in effect on the date of and immediately prior to such issue, then, and in such event, the applicable Conversion Price shall be reduced, concurrently with such issue, to a price (calculated to the nearest cent) determined by multiplying the Conversion Price by a fraction, the numerator of which shall be the number of shares of Common Stock deemed outstanding (as defined below) immediately prior to such issuance plus the number of shares of Common Stock which the aggregate consideration received by the Company for the total number of Additional Shares of Common Stock so issued would purchase at the Conversion Price in effect immediately prior to such issuance, and the

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denominator of which shall be the number of shares of Common Stock deemed outstanding (as defined below) immediately prior to such issuance plus the number of such Additional Shares of Common Stock so issued. For the purpose of the above calculation, the number of shares of Common Stock outstanding immediately prior to such issue shall be calculated on a fully diluted basis, as if all shares of Preferred Stock and all outstanding Convertible Securities had been fully converted into shares of Common Stock and any outstanding warrants, outstanding options or other rights outstanding for the purchase of shares of stock or convertible securities had been fully exercised (and the resulting securities fully converted into shares of Common Stock, if so convertible) as of such date. For the purposes of adjusting the applicable Conversion Price of a series of Preferred Stock, the grant, issue or sale of Additional Shares of Common consisting of the same class of security and warrants to purchase such security issued or issuable at the same price at two or more closings held within a six (6) month period shall be aggregated and shall be treated as one sale of Additional Shares of Common occurring on the earliest date on which such securities were granted, issued or sold.

(v)Determination of Consideration. For purposes of this Section 4.d, the consideration received by the Company for the issue of any Additional Shares of Common Stock shall be computed as follows:

(1)Cash and Property. Such consideration shall:

(A)insofar as it consists of cash, be computed at the aggregate amount of cash received by the Company, excluding amounts paid or payable for accrued interest or declared but unpaid dividends;

(B)insofar as it consists of property other than cash, be computed at the fair value thereof at the time of such issue, as determined in good faith by the Board of Directors; and

(C)in the event Additional Shares of Common Stock are issued together with other shares or securities or other assets of the Company for consideration which covers both, be the proportion of such consideration so received, computed as provided in clauses (A) and (B) above, as determined in good faith by the Board of Directors.

(2)Options and Convertible Securities. The consideration per share received by the Company for Additional Shares of Common Stock deemed to have been issued pursuant to Section 4.d(iii), relating to Options and Convertible Securities shall be determined by dividing

(A)the total amount, if any, received or receivable by the Company as consideration for the issue of such Options or Convertible Securities, plus the minimum aggregate amount of additional consideration (as set forth in the instruments relating thereto, without regard to any provision contained therein designed to protect against dilution) payable to the Company upon the exercise of such Options or the conversion or exchange of such Convertible Securities, or in the case of Options for Convertible Securities, the exercise of such Options for Convertible Securities and the conversion or exchange of such Convertible Securities by

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(B)the maximum number of shares of Common Stock (as set forth in the instruments relating thereto, without regard to any provision contained therein designed to protect against the dilution) issuable upon the exercise of such Options or conversion or exchange of such Convertible Securities.

e.Adjustments for Stock Dividends and for Combinations or Subdivisions of Common Stock. In the event that this Company at any time or from time to time after the Original Issue Date shall declare or pay, without consideration, any dividend on the Common Stock payable in Common Stock or in any right to acquire Common Stock for no consideration, or shall effect a subdivision of the outstanding shares of Common Stock into a greater number of shares of Common Stock (by stock split, reclassification or otherwise than by payment of a dividend in Common Stock or in any right to acquire Common Stock), or in the event the outstanding shares of Common Stock shall be combined or consolidated, by reclassification or otherwise, into a lesser number of shares of Common Stock, then the conversion price for any series of Preferred Stock in effect immediately prior to such event shall, concurrently with the effectiveness of such event, be proportionately decreased or increased, as appropriate. In the event that the Company shall declare or pay, without consideration, any dividend on the Common Stock payable in any right to acquire Common Stock for no consideration then the Company shall be deemed to have made a dividend payable in Common Stock in an amount of shares equal to the maximum number of shares issuable upon exercise of such rights to acquire Common Stock.

f.Adjustments for Reclassification and Reorganization. If the Common Stock issuable upon conversion of any series of Preferred Stock shall be changed into the same or a different number of shares of any other class or classes of stock, whether by capital reorganization, reclassification or otherwise (other than a subdivision or combination of shares provided for in Section 4.e above or a merger or other reorganization referred to in Section 2.d above), the Conversion Price for any series of Preferred Stock then in effect shall, concurrently with the effectiveness of such reorganization or reclassification, be proportionately adjusted so that the Preferred Stock shall be convertible into, in lieu of the number of shares of Common Stock which the holders would otherwise have been entitled to receive, a number of shares of such other class or classes of stock equivalent to the number of shares of Common Stock that would have been subject to receipt by the holders upon conversion of the Preferred Stock immediately before that change, respectively.

g.Certificates as to Adjustments. Upon the occurrence of each adjustment or readjustment of any conversion price pursuant to this Section 4, the Company at its expense shall promptly compute such adjustment or readjustment in accordance with the terms hereof and prepare and furnish to each holder of Preferred Stock a certificate executed by the Company's President or a Vice President setting forth such adjustment or readjustment and showing in detail the facts upon which such adjustment or readjustment is based. The Company shall, upon the written request at any time of any holder of Preferred Stock, furnish or cause to be furnished to such holder a like certificate setting forth (i) such adjustments and readjustments, (ii) the conversion price for such series of Preferred Stock at the time in effect, and (iii) the number of shares of Common Stock and the amount, if any, of other property which at the time would be received upon the conversion of the Preferred Stock.

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h.Notices of Record Date. In the event that the Company shall propose at any time (i) to declare any dividend or distribution upon its Common Stock, whether in cash, property, stock or other securities, whether or not a regular cash dividend and whether or not out of earnings or earned surplus, (ii) a Liquidation or any voluntary or involuntary dissolution or winding up of the Company, or (iii) to offer for subscription pro rata to the holders of any class or series of its stock any additional shares of stock of any class or series or other rights, then, in connection with each such event, unless otherwise waived by a majority of Preferred Stock, the Company shall send to the holders of Preferred Stock at least twenty (20) days' prior written notice of the date on which a record shall be taken for such dividend, distribution, Liquidation, dissolution, winding up or subscription rights.

i.Reservation of Stock Issuable Upon Conversion. The Company shall at all times reserve and keep available out of its authorized but unissued shares of Common Stock, solely for the purpose of effecting the conversion of the shares of the Preferred Stock, such number of its shares of Common Stock as shall from time to time be sufficient to effect the conversion of all outstanding shares of the Preferred Stock; and if at any time the number of authorized but unissued shares of Common Stock shall not be sufficient to effect the conversion of all then outstanding shares of the Preferred Stock, the Company will take such corporate action as may, in the opinion of its counsel, be necessary to increase its authorized but unissued shares of Common Stock to such number of shares as shall be sufficient for such purpose, including, without limitation, engaging in best efforts to obtain the requisite stockholder approval of any necessary amendment to this Restated Certificate.

j.Fractional Shares. No fractional share shall be issued upon the conversion of any share or shares of Preferred Stock. All shares of Common Stock (including fractions thereof) issuable upon conversion of more than one share of Preferred Stock by a holder thereof shall be aggregated for purposes of determining whether the conversion would result in the issuance of any fractional share. If, after the aforementioned aggregation, the conversion would result in the issuance of a fraction of a share of Common Stock, the Company shall, in lieu of issuing any fractional share, pay the holder otherwise entitled to such fraction a sum in cash equal to the fair market value of such fraction on the date of conversion (as determined in good faith by the Board of Directors).

k.Notices. Any notice required by the provisions of this Section 4 shall be in writing and shall be deemed effectively given: (i) upon personal delivery to the party to be notified, (ii) when sent by confirmed electronic mail or facsimile if sent during normal business hours of the recipient; if not, then on the next business day, (iii) five (5) days after deposit in the United States mail, by registered or certified mail, postage prepaid and properly addressed to the party to be notified, or (iv) one (1) day after deposit with a nationally recognized overnight courier, specifying next day delivery, with written verification of receipt. All notices shall be addressed to each holder of record at the address of such holder appearing on the books of the Company.

5.Board Representation. In addition to the rights of the holders of Preferred Stock to vote on an as converted basis with holders of Common Stock pursuant to Section 3 above, with respect to election of directors:

13

a.For so long as any shares of Series A Preferred Stock remain outstanding, the holders of Series A Preferred Stock, voting as a separate class, shall be entitled to elect three (3) members of the Board of Directors (each a “Series A Director”) at each meeting or pursuant to each consent of the Company's stockholders for the election of directors, and to remove from office such directors and to fill any vacancy caused by the resignation, death or removal of such directors.

b.The holders of Common Stock, voting as a separate class, shall be entitled to elect two (2) members of the Board of Directors (each a “Common Director”) at each meeting or pursuant to each consent of the Company's stockholders for the election of directors, and to remove from office such directors and to fill any vacancy caused by the resignation, death or removal of such directors.

c.The holders of Preferred Stock and the holders of Common Stock, voting together as a single class on an as-if converted basis, shall be entitled to elect any additional members of the Board of Directors (each an “Independent Director”), and to remove from office such directors and to fill any vacancy caused by the resignation, death or removal of such directors.

6.Redemption. The Preferred Stock shall not be redeemable.

7.Restrictions and Limitations. So long as at least 20% of the shares of the Preferred Stock sold by the Company (as adjusted for stock splits, dividends, combinations, recapitalizations and the like) remain outstanding, consent of the holders of at least the majority of the Preferred Stock shall be required for any action that (whether by amendment, merger, reorganization or otherwise):

a.alters or changes the rights, preferences or privileges of the Common Stock or the Preferred Stock,

b.increases or decreases the authorized number of shares of Common or Preferred Stock,

c.creates (by reclassification or otherwise) any new class or series of shares having rights, preferences or privileges senior to or on a parity with the Preferred Stock,

d.results in the redemption of any shares of Preferred Stock or Common Stock (other than pursuant to equity incentive agreements with employees and other service providers giving the Company the right to repurchase shares upon the termination of employment or such other service relationship, at their original cost),

e.results in a Liquidation or other corporate reorganization, including any reorganization or other transaction involving any parent or subsidiary of the Company,

f.amends or waives any provision of the Company's certificate of incorporation or bylaws,

g.increases or decreases the authorized size of the Company's Board of Directors, or

14

h.results in the payment or declaration of any dividend on any shares of Common or Preferred Stock;

provided, however, that for any amendment or waiver of any provision of the Company's certificate of incorporation or bylaws that would have a material, adverse and disproportionate effect on a series of Preferred Stock relative to any other series of Preferred Stock, consent of the holders of at least the majority of such series of Preferred Stock voting as a separate class shall be required.

8.No Reissuance of Preferred Stock. No share or shares of Preferred Stock acquired by the Company by reason of redemption, purchase, conversion, or otherwise shall be reissued; and, in addition, the certificate of incorporation shall be appropriately amended to effect the corresponding reduction in the Company's authorized stock.

ARTICLE V: PREEMPTIVE RIGHTS.

No stockholder of the Corporation shall have a right to purchase shares of capital stock of the Corporation sold or issued by the Corporation except to the extent that such a right may from time to time be set forth in a written agreement between the Corporation and any stockholder.

ARTICLE VI: STOCK REPURCHASES.

In connection with repurchases by the Corporation of its Common Stock from Service Providers pursuant to agreements under which the Corporation has the option to repurchase such shares at cost upon the occurrence of certain events, such as the termination of employment, Sections 502 and 503 of the Corporations Code of the State of California shall not apply in all or in part with respect to such repurchases.

ARTICLE VII: BYLAW PROVISIONS.

A.AMENDMENT OF BYLAWS. Subject to any additional vote required by the Restated Certificate or Bylaws, in furtherance and not in limitation of the powers conferred by statute, the Board is expressly authorized to make, repeal, alter, amend and rescind any or all of the Bylaws of the Corporation.

B.NUMBER OF DIRECTORS. Subject to any additional vote required by the Restated Certificate, the number of directors of the Corporation shall be determined in the manner set forth in the Bylaws of the Corporation.

C.BALLOT. Elections of directors need not be by written ballot unless the Bylaws of the Corporation shall so provide.

D.MEETINGS AND BOOKS. Meetings of stockholders may be held within or without the State of Delaware, as the Bylaws of the Corporation may provide. The books of the Corporation may be kept outside the State of Delaware at such place or places as may be designated from time to time by the Board or in the Bylaws of the Corporation.

15

ARTICLE VIII: DIRECTOR LIABILITY.

A.LIMITATION. To the fullest extent permitted by law, a director of the Corporation shall not be personally liable to the Corporation or its stockholders for monetary damages for breach of fiduciary duty as a director. If the General Corporation Law or any other law of the State of Delaware is amended after approval by the stockholders of this Article VIII to authorize corporate action further eliminating or limiting the personal liability of directors, then the liability of a director of the Corporation shall be eliminated or limited to the fullest extent permitted by the General Corporation Law as so amended. Any repeal or modification of the foregoing provisions of this Article VIII by the stockholders of the Corporation shall not adversely affect any right or protection of a director of the Corporation existing at the time of, or increase the liability of any director of the Corporation with respect to any acts or omissions of such director occurring prior to, such repeal or modification.

B.INDEMNIFICATION. To the fullest extent permitted by applicable law, the Corporation is authorized to provide indemnification of (and advancement of expenses to) directors, officers and agents of the Corporation (and any other persons to which General Corporation Law permits the Corporation to provide indemnification) through Bylaw provisions, agreements with such agents or other persons, vote of stockholders or disinterested directors or otherwise, in excess of the indemnification and advancement otherwise permitted by Section 145 of the General Corporation Law.

C.MODIFICATION. Any amendment, repeal or modification of the foregoing provisions of this Article VIII shall not adversely affect any right or protection of any director, officer or other agent of the Corporation existing at the time of such amendment, repeal or modification.

ARTICLE IX:CREDITOR AND STOCKHOLDER COMPROMISES

Whenever a compromise or arrangement is proposed between the Corporation and its creditors or any class of them and/or between the Corporation and its stockholders or any class of them, any court of equitable jurisdiction within the State of Delaware may, on the application in a summary way of the Corporation or of any creditor or stockholder thereof or on the application of any receiver or receivers appointed for the Corporation under the provisions of §291 of Title 8 of the General Corporation Law or on the application of trustees in dissolution or of any receiver or receivers appointed for this Corporation under §279 of Title 8 of the General Corporation Law order a meeting of the creditors or class of creditors, and/or of the stockholders or class of stockholders of the Corporation, as the case may be, to be summoned in such manner as the said court directs. If a majority in number representing three-fourths in value of the creditors or class of creditors, and/or of the stockholders or class of stockholders of the Corporation, as the case may be, agree to any compromise or arrangement and to any reorganization of the Corporation as a consequence of such compromise or arrangement, the said compromise or arrangement and the said reorganization shall, if sanctioned by the court to which the said application has been made, be binding on all the creditors or class of creditors, and/or on all the stockholders or class of stockholders, of the Corporation, as the case may be, and also on the Corporation.

* * * * *

16

EXHIBIT B

CERTIFICATE OF MERGER OF AMEYRIS BIOTECHNOLOGIES, INC.

WITH AND INTO

AMYRIS BIOTECHNOLOGIES, INC.

D1025001

State of California

Secretary of State

I, DEBRA BOWEN, Secretary of State of the State of California, hereby certify:

That the attached transcript of 20 page(s) is a full, true and correct copy of the original record in the custody of this office.

IN WITNESS WHEREOF, I execute this certificate and affix the Great Seal of the State of California this day of

JUN 10 2010                    

/s/ Debra Bowen

DEBRA BOWEN

Secretary of State

D1025001

ENDORSED - FILED

in the office of the Secretary of State

of the State of California

JUN 10 2010

DELAWARE

The First State

I, JEFFREY W. BULLOCK, SECRETARY OF STATE OF THE STATE OF DELAWARE, DO HEREBY CERTIFY THE ATTACHED IS A TRUE AND CORRECT COPY OF THE CERTIFICATE OF MERGER, WHICH MERGES:

"AMYRIS BIOTECHNOLOGIES, INC.", A CALIFORNIA CORPORATION,

WITH AND INTO "AMYRIS BIOTECHNOLOGIES, INC." UNDER THE NAME OF "AMYRIS BIOTECHNOLOGIES, INC.', A CORPORATION ORGANIZED AND EXISTING UNDER THE LAWS OF THE STATE OF DELAWARE, AS RECEIVED AND FILED IN THIS OFFICE THE TENTH DAY OF JUNE, A.D. 2010, AT 2:10 O'CLOCK P.M.

A FILED COPY OF THIS CERTIFICATE HAS BEEN FORWARDED TO THE KENT COUNTY RECORDER OF DEEDS.

/s/ Jeffrey W. Bullock                

Jeffrey W. Bullock, Secretary of State

AUTHENTICATION: 8046722

DATE: 06-10-10

4768633 8100M

100646250

You may verify this certificate online

at corp.delaware.gov/authver.shtml

State of Delaware

Secretary of State

Division of Corporations

Delivered 02:10 PM 06/10/2010

FILED 02:10 PM 06/10/2010

SRV 100646250 - 4768633 FILE

CERTIFICATE OF MERGER OF

AMYRIS BIOTECHNOLOGIES, INC., a California corporation

WITH AND INTO

AMYRIS BIOTECHNOLOGIES, INC., a Delaware corporation

Pursuant to Section 252(c) of the

General Corporation Law of the State of Delaware

Amyris Biotechnologies, Inc., a Delaware corporation (“Amyris Delaware”), does hereby certify to the following facts relating to the merger (the “Merger”) of Amyris Biotechnologies, Inc., a California corporation (“Amyris California”), with and into Amyris Delaware, with Amyris Delaware remaining as the surviving corporation of the Merger (the “Surviving Corporation”):

FIRST: Amyris Delaware is incorporated pursuant to the General Corporation Law of the State of Delaware (“DGCL”). Amyris California is incorporated pursuant to the General Corporation Law of the State of California. Amyris Delaware and Amyris California are the constituent corporations in the Merger.

SECOND: An Agreement and Plan of Merger has been approved, adopted, certified, executed and acknowledged by Amyris Delaware and Amyris California in accordance with the provisions of subsection (c) of Section 252 of the DGCL.

THIRD: The name of the Surviving Corporation shall be Amyris Biotechnologies, Inc.

FOURTH: Upon the effectiveness of the Merger, the certificate of incorporation of the Surviving Corporation shall be amended and restated to read in its entirety as set forth in the Restated Certificate of Incorporation attached hereto as Attachment A.

FIFTH: The executed Agreement and Plan of Merger is on file at the principal place of business of Amyris Delaware, the Surviving Corporation, 5885 Hollis Street, Suite 100, Emeryville, CA 94608, United States of America.

SIXTH: A copy of the executed Agreement and Plan of Merger will be furnished by Amyris Delaware, the Surviving Corporation, on request and without cost, to any stockholder of any constituent corporation of the Merger

SEVENTH: The authorized capital stock of Amyris California is 38,000,000 shares of Common Stock, no par value, and 23,862,355 shares of Preferred Stock, no par value.

EIGHTH: The Surviving Corporation is a corporation formed and existing under the laws of Delaware.

NINTH: This Certificate of Merger shall become effective upon filing.

IN WITNESS WHEREOF, Amyris Delaware has caused this Certificate of Merger to be executed by its duly authorized officers as of June 10, 2010.

AMYRIS BIOTECHNOLOGIES, INC.

By: /s/ John Melo            

John G. Melo, President

By: /s/ Tamara Tompkins        

Tamara Tompkins, Secretary

Attachment A

Restated Certificate of Incorporation

(see Exhibit "A" to the Exhibit A Agreement and Plan of Merger)

EXHIBIT C

RESTATED CERTIFICATE OF INCORPORATION

DELAWARE

The First State

I, JEFFREY W. BULLOCK, SECRETARY OF STATE OF THE STATE OF DELAWARE, DO HEREBY CERTIFY THE ATTACHED IS A TRUE AND CORRECT COPY OF THE RESTATED CERTIFICATE OF "AMYRIS BIOTECHNOLOGIES, INC.", CHANGING ITS NAME FROM "AMYRIS BIOTECHNOLOGIES, INC." TO "AMYRIS, INC.", FILED IN THIS OFFICE ON THE TWENTY-FIRST DAY OF JUNE, A.D. 2010, AT 8:25 O'CLOCK A.M.

A FILED COPY OF THIS CERTIFICATE HAS BEEN FORWARDED TO THE KENT COUNTY RECORDER OF DEEDS.

/s/ Jeffrey W. Bullock                

Jeffrey W. Bullock, Secretary of State

AUTHENTICATION: 8064893

DATE: 06-21-10

4768633 8100

100672905

You may verify this certificate online

at corp.delaware.gov/authver.shtml

State of Delaware

Secretary of State

Division of Corporations

Delivered 08:29 AM 06/21/2010

FILED 08:25 AM 06/21/2010

SRV 100672905 - 4768633 FILE

AMYRIS BIOTECHNOLOGIES, INC.

RESTATED CERTIFICATE OF INCORPORATION

(Pursuant to Sections 242 and 245 of the

General Corporation Law of the State of Delaware)

Amyris Biotechnologies, Inc., a corporation organized and existing under and by virtue of the provisions of the General Corporation Law of the State of Delaware (the “General Corporation Law”), does hereby certify as follows.

1.The name of this corporation is Amyris Biotechnologies, Inc. and that this corporation was originally incorporated pursuant to the General Corporation Law on April 15, 2010 under the name Amyris Biotechnologies, Inc.

2.The Board of Directors of this corporation duly adopted resolutions proposing to amend and restate the Certificate of Incorporation of this corporation, declaring said amendment and restatement to be advisable and in the best interests of this corporation and its stockholders, and authorizing the appropriate officers of this corporation to solicit the consent of the stockholders therefor, which resolution setting forth the proposed amendment and restatement is as follows.

RESOLVED, that the Certificate of Incorporation of this corporation be amended and restated in its entirety to read as set forth on Exhibit A attached hereto and incorporated herein by this reference.

3.    Exhibit A referred to above is attached hereto as Exhibit A and is hereby incorporated herein by this reference. This Restated Certificate of Incorporation was approved by the holders of the requisite number of shares of this corporation in accordance with Section 228 of the General Corporation Law.

4.    This Restated Certificate of Incorporation, which restates and integrates and further amends the provisions of this corporation's Certificate of Incorporation, has been duly adopted in accordance with Sections 242 and 245 of the General Corporation Law.

IN WITNESS WHEREOF, this Restated Certificate of Incorporation has been executed by a duly authorized officer of this corporation on this 18th day of June, 2010.

By: /s/ John Melo        

John Melo, President

EXHIBIT A

AMYRIS BIOTECHNOLOGIES, INC.

RESTATED CERTIFICATE OF INCORPORATION

ARTICLE I: NAME

The name of the corporation is Amyris, Inc. (the “Company”).

ARTICLE II: REGISTERED OFFICE

The address of the registered office of the Corporation in the State of Delaware is 3500 South Dupont Highway, in the City of Dover, County of Kent, Delaware 19901. The name of its registered agent at such address is Incorporation Services, Ltd.

ARTICLE III: PURPOSE

The nature of the business or purposes to be conducted or promoted is to engage in any lawful act or activity for which corporations may be organized under the General Corporation Law.

ARTICLE IV: AUTHORIZED SHARES

The total number of shares of all classes of stock which the Corporation shall have authority to issue is (a) 70,000,000 shares of Common Stock, $0.0001 par value per share (“Common Stock”), and (b) 30,963,903 shares of Preferred Stock, $0.0001 par value per share (“Preferred Stock”). The Preferred Stock may be issued from time to time in one or more series, each of such series to consist of such number of shares and to have such terms, powers, preferences or rights, and the qualifications and limitations with respect thereto, as stated or expressed herein. As of the effective date of this Restated Certificate of Incorporation (this “Restated Certificate”), 9,475,000 shares of the authorized Preferred Stock of the Corporation are hereby designated “Series A Preferred Stock”, 1,929,641 shares of the authorized Preferred Stock of the Corporation are hereby designated “Series B Preferred Stock”, 4,700,000 shares of the authorized Preferred Stock of the Corporation are hereby designated “Series B-1 Preferred Stock”, 4,976,000 shares of the authorized Preferred Stock of the Corporation are hereby designated “Series C Preferred Stock”, 2,781,714 shares of the authorized Preferred Stock of the Corporation are hereby designated “Series C-1 Preferred Stock”, and 7,101,548 shares of the authorized Preferred Stock of the Corporation are hereby designated “Series D Preferred Stock”. The following is a statement of the designations and the powers, preferences or rights, and the qualifications, limitations or restrictions thereof, in respect of each class of capital stock of the Corporation.

A.    COMMON STOCK

1.General. The voting, dividend and liquidation rights of the holders of the Common Stock are subject to and qualified by the rights, powers and privileges of the holders of the Preferred Stock set forth herein.

2.Voting. The holders of the Common Stock are entitled to one vote for each share of Common Stock held at all meetings of stockholders (and written actions in lieu of meetings). Unless required by law, there shall be no cumulative voting. The number of authorized shares of Common Stock may be increased or decreased (but not below the number of shares thereof then outstanding) by (in addition to any vote of the holders of one or more series of Preferred Stock that may be required by the terms of the Certificate of Incorporation) the affirmative vote of the holders of shares of capital stock of the Corporation representing a majority of the votes represented by all outstanding shares of capital stock of the Corporation entitled to vote, irrespective of the provisions of Section 242(b)(2) of the General Corporation Law.

B.    PREFERRED STOCK

The following rights, powers and privileges, and restrictions, qualifications and limitations, shall apply to the Preferred Stock. Unless otherwise indicated, references to “Sections” in this Part B of this Article IV refer to sections of this Part B.

1.Dividends.

a.Preferred Stock Dividends. The holders of Series A Preferred Stock, Series B Preferred Stock, Series B-1 Preferred Stock, Series C Preferred Stock, Series C-1 Preferred Stock and Series D Preferred Stock shall be entitled to receive non-cumulative dividends, on a pari passu basis, at the rate of 8% of the Series A Issue Price as defined in Section 2.a. (as adjusted for any stock dividends, combinations or splits with respect to such shares) per annum for the Series A Preferred Stock, at the rate of 8% of the Series B Issue Price as defined in Section 2.a (as adjusted for any stock dividends, combinations or splits with respect to such shares) per annum for the Series B Preferred Stock, at the rate of 8% of the Series B-1 Issue Price as defined in Section 2.a. (as adjusted for any stock dividends, combinations or splits with respect to such shares) per annum for the Series B-1 Preferred Stock, at the rate of 8% of the Series C Issue Price as defined in Section 2.a. (as adjusted for any stock dividends, combinations or splits with respect to such shares) per annum for the Series C Preferred Stock, at the rate of 8% of the Series C-1 Issue Price as defined in Section 2.a. (as adjusted for any stock dividends, combinations or splits with respect to such shares) per annum for the Series C-1 Preferred Stock, and at the rate of 8% of the Series D Issue Price as defined in Section 2.a. (as adjusted for any stock dividends, combinations or splits with respect to such shares) per annum for the Series D Preferred Stock, payable out of funds legally available therefor. Such dividends shall be payable only when, as, and if declared by the Board of Directors and shall be non-cumulative.

No dividends (other than those payable solely in the Common Stock of the Company) shall be paid or other distribution made on any Common Stock of the Company, or purchase, redemption or other acquisition of Common Stock for value during any fiscal year of the

Company until dividends, in the amount of 8% of the Series A Issue Price (as adjusted for any stock dividends, combinations or splits with respect to such shares) on the Series A Preferred Stock, 8% of the Series B Issue Price as defined in Section 2.a (as adjusted for any stock dividends, combinations or splits with respect to such shares) on the Series B Preferred Stock, 8% of the Series B-1 Issue Price as defined in Section 2.a (as adjusted for any stock dividends, combinations or splits with respect to such shares) on the Series B-1 Preferred Stock, 8% of the Series C Issue Price as defined in Section 2.a (as adjusted for any stock dividends, combinations or splits with respect to such shares) on the Series C Preferred Stock, 8% of the Series C-1 Issue Price as defined in Section 2.a (as adjusted for any stock dividends, combinations or splits with respect to such shares) on the Series C-1 Preferred Stock, and 8% of the Series D Issue Price as defined in Section 2.a (as adjusted for any stock dividends, combinations or splits with respect to such shares) on the Series D Preferred Stock shall have been paid or declared and set apart during that fiscal year, except for:

(i)acquisitions of Common Stock by the Company pursuant to agreements which permit the Company to repurchase such shares at cost (or the lesser of cost or fair market value) upon termination of services to the Company;

(ii)acquisitions of Common Stock in exercise of the Company's right of first refusal to repurchase such shares; or

(iii)distributions to holders of Common Stock in accordance with Section 2.

b.Common Stock Dividends. In the event the Company shall declare a distribution or dividend on any Common Stock (other than dividends payable solely in Common Stock of the Company), then, in each such case, the holders of the Preferred Stock shall be entitled to a proportionate share of any such distribution as though the holders of the Preferred Stock were the holders of the number of shares of Common Stock of the Company into which their respective shares of Preferred Stock are convertible as of the record date fixed for the determination of the holders of Common Stock of the Company entitled to receive such distribution.

2.Liquidation Preference.

a.Payments to Holders of Preferred Stock. In the event of any liquidation, dissolution or winding up of the Company (a “Liquidation”), whether voluntary or involuntary, the holders of the Series A Preferred Stock, Series B Preferred Stock, Series B-1 Preferred Stock, Series C Preferred Stock, Series C-1 Preferred Stock and Series D Preferred Stock shall be entitled to receive, on a pari passu basis but prior and in preference to any distribution of any of the legally available assets or surplus funds of the Company to the holders of the Common Stock by reason of their ownership thereof, (i) in the case of Series A Preferred Stock, the amount of $2.174 per share, as adjusted for any stock dividends, combinations or splits with respect to such shares, (the “Series A Issue Price”), plus all declared but unpaid dividends, on each such share then held by them, (ii) in the case of Series B Preferred Stock, the amount of $24.88 per share, as adjusted for any stock dividends, combinations or splits with respect to such shares (the “Series B Issue Price”), plus all declared but unpaid dividends, on

each such share then held by them, (iii) in the case of Series B-1 Preferred Stock, the amount of $25.26 per share, as adjusted for any stock dividends, combinations or splits with respect to such shares (the “Series B-1 Issue Price”), plus all declared but unpaid dividends, on each such share then held by them, (iv) in the case of Series C Preferred Stock, the amount of $12.46 per share, as adjusted for any stock dividends, combinations or splits with respect to such shares (the “Series C Issue Price”), (v) in the case of Series C-1 Preferred Stock, the amount of $17.56 per share, as adjusted for any stock dividends, combinations or splits with respect to such shares (the “Series C-1 Issue Price”), and (vi) in the case of Series D Preferred Stock, the amount of $18.75 per share, as adjusted for any stock dividends, combinations or splits with respect to such shares (the “Series D Issue Price”). If upon the occurrence of such event, the assets and funds thus distributed among the holders of the Preferred Stock shall be insufficient to permit the payment to such holders of the full aforesaid preferential amount, then the entire assets and funds of the Company legally available for distribution shall be distributed ratably among the holders of the Preferred Stock in proportion to the preferential amount each such holder is otherwise entitled to receive.

b.Payments to Holders of Common Stock. After payment to the holders of the Preferred Stock of the amounts set forth in Section 2.a above, the entire remaining

assets and funds of the Company legally available for distribution, if any, shall be distributed ratably among the holders of the Common Stock pro rata based on the number of shares of Common Stock held by each.

c.Conversion for Payments. Notwithstanding paragraphs (a) and (b) above, solely for purposes of determining the amount each holder of shares of Preferred Stock is entitled to receive with respect to a Liquidation, each series of Preferred Stock shall be treated as if all holders of such series had converted such holder's shares of such series into shares of Common Stock immediately prior to the Liquidation if, as a result of an actual conversion of any series of Preferred Stock (including taking into account the operation of this paragraph (c) with respect to all series of Preferred Stock), holders of such series would receive (with respect to such series), in the aggregate, an amount greater than the amount that would be distributed to holders of such series if such holders had not converted such series of Preferred Stock into shares of Common Stock.

d.Deemed Liquidation. For purposes of this Section 2, (i) any acquisition of the Company by means of merger or other form of corporate reorganization in which outstanding shares of the Company are exchanged for securities or other consideration issued, or caused to be issued, by the acquiring company or its subsidiary (other than a transaction effected solely to reincorporate the Company in another jurisdiction) and pursuant to which the holders of the outstanding voting securities of the Company immediately prior to such consolidation, merger or other transaction fail to hold equity securities representing a majority of the voting power of the Company or surviving entity immediately following such consolidation, merger or other transaction (an “Acquisition”) or (ii) a sale of all or substantially all of the assets of the Company (an “Asset Sale”), shall be treated as a Liquidation of the Company and shall entitle the holders of Preferred Stock to receive at the closing of such transaction in cash, securities or other property (valued as provided in Section 2.e below) the amounts as specified in Section 2.a above; provided that an Acquisition shall not include any transaction or series of transactions principally for bona fide equity financing purposes in which cash is received by the

Company or any successor or indebtedness of the Company is cancelled or converted or a combination thereof.

e.Amount Deemed Paid or Distributed. Whenever the distribution provided for in this Section 2 shall be payable in securities or property other than cash, the value of such distribution shall be the fair market value of such securities or other property. Any securities shall be valued as follows:

(i)If traded on a securities exchange, the value shall be deemed to be the average of the closing prices of the securities on such exchange or system over the thirty (30) day period ending three (3) days prior to the closing;

(ii)If actively traded over-the-counter, the value shall be deemed to be the average of the closing bid or sale prices (whichever is applicable) over the thirty (30) day period ending three (3) days prior to the closing; and

(iii)If there is no active market, the value shall be the fair market value thereof, as determined in good faith by the Board of Directors of the Company.

3.Voting Rights. Except as otherwise provided herein or as required by law, the Preferred Stock will be voted equally with the shares of the Common Stock and not as a separate class, at any annual or special meeting of stockholders of the Company, and may act by written consent in the same manner as the Common Stock, in either case upon the following basis: each holder of shares of the Preferred Stock shall be entitled to the number of votes equal to the respective number of shares of Common Stock into which such shares of Preferred Stock could be converted immediately after the close of business on the record date fixed for such meeting or the effective date of such written consent, and shall be entitled to notice of any stockholders' meeting in accordance with the Bylaws of the Company. Fractional votes shall not, however, be permitted and any fractional voting rights resulting from the above formula (after aggregating all shares into which shares of Preferred Stock held by each holder could be converted) shall be rounded to the nearest whole number (with one-half being rounded upward).

4.Conversion. The holders of the Preferred Stock shall have conversion rights as follows:

a.Right to Convert. Each share of Preferred Stock shall be convertible, at the option of the holder thereof, at any time after the date of issuance of such share, at the office of the Company or any transfer agent for such stock, into fully paid and nonassessable shares of Common Stock. The number of shares of Common Stock to which a holder of Preferred Stock shall be entitled upon conversion shall be determined by dividing the Series A Issue Price, Series B Issue Price, Series B-1 Issue Price, Series C Issue Price, Series C-1 Issue Price or Series D Issue Price, as applicable, by the conversion price for such share in effect at the time that such certificate is surrendered for conversion, and then multiplying by the number of shares of Preferred Stock being converted. The conversion price per share (the “Conversion Price”) as of the Original Issue Date (as defined below) shall be (i) for shares of Series A Preferred Stock $2.174 per share, (ii) for shares of Series B Preferred Stock shall be $22.24 per share, (iii) for shares of Series B-1 Preferred Stock shall be $22.52 per share, (iv) for

shares of Series C Preferred Stock shall be $12.46 per share, (v) for shares of Series C-1 Preferred Stock, $17.56 per share, and (vi) for shares of Series D Preferred Stock, $18.75 per share, in each case each subject to adjustment as hereinafter provided.

b.Automatic Conversion.

(i)Each share of Series A Preferred Stock shall automatically be converted into shares of Common Stock at the then applicable Conversion Price upon the earlier to occur of (i) the date specified by written consent or agreement of stockholders holding at least a majority of the then outstanding shares of Series A Preferred Stock, voting together as a single class, or (ii) immediately upon the closing of the sale of the Company's Common Stock in a firm commitment, underwritten public offering registered under the Securities Act of 1933, as amended (the “Securities Act”), which results in aggregate proceeds to the Company (before deduction for underwriters' discounts and expenses relating to the issuance, including without limitation fees of the Company's counsel) equal to at least $30,000,000 (a “Qualified IPO”). Upon such automatic conversion, any declared and unpaid dividends shall be paid in accordance with the provisions of Section 1.

(ii)Each share of Series B Preferred Stock shall automatically be converted into shares of Common Stock at the then applicable Conversion Price upon the earlier to occur of (i) the date specified by written consent or agreement of (A) stockholders holding at least a majority of the then outstanding shares of Preferred Stock, voting together as a single class, and (B) stockholders holding at least a majority of the then outstanding shares of Series B Preferred Stock, voting together as a single class, or (ii) immediately upon the closing of a Qualified IPO. Upon such automatic conversion, any declared and unpaid dividends shall be paid in accordance with the provisions of Section 1.

(iii)Each share of Series B-1 Preferred Stock shall automatically be converted into shares of Common Stock at the then applicable Conversion Price upon the earlier to occur of (i) the date specified by written consent or agreement of (A) stockholders holding at least a majority of the then outstanding shares of Preferred Stock, voting together as a single class, and (B) stockholders holding at least a majority of the then outstanding shares of Series B-1 Preferred Stock, voting together as a single class, or (ii) immediately upon the closing of a Qualified IPO. Upon such automatic conversion, any declared and unpaid dividends shall be paid in accordance with the provisions of Section 1.

(iv)Each share of Series C Preferred Stock shall automatically be converted into shares of Common Stock at the then applicable Conversion Price upon the earlier to occur of (i) the date specified by written consent or agreement of (A) stockholders holding at least a majority of the then outstanding shares of Preferred Stock, voting together as a single class, and (B) stockholders holding at least a majority of the then outstanding shares of Series C Preferred Stock, voting together as a single class, or (ii) immediately upon the closing of a Qualified IPO. Upon such automatic conversion, any declared and unpaid dividends shall be paid in accordance with the provisions of Section 1.

(v)Each share of Series C-1 Preferred Stock shall automatically be converted into shares of Common Stock at the then applicable Conversion Price

upon the earlier to occur of (i) the date specified by written consent or agreement of (A) stockholders holding at least a majority of the then outstanding shares of Preferred Stock, voting together as a single class, and (B) stockholders holding at least a majority of the then outstanding shares of Series C-1 Preferred Stock, voting together as a single class, or (ii) immediately upon the closing of a Qualified IPO. Upon such automatic conversion, any declared and unpaid dividends shall be paid in accordance with the provisions of Section 1.

(vi)Each share of Series D Preferred Stock shall automatically be converted into shares of Common Stock at the then applicable Conversion Price upon the earlier to occur of (A) the date specified by written consent or agreement of stockholders holding at least a majority of the then outstanding shares of Preferred Stock, voting together as a single class (provided that all other shares of Preferred Stock are converted into shares of Common Stock at the same time that the shares of Series D Preferred Stock are converted into shares of Common Stock), or (B) immediately upon the closing of a Qualified IPO. Upon such automatic conversion, any declared and unpaid dividends shall be paid in accordance with the provisions of Section 1. Notwithstanding the foregoing subclause (A), the consent of the holders of a majority of the Series D Preferred Stock shall also be required if the conversion of the shares of Series D Preferred Stock into shares of Common Stock is effected in connection with an Acquisition or Asset Sale in which the value of the consideration to be received (as determined in good faith by the Company's Board of Directors) in respect of the share or shares of Common Stock issuable upon conversion of a share of Series D Preferred Stock is less than the product of one hundred fifty percent (150%) multiplied by the Series D Issue Price.

c.Mechanics of Conversion.

(i)Except in the case of an automatic conversion pursuant to Section 4.b., before any holder of Preferred Stock shall be entitled to convert the same into shares of Common Stock, such holder shall surrender the certificate or certificates therefor, duly endorsed, at the office of the Company or of any transfer agent for such stock, and shall give written notice to the Company at such office that such holder elects to convert the same and shall state therein the name or names in which such holder wishes the certificate or certificates for shares of Common Stock to be issued. The Company shall, as soon as practicable thereafter, issue and deliver at such office to such holder of Preferred Stock a certificate or certificates for the number of shares of Common Stock to which such holder shall be entitled as aforesaid and shall promptly pay (i) in cash or, to the extent sufficient funds are not then legally available therefor, in Common Stock (at the Common Stock's fair market value determined by the Board as of the date of such conversion), any declared and unpaid dividends on the shares of Preferred Stock being converted and (ii) in cash (at the Common Stock's fair market value determined by the Board as of the date of conversion) the value of any fractional share of Common Stock otherwise issuable to any holder of Preferred Stock. Such conversion shall be deemed to have been made immediately prior to the close of business on the date of surrender of the shares of Preferred Stock to be converted, and the person or persons entitled to receive the shares of Common Stock issuable upon such conversion shall be treated for all purposes as the record holder or holders of such shares of Common Stock on such date.

(ii)If the conversion is in connection with an underwritten offering of securities pursuant to the Securities Act, the conversion may, at the option of any

holder tendering shares of Preferred Stock for conversion, be conditioned upon the closing with the underwriters of the sale of securities pursuant to such offering, in which event the person(s) entitled to receive the Common Stock upon conversion of the Preferred Stock shall not be deemed to have converted such Preferred Stock until immediately prior to the closing of such sale of securities.

d.Adjustments to Conversion Price for Certain Diluting Issues.

(i)Special Definitions. For purposes of this Section 4, the following definitions apply:

(1)“Options” shall mean rights, options or warrants to subscribe for, purchase or otherwise acquire either Common Stock or Convertible Securities (as defined below).

(2)“Original Issue Date” shall mean the date on which the first share of Series D Preferred Stock is issued.

(3)“Convertible Securities” shall mean any evidences of indebtedness, shares (other than Common Stock, Series A Preferred Stock, Series B Preferred Stock, Series B-1 Preferred Stock, Series C Preferred Stock, Series C-1 Preferred Stock or Series D Preferred Stock) or other securities convertible into or exchangeable for Common Stock, including securities described in Section 4.d.(i)(4).

(4)“Additional Shares of Common Stock” shall mean all shares of Common Stock issued (or, pursuant to Section 4.d(iii) deemed to be issued) by the Company after the Original Issue Date, other than shares of Common Stock issued or issuable after the Original Issue Date:

(A)upon conversion of shares of Series A Preferred Stock, Series B Preferred Stock, Series B-1 Preferred Stock, Series C Preferred Stock, Series C-1 Preferred Stock or Series D Preferred Stock;

(B)pursuant to or issuable upon exercise of options or warrants to purchase shares of Common stock, issued to employees, officers, directors or consultants of the Company or a subsidiary pursuant to stock option or stock purchase plans or other arrangements in each case on terms approved by at least 76% of the members of the Board of Directors of the Company;

(C)pursuant to transactions involving research or development funding, technology licensing, joint ventures, strategic alliances, partnering arrangements, bank financings or lease arrangements pursuant to agreements in each case approved by at least 76% of the members of the Board of Directors of the Company;

(D)pursuant to the acquisition of another corporation or entity by the corporation by way of merger, purchase of assets, stock for stock exchange or other reorganization or recapitalization in each case approved by at least 76% of the members of the Board of Directors of the Company;

(E)in a Qualified IPO;

(F)pursuant to a transaction described in Section 4.e or 4.f;

(G)for which adjustment of the applicable Conversion Price is made pursuant to this Section 4;

(H)pursuant to or issuable upon exercise of warrants, options or other rights to acquire securities of the Company outstanding as of the Original Issue Date and any securities issuable upon conversion thereof;

(I)pursuant to or issuable upon conversion, exchange or cancellation of shares of Amyris Brasil S.A., a majority-owned subsidiary of the Company; or

(J)upon the affirmative vote of at least a majority of the then outstanding shares of Preferred Stock, voting together as a single class on an as-if converted basis.

(ii)No Adjustment of Conversion Price. Any provision herein to the contrary notwithstanding, no adjustment in the applicable Conversion Price shall be made in respect of the issuance of Additional Shares of Common Stock unless the consideration per share (determined pursuant to Section 4.d(v) hereof) for an Additional Share of Common Stock issued or deemed to be issued by the Company is less than the applicable Conversion Price in effect immediately prior to such issue.

(iii)Deemed Issue of Additional Shares of Common Stock. In the event the Company at any time or from time to time after the Original Issue Date shall issue any Options or Convertible Securities or shall fix a record date for the determination of holders of any class of securities then entitled to receive any such Options or Convertible Securities, then the maximum number of shares (as set forth in the instrument relating thereto without regard to any provisions contained therein designed to protect against dilution) of Common Stock issuable upon the exercise of such Options or, in the case of Convertible Securities and Options therefor, the conversion or exchange of such Convertible Securities, shall be deemed to be Additional Shares of Common Stock issued as of the time of such issue or, in case such a record date shall have been fixed, as of the close of business on such record date, provided further that in any such case in which Additional Shares of Common Stock are deemed to be issued:

(1)no further adjustments in the applicable Conversion Price shall be made upon the subsequent issue of Convertible Securities or shares of Common Stock upon the exercise of such Options or conversion or exchange of such Convertible Securities;

(2)if such Options or Convertible Securities by their terms provide, with the passage of time or otherwise, for any increase in the consideration payable to the Company, or decrease in the number of shares of Common Stock issuable, upon the exercise, conversion or exchange thereof, the applicable Conversion Price computed upon the

original issue thereof (or upon the occurrence of a record date with respect thereto), and any subsequent adjustments based thereon, shall, upon any such increase or decrease becoming effective, be recomputed to reflect such increase or decrease insofar as it affects such Options or the rights of conversion or exchange under such Convertible Securities (provided, however, that no such adjustment of the Conversion Price shall affect Common Stock previously issued upon conversion of the Preferred Stock);

(3)upon the expiration of any such options or rights, the termination of any such rights to convert or exchange or the expiration of any options or rights related to such convertible or exchangeable securities, the applicable Conversion Price to the extent in any way affected by or computed using such options, rights or securities or options or rights related to such securities, shall be recomputed to reflect the issuance of only the number of shares of Common Stock (and convertible or exchangeable securities which remain in effect) actually issued upon the exercise of such options or rights, upon the conversion or exchange of such securities or upon the exercise of the options or rights related to such securities;

(4)no readjustment pursuant to clause (2) or (3) above shall have the effect of increasing the applicable Conversion Price to an amount which exceeds the lower of (a) the Conversion Price on the original adjustment date or (b) the Conversion Price that would have resulted from any issuance of Additional Shares of Common Stock between the original adjustment date and such readjustment date.

(iv)Adjustment of Conversion Price Upon Issuance of Additional Shares of Common Stock. In the event the Company, at any time after the Original Issue Date shall issue Additional Shares of Common Stock (including Additional Shares of Common Stock deemed to be issued pursuant to Section 4.d(iii)) without consideration or for a consideration per share less than the applicable Conversion Price in effect on the date of and immediately prior to such issue, then, and in such event, the applicable Conversion Price shall be reduced, concurrently with such issue, to a price (calculated to the nearest cent) determined by multiplying the Conversion Price by a fraction, the numerator of which shall be the number of shares of Common Stock deemed outstanding (as defined below) immediately prior to such issuance plus the number of shares of Common Stock which the aggregate consideration received by the Company for the total number of Additional Shares of Common Stock so issued would purchase at the Conversion Price in effect immediately prior to such issuance, and the denominator of which shall be the number of shares of Common Stock deemed outstanding (as defined below) immediately prior to such issuance plus the number of such Additional Shares of Common Stock so issued. For the purpose of the above calculation, the number of shares of Common Stock outstanding immediately prior to such issue shall be calculated on a fully diluted basis, as if all shares of Preferred Stock and all outstanding Convertible Securities had been fully converted into shares of Common Stock and any outstanding warrants, outstanding options or other rights outstanding for the purchase of shares of stock or convertible securities had been fully exercised (and the resulting securities fully converted into shares of Common Stock, if so convertible) as of such date. For the purposes of adjusting the applicable Conversion Price of a series of Preferred Stock, the grant, issue or sale of Additional Shares of Common consisting of the same class of security and warrants to purchase such security issued or issuable at the same price at two or more closings held within a six (6) month period shall be aggregated and shall be

treated as one sale of Additional Shares of Common occurring on the earliest date on which such securities were granted, issued or sold.

(v)Determination of Consideration. For purposes of this Section 4.d, the consideration received by the Company for the issue of any Additional Shares of Common Stock shall be computed as follows:

(1)Cash and Property. Such consideration shall:

(A)insofar as it consists of cash, be computed at the aggregate amount of cash received by the Company, excluding amounts paid or payable for accrued interest or declared but unpaid dividends;

(B)insofar as it consists of property other than cash, be computed at the fair value thereof at the time of such issue, as determined in good faith by the Board of Directors; and

(C)in the event Additional Shares of Common Stock are issued together with other shares or securities or other assets of the Company for consideration which covers both, be the proportion of such consideration so received, computed as provided in clauses (A) and (B) above, as determined in good faith by the Board of Directors.

(2)Options and Convertible Securities. The consideration per share received by the Company for Additional Shares of Common Stock deemed to have been issued pursuant to Section 4.d(iii), relating to Options and Convertible Securities shall be determined by dividing

(A)the total amount, if any, received or receivable by the Company as consideration for the issue of such Options or Convertible Securities, plus the minimum aggregate amount of additional consideration (as set forth in the instruments relating thereto, without regard to any provision contained therein designed to protect against dilution) payable to the Company upon the exercise of such Options or the conversion or exchange of such Convertible Securities, or in the case of Options for Convertible Securities, the exercise of such Options for Convertible Securities and the conversion or exchange of such Convertible Securities by

(B)the maximum number of shares of Common Stock (as set forth in the instruments relating thereto, without regard to any provision contained therein designed to protect against the dilution) issuable upon the exercise of such Options or conversion or exchange of such Convertible Securities.

e.Adjustment of Conversion Price of Series D Preferred Stock Upon Qualified IPO. In the event of a Qualified IPO that closes (i) on or before September 30, 2010, in which the initial public offering price for the Common Stock in such Qualified IPO (the “IPO Price”) is less than the product of (a) 1.16 multiplied by (b) the Series D Preferred Stock Conversion Price then in effect, the Series D Preferred Stock Conversion Price shall be reduced to the quotient obtained by dividing (w) the IPO Price by (x) 1.16; or (ii) after September 30, 2010, in which the IPO Price is less than the product of (c) 1.30 multiplied by (d) the Series D Preferred Stock Conversion Price then in effect, the Series D Preferred Stock Conversion Price shall be reduced to the quotient obtained by dividing (y) the IPO Price by (z) 1.30.

f.Adjustments for Stock Dividends and for Combinations or Subdivisions of Common Stock. In the event that this Company at any time or from time to time after the Original Issue Date shall declare or pay, without consideration, any dividend on the Common Stock payable in Common Stock or in any right to acquire Common Stock for no consideration, or shall effect a subdivision of the outstanding shares of Common Stock into a greater number of shares of Common Stock (by stock split, reclassification or otherwise than by payment of a dividend in Common Stock or in any right to acquire Common Stock), or in the event the outstanding shares of Common Stock shall be combined or consolidated, by reclassification or otherwise, into a lesser number of shares of Common Stock, then the conversion price for any series of Preferred Stock in effect immediately prior to such event shall, concurrently with the effectiveness of such event, be proportionately decreased or increased, as appropriate. In the event that the Company shall declare or pay, without consideration, any dividend on the Common Stock payable in any right to acquire Common Stock for no consideration then the Company shall be deemed to have made a dividend payable in Common Stock in an amount of shares equal to the maximum number of shares issuable upon exercise of such rights to acquire Common Stock.

g.Adjustments for Reclassification and Reorganization. If the Common Stock issuable upon conversion of any series of Preferred Stock shall be changed into the same or a different number of shares of any other class or classes of stock, whether by capital reorganization, reclassification or otherwise (other than a subdivision or combination of shares provided for in Section 4.e above or a merger or other reorganization referred to in Section 2.d above), the Conversion Price for any series of Preferred Stock then in effect shall, concurrently with the effectiveness of such reorganization or reclassification, be proportionately adjusted so that the Preferred Stock shall be convertible into, in lieu of the number of shares of Common Stock which the holders would otherwise have been entitled to receive, a number of shares of such other class or classes of stock equivalent to the number of shares of Common Stock that would have been subject to receipt by the holders upon conversion of the Preferred Stock immediately before that change, respectively.

h.Certificates as to Adjustments. Upon the occurrence of each adjustment or readjustment of any conversion price pursuant to this Section 4, the Company at its expense shall promptly compute such adjustment or readjustment in accordance with the terms hereof and prepare and furnish to each holder of Preferred Stock a certificate executed by the Company's President, Chief Financial Officer or a Vice President setting forth such adjustment or readjustment and showing in detail the facts upon which such adjustment or readjustment is based. The Company shall, upon the written request at any time of any holder of Preferred Stock, furnish or cause to be furnished to such holder a like certificate setting forth (i) such adjustments and readjustments, (ii) the conversion price for such series of Preferred Stock at the time in effect, and (iii) the number of shares of Common Stock and the amount, if any, of other property which at the time would be received upon the conversion of the Preferred Stock.

i.Notices of Record Date. In the event that the Company shall propose at any time (i) to declare any dividend or distribution upon its Common Stock, whether

in cash, property, stock or other securities, whether or not a regular cash dividend and whether or not out of earnings or earned surplus, (ii) a Liquidation or any voluntary or involuntary dissolution or winding up of the Company, or (iii) to offer for subscription pro rata to the holders of any class or series of its stock any additional shares of stock of any class or series or other rights, then, in connection with each such event, unless otherwise waived by a majority of Preferred Stock, the Company shall send to the holders of Preferred Stock at least twenty (20) days' prior written notice of the date on which a record shall be taken for such dividend, distribution, Liquidation, dissolution, winding up or subscription rights.

j.Reservation of Stock Issuable Upon Conversion. The Company shall at all times reserve and keep available out of its authorized but unissued shares of Common Stock, solely for the purpose of effecting the conversion of the shares of the Preferred Stock, such number of its shares of Common Stock as shall from time to time be sufficient to effect the conversion of all outstanding shares of the Preferred Stock; and if at any time the number of authorized but unissued shares of Common Stock shall not be sufficient to effect the conversion of all then outstanding shares of the Preferred Stock, the Company will take such corporate action as may, in the opinion of its counsel, be necessary to increase its authorized but unissued shares of Common Stock to such number of shares as shall be sufficient for such purpose, including, without limitation, engaging in best efforts to obtain the requisite stockholder approval of any necessary amendment to this Restated Certificate.

k.Fractional Shares. No fractional share shall be issued upon the conversion of any share or shares of Preferred Stock. All shares of Common Stock (including fractions thereof) issuable upon conversion of more than one share of Preferred Stock by a holder thereof shall be aggregated for purposes of determining whether the conversion would result in the issuance of any fractional share. If, after the aforementioned aggregation, the conversion would result in the issuance of a fraction of a share of Common Stock, the Company shall, in lieu of issuing any fractional share, pay the holder otherwise entitled to such fraction a sum in cash equal to the fair market value of such fraction on the date of conversion (as determined in good faith by the Board of Directors).

l.Notices. Any notice required by the provisions of this Section 4 shall be in writing and shall be deemed effectively given: (i) upon personal delivery to the party to be notified, (ii) when sent by confirmed electronic mail or facsimile if sent during normal business hours of the recipient; if not, then on the next business day, (iii) five (5) days after deposit in the United States mail, by registered or certified mail, postage prepaid and properly addressed to the party to be notified, or (iv) one (1) day after deposit with a nationally recognized overnight courier, specifying next day delivery, with written verification of receipt. All notices shall be addressed to each holder of record at the address of such holder appearing on the books of the Company.

5.Board Representation. In addition to the rights of the holders of Preferred Stock to vote on an as converted basis with holders of Common Stock pursuant to Section 3 above, with respect to election of directors:

a.For so long as any shares of Series A Preferred Stock remain outstanding, the holders of Series A Preferred Stock, voting as a separate class, shall be entitled

to elect three (3) members of the Board of Directors (each a “Series A Director”) at each meeting or pursuant to each consent of the Company's stockholders for the election of directors, and to remove from office such directors and to fill any vacancy caused by the resignation, death or removal of such directors. Notwithstanding the foregoing, the right of the holders of Series A Preferred Stock to elect the Series A Directors shall terminate upon the earliest to occur of the following: (i) an Acquisition; or (ii) an Asset Sale.

b.The holders of Series D Preferred Stock, voting as a separate class, shall be entitled to elect one (1) member of the Board of Directors (the “Series D Director”) at each meeting or pursuant to each consent of the Company's stockholders for the election of directors, and to remove from office such directors and to fill any vacancy caused by the resignation, death or removal of such directors. Notwithstanding the foregoing, the right of the holders of Series D Preferred Stock to elect the Series D Director shall terminate upon the earliest to occur of the following: (i) such time as the Investor (as defined in that certain Series D Preferred Stock Purchase Agreement dated on or about the date of filing of this Restated Certificate by and between the Company and the Investor (the “Purchase Agreement”)), together with its Affiliates (as defined below), holds less than fifty percent (50%) of the shares of Series D Preferred Stock purchased by it pursuant to the Purchase Agreement; (ii) an Acquisition; or (iii) an Asset Sale. “Affiliate” means with respect to a Person (as defined below), any Person that, directly or indirectly, through one or more intermediaries, controls, is controlled by or is under common control with such first Person. For purposes of this definition, “control” and, with correlative meanings, the terms “controlled by” and “under common control with” mean (x) the possession, directly or indirectly, of the power to direct the management or policies of a Person, whether through the ownership of voting securities, by contract relating to voting rights or corporate governance, or otherwise, or (y) the ownership, directly or indirectly, of more than 50% of the voting securities or other ownership interest of a Person. “Person” means an individual, sole proprietorship, partnership, limited partnership, limited liability partnership, corporation, limited liability company, business trust, joint stock company, trust, unincorporated association, joint venture or other similar entity or organization, including a government or political subdivision, department or agency of a government.

c.The holders of Common Stock, voting as a separate class, shall be entitled to elect two (2) members of the Board of Directors (each a “Common Director”) at each meeting or pursuant to each consent of the Company's stockholders for the election of directors, and to remove from office such directors and to fill any vacancy caused by the resignation, death or removal of such directors.

d.The holders of Preferred Stock and the holders of Common Stock, voting together as a single class on an as-if converted basis, shall be entitled to elect any additional members of the Board of Directors (each an “Independent Director”), and to remove from office such directors and to fill any vacancy caused by the resignation, death or removal of such directors.

6.Redemption. The Preferred Stock shall not be redeemable.

7.Restrictions and Limitations. So long as at least 20% of the shares of the Preferred Stock sold by the Company (as adjusted for stock splits, dividends, combinations,

recapitalizations and the like) remain outstanding, consent of the holders of at least the majority of the then outstanding shares of Preferred Stock shall be required for any action that (whether by amendment, merger, reorganization or otherwise):

a.alters or changes the powers, preferences or rights of the Common Stock or the Preferred Stock,

b.increases or decreases the authorized number of shares of Common or Preferred Stock,

c.creates (whether by amendment, merger, reorganization or otherwise) any new class or series of shares having powers, preferences or rights senior to or on a parity with the Preferred Stock,

d.results in the redemption of any shares of Preferred Stock or Common Stock (other than pursuant to equity incentive agreements with employees and other service providers giving the Company the right to repurchase shares upon the termination of employment or such other service relationship, at their original cost),

e.results in a Liquidation or other corporate reorganization, including any reorganization or other transaction involving any parent or subsidiary of the Company,

f.amends or waives any provision of the Company's certificate of incorporation or bylaws,

g.increases or decreases the authorized size of the Company's Board of Directors, or

h.results in the payment or declaration of any dividend on any shares of Common or Preferred Stock.

8.Further Restrictions and Limitations. So long as at least 50% of the shares of the Series D Preferred Stock sold by the Company (as adjusted for stock splits, dividends, combinations, recapitalizations and the like with respect to such shares) remain outstanding, consent of the holders of at least the majority of the then outstanding shares of the Series D Preferred Stock shall be required for any action that (whether by amendment, merger, reorganization or otherwise):

a.approves or permits the approval of a “drag-along” provision, or any provision that functions as a “drag-along” that would require the holders of Series D Preferred Stock to vote in favor of or otherwise support an Acquisition or Asset Sale,

b.amends, alters or changes the powers, preferences or rights of the Series D Preferred Stock (provided that the creation (whether by amendment, merger, reorganization or otherwise) of any new class or series of shares having powers, preferences or rights on parity with the Series D Preferred Stock shall not constitute an amendment, alteration or change of the powers, preferences or rights of the Series D Preferred Stock),

c.increases the number of authorized shares of Series D Preferred Stock,

d.creates (whether by amendment, merger, reorganization or otherwise) any new class or series of shares having powers, preferences or rights senior to the Series D Preferred Stock, or

e.results in the redemption of any shares of Preferred Stock or Common Stock (other than (i) pursuant to equity incentive agreements with employees and other service providers giving the Company the right to repurchase shares upon the termination of employment or such other service relationship, at their original cost, or (ii) repurchases or redemptions of shares from any founder or service provider upon terms approved by the Company's Board of Directors),

f.increases the authorized size of the Board of Directors to more than eleven (11) members,

9.No Reissuance of Preferred Stock. No share or shares of Preferred Stock acquired by the Company by reason of redemption, purchase, conversion, or otherwise shall be reissued; and, in addition, the certificate of incorporation shall be appropriately amended to effect the corresponding reduction in the Company's authorized stock.

ARTICLE V: PREEMPTIVE RIGHTS.

No stockholder of the Corporation shall have a right to purchase shares of capital stock of the Corporation sold or issued by the Corporation except to the extent that such a right may from time to time be set forth in a written agreement between the Corporation and any stockholder.

ARTICLE VI: STOCK REPURCHASES.

In connection with repurchases by the Corporation of its Common Stock from Service Providers pursuant to agreements under which the Corporation has the option to repurchase such shares at cost upon the occurrence of certain events, such as the termination of employment, Sections 502 and 503 of the Corporations Code of the State of California shall not apply in all or in part with respect to such repurchases.

ARTICLE VII: BYLAW PROVISIONS.

A.AMENDMENT OF BYLAWS. Subject to any additional vote required by the Restated Certificate or Bylaws, in furtherance and not in limitation of the powers conferred by statute, the Board is expressly authorized to make, repeal, alter, amend and rescind any or all of the Bylaws of the Corporation.

B.NUMBER OF DIRECTORS. Subject to any additional vote required by the Restated Certificate, the number of directors of the Corporation shall be determined in the manner set forth in the Bylaws of the Corporation.

C.BALLOT. Elections of directors need not be by written ballot unless the Bylaws of the Corporation shall so provide.

D.MEETINGS AND BOOKS. Meetings of stockholders may be held within or without the State of Delaware, as the Bylaws of the Corporation may provide. The books of the Corporation may be kept outside the State of Delaware at such place or places as may be designated from time to time by the Board or in the Bylaws of the Corporation.

ARTICLE VIII: DIRECTOR LIABILITY.

A.LIMITATION. To the fullest extent permitted by law, a director of the Corporation shall not be personally liable to the Corporation or its stockholders for monetary damages for breach of fiduciary duty as a director. If the General Corporation Law or any other law of the State of Delaware is amended after approval by the stockholders of this Article VIII to authorize corporate action further eliminating or limiting the personal liability of directors, then the liability of a director of the Corporation shall be eliminated or limited to the fullest extent permitted by the General Corporation Law as so amended. Any repeal or modification of the foregoing provisions of this Article VIII by the stockholders of the Corporation shall not adversely affect any right or protection of a director of the Corporation existing at the time of, or increase the liability of any director of the Corporation with respect to any acts or omissions of such director occurring prior to, such repeal or modification.

B.INDEMNIFICATION. To the fullest extent permitted by applicable law, the Corporation is authorized to provide indemnification of (and advancement of expenses to) directors, officers and agents of the Corporation (and any other persons to which General Corporation Law permits the Corporation to provide indemnification) through Bylaw provisions, agreements with such agents or other persons, vote of stockholders or disinterested directors or otherwise, in excess of the indemnification and advancement otherwise permitted by Section 145 of the General Corporation Law.

C.MODIFICATION. Any amendment, repeal or modification of the foregoing provisions of this Article VIII shall not adversely affect any right or protection of any director, officer or other agent of the Corporation existing at the time of such amendment, repeal or modification.

ARTICLE IX: CREDITOR AND STOCKHOLDER COMPROMISES

Whenever a compromise or arrangement is proposed between the Corporation and its creditors or any class of them and/or between the Corporation and its stockholders or any class of them, any court of equitable jurisdiction within the State of Delaware may, on the application in a summary way of the Corporation or of any creditor or stockholder thereof or on the application of any receiver or receivers appointed for the Corporation under the provisions of §291 of Title 8 of the General Corporation Law or on the application of trustees in dissolution or of any receiver or receivers appointed for this Corporation under §279 of Title 8 of the General Corporation Law order a meeting of the creditors or class of creditors, and/or of the stockholders or class of stockholders of the Corporation, as the case may be, to be summoned in such manner as the said court directs. If a majority in number representing three-fourths in value of the creditors or class

of creditors, and/or of the stockholders or class of stockholders of the Corporation, as the case may be, agree to any compromise or arrangement and to any reorganization of the Corporation as a consequence of such compromise or arrangement, the said compromise or arrangement and the said reorganization shall, if sanctioned by the court to which the said application has been made, be binding on all the creditors or class of creditors, and/or on all the stockholders or class of stockholders, of the Corporation, as the case may be, and also on the Corporation.

* * * * *

EXHIBIT D

RECIPIENT CHANGE REQUEST QUESTIONNAIRE

RECIPIENT CHANGE REQUEST QUESTIONNAIRE

Recipient Name: Amyris Biotechnologies, Inc.

Address: 5885 Hollis Street, Suite 100, Emeryville, CA 94608

Principal Investigator: Neil Renninger

DOE Award #: DE-EE0002869

Type of Award: XX Competitive (FOA #DE-FOA-0000096)

(Check one) __ Congressionally Directed Project (CDP#_________)

                                 __ Unsolicited Proposal

Primary Nature of the Project: __ Education and Outreach

(Check one) __ Research and Development

                                                         XX Demonstration or Commercialization

Date of Selection for Negotiation of Award: December 4, 2009

Date of Award: December 28, 2009

Date of event precipitating the need for this change request: June 10, 2010

Page 1 of 6

Approximate percentage of project completed to date: 40% (based on projected duration)

Total amount of award (total project cost): $24,341,409.00 ($34,932,999.00)

Required Cost Share Percentage: 29.6%

List any other DOE Financial Assistance Awards or DOE Contracts currently held by Recipient:

Subcontract ZFT-0-40623-01 under prime contract number DE-AC36-08GO28308.

Proposed Transferee: Amyris, Inc.

Address: 5885 Hollis Street, Suite 100, Emeryville, CA 94608

Principal Investigator: Neil Renninger

"Recipient"    = the existing awardee or entity selected for negotiation of award

"Proposed Transferee"    = the entity agreeing to perform the award and accept the Recipient's rights and responsibilities under the DOE Award

Page 2 of 6

1. Please describe, in detail, the reason for the requested transfer of the DOE Award from Recipient to Proposed Transferee (attach additional pages if necessary):

Amyris Biotechnologies, Inc., a California corporation, WAS reincorporated in Delaware as Amyris Biotechnologies, Inc., a Delaware corporation, in connection with the company's initial public offering. There was no change in ownership of the company. The reincorporation was accomplished effective June 10, 2010, and name change of the surviving Delaware entity (from Amyris Biotechnologies, Inc. to Amyris, Inc.) was completed effective June 21, 2010.

2. Please describe any financial considerations (including, for example, threat of bankruptcy) that are contributing to the reason for the requested transfer:

Amyris reincorporated in Delaware in connection with its initial public offering, which closed in September 2010. There were no financial considerations that contributed to the subsequent change in the name of the company.

3. What is the existing legal relationship between the Recipient and the Proposed Transferee

(Check all that apply):

___    Unrelated entities (e.g. no common owner(s), assets, or employees)

___    Parent: __________ Subsidiary: ___________ % Owned: ____

(Please specify which entity is parent and which entity is Subsidiary)

___    Joint venture partner. Please describe the nature of the joint venture: ___________________

___    Proposed Transferee does not yet exist. Please note details re: formation of proposed Transferee,

e.g. formation date, founder, and reason for the formation of the Proposed Transferee:

XX    Recipient is legally changing name to Amyris, Inc., but no assets, stock, employees, or other

ownership interests are changing. Effective date of name change is: June 21, 2010

*Attach a certified copy of the document effecting the name change.

XX    Recipient and Proposed Transferee are Associate or Affiliate Companies (e.g., common owner(s),

assets or employees)

___    Proposed Transferee is a sub-recipient under the award.

___    Proposed Transferee is a vendor tinder the award.

XX    Other, please describe:

Page 3 of 6

Above answers reflect a reincorporation of the Recipient in Delaware (from California) and a subsequent

name change. Copies of the Certificate of Merger (Reincorporation) and Restated Certificate of

Incorporation (name change) are attached for reference.

4. What type of agreement has been or will be executed between the Recipient and the Proposed

Transferee that is precipitating the request for n change to the DOE Award:

___ Acquisition - of Recipient by Proposed Transferee

(Purchase of all assets and liabilities; Requiring company continues to function and acquired

company ceases to exist)

___    Asset Sale - from Recipient to Proposed Transferee

(No liabilities transferred, e.g. liquidation pursuant to bankruptcy)

XX     Merger - of Recipient and Proposed Transferee

(Exchange of stock between Recipient and another company resulting in a single company, the

Proposed Transferee, replacing both of the old companies)

___    Consolidation - of Recipient into Proposed Transferee

(All assets and liabilities of Recipient are absorbed by Proposed Transferee and Proposed

Transferee retains original identity)

___    Downstream Merger - of Recipient into Proposed Transferee

(Partially owned subsidiary takes over its parent company)

XX    No agreement will be executed because Proposed Transferee is not a legally separate entity from

Recipient and Recipient is only changing !lame to that of Proposed Transferee.

___    Assignment and Assumption of Award Agreement from Recipient to Sub-Recipient

XX     Other, please explain: Above answers reflect a reincorporation of the Recipient in Delaware (from

California) and a subsequent name change. Copies of the Certificate of Merger (Reincorporation)

and Restated Certificate of Incorporation (name change) are attached for reference

Page 4 of 6

5. Are there any Assets, stock, or ownership interests being sold or transferred to any person or entity

other than the Proposed Transferee:

___    Yes             XX No            ___ N/A

6. Will the indirect cost rates change as a result of the transfer of the award from the Recipient to the Proposed Transferee:

___    Yes             XX No

7. Please provide (he following information:

Actual Federal Share Spent, As of Oct 31, 2010	Cost Share Accrued As of Oct 31, 2010
$7,587,029	$3,482,977

DUNS # of Proposed Transferee: 185930182

Taxpayer ID (TIN) of Proposed Transferee: 55-0856151

8. Attach any diagrams depicting the existing and/or restructured relationship between the Recipient and the Proposed Transferee.

Not applicable

9. Attach a list of assets related to the Award (including any Intellectual Property, cash or cash equivalents, service agreements, sublease agreements, and transferred licenses) that have been or are being transferred between the Recipient find the Proposed Transferee.

Any and all assets of the Recipient, related to the award or otherwise, are now owned by the Transferee.

10. Attach a certified copy of the Proposed Transferee's formation documentation (e.g. Certificate of

Incorporation or Organization).

Copy of Restated Certificate of Incorporation of Amyris, Inc. attached.

11. Attach a copy of the instrument(s) effecting the transfer of assets from the Recipient to the Proposed Transferee (e.g., bill of sale, certificate of merger, contract, deed, agreement, court decree, etc.)

Copies of the Agreement and Plan of Merger (Reincorporation), Certificate of Merger

(Reincorporation) and Restated Certificate of Incorporation (name change) are attached for reference.

Page 5 of 6

I am a duly authorized representative of the Recipient and I certify that the answers above are correct to

the best of my knowledge.

/s/ Tamara Tompkins                December 17, 2010    

(Signature of Authorized Official)            Date

Recipient/Transferor

Printed Name of Official: Tamara Tompkins    

Title: SVP, General Counsel and Secretary    

I am a duly authorized Representative of the Proposed Transferee and I certify that i have reviewed and agree with the Recipients' answers contained in the questionnaire.

/s/ Tamara Tompkins                December 17, 2010    

(Signature of Authorized Official)            Date

Proposed Transferee

Printed Name of Official: Tamara Tompkins    

Title: SVP, General Counsel and Secretary    

Page 6 of 6

EXHIBIT E

LEGAL OPINION LETTER DATED NOVEMBER 8, 2011

November 8, 2011

Jon Olsen

Contracting Officer

U.S. Department of Energy

Golden Field Office

1617 Cole Boulevard

Golden, CO 80401

RE: Opinion Letter - Amyris Reincorporation & Name Change

Dear Mr. Olsen,

Pursuant to your request in relation to the Department oF Energy formally recognizing Amyris, Inc. as the successor in interest to Amyris Biotechnologies, Inc., the recipient of that certain Department of Energy Award under Cooperative agreement Number DE-EE0002869 (the "Award"), on behalf of Amyris, Inc., the undersigned, EVP, General Counsel and Secretary of Amyris, Inc., hereby warrants and represents the following facts:

1. That upon a merger of amyris Biotechnologies, Inc., a California corporation ("Amyris California") with and into amyris, Inc., a Delaware corporation ("Amyris Delaware") in connection with a reincorporation of Amyris California in the State of Delaware (the "Reincorporation") as part of an initial public offering of Amyris Delaware assumed all rights and obligations of Amyris California by operation of law;

2. Amyris Delaware has the same Employer Identification Number as Amyris California, is engaged in essentially the same business activities as Amyris California was, and is otherwise the same enterprise in all material respects (other than the jurisdiction of incorporation and changes in the charter and similar documents necessitated by the Reincorporation and IPO);

3. The merger of Amyris California and into Amyris Delaware was effected in accordance with applicable law and was effective on the date set forth in Certificate of Merger, a copy of which was previously provided to you; and as, a result of that merger, Amyris California no longer exists as a legal entity;

4. The merger of Amyris California into Amyris Delaware did not itself result in any significant change to finances, assets, key personnel or other aspects of the business conducted by Amyris California and assumed by Amyris Delaware; and Amyris Delaware was, and continues to be, in substantially the same or better position to perform the Award as was Amyris California; and

5. There have been no material changes in ownership of Amyris Delaware, such that it is still an eligible entity under the original requirements of the Funding Opportunity Announcement under which the Award was made.

Sincerely,

/s/ Tamara L. Tompkins        

Tamara L. Tompkins

EVP, General Counsel & Secretary

ASSISTANCE AGREEMENT
1. Award No. DE-EE0002869		2. Modification No. 008		3. Effective Date 12/28/2009		4. CFDA No. 81.087
5. Awarded To AMYRIS, INC. Attn: NEIL RENNINGER 5885 HOLLIS STREET SUITE 100 EMERYVILLE CA 946082059			6. Sponsoring Office Energy Effcy & Renewable Energy				7. Period of Performance 12/28/2009 through 12/31/2012
8. Type of Agreement _ Grant x Cooperative Agreement _ Other	9. Authority 109-58 Energy Policy Act (2005) 111-5 Recovery Act (2009)				10. Purchase Request or Funding Document No. 12EE003800
11. Remittance Address			12. Total Amount				13. Funds Obligated
AMYRIS, INC. Attn: NEIL RENNINGER 5885 HOLLIS STREET SUITE 100 EMERYVILLE CA 946082059			Govt. Share: $ 24,341,409.00 Cost Share: $ 10,591,590.00 Total: $ 34,932,999.00				This action: $0.00 Total: $24,341,409.00
14. Principal Investigator Todd Pray Phone: 510-740-7441	15. Program Manager Bryna E. Berendzen Phone: 720-356-1442				16. Administrator Golden Field Office U.S. Department of Energy Golden Field Office 1617 Cole Blvd. Golden CO 80401-3393
17. Submit Payment Requests To OR for Golden U.S. Department of Energy Oak Ridge Financial Service Center P.O. Box 4517 Oak Ridge TN 37831			18. Paying Office OR for Golden U.S. Department of Energy Oak Ridge Financial Service Center P.O. Box 4517 Oak Ridge TN 37831				19. Submit Reports To
20. Accounting and Appropriation Data See Schedule
21. Research Title and/or Description of Project RECOVERY ACT: SCALE-UP & MOBILIZATION OF RENEWABLE DIESEL & CHEMICAL PRODUCTION FROM COMMON INTERMEDIATE USING US-BASED FERMENTABLE SUGAR FEEDSTOCKS
For the Recipient				For the United States of America
22. Signature of Person Authorized to Sign				25. Signature of Grants/Agreements Officer Signature on File
23. Name and Title	24. Date Signed			26. Name of Officer Jon F. Olsen				27. Date Signed 07/10/2012

CONTINUATION SHEET		REFERENCE NO. OF DOCUMENT BEING CONTINUED DE-EE0002869/008			PAGE 2 OF 3
NAME OF OFFEROR OR CONTRACTOR AMYRIS, INC.
ITEM  NO. (A)	SUPPLIES/SERVICES (B)	QUANTITY (C)	UNIT (D)	UNIT PRICE (E)	AMOUNT (F)
	DUNS Number: 185930182 The purpose of this modification is to revise the budgets for Phase 1 and Phase 2. Accordingly, the following changes are made: 1) Extend the Period of Performance end date, as noted in Block 7; 2) Delete and replace Attachment #2, Statement of Project Objectives; 3) Delete and replace Attachment #4, Budget Information;All others and conditions remain unchanged. 4) In the Special Terms and Conditions, change the following:      a) Delete and replace Provision 2, "Award Agreement Terms and Conditions";      b) Delete and replace Provision 4, "Award Project Period and Budget Periods";      c) Delete and replace Provision 5, "Payment Procedures";      d) Delete and replace Provision 6, "Cost Sharing";      e) Delete and replace Provision 15, "Intellectual Property Provisions and Contact Information";      f) Add Provision 32, "Subcontractor Approvals", and 5) Update the Recipient Principal Investigator, as noted below and in Block 14 of the Assistance Agreement. All other terms and conditions remain unchanged. In Block 7 of the Assistance Agreement, the Period of Performance reflects the beginning of the Project Period through the end of the current Budget Period. The total amounts reflected in Blocks 12 and 13 of the Assistance Agreement do not include the Federally Funded Research and Development Center (FFRDC) funding amount of $658,591, which is funded directly during Phase 2. DOE Award Administrator: Brenda Dias E-mail: brenda.dias@go.doe.gov Phone: 720-356-1519 Continued...
JULY 2004

CONTINUATION SHEET		REFERENCE NO. OF DOCUMENT BEING CONTINUED DE-EE0002869/008			PAGE 3 OF 3
NAME OF OFFEROR OR CONTRACTOR AMYRIS, INC.
ITEM  NO. (A)	SUPPLIES/SERVICES (B)	QUANTITY (C)	UNIT (D)	UNIT PRICE (E)	AMOUNT (F)
	DOE Project Officer: Bryna Berendzen E-mail: bryna.berendzen@go.doe.gov Phone: 720-356-1442 Recipient Business Officer: Todd Pray E-mail: pray@amyris.com Phone: 510-740-7441 Recipient Principal Investigator: Todd Pray E-mail: pray@amyris.com Phone: 510-740-7441 “Electronic signature or signatures as used in this document means a method of signing an electronic message that-- (A) Identifies and authenticates a particular person as the source of the electronic message; (B) Indicates such person's approval of the information contained in the electronic message; and, (C) Submission via FedConnect constitutes electronically signed documents.” ASAP: NO: STD IMMEDIATE Extent Competed: COMPETED Davis-Bacon Act: YES
JULY 2004

DE-EE0002869/008

Attachment #2

STATEMENT OF PROJECT OBJECTIVES

Amyris Biotechnologies, Inc.

Recovery Act: Scale-up and Mobilization of Renewable Diesel and Chemical Production from Common

Intermediate using US-based Fermentable Sugar Feedstocks

A. PROJECT OBJECTIVES

The Amyris pilot-scale Integrated Biorefinery (IBR) will leverage and upgrade Amyris's existing Emeryville, California pilot plant and support labs to develop US-based production capabilities for No Compromise® renewable diesel fuel and petrochemical substitutes such as lubricants and polymers. These products will be derived semi-synthetically from high-impact biomass feedstocks via microbial fermentation to the same 15- carbon isoprenoid intermediate and subsequent chemical finishing. In particular, Amyris will adapt its current sugarcane juice-based processes to instead utilize sweet sorghum juice and lignocellulosic sugars as a domestic feedstock alternative. To this end, the Amyris IBR team will prepare standard operating procedures (SOPs) for diesel and chemical manufacturing from sweet sorghum, and potentially other high-impact feedstocks, at pilot scale. This will enable robust ongoing techno-economic analysis (TEA), regulatory approvals, and a conceptual design for demonstration- and commercial-scale manufacturing facilities at project closure.

B. PROJECT SCOPE

The primary product of the Amyris IBR is Amyris Renewable Diesel. Secondary products will include lubricants, polymers and other petro-chemical substitutes -- in particular, plasticizers present a significant opportunity as a polymer component used at very high percentages in bulk plastics. Amyris and its project partners will execute on a rapid project to integrate and leverage their collective expertise to enable the conversion of high-impact biomass feedstocks to these advanced, infrastructure-compatible fuel and chemical products. Amyris will perform large scale contract manufacturing for process and product testing to support regulatory and end-user acceptance for domestic production and utilization. Amyris will double the fermentation capacity at its pilot plant and add significant functionality to enable more flexible sugar-stream handling and product finishing unit operations.

For Amyris's IBR project the key feedstock focus will be the utilization of sweet sorghum in collaboration with project partners. The team will plant and harvest sweet sorghum within existing agricultural footprints, concentrate juice to syrup and ship syrup to Amyris and bagasse to Amyris's pretreatment partner. Sweet sorghum bagasse pretreatment conditions will be developed first at lab scale and then at pilot scale, based on feedback from Amyris regarding fermentation performance using different bagasse-derived sugar streams. Other lignocellulosic sugar streams are options as well, either as risk mitigation for sweet sorghum or as feedstock alternatives once sweet sorghum has been validated. Continuing to use its defined media and cane juice-based fermentation processing as reference points, Amyris will optimize sweet sorghum juice- and lignocellulosic sugar-based C15 production in its pilot plant and support labs using its suite of C6 sugar-utilizing Saccharomyces cerevisiae yeast strains. For downstream integration with product finishing and to utilize unfermented C5 sugars from bagasse, fermentation effluent vinasse will be treated by anaerobic digestion for biogas production. Biogas cleanup procedures will be developed and modeled for production of highly pure methane for conversion to hydrogen - a key component for Amyris product finishing - via steam-methane reformation.

Development of alternative products, in addition to diesel, is a core focus of the Amyris IBR project, with both scale-up efforts relying on a robust TEA. Amyris will leverage a variety of vendors with expertise in large-scale production and fuel and chemical product testing to support product acceptance objectives. Supplementing existing product approvals from 20% Amyris Diesel to higher blend percentages and

additional products is a focus area. Finally, readying Amyris from a regulatory standpoint for domestic manufacturing will be a component of this IBR project.

C. TASKS TO BE PERFORMED

Task A.0 Amyris Pilot Plant Upgrades and Operations

Unit operation upgrades and capacity augmentation for both fermentation and chemical processing at Amyris's existing Emeryville pilot plant form a core component of this IBR project. During the two budget periods of the project Amyris will leverage its experience in pilot plant design, construction and operation to rapidly execute with minimal incremental permitting required. In particular, Amyris anticipates little or no downtime of ongoing pilot operations during upgrade design and installation.

Subtask A.1 Amyris pilot plant upgrade design and approvals (Phase 1)

Amyris has scoped initial facility design and will rapidly move to complete this effort. Equipment has already been selected and a general contractor has been engaged. Working with the Department of Energy (DOE) Amyris will adapt a risk management plan from the original construction and initial start-up of the pilot plant in 2008 and ensure that necessary permitting is completed. During the design phase Amyris' pilot plant will continue to operate with current capacity using defined media and real-world feedstocks, such as cane syrup, in order to prototype and develop standard operating procedures (SOPs) and performance metrics for adaptation to sorghum utilization.

Subtask A.2 Amyris pilot plant upgrade installation (Phase 2)

This subtask will include construction and installation activities. Fermentors have the longest lead time and will most likely require nine months for delivery. Other unit operations for downstream processing and upstream feedstock handling will be installed earlier and as delivered pending construction completion in relevant process areas. Amyris's pilot plant will begin handling sweet sorghum-derived feedstreams from a contractor to develop early benchmark data and validate performance targets. During the course of upgrading the pilot plant facility, Amyris will continue ongoing operations and prototyping with defined media and cane-derived feedstreams to simulate and facilitate conversion of sorghum sugars to finished products. This will be accomplished using Amyris's existing pilot plant capacity and by integrating with additional unit operations as they come online.

Subtask A.3 Post-upgrade Amyris pilot plant operations (Phase 2)

Following installation and commissioning of pilot plant upgrades, Amyris will operate the pilot plant to produce comprehensive technical, operating and financial data facilitating conceptual design of a demonstration or commercial scale facility acceptable to DOE.

In addition to developing sweet sorghum pilot scale data, this operations phase will include continuing work with simulated sorghum juice (defined media) and cane-derived feedstreams to maintain reference processes in which the Amyris team has demonstrated consistent performance both in terms of communication and reporting.

Current in-process controls and SOPs will be expanded upon to ensure continued robust data collection and safe operations, leading to enabling data for the design of a US commercial plant using sweet sorghum or other highimpact feedstocks.

Task B.0 Scale-up and economic analysis of Amyris diesel production from sweet sorghum

To complement the pilot plant upgrades and operations in Task 1, Amyris and partners will focus significant effort on process optimization and integration from feedstock to final diesel product finishing processes and waste treatment.

Subtask B.1 Sweet sorghum development, syrup and bagasse production (Phase 1-2)

Amyris's partner will provide both sweet sorghum bagasse and syrup to support integrated processing to Amyris Renewable Diesel. This feedstock partner will manage all aspects of feedstock development and handling including land management, planting within existing agricultural footprints, harvesting, bagasse drying and juice concentration to syrup. They will ship syrup samples to Amyris and will also ship chopped and dried bagasse for lignocellulosic biomass pre-treatment to Amyris's pre-treatment partner.

Subtask B.2 Lignocellulosic pre-treatment development and scale-up (Phase 2)

Following receipt of dried, chopped biomass from sweet sorghum or other feedstocks Amyris's pretreatment partner will undertake three key research and development and scale-up activities. First, they will perform wet chemical compositional analysis of each biomass lot. Second, the partner will undertake parametric pilot-scale pretreatment studies to determine the effect of varying pretreatment conditions on hemi-cellulose conversion yields, enzymatic cellulose digestibility and fermentation performance at Amyris. Third, they will perform pilotscale pretreatment and enzymatic hydrolysis campaigns to produce concentrated sugar solutions. These sugar streams will be shipped to Amyris for fermentation and downstream process performance testing and scale-up.

Subtask B.3 Fermentation scale-up (Phase 1-2) Utilization of sugar streams from such sources as lignocellulosic bagasse and sweet sorghum syrup, as well as other potential feedstocks will result in significant need for medium optimization. This includes optimization of pre-treatment steps to precipitate undesired species, removal of particulates, and sterilization of the medium, as well as supplementation of trace nutrients needed for cost-effective gains in fermentation yield. Additionally, converting current processes to use syrup and lignocellulosic fermentable sugars will likely require significant changes to pre-fermentation handling of sugar streams as well as to operating conditions for fermentation itself.

Initially Amyris will acquire baseline fermentation process data using sweet sorghum syrup and bagasse sugar streams, along with defined and cane-derived media, in its support labs. Later in the project Amyris will develop sweet sorghum SOPs for comparison to cane-based media performance in terms of product yield and sugar utilization rates. Throughout the project Amyris will test S. cerevisiae yeast strains to monitor relative and absolute performance comparing production from defined, cane-derived and sweet sorghum-based media.

Subtask B.4 Anaerobic digestion development and hydrogen production (Phase 2)

In collaboration with partners, Amyris will develop and optimize an integrated hydrogen production process to utilize residual unfermented C5 sugars from fermentation effluent. This effluent, vinasse, will be exposed to one or two anaerobic digestion conditions for biogas production. Amyris will then lead collaborative efforts to develop and model proper biogas cleanup procedures to ensure effective conversion of methane to hydrogen via steam methane reforming.

Subtask B.5 Recovery, purification and diesel finishing scale-up (Phase 1-2)

Recovery yield and purity indicators will drive scale-up and process optimization for isolation of the waterimmiscible C15 isoprenoid oil phase from fermentation broth aqueous phase and solids components. Various product recovery unit operations will be adapted from defined media and cane syrup-based fermentation recovery processes and tested with sorghum syrup and bagasse sugar-derived media. Amyris

will first focus on developing baseline recovery data from sorghum media relative to defined and cane based fermentations. Later, Amyris will optimize and scale robust recovery processes with sorghum or other feedstocks.

The current base-case chemical finishing process for Amyris Diesel is catalytic hydrogenation of the C15 fermentation intermediate. Product yields are high under current process conditions, and the Amyris team will validate that sweet sorghum utilization in fermentation does not result in degradation of hydrogenation specificity and yield via impurities carried over from recovery. In addition, process engineering expertise will be required to test and ensure that potential impurities identified during biogas clean-up and hydrogen production do not impact final Amyris Diesel quality or cost.

Subtask B.6 TEA and LCA for Amyris Diesel production (Phase 1-2)

Amyris will lead efforts to merge pre-treatment process models with sugar-to-diesel conversion for an

overall TEA of the integrated process for sweet sorghum conversion to Amyris Diesel using Aspen Plus and other software tools. In addition, life cycle analyses (LCA) will be further refined to reflect up-to-date process configuration and conceptual designs for commercial scale production.

Task C.0 Development and scale-up of value-added products from diesel fermentation intermediate

The third task in this project focuses on the use of the C15 isoprenoid fermentation product used for diesel production as a raw material for the synthesis of a number of large-market, high-value chemicals. The work required in this task will be divided into the following sections:

Subtask C.1 Laboratory-scale development and chemical product synthesis (Phase 1-2)

High-volume or high-value market needs that are amenable to solutions using the C15 isoprenoid fermentation product will be identified. Scientific literature searches will be continuously performed to determine prior art for candidate product molecules. If patented, Amyris will evaluate whether these patents and patent applications would pose freedom to operate issues to Amyris. Screening experiments on a small (e.g. grams or less) scale will be used to identify an effective (but not necessarily optimum) synthesis and a full characterization of the product. The initial synthesis may have to be scaled up to tens of grams depending on the sample amounts required for any performance testing. Design and initial synthesis of a target product will be followed by comprehensive product and byproduct characterization and application-related product property testing. In particular, plasticizers are contemplated as a key focus in Phase 2 as high-volume, value-add complements to Amyris Diesel production.

Subtask C.2 Mid-scale synthesis and characterization (Phase 2)

Initial scale-up/optimization will be accomplished by using statistical design of experiments to identify and optimize the important process variables with a minimum number of experiments. This will provide an optimized scaled process for each candidate chemical product that will allow for a preliminary cost assessment, a safety evaluation and a process design that can be the basis of preparing a SOP for technology transfer to the pilot plant. In addition, it will provide large scale samples for more thorough characterization of product properties and sampling to potential customers, for their preliminary application testing, if applicable.

Subtask C.3 Pilot-scale production and chemical process technoeconomics (Phase 2)

Pre-pilot chemical product scale-up support efforts will comprise determining how the process described performs at scale and the collection of engineering data for plant design and process economics. It will also enable the pilotscale in-house manufacture of quantities of product suitable for larger scale customer

sampling. For any unit operations beyond the capabilities of the pilot plant Amyris IBR will rely on specialized contract research organizations offering custom synthesis and scale-up services.

The final phase of new chemical product development would be initiated by a reevaluation of project justification, cost scenarios and market status. These would build upon modeling throughout the project life span that is refined as data becomes available. The final outcome would indicate whether a toll manufacturing option or in house manufacture would be preferable. Either scenario would require preparation of the appropriate engineering data packages, preliminary commercial scale process design and costing and Capital Expenditure/Operating Expenditure assessments to integrate with the Amyris Diesel TEA and LCA performed in Task B.6.

Task D.0 Regulatory and end-user process and product acceptance

The establishment of market readiness for Amyris Diesel and chemical products is an essential component of the IBR project.

Subtask D.1 Fuel product approval and acceptance (Phase 1-2)

Under the scope of this project, registration of higher diesel fuel blend ratios (above the current Environmental Protection Agency (EPA) registration at 20% Amyris Diesel) will be pursued. Amyris will perform contract manufacturing and third-party laboratory testing to validate product properties and determine potential toxicity of chemical substances under EPA test procedures, fuel properties and combustion effects. Additional toxicity data collection will include occupational exposure risk assessment, if necessary.

Subtask D.2 Chemical product approval and acceptance (Phase 1-2)

Chemical registration dossiers for selected products, either as new products or bio-derived product equivalents will be submitted to EPA for pre-manufacture notice and to fulfill the reporting requirements of EPA under the North American Free Trade Agreement Chemical Assessment and Management Program obligations. Amyris will use contract manufacturing for volume production required for product acceptance testing and validation by potential end-users, contract laboratories, and regulatory agencies.

Subtask D.3 Use approvals for genetically modified microbes (Phase 1-2)

During the course of the IBR project Amyris will develop the strategy and data required to submit a microbial commercial activity notice (MCAN) for use of genetically modified microorganisms (GMM) in commercial US production.

Subtask D.4 Commercial production process approvals and acceptance (Phase 1-2)

During the course of the IBR project Amyris will develop and refine the path for commercial process and installation approvals, including any National Environmental Policy Act (NEPA), state or local regulations governing chemical manufacturing. Amyris will focus on states such as Hawaii, Florida, California, Louisiana and Alabama as potential sites for early US production from sweet sorghum and other feedstocks.

Task E.0 Project Management and Reporting (Phase 1-2)

Management of the timelines and key decision points will be monitored by Amyris using the Earned Value system using percentage completion of each task as a monthly performance-to-plan metric. A detailed baseline plan will be developed with project partners, and progress will be monitored using task start and finish dates to identify variance, major performance issues, key risks to completion, and to enable more accurate forecasting in later quarters. Linkage between task completion and project expenditures will be accomplished using project based accounting.

Applicant Name: Amyris, Inc.        Award Number: DE-EE0002869/008        Attachment #4

BUDGET INFORMATION - NON CONSTRUCTION PROGRAMS

OMB Approval No. 0348-044

Section A - Budget Summary
		Estimated Unobligated Funds				New or Revised Budget
Grant Program Function or Activity (a)	Catalog of Federal Domestic Assistance Number (b)	Federal (c)		Non-Federal (d)		Federal (e)		Non-Federal (f)		Total (g)
1. Phase 1						$	3,008,260	$	1,702,920	$	4,711,180
2. Phase 2						$	21,991,740	$	8,230,079	$	30,221,819
3.
4.
5. Totals		$	—	$	—	$	25,000,000	$	9,932,999	$	34,932,999
Section B - Budget Categories
6. Object Class Categories		Grant Program, Function or Activity
		(1) Phase 1		(2) Phase 2						Total (5)
a. Personnel		$	1,342,119	$	7,245,746					$	8,587,865
b. Fringe Benefits		$	289,629	$	1,563,632					$	1,853,261
c. Travel		$	9,168	$	18,064					$	27,232
d. Equipment		$	592,541	$	1,925,314					$	2,517,855
e. Supplies		$	209,745	$	2,074,668					$	2,284,413
f. Contractual		$	84,772	$	5,446,373					$	5,531,145
g. Construction		$	—	$	—					$	—
h. Other		$	304,239	$	1,803,978					$	2,108,217
i. Total Direct Charges (sum of 6a-6h)		$	2,832,213	$	20,077,775					$	22,909,988
j. Indirect Charges		$	1,878,967	$	10,144,044					$	12,023,011
k. Totals (sum of 6i-6j)		$	4,711,180	$	30,221,819					$	34,932,999
7. Program Income		$	—	$	—					$	—

SF-424A (Rev. 4-92)

Prescribed by OMB Circular A-102

Previous Edition Usable            Authorized for Local Reproduction

DE-EE0002869/008

SPECIAL TERMS AND CONDITIONS

Table of Contents

Number SubjectPage

1. RESOLUTION OF CONFLICTING CONDITIONS    2

2. AWARD AGREEMENT TERMS AND CONDITIONS2

3. ELECTRONIC AUTHORIZATION OF AWARD DOCUMENTS2

4. AWARD PROJECT PERIOD AND BUDGET PERIODS2

5. PAYMENT PROCEDURES3

6. COST SHARING4

7. REBUDGETING AND RECOVERY OF INDIRECT COSTS5

8. FINAL INCURRED COST AUDIT5

9. STATEMENT OF FEDERAL STEWARDSHIP5

10. STATEMENT OF SUBSTANTIAL INVOLVEMENT5

11. SITE VISITS6

12. REPORTING REQUIREMENTS7

13. PUBLICATIONS7

14. FEDERAL, STATE, AND MUNICIPAL REQUIREMENTS8

15. INTELLECTUAL PROPERTY PROVISIONS AND CONTACT

INFORMATION8

16. NATIONAL SECURITY: CLASSIFIABLE RESULTS ORIGINATING

UNDER AN AWARD8

17. LOBBYING RESTRICTIONS9

18. NOTICE REGARDING THE PURCHASE OF AMERICAN-MADE EQUIPMENT

AND PRODUCTS -- SENSE OF CONGRESS9

19. PROPERTY10

20. DECONTAMINATION AND/OR DECOMMISSIONING (D&D) COSTS10

21. INSOLVENCY, BANKRUPTCY OR RECEIVERSHIP10

22. INDEMNITY11

23. SPECIAL PROVISIONS RELATING TO WORK FUNDED UNDER

AMERICAN RECOVERY AND REINVESTMENT ACT OF 2009 (May 2009)11

24. REPORTING AND REGISTRATION REQUIREMENTS UNDER SECTION 1512

OF THE RECOVERY ACT16

25. REQUIRED USE OF AMERICAN IRON, STEEL, AND MANUFACTURED GOODS - SECTION 1605 OF THE AMERICAN RECOVERY AND REINVESTMENT ACT OF 200916

26. REQUIRED USE OF AMERICAN IRON, STEEL, AND MANUFACTURED GOODS (COVERED UNDER INTERNATIONAL AGREEMENTS) -

SECTION 1605 OF THE AMERICAN RECOVERY AND REINVESTMENT

ACT OF 200919

27. RECOVERY ACT TRANSACTIONS LISTED IN SCHEDULE OF EXPENDITURES

OF FEDERAL AWARDS AND RECIPIENT RESPONSIBILITIES FOR INFORMING SUBRECIPIENTS23

28. WAGE RATE REQUIREMENTS UNDER SECTION 1606 OF THE

RECOVERY ACT24

29. DAVIS BACON ACT AND CONTRACT WORK HOURS AND SAFETY STANDARDS ACT25

30. CONTINGENCY35

31. NATIONAL ENVIRONMENTAL POLICY ACT (NEPA) REQUIREMENTS36

32. SUBCONTRACT APPROVALS36

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1. RESOLUTION OF CONFLICTING CONDITIONS

Any apparent inconsistency between Federal statutes and regulations and the terms and conditions contained in this award must be referred to the DOE Award Administrator for guidance.

2. AWARD AGREEMENT TERMS AND CONDITIONS

This award/agreement consists of the Assistance Agreement, plus the following:

a. Special Terms and Conditions.

b. Attachments:

Attachment Number        Title

1.        Intellectual Property Provisions

2.        Statement of Project Objectives

3.        Federal Assistance Reporting Checklist and Instructions

4.        Budget Pages (SF 424A)     

5.        Requirements for Contingency Funds for Integrated Biorefinery Projects    

c. Applicable program regulations.

d. DOE Assistance Regulations, 10 CFR Part 600 at http://ecfr.gpoaccess.gov.

e. If the award is for research and the award is for a university or non-profit, the Research Terms & Conditions and the DOE Agency Specific Requirements at http://www.nsf.gov/bfa/dias/policy/rtc/index.jsp apply.

f. Application/proposal as approved by DOE.

g. National Policy Assurances to be incorporated as award terms in effect on date of award at http://energy.gov/management/downloads/national-policy-assurances-be-incorporated-award-terms

3. ELECTRONIC AUTHORIZATION OF AWARD DOCUMENTS

Acknowledgement of award documents by the Recipient's authorized representative through electronic systems used by the Department of Energy, specifically FedConnect, constitutes the Recipient's acceptance of the terms and conditions of the award. Acknowledgement via FedConnect by the Recipient's authorized representative constitutes the Recipient's electronic signature.

4. AWARD PROJECT PERIOD AND BUDGET PERIODS

The Project Period for this award is 12/28/2009 through 12/31/2012, consisting of the following Budget Periods:

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Budget Period	Phase	Start Date	End Date
1	1	12/28/2009	4/21/2010
	2	4/22/2010	12/31/2012

5. PAYMENT PROCEDURES

a. Method of Payment. Payment will be made by reimbursement through ACH.

b. Requesting Reimbursement. Requests for reimbursements must be made electronically through Department of Energy's Oak Ridge Financial Service Center (ORFSC) VIPERS. To access and use VIPERS, you must enroll at https://vipers.oro.doe.gov. Detailed instructions on how to enroll are provided on the web site.

For non-construction awards, you must submit a Standard Form (SF) 270, “Request for Advance or Reimbursement,” at https://vipers.oro.doe.gov and attach a file containing appropriate supporting documentation. The file attachment must show the total Federal share claimed on the SF 270, the non-Federal share claimed for the billing period if cost sharing is required, and cumulative expenditures to date (both Federal and non-Federal) for each of the following categories: salaries/wages and fringe benefits; equipment; travel; participant/training support costs, if any; other direct costs, including subawards/contracts; and indirect costs. For construction awards, you must submit a SF 271, “Outlay Report and Request for Reimbursement for Construction Programs,” through VIPERS.

c. Timing of submittals. Submittal of the SF 270 or SF 271 should coincide with your normal billing pattern, but not more frequently than every two weeks. Requests for reimbursement must be limited to the amount of disbursements made during the billing period for the Federal share of direct project costs and the proportionate share of any allowable indirect costs incurred during that billing period.

d. Adjusting payment requests for available cash. You must disburse any funds that are available from repayments to and interest earned on a revolving fund, program income, rebates, refunds, contract settlements, audit recoveries, credits, discounts, and interest earned on any of those funds before requesting additional cash payments from DOE.

e. Payments. The DOE approving official will approve the invoice as soon as practical, but not later than 30 days after your request is received, unless the billing is improper. Upon receipt of an invoice payment authorization from the DOE approving official, the ORFSC will disburse payment to you. You may check the status of payments at the VIPER web site. All payments are made by electronic funds transfer to the bank account identified on the ACH Vendor/Miscellaneous Payment Enrollment Form (SF 3881) that you filed.

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6. COST SHARING

a. Total Estimated Project Cost is the sum of the Federal Government share, including Federally Funded Research and Development Center (FFRDC) contractor costs, and Recipient share of the estimated project costs. The DOE FFRDC contractor cost is not included in the total approved budget for this award, because DOE will pay the DOE FFRDC contractor portion of the effort under an existing DOE contract. The Recipient is not responsible for reporting on that portion of the total estimated cost that is paid directly to the DOE FFRDC contractor.

The Recipient's cost share must come from non-Federal sources unless otherwise allowed by law. By accepting Federal funds under this award, you agree that you are liable for your percentage share of allowable project costs, on a budget period basis, even if the project is terminated early or is not funded to its completion. This cost is shared as follows:

Budget Period 1	Phase	DOE Cost Share, including FFRDC Costs		Recipient Cost Share $ / %	Total Estimated Costs
		DOE $ / %	FFRDC $ / %
	1	$3,008,260/63.1%	—	$1,702,920/36.9%	$4,711,180
	2	$21,333,149/69.1%	$658,591/2.1%	$8,888,670/28.8%	$30,880,410
	Total Project	$24,341,409/68.4%	$658,591/2.0%	$10,591,590/29.8%	$35,591,590

b. If you discover that you may be unable to provide cost sharing of at least the amount identified in paragraph a of this Article, you should immediately provide written notification to the DOE Award Administrator, indicating whether you will continue the project or phase out the project. If you plan to continue the project, the notification must describe how replacement cost sharing will be secured.

c. You must maintain records of all project costs you claim as cost sharing, including in-kind costs, as well as records of costs to be paid by DOE. Such records are subject to audit.

d. Failure to provide the cost share required by this Article may result in the subsequent recovery by DOE of some or all the funds provided under the award.

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7. REBUDGETING AND RECOVERY OF INDIRECT COSTS

a. If actual allowable indirect costs are less than those budgeted and funded under the award, you may use the difference to pay additional allowable direct costs during the project period. If at the completion of the award the Government's share of total allowable costs (i.e., direct and indirect), is less than the total costs reimbursed, you must refund the difference.

b. Recipients are expected to manage their indirect costs. DOE will not amend an award solely to provide additional funds for changes in indirect cost rates. DOE recognizes that the inability to obtain full reimbursement for indirect costs means the Recipient must absorb the underrecovery. Such underrecovery may be allocated as part of the organization's required cost sharing.

8. FINAL INCURRED COST AUDIT

In accordance with 10 CFR 600, DOE reserves the right to initiate a final incurred cost audit on this award. If the audit has not been performed or completed prior to the closeout of the award, DOE retains the right to recover an appropriate amount after fully considering the recommendations on disallowed costs resulting from the final audit.

9. STATEMENT OF FEDERAL STEWARDSHIP

DOE will exercise normal Federal stewardship in overseeing the project activities performed under this award. Stewardship activities include, but are not limited to, conducting site visits; reviewing performance and financial reports; providing technical assistance and/or temporary intervention in unusual circumstances to correct deficiencies which develop during the project; assuring compliance with terms and conditions; and reviewing technical performance after project completion to ensure that the award objectives have been accomplished.

10. STATEMENT OF SUBSTANTIAL INVOLVEMENT

a. Government Insight

In order to adequately monitor project progress and provide technical direction and/or redirection to the Recipient, DOE must be provided an adequate level of insight into various Recipient activities. Government Insight activities by DOE include attendance at Recipient meetings, reviews and tests, as well as access for DOE's consultants to perform independent evaluations of Recipient's plans and processes. Recipient shall notify the DOE Project Officer of meetings, reviews, and tests in sufficient time to permit DOE participation, and provide all appropriate documentation for DOE review.

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b. Specific activities to be conducted by DOE

1. Risk Evaluation - DOE will review the Recipient's initial Risk Mitigation Plan (RMP) for quality and completeness. DOE will also monitor updates to the RMP and actions taken by the Recipient during the performance of its award to mitigate risks and improve the probability of successful execution of the integrated Biorefinery project. At DOE's discretion, additional independent risk analyses of the project by DOE consultants may be requested.

2. Independent Engineering Assessments -DOE will engage a private, independent engineering (IE) firm to assist in assessing the progress of the project and provide timely and accurate reports to DOE. The Recipient will ensure that the IE has access to any and all relevant documentation sufficient to allow the IE to provide independent evaluations to DOE on the progress of the project. Such documentation includes but is not limited to the following:

•Drawings and specifications

•Construction and Execution plans

•Resource loaded schedules

•Design functions and requirements for the site final design review

•Risk management plans

•Value management and engineering studies and/or plans

•Acquisition strategies

•Project execution plans

•Project controls including earned value management systems

•Qualifications of the integrated project team.

•Financial strategy for funding the construction project

•Updated marketing and business plan

•Invoices submitted to DOE

DOE will evaluate the quality and completeness of information and documentation provided by the Recipient to DOE and its consultants in order to allow DOE to provide technical direction and/or redirection to the Recipient about how best to achieve the purposes of the award. Consultants to DOE may not provide technical direction and/or redirection to the Recipient.

11. SITE VISITS

DOE's authorized representatives have the right to make site visits at reasonable times to review project accomplishments and management control systems and to provide technical assistance, if required. You must provide, and must require your subawardees to provide, reasonable access to facilities, office space, resources, and assistance for the safety and convenience of the government representatives in the performance of their duties. All site visits and evaluations must be performed in a manner that does not unduly interfere with or delay the work.

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12. REPORTING REQUIREMENTS

a. Requirements. The reporting requirements for this award are identified on the Federal Assistance Reporting Checklist, DOE F 4600.2, attached to this award. Failure to comply with these reporting requirements is considered a material noncompliance with the terms of the award. Noncompliance may result in withholding of future payments, suspension or termination of the current award, and withholding of future awards. A willful failure to perform, a history of failure to perform, or unsatisfactory performance of this and/or other financial assistance awards, may also result in a debarment action to preclude future awards by Federal agencies.

b. Dissemination of scientific/technical reports. Scientific/technical reports submitted under this award will be disseminated on the Internet via the DOE Information Bridge (www.osti.gov/bridge), unless the report contains patentable material, protected data or SBIR/STTR data. Citations for journal articles produced under the award will appear on the DOE Energy Citations Database (www.osti.gov/energycitations).

c. Restrictions. Reports submitted to the DOE Information Bridge must not contain any Protected Personal Identifiable Information (PII), limited rights data (proprietary data), classified information, information subject to export control classification, or other information not subject to release.

13. PUBLICATIONS

a. You are encouraged to publish or otherwise make publicly available the results of the work conducted under the award.

b. An acknowledgment of DOE support and a disclaimer must appear in the publication of any material, whether copyrighted or not, based on or developed under this project, as follows:

Acknowledgment: “This material is based upon work supported by the Department of Energy [National Nuclear Security Administration] [add name(s) of other agencies, if applicable] under Award Number(s) [enter the award number(s)].”

Disclaimer: “This report was prepared as an account of work sponsored by an agency of the United States Government. Neither the United States Government nor any agency thereof, nor any of their employees, makes any warranty, express or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights. Reference herein to any specific commercial product, process, or service by trade name, trademark, manufacturer, or otherwise does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States Government or any agency thereof. The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States Government or any agency thereof.”

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14. FEDERAL, STATE, AND MUNICIPAL REQUIREMENTS

You must obtain any required permits and comply with applicable federal, state, and municipal laws, codes, and regulations for work performed under this award.

15. INTELLECTUAL PROPERTY PROVISIONS AND CONTACT INFORMATION

a. The intellectual property provisions applicable to this award are provided as an attachment to this award or are referenced in the Assistance Agreement.

b. Questions regarding intellectual property matters should be referred to the DOE Award Administrator identified and the Patent Counsel designated as the service provider for the DOE office that issued the award.

Patent Counsel for the Golden Field Office is Julia Moody, who may be reached at julia.moody@go.doe.gov or 720-356-1669.

16. NATIONAL SECURITY: CLASSIFIABLE RESULTS ORIGINATING UNDER AN AWARD

a. This award is intended for unclassified, publicly releasable research. You will not be granted access to classified information. DOE does not expect that the results of the research project will involve classified information. Under certain circumstances, however, a classification review of information originated under the award may be required. The Department may review research work generated under this award at any time to determine if it requires classification.

b. Executive Order 12958 (60 Fed. Reg. 19,825 (1995)) states that basic scientific research information not clearly related to the national security shall not be classified. Nevertheless, some information concerning (among other things) scientific, technological, or economic matters relating to national security or cryptology may require classification. If you originate information during the course of this award that you believe requires classification, you must promptly:

1. Notify the DOE Project Officer and the DOE Award Administrator;

2. Submit the information by registered mail directly to the Director, Office of Classification and Information Control, SO-10.2; U.S. Department of Energy; P.O. Box A; Germantown, MD 20875-0963, for classification review.

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3. Restrict access to the information to the maximum extent possible until you are informed that the information is not classified, but no longer than 30 days after receipt by the Director, Office of Classification and Information Control

c. If you originate information concerning the production or utilization of special nuclear material (i.e., plutonium, uranium enriched in the isotope 233 or 235, and any other material so determined under section 51 of the Atomic Energy Act) or nuclear energy, you must:

1. Notify the DOE Project Officer and the DOE Award Administrator;

2. Submit the information by registered mail directly to the Director, Office of Classification and Information Control, SO-10.2; U.S. Department of Energy; P. O. Box A; Germantown, MD 20875-0963 for classification review within 180 days of the date the Recipient first discovers or first has reason to believe that the information is useful in such production or utilization; and

3. Restrict access to the information to the maximum extent possible until you are informed that the information is not classified, but no longer than 90 days after receipt by the Director, Office of Classification and Information Control.

d. If DOE determines any of the information requires classification, you agree that the Government may terminate the award by mutual agreement in accordance with 10 CFR 600.25(d). All material deemed to be classified must be forwarded to DOE, in a manner specified by DOE.

e. If DOE does not respond within the specified time periods, you are under no further obligation to restrict access to the information.

17. LOBBYING RESTRICTIONS

By accepting funds under this award, you agree that none of the funds obligated on the award shall be expended, directly or indirectly, to influence congressional action on any legislation or appropriation matters pending before Congress, other than to communicate to Members of Congress as described in 18 U.S.C. 1913. This restriction is in addition to those prescribed elsewhere in statute and regulation.

18. NOTICE REGARDING THE PURCHASE OF AMERICAN-MADE EQUIPMENT AND PRODUCTS -- SENSE OF CONGRESS

It is the sense of the Congress that, to the greatest extent practicable, all equipment and products purchased with funds made available under this award should be American-made.

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19. PROPERTY

Real property and equipment acquired by the Recipient shall be subject to the rules set forth in 10 CFR 600.130-137, 10 CFR 600.231-233, or 10 CFR 600.320-324, as applicable.

Consistent with the goals and objectives of this project, the Recipient may continue to use Recipient acquired property beyond the Period of Performance, without obligation, during the period of such use, to extinguish DOE's conditional title to such property as described in 10 CFR 600.132-135, 10 CFR 600.231-233, or 600.321-324, subject to the following: (a) the Recipient continues to utilize such property for the objectives of the project as set forth in the Statement of Project Objectives; (b) DOE retains the right to periodically ask for, and the Recipient agrees to provide, reasonable information concerning the use and condition of the property; and (c) the Recipient follows the property disposition rules set forth in the applicable sections of 10 CFR Part 600, if the property is no longer used by the Recipient for the objectives of the project, and the fair market value of property exceeds $5,000.

Once the per unit fair market value of the property is less than $5,000, pursuant to the applicable sections of 10 CFR Part 600, DOE's residual interest in the property shall be extinguished and the Recipient shall have no further obligation to the DOE with respect to the property.

The regulations as set forth in 10 CFR Part 600 and the requirements of this article shall also apply to property in the possession of any team member, sub-recipient or other entity where such property was acquired in whole or in part with funds provided by DOE under this award or where such property was counted as cost-sharing under the award.

20. DECONTAMINATION AND/OR DECOMMISSIONING (D&D) COSTS

Notwithstanding any other provisions of this Agreement, the Government shall not be responsible for or have any obligation to the Recipient for (i) Decontamination and/or Decommissioning (D&D) of any of the Recipient's facilities, or (ii) any costs which may be incurred by the Recipient in connection with the D&D of any of its facilities due to the performance of the work under this Agreement, whether said work was performed prior to or subsequent to the effective date of the Agreement.

21. INSOLVENCY, BANKRUPTCY OR RECEIVERSHIP

a. You shall immediately notify the DOE of the occurrence of any of the following events: (i) you or your parent's filing of a voluntary case seeking liquidation or reorganization under the Bankruptcy Act; (ii) your consent to the institution of an involuntary case under the Bankruptcy Act against you or your parent; (iii) the filing of any similar proceeding for or against you or your parent, or your consent to the dissolution, winding-up or readjustment of your debts, appointment of a receiver, conservator, trustee, or other officer with similar powers over you, under any other applicable state or federal law; or (iv) your insolvency due to its inability to pay debts generally as they become due.

10

b. Such notification shall be in writing and shall: (i) specifically set out the details of the occurrence of an event referenced in paragraph (a); (ii) provide the facts surrounding that event; and (iii) provide the impact such event will have on the project being funded by this award.

c. Upon the occurrence of any of the four events described in paragraph a. of this provision, DOE reserves the right to conduct a review of your award to determine your compliance with the required elements of the award (including such items as cost share, progress towards technical project objectives, and submission of required reports). If the DOE review determines that there are significant deficiencies or concerns with your performance under the award, DOE reserves the right to impose additional requirements, as needed, including (i) change of payment method; or (ii) institute payment controls.

d. Failure of the Recipient to comply with this provision may be considered a material noncompliance of this financial assistance award by the Contracting Officer.

22. INDEMNITY

The Recipient shall indemnify the Government and its officers, agents, or employees for any and all liability, including litigation expenses and attorneys' fees, arising from suits, actions, or claims of any character for death, bodily injury, or loss of or damage to property or to the environment, resulting from the project, except to the extent that such liability results from the direct fault or negligence of Government officers, agents or employees, or to the extent such liability may be covered by applicable allowable costs provisions. 

23. SPECIAL PROVISIONS RELATING TO WORK FUNDED UNDER AMERICAN RECOVERY AND REINVESTMENT ACT OF 2009 (May 2009)

Preamble

The American Recovery and Reinvestment Act of 2009, Pub. L. 111-5, (Recovery Act) was enacted to preserve and create jobs and promote economic recovery, assist those most impacted by the recession, provide investments needed to increase economic efficiency by spurring technological advances in science and health, invest in transportation, environmental protection, and other infrastructure that will provide long-term economic benefits, stabilize State and local government budgets, in order to minimize and avoid reductions in essential services and counterproductive State and local tax increases. Recipients shall use grant funds in a manner that maximizes job creation and economic benefit.

11

The Recipient shall comply with all terms and conditions in the Recovery Act relating generally to governance, accountability, transparency, data collection and resources as specified in Act itself and as discussed below.

Recipients should begin planning activities for their first tier subrecipients, including obtaining a DUNS number (or updating the existing DUNS record), and registering with the Central Contractor Registration (CCR).

Be advised that Recovery Act funds can be used in conjunction with other funding as necessary to complete projects, but tracking and reporting must be separate to meet the reporting requirements of the Recovery Act and related guidance. For projects funded by sources other than the Recovery Act, Contractors must keep separate records for Recovery Act funds and to ensure those records comply with the requirements of the Act.

The Government has not fully developed the implementing instructions of the Recovery Act, particularly concerning specific procedural requirements for the new reporting requirements. The Recipient will be provided these details as they become available. The Recipient must comply with all requirements of the Act. If the recipient believes there is any inconsistency between ARRA requirements and current award terms and conditions, the issues will be referred to the Contracting Officer for reconciliation.

Definitions

For purposes of this clause, Covered Funds means funds expended or obligated from appropriations under the American Recovery and Reinvestment Act of 2009, Pub. L. 111-5. Covered Funds will have special accounting codes and will be identified as Recovery Act funds in the grant, cooperative agreement or TIA and/or modification using Recovery Act funds. Covered Funds must be reimbursed by September 30, 2015.

Non-Federal employer means any employer with respect to covered funds -- the contractor, subcontractor, grantee, or recipient, as the case may be, if the contractor, subcontractor, grantee, or recipient is an employer; and any professional membership organization, certification of other professional body, any agent or licensee of the Federal government, or any person acting directly or indirectly in the interest of an employer receiving covered funds; or with respect to covered funds received by a State or local government, the State or local government receiving the funds and any contractor or subcontractor receiving the funds and any contractor or subcontractor of the State or local government; and does not mean any department, agency, or other entity of the federal government.

Recipient means any entity that receives Recovery Act funds directly from the Federal government (including Recovery Act funds received through grant, loan, or contract) other than an individual and includes a State that receives Recovery Act Funds.

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Special Provisions

A. Flow Down Requirement

Recipients must include these special terms and conditions in any subaward.

B. Segregation of Costs

Recipients must segregate the obligations and expenditures related to funding under the Recovery Act. Financial and accounting systems should be revised as necessary to segregate, track and maintain these funds apart and separate from other revenue streams. No part of the funds from the Recovery Act shall be commingled with any other funds or used for a purpose other than that of making payments for costs allowable for Recovery Act projects.

C. Prohibition on Use of Funds

None of the funds provided under this agreement derived from the American Recovery and Reinvestment Act of 2009, Pub. L. 111-5, may be used by any State or local government, or any private entity, for any casino or other gambling establishment, aquarium, zoo, golf course, or swimming pool.

D. Access to Records

With respect to each financial assistance agreement awarded utilizing at least some of the funds appropriated or otherwise made available by the American Recovery and Reinvestment Act of 2009, Pub. L. 111-5, any representative of an appropriate inspector general appointed under section 3 or 8G of the Inspector General Act of 1988 (5 U.S.C. App.) or of the Comptroller General is authorized --

(1) to examine any records of the contractor or grantee, any of its subcontractors or subgrantees, or any State or local agency administering such contract that pertain to, and involve transactions that relate to, the subcontract, subcontract, grant, or subgrant; and

(2) to interview any officer or employee of the contractor, grantee, subgrantee, or agency regarding such transactions.

E. Publication

An application may contain technical data and other data, including trade secrets and/or privileged or confidential information, which the applicant does not want disclosed to the public or used by the Government for any purpose other than the application. To protect such data, the applicant should specifically identify each page including each line or paragraph thereof containing the data to be protected and mark the cover sheet of the application with the following Notice as well as referring to the Notice on each page to which the Notice applies:

Notice of Restriction on Disclosure and Use of Data

The data contained in pages ---- of this application have been submitted in confidence and contain trade secrets or proprietary information, and such data shall be used or disclosed only for

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evaluation purposes, provided that if this applicant receives an award as a result of or in connection with the submission of this application, DOE shall have the right to use or disclose the data here to the extent provided in the award. This restriction does not limit the Government's right to use or disclose data obtained without restriction from any source, including the applicant.

Information about this agreement will be published on the Internet and linked to the website www.recovery.gov, maintained by the Accountability and Transparency Board. The Board may exclude posting contractual or other information on the website on a case-by-case basis when necessary to protect national security or to protect information that is not subject to disclosure under sections 552 and 552a of title 5, United States Code.

F. Protecting State and Local Government and Contractor Whistleblowers.

The requirements of Section 1553 of the Act are summarized below. They include, but are not limited to:

Prohibition on Reprisals: An employee of any non-Federal employer receiving covered funds under the American Recovery and Reinvestment Act of 2009, Pub. L. 111-5, may not be discharged, demoted, or otherwise discriminated against as a reprisal for disclosing, including a disclosure made in the ordinary course of an employee's duties, to the Accountability and Transparency Board, an inspector general, the Comptroller General, a member of Congress, a State or Federal regulatory or law enforcement agency, a person with supervisory authority over the employee (or other person working for the employer who has the authority to investigate, discover or terminate misconduct), a court or grant jury, the head of a Federal agency, or their representatives information that the employee believes is evidence of:

- gross management of an agency contract or grant relating to covered funds;

- a gross waste of covered funds;

- a substantial and specific danger to public health or safety related to the implementation or use of covered funds;

- an abuse of authority related to the implementation or use of covered funds; or

- as violation of law, rule, or regulation related to an agency contract (including the competition for or negotiation of a contract) or grant, awarded or issued relating to covered funds.

Agency Action: Not later than 30 days after receiving an inspector general report of an alleged reprisal, the head of the agency shall determine whether there is sufficient basis to conclude that the non-Federal employer has subjected the employee to a prohibited reprisal. The agency shall either issue an order denying relief in whole or in part or shall take one or more of the following actions:

- Order the employer to take affirmative action to abate the reprisal.

- Order the employer to reinstate the person to the position that the person held before the reprisal, together with compensation including back pay, compensatory damages, employment benefits, and other terms and conditions of employment that would apply to the person in that position if the reprisal had not been taken.

- Order the employer to pay the employee an amount equal to the aggregate amount of all

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costs and expenses (including attorneys' fees and expert witnesses' fees) that were reasonably incurred by the employee for or in connection with, bringing the complaint regarding the reprisal, as determined by the head of a court of competent jurisdiction.

Nonenforceablity of Certain Provisions Waiving Rights and remedies or Requiring Arbitration: Except as provided in a collective bargaining agreement, the rights and remedies provided to aggrieved employees by this section may not be waived by any agreement, policy, form, or condition of employment, including any predispute arbitration agreement. No predispute arbitration agreement shall be valid or enforceable if it requires arbitration of a dispute arising out of this section.

Requirement to Post Notice of Rights and Remedies: Any employer receiving covered funds under the American Recovery and Reinvestment Act of 2009, Pub. L. 111-5, shall post notice of the rights and remedies as required therein. (Refer to section 1553 of the American Recovery and Reinvestment Act of 2009, Pub. L. 111-5, www.Recovery.gov, for specific requirements of this section and prescribed language for the notices.).

G. RESERVED

H. False Claims Act

Recipient and sub-recipients shall promptly refer to the DOE or other appropriate Inspector General any credible evidence that a principal, employee, agent, contractor, sub-grantee, subcontractor or other person has submitted a false claim under the False Claims Act or has committed a criminal or civil violation of laws pertaining to fraud, conflict of interest, bribery, gratuity or similar misconduct involving those funds.

I. Information in Support of Recovery Act Reporting

Recipient may be required to submit backup documentation for expenditures of funds under the Recovery Act including such items as timecards and invoices. Recipient shall provide copies of backup documentation at the request of the Contracting Officer or designee.

J. Availability of Funds

Funds appropriated under the Recovery Act and obligated to this award are available for reimbursement of costs until September 30, 2015.

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24. REPORTING AND REGISTRATION REQUIREMENTS UNDER SECTION 1512 OF THE RECOVERY ACT

(a) This award requires the recipient to complete projects or activities which are funded under the American Recovery and Reinvestment Act of 2009 (Recovery Act) and to report on use of Recovery Act funds provided through this award. Information from these reports will be made available to the public.

(b) The reports are due no later than ten calendar days after each calendar quarter in which the Recipient receives the assistance award funded in whole or in part by the Recovery Act.

(c) Recipients and their first-tier subrecipients must maintain current registrations in the Central Contractor Registration (http://www.ccr.gov) at all times during which they have active federal awards funded with Recovery Act funds. A Dun and Bradstreet Data Universal Numbering System (DUNS) Number (http://www.dnb.com) is one of the requirements for registration in the Central Contractor Registration.

(d) The recipient shall report the information described in section 1512(c) of the Recovery Act using the reporting instructions and data elements that will be provided online at http://www.FederalReporting.gov and ensure that any information that is pre-filled is corrected or updated as needed.

25. REQUIRED USE OF AMERICAN IRON, STEEL, AND MANUFACTURED GOODS - SECTION 1605 OF THE AMERICAN RECOVERY AND REINVESTMENT ACT OF 2009

If the Recipient determines at any time that any construction, alteration, or repair activity on a public building or public works will be performed during the course of the project, the Recipient shall notify the Contracting Officer prior to commencing such work and the following provisions shall apply.

(a) Definitions. As used in this award term and condition-

(1) Manufactured good means a good brought to the construction site for incorporation into the building or work that has been-

(i) Processed into a specific form and shape; or

(ii) Combined with other raw material to create a material that has different properties than the properties of the individual raw materials.

(2) Public building and public work means a public building of, and a public work of, a governmental entity (the United States; the District of Columbia; commonwealths, territories, and minor outlying islands of the United States; State and local governments; and multi-State, regional, or interstate entities which have governmental functions). These buildings and works may include, without limitation, bridges, dams, plants, highways, parkways, streets, subways, tunnels, sewers, mains, power lines, pumping stations, heavy generators, railways, airports, terminals, docks, piers, wharves, ways, lighthouses, buoys, jetties, breakwaters, levees, and canals, and the construction, alteration, maintenance, or repair of such buildings and works.

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(3) Steel means an alloy that includes at least 50 percent iron, between .02 and 2 percent carbon, and may include other elements.

(b) Domestic preference. (1) This award term and condition implements Section 1605 of the American Recovery and Reinvestment Act of 2009 (Recovery Act) (Pub. L. 111-5), by requiring that all iron, steel, and manufactured goods used in the project are produced in the United States except as provided in paragraph (b)(3) of this section and condition.

(2) This requirement does not apply to the material listed by the Federal Government as follows:

none

(3) The award official may add other iron, steel, and/or manufactured goods to the list in paragraph (b)(2) of this section and condition if the Federal Government determines that-

(i) The cost of the domestic iron, steel, and/or manufactured goods would be unreasonable. The cost of domestic iron, steel, or manufactured goods used in the project is unreasonable when the cumulative cost of such material will increase the cost of the overall project by more than 25 percent;

(ii) The iron, steel, and/or manufactured good is not produced, or manufactured in the United States in sufficient and reasonably available quantities and of a satisfactory quality; or

(iii) The application of the restriction of section 1605 of the Recovery Act would be inconsistent with the public interest.

(c) Request for determination of inapplicability of Section 1605 of the Recovery Act . (1)(i) Any recipient request to use foreign iron, steel, and/or manufactured goods in accordance with paragraph (b)(3) of this section shall include adequate information for Federal Government evaluation of the request, including-

(A) A description of the foreign and domestic iron, steel, and/or manufactured goods;

(B) Unit of measure;

(C) Quantity;

(D) Cost;

(E) Time of delivery or availability;

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(F) Location of the project;

(G) Name and address of the proposed supplier; and

(H) A detailed justification of the reason for use of foreign iron, steel, and/or manufactured goods cited in accordance with paragraph (b)(3) of this section.

(ii) A request based on unreasonable cost shall include a reasonable survey of the market and a completed cost comparison table in the format in paragraph (d) of this section.

(iii) The cost of iron, steel, and/or manufactured goods material shall include all delivery costs to the construction site and any applicable duty.

(iv) Any recipient request for a determination submitted after Recovery Act funds have been obligated for a project for construction, alteration, maintenance, or repair shall explain why the recipient could not reasonably foresee the need for such determination and could not have requested the determination before the funds were obligated. If the recipient does not submit a satisfactory explanation, the award official need not make a determination.

(2) If the Federal Government determines after funds have been obligated for a project for construction, alteration, maintenance, or repair that an exception to section 1605 of the Recovery Act applies, the award official will amend the award to allow use of the foreign iron, steel, and/or relevant manufactured goods. When the basis for the exception is nonavailability or public interest, the amended award shall reflect adjustment of the award amount, redistribution of budgeted funds, and/or other actions taken to cover costs associated with acquiring or using the foreign iron, steel, and/or relevant manufactured goods. When the basis for the exception is the unreasonable cost of the domestic iron, steel, or manufactured goods, the award official shall adjust the award amount or redistribute budgeted funds by at least the differential established in 2 CFR 176.110(a).

(3) Unless the Federal Government determines that an exception to section 1605 of the Recovery Act applies, use of foreign iron, steel, and/or manufactured goods is noncompliant with section 1605 of the American Recovery and Reinvestment Act.

(d) Data. To permit evaluation of requests under paragraph (b) of this section based on unreasonable cost, the Recipient shall include the following information and any applicable supporting data based on the survey of suppliers:

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Foreign and Domestic Items Cost Comparison

Description	Unit of measure	Quantity	Cost (dollars)*
Item 1:
Foreign steel, iron, or manufactured good	_________	_________	_________
Domestic steel, iron, or manufactured good	_________	_________	_________
Item 2:
Foreign steel, iron, or manufactured good	_________	_________	_________
Domestic steel, iron, or manufactured good	_________	_________	_________

List name, address, telephone number, email address, and contact for suppliers surveyed. Attach copy of response; if oral, attach summary.

Include other applicable supporting information.

*Include all delivery costs to the construction site.

26. REQUIRED USE OF AMERICAN IRON, STEEL, AND MANUFACTURED GOODS (COVERED UNDER INTERNATIONAL AGREEMENTS) - SECTION 1605 OF THE AMERICAN RECOVERY AND REINVESTMENT ACT OF 2009

(a) Definitions. As used in this award term and condition-

Designated country - (1) A World Trade Organization Government Procurement Agreement country (Aruba, Austria, Belgium, Bulgaria, Canada, Cyprus, Czech Republic, Denmark, Estonia, Finland, France, Germany, Greece, Hong Kong, Hungary, Iceland, Ireland, Israel, Italy, Japan, Korea (Republic of), Latvia, Liechtenstein, Lithuania, Luxembourg, Malta, Netherlands, Norway, Poland, Portugal, Romania, Singapore, Slovak Republic, Slovenia, Spain, Sweden, Switzerland, and United Kingdom;

(2) A Free Trade Agreement (FTA) country (Australia, Bahrain, Canada, Chile, Costa Rica, Dominican Republic, El Salvador, Guatemala, Honduras, Israel, Mexico, Morocco, Nicaragua, Oman, Peru, or Singapore); or

(3) A United States-European Communities Exchange of Letters (May 15, 1995) country: Austria, Belgium, Bulgaria, Cyprus, Czech Republic, Denmark, Estonia, Finland, France, Germany, Greece, Hungary, Ireland, Italy, Latvia, Lithuania, Luxembourg, Malta, Netherlands, Poland, Portugal, Romania, Slovak Republic, Slovenia, Spain, Sweden, and United Kingdom.

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Designated country iron, steel, and/or manufactured goods - (1) Is wholly the growth, product, or manufacture of a designated country; or

(2) In the case of a manufactured good that consist in whole or in part of materials from another country, has been substantially transformed in a designated country into a new and different manufactured good distinct from the materials from which it was transformed.

Domestic iron, steel, and/or manufactured good - (1) Is wholly the growth, product, or manufacture of the United States; or

(2) In the case of a manufactured good that consists in whole or in part of materials from another country, has been substantially transformed in the United States into a new and different manufactured good distinct from the materials from which it was transformed. There is no requirement with regard to the origin of components or subcomponents in manufactured goods or products, as long as the manufacture of the goods occurs in the United States.

Foreign iron, steel, and/or manufactured good means iron, steel and/or manufactured good that is not domestic or designated country iron, steel, and/or manufactured good.

Manufactured good means a good brought to the construction site for incorporation into the building or work that has been-

(1) Processed into a specific form and shape; or

(2) Combined with other raw material to create a material that has different properties than the properties of the individual raw materials.

Public building and public work means a public building of, and a public work of, a governmental entity (the United States; the District of Columbia; commonwealths, territories, and minor outlying islands of the United States; State and local governments; and multi-State, regional, or interstate entities which have governmental functions). These buildings and works may include, without limitation, bridges, dams, plants, highways, parkways, streets, subways, tunnels, sewers, mains, power lines, pumping stations, heavy generators, railways, airports, terminals, docks, piers, wharves, ways, lighthouses, buoys, jetties, breakwaters, levees, and canals, and the construction, alteration, maintenance, or repair of such buildings and works.

Steel means an alloy that includes at least 50 percent iron, between .02 and 2 percent carbon, and may include other elements.

(b) Iron, steel, and manufactured goods. (1) The award term and condition described in this section implements-

(i) Section 1605(a) of the American Recovery and Reinvestment Act of 2009 (Pub. L. 111-5) (Recovery Act), by requiring that all iron, steel, and manufactured goods used in the project are produced in the United States; and

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(ii) Section 1605(d), which requires application of the Buy American requirement in a manner consistent with U.S. obligations under international agreements. The restrictions of section 1605 of the Recovery Act do not apply to designated country iron, steel, and/or manufactured goods. The Buy American requirement in section 1605 shall not be applied where the iron, steel or manufactured goods used in the project are from a Party to an international agreement that obligates the recipient to treat the goods and services of that Party the same as domestic goods and services. This obligation shall only apply to projects with an estimated value of $7,443,000 or more.

(2) The recipient shall use only domestic or designated country iron, steel, and manufactured goods in performing the work funded in whole or part with this award, except as provided in paragraphs (b)(3) and (b)(4) of this section.

(3) The requirement in paragraph (b)(2) of this section does not apply to the iron, steel, and manufactured goods listed by the Federal Government as follows:

none

(4) The award official may add other iron, steel, and manufactured goods to the list in paragraph (b)(3) of this section if the Federal Government determines that-

(i) The cost of domestic iron, steel, and/or manufactured goods would be unreasonable. The cost of domestic iron, steel, and/or manufactured goods used in the project is unreasonable when the cumulative cost of such material will increase the overall cost of the project by more than 25 percent;

(ii) The iron, steel, and/or manufactured good is not produced, or manufactured in the United States in sufficient and reasonably available commercial quantities of a satisfactory quality; or

(iii) The application of the restriction of section 1605 of the Recovery Act would be inconsistent with the public interest.

(c) Request for determination of inapplicability of section 1605 of the Recovery Act or the Buy American Act. (1)(i) Any recipient request to use foreign iron, steel, and/or manufactured goods in accordance with paragraph (b)(4) of this section shall include adequate information for Federal Government evaluation of the request, including-

(A) A description of the foreign and domestic iron, steel, and/or manufactured goods;

(B) Unit of measure;

(C) Quantity;

(D) Cost;

(E) Time of delivery or availability;

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(F) Location of the project;

(G) Name and address of the proposed supplier; and

(H) A detailed justification of the reason for use of foreign iron, steel, and/or manufactured goods cited in accordance with paragraph (b)(4) of this section.

(ii) A request based on unreasonable cost shall include a reasonable survey of the market and a completed cost comparison table in the format in paragraph (d) of this section.

(iii) The cost of iron, steel, or manufactured goods shall include all delivery costs to the construction site and any applicable duty.

(iv) Any recipient request for a determination submitted after Recovery Act funds have been obligated for a project for construction, alteration, maintenance, or repair shall explain why the recipient could not reasonably foresee the need for such determination and could not have requested the determination before the funds were obligated. If the recipient does not submit a satisfactory explanation, the award official need not make a determination.

(2) If the Federal Government determines after funds have been obligated for a project for construction, alteration, maintenance, or repair that an exception to section 1605 of the Recovery Act applies, the award official will amend the award to allow use of the foreign iron, steel, and/or relevant manufactured goods. When the basis for the exception is nonavailability or public interest, the amended award shall reflect adjustment of the award amount, redistribution of budgeted funds, and/or other appropriate actions taken to cover costs associated with acquiring or using the foreign iron, steel, and/or relevant manufactured goods. When the basis for the exception is the unreasonable cost of the domestic iron, steel, or manufactured goods, the award official shall adjust the award amount or redistribute budgeted funds, as appropriate, by at least the differential established in 2 CFR 176.110(a).

(3) Unless the Federal Government determines that an exception to section 1605 of the Recovery Act applies, use of foreign iron, steel, and/or manufactured goods other than designated country iron, steel, and/or manufactured goods is noncompliant with the applicable Act.

(d) Data. To permit evaluation of requests under paragraph (b) of this section based on unreasonable cost, the applicant shall include the following information and any applicable supporting data based on the survey of suppliers:

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Foreign and Domestic Items Cost Comparison

Description	Unit of measure	Quantity	Cost (dollars)*
Item 1:
Foreign steel, iron, or manufactured good	_________	_________	_________
Domestic steel, iron, or manufactured good	_________	_________	_________
Item 2:
Foreign steel, iron, or manufactured good	_________	_________	_________
Domestic steel, iron, or manufactured good	_________	_________	_________

List name, address, telephone number, email address, and contact for suppliers surveyed. Attach copy of response; if oral, attach summary.

Include other applicable supporting information.

*Include all delivery costs to the construction site.

27. RECOVERY ACT TRANSACTIONS LISTED IN SCHEDULE OF EXPENDITURES OF FEDERAL AWARDS AND RECIPIENT RESPONSIBILITIES FOR INFORMING SUBRECIPIENTS

(a) To maximize the transparency and accountability of funds authorized under the American Recovery and Reinvestment Act of 2009 (Pub. L. 111-5) (Recovery Act) as required by Congress and in accordance with 2 CFR 215.21 “Uniform Administrative Requirements for Grants and Agreements” and OMB Circular A-102 Common Rules provisions, recipients agree to maintain records that identify adequately the source and application of Recovery Act funds. OMB Circular A-102 is available at http://www.whitehouse.gov/omb/circulars/a102/a102.html.

(b) For recipients covered by the Single Audit Act Amendments of 1996 and OMB Circular A-133, “Audits of States, Local Governments, and Non-Profit Organizations,” recipients agree to separately identify the expenditures for Federal awards under the Recovery Act on the Schedule of Expenditures of Federal Awards (SEFA) and the Data Collection Form (SF-SAC) required by OMB Circular A-133. OMB Circular A-133 is available at http://www.whitehouse.gov/omb/circulars/a133/a133.html. This shall be accomplished by identifying expenditures for Federal awards made under the Recovery Act separately on the SEFA, and as separate rows under Item 9 of Part III on the SF-SAC by CFDA number, and inclusion of the prefix “ARRA-” in identifying the name of the Federal program on the SEFA and as the first characters in Item 9d of Part III on the SF-SAC.

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(c) Recipients agree to separately identify to each subrecipient, and document at the time of subaward and at the time of disbursement of funds, the Federal award number, CFDA number, and amount of Recovery Act funds. When a recipient awards Recovery Act funds for an existing program, the information furnished to subrecipients shall distinguish the subawards of incremental Recovery Act funds from regular subawards under the existing program.

(d) Recipients agree to require their subrecipients to include on their SEFA information to specifically identify Recovery Act funding similar to the requirements for the recipient SEFA described above. This information is needed to allow the recipient to properly monitor subrecipient expenditure of ARRA funds as well as oversight by the Federal awarding agencies, Offices of Inspector General and the Government Accountability Office.

28. WAGE RATE REQUIREMENTS UNDER SECTION 1606 OF THE RECOVERY ACT

(a) Section 1606 of the Recovery Act requires that all laborers and mechanics employed by contractors and subcontractors on projects funded directly by or assisted in whole or in part by and through the Federal Government pursuant to the Recovery Act shall be paid wages at rates not less than those prevailing on projects of a character similar in the locality as determined by the Secretary of Labor in accordance with subchapter IV of chapter 31 of title 40, United States Code.

Pursuant to Reorganization Plan No. 14 and the Copeland Act, 40 U.S.C. 3145, the Department of Labor has issued regulations at 29 CFR parts 1, 3, and 5 to implement the Davis-Bacon and related Acts. Regulations in 29 CFR 5.5 instruct agencies concerning application of the standard Davis-Bacon contract clauses set forth in that section. Federal agencies providing grants, cooperative agreements, and loans under the Recovery Act shall ensure that the standard Davis-Bacon contract clauses found in 29 CFR 5.5(a) are incorporated in any resultant covered contracts that are in excess of $2,000 for construction, alteration or repair (including painting and decorating).

(b) For additional guidance on the wage rate requirements of section 1606, contact your awarding agency. Recipients of grants, cooperative agreements and loans should direct their initial inquiries concerning the application of Davis-Bacon requirements to a particular federally assisted project to the Federal agency funding the project. The Secretary of Labor retains final coverage authority under Reorganization Plan Number 14.

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29. DAVIS BACON ACT AND CONTRACT WORK HOURS AND SAFETY STANDARDS ACT

If the Recipient determines at any time that any construction, alteration, or repair activity as defined by 29 CFR 5.2(j) (http://cfr.vlex.com/vid/5-2-definitions-19681309) will be performed during the course of the project, the Recipient shall notify the Contracting Officer prior to commencing such work and the following provisions shall apply. A modification to the award which incorporates the appropriate Davis-Bacon wage rate determination(s) will constitute the Contracting Officer's approval to proceed.

Definitions: For purposes of this provision, “Davis Bacon Act and Contract Work Hours and Safety Standards Act,” the following definitions are applicable:

(1) “Award” means any grant, cooperative agreement or technology investment agreement made with Recovery Act funds by the Department of Energy (DOE) to a Recipient. Such Award must require compliance with the labor standards clauses and wage rate requirements of the Davis-Bacon Act (DBA) for work performed by all laborers and mechanics employed by Recipients (other than a unit of State or local government whose own employees perform the construction) Subrecipients, Contractors, and subcontractors.

(2) “Contractor” means an entity that enters into a Contract. For purposes of these clauses, Contractor shall include (as applicable) prime contractors, Recipients, Subrecipients, and Recipients' or Subrecipients' contractors, subcontractors, and lower-tier subcontractors. “Contractor” does not mean a unit of State or local government where construction is performed by its own employees.”

(3) “Contract” means a contract executed by a Recipient, Subrecipient, prime contractor, or any tier subcontractor for construction, alteration, or repair. It may also mean (as applicable) (i) financial assistance instruments such as grants, cooperative agreements, technology investment agreements, and loans; and, (ii) Sub awards, contracts and subcontracts issued under financial assistance agreements. “Contract” does not mean a financial assistance instrument with a unit of State or local government where construction is performed by its own employees.

(4) “Contracting Officer” means the DOE official authorized to execute an Award on behalf of DOE and who is responsible for the business management and non-program aspects of the financial assistance process.

(5) “Recipient” means any entity other than an individual that receives an Award of Federal funds in the form of a grant, cooperative agreement, or technology investment agreement directly from the Federal Government and is financially accountable for the use of any DOE funds or property, and is legally responsible for carrying out the terms and conditions of the program and Award.

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(6) “Subaward” means an award of financial assistance in the form of money, or property in lieu of money, made under an award by a Recipient to an eligible Subrecipient or by a Subrecipient to a lower-tier subrecipient. The term includes financial assistance when provided by any legal agreement, even if the agreement is called a contract, but does not include the Recipient's procurement of goods and services to carry out the program nor does it include any form of assistance which is excluded from the definition of “Award” above.

(7) “Subrecipient” means a non-Federal entity that expends Federal funds received from a Recipient to carry out a Federal program, but does not include an individual that is a beneficiary of such a program.

(a) Davis Bacon Act

(1) Minimum wages.

(i) All laborers and mechanics employed or working upon the site of the work (or under the United States Housing Act of 1937 or under the Housing Act of 1949 in the construction or development of the project), will be paid unconditionally and not less often than once a week, and, without subsequent deduction or rebate on any account (except such payroll deductions as are permitted by regulations issued by the Secretary of Labor under the Copeland Act (29 CFR part 3)), the full amount of wages and bona fide fringe benefits (or cash equivalents thereof) due at time of payment computed at rates not less than those contained in the wage determination of the Secretary of Labor which is attached hereto and made a part hereof, regardless of any contractual relationship which may be alleged to exist between the Contractor and such laborers and mechanics.

Contributions made or costs reasonably anticipated for bona fide fringe benefits under section 1(b)(2) of the Davis-Bacon Act on behalf of laborers or mechanics are considered wages paid to such laborers or mechanics, subject to the provisions of paragraph (a)(1)(iv) of this section; also, regular contributions made or costs incurred for more than a weekly period (but not less often than quarterly) under plans, funds, or programs which cover the particular weekly period, are deemed to be constructively made or incurred during such weekly period. Such laborers and mechanics shall be paid the appropriate wage rate and fringe benefits on the wage determination for the classification of work actually performed, without regard to skill, except as provided in § 5.5(a)(4). Laborers or mechanics performing work in more than one classification may be compensated at the rate specified for each classification for the time actually worked therein, provided that the employer's payroll records accurately set forth the time spent in each classification in which work is performed. The wage determination (including any additional classification and wage rates conformed under paragraph (a)(1)(ii) of this section) and the Davis-Bacon poster (WH-1321) shall be posted at all times by the Contractor and its subcontractors at the site of the work in a prominent and accessible place where it can be easily seen by the workers.

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(ii) (A) The Contracting Officer shall require that any class of laborers or mechanics, including helpers, which is not listed in the wage determination and which is to be employed under the Contract shall be classified in conformance with the wage determination. The Contracting Officer shall approve an additional classification and wage rate and fringe benefits therefore only when the following criteria have been met:

(1) The work to be performed by the classification requested is not performed by a classification in the wage determination;

(2) The classification is utilized in the area by the construction industry; and

(3) The proposed wage rate, including any bona fide fringe benefits, bears a reasonable relationship to the wage rates contained in the wage determination.

(B) If the Contractor and the laborers and mechanics to be employed in the classification (if known), or their representatives, and the Contracting Officer agree on the classification and wage rate (including the amount designated for fringe benefits where appropriate), a report of the action taken shall be sent by the Contracting Officer to the Administrator of the Wage and Hour Division, U.S. Department of Labor, Washington, DC 20210. The Administrator, or an authorized representative, will approve, modify, or disapprove every additional classification action within 30 days of receipt and so advise the Contracting Officer or will notify the Contracting Officer within the 30-day period that additional time is necessary.

(C) In the event the Contractor, the laborers or mechanics to be employed in the classification or their representatives, and the Contracting Officer do not agree on the proposed classification and wage rate (including the amount designated for fringe benefits, where appropriate), the Contracting Officer shall refer the questions, including the views of all interested parties and the recommendation of the Contracting Officer, to the Administrator for determination. The Administrator, or an authorized representative, will issue a determination within 30 days of receipt and so advise the Contracting Officer or will notify the Contracting Officer within the 30-day period that additional time is necessary.

(D) The wage rate (including fringe benefits where appropriate) determined pursuant to paragraphs (a)(1)(ii)(B) or (C) of this section, shall be paid to all workers performing work in the classification under this Contract from the first day on which work is performed in the classification.

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(iii) Whenever the minimum wage rate prescribed in the Contract for a class of laborers or mechanics includes a fringe benefit which is not expressed as an hourly rate, the Contractor shall either pay the benefit as stated in the wage determination or shall pay another bona fide fringe benefit or an hourly cash equivalent thereof.

(iv) If the Contractor does not make payments to a trustee or other third person, the Contractor may consider as part of the wages of any laborer or mechanic the amount of any costs reasonably anticipated in providing bona fide fringe benefits under a plan or program, provided that the Secretary of Labor has found, upon the written request of the Contractor, that the applicable standards of the Davis-Bacon Act have been met. The Secretary of Labor may require the Contractor to set aside in a separate account assets for the meeting of obligations under the plan or program.

(2) Withholding. The Department of Energy or the Recipient or Subrecipient shall upon its own action or upon written request of an authorized representative of the Department of Labor withhold or cause to be withheld from the Contractor under this Contract or any other Federal contract with the same prime contractor, or any other federally-assisted contract subject to Davis-Bacon prevailing wage requirements, which is held by the same prime contractor, so much of the accrued payments or advances as may be considered necessary to pay laborers and mechanics, including apprentices, trainees, and helpers, employed by the Contractor or any subcontractor the full amount of wages required by the Contract. In the event of failure to pay any laborer or mechanic, including any apprentice, trainee, or helper, employed or working on the site of the work (or under the United States Housing Act of 1937 or under the Housing Act of 1949 in the construction or development of the project), all or part of the wages required by the Contract, the Department of Energy, Recipient, or Subrecipient, may, after written notice to the Contractor, sponsor, applicant, or owner, take such action as may be necessary to cause the suspension of any further payment, advance, or guarantee of funds until such violations have ceased.

(3) Payrolls and basic records.

(i) Payrolls and basic records relating thereto shall be maintained by the Contractor during the course of the work and preserved for a period of three years thereafter for all laborers and mechanics working at the site of the work (or under the United States Housing Act of 1937, or under the Housing Act of 1949, in the construction or development of the project). Such records shall contain the name, address, and social security number of each such worker, his or her correct classification, hourly rates of wages paid (including rates of contributions or costs anticipated for bona fide fringe benefits or cash equivalents thereof of the types described in section 1(b)(2)(B) of the Davis-Bacon Act), daily and weekly number of hours worked, deductions made, and actual wages paid. Whenever the Secretary of Labor has found under 29 CFR 5.5(a)(1)(iv) that the wages of any laborer or mechanic include the amount of any costs reasonably anticipated in

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providing benefits under a plan or program described in section 1(b)(2)(B) of the Davis-Bacon Act, the Contractor shall maintain records which show that the commitment to provide such benefits is enforceable, that the plan or program is financially responsible, and that the plan or program has been communicated in writing to the laborers or mechanics affected, and records which show the costs anticipated or the actual cost incurred in providing such benefits. Contractors employing apprentices or trainees under approved programs shall maintain written evidence of the registration of apprenticeship programs and certification of trainee programs, the registration of the apprentices and trainees, and the ratios and wage rates prescribed in the applicable programs.

(ii) (A) The Contractor shall submit weekly for each week in which any Contract work is performed a copy of all payrolls to the Department of Energy if the agency is a party to the Contract, but if the agency is not such a party, the Contractor will submit the payrolls to the Recipient or Subrecipient (as applicable), applicant, sponsor, or owner, as the case may be, for transmission to the Department of Energy. The payrolls submitted shall set out accurately and completely all of the information required to be maintained under 29 CFR 5.5(a)(3)(i), except that full social security numbers and home addresses shall not be included on weekly transmittals. Instead, the payrolls shall only need to include an individually identifying number for each employee (e.g., the last four digits of the employee's social security number). The required weekly payroll information may be submitted in any form desired. Optional Form WH-347 is available for this purpose from the Wage and Hour Division Web site at http://www.dol.gov/esa/whd/forms/wh347instr.htm or its successor site. The prime Contractor is responsible for the submission of copies of payrolls by all subcontractors. Contractors and subcontractors shall maintain the full social security number and current address of each covered worker, and shall provide them upon request to the Department of Energy if the agency is a party to the Contract, but if the agency is not such a party, the Contractor will submit them to the Recipient or Subrecipient (as applicable), applicant, sponsor, or owner, as the case may be, for transmission to the Department of Energy, the Contractor, or the Wage and Hour Division of the Department of Labor for purposes of an investigation or audit of compliance with prevailing wage requirements. It is not a violation of this section for a prime contractor to require a subcontractor to provide addresses and social security numbers to the prime contractor for its own records, without weekly submission to the sponsoring government agency (or the Recipient or Subrecipient (as applicable), applicant, sponsor, or owner).

(B) Each payroll submitted shall be accompanied by a “Statement of Compliance,” signed by the Contractor or subcontractor or his or her agent who pays or supervises the payment of the persons employed under the Contract and shall certify the following:

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(1) That the payroll for the payroll period contains the information required to be provided under § 5.5 (a)(3)(ii) of Regulations, 29 CFR part 5, the appropriate information is being maintained under § 5.5 (a)(3)(i) of Regulations, 29 CFR part 5, and that such information is correct and complete;

(2) That each laborer or mechanic (including each helper, apprentice, and trainee) employed on the Contract during the payroll period has been paid the full weekly wages earned, without rebate, either directly or indirectly, and that no deductions have been made either directly or indirectly from the full wages earned, other than permissible deductions as set forth in Regulations, 29 CFR part 3;

(3) That each laborer or mechanic has been paid not less than the applicable wage rates and fringe benefits or cash equivalents for the classification of work performed, as specified in the applicable wage determination incorporated into the Contract.

(C) The weekly submission of a properly executed certification set forth on the reverse side of Optional Form WH-347 shall satisfy the requirement for submission of the “Statement of Compliance” required by paragraph (a)(3)(ii)(B) of this section.

(D) The falsification of any of the above certifications may subject the Contractor or subcontractor to civil or criminal prosecution under section 1001 of title 18 and section 3729 of title 31 of the United States Code.

(iii) The Contractor or subcontractor shall make the records required under paragraph (a)(3)(i) of this section available for inspection, copying, or transcription by authorized representatives of the Department of Energy or the Department of Labor, and shall permit such representatives to interview employees during working hours on the job. If the Contractor or subcontractor fails to submit the required records or to make them available, the Federal agency may, after written notice to the Contractor, sponsor, applicant, or owner, take such action as may be necessary to cause the suspension of any further payment, advance, or guarantee of funds. Furthermore, failure to submit the required records upon request or to make such records available may be grounds for debarment action pursuant to 29 CFR 5.12.

(4) Apprentices and trainees-

(i) Apprentices. Apprentices will be permitted to work at less than the predetermined rate for the work they performed when they are employed pursuant to and individually registered in a bona fide apprenticeship program registered with the U.S. Department of Labor, Employment and Training Administration, Office of Apprenticeship Training, Employer and Labor Services, or with a State

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Apprenticeship Agency recognized by the Office, or if a person is employed in his or her first 90 days of probationary employment as an apprentice in such an apprenticeship program, who is not individually registered in the program, but who has been certified by the Office of Apprenticeship Training, Employer and Labor Services or a State Apprenticeship Agency (where appropriate) to be eligible for probationary employment as an apprentice. The allowable ratio of apprentices to journeymen on the job site in any craft classification shall not be greater than the ratio permitted to the Contractor as to the entire work force under the registered program. Any worker listed on a payroll at an apprentice wage rate, who is not registered or otherwise employed as stated above, shall be paid not less than the applicable wage rate on the wage determination for the classification of work actually performed. In addition, any apprentice performing work on the job site in excess of the ratio permitted under the registered program shall be paid not less than the applicable wage rate on the wage determination for the work actually performed. Where a Contractor is performing construction on a project in a locality other than that in which its program is registered, the ratios and wage rates (expressed in percentages of the journeyman's hourly rate) specified in the Contractor's or subcontractor's registered program shall be observed. Every apprentice must be paid at not less than the rate specified in the registered program for the apprentice's level of progress, expressed as a percentage of the journeymen hourly rate specified in the applicable wage determination. Apprentices shall be paid fringe benefits in accordance with the provisions of the apprenticeship program. If the apprenticeship program does not specify fringe benefits, apprentices must be paid the full amount of fringe benefits listed on the wage determination for the applicable classification. If the Administrator determines that a different practice prevails for the applicable apprentice classification, fringes shall be paid in accordance with that determination. In the event the Office of Apprenticeship Training, Employer and Labor Services, or a State Apprenticeship Agency recognized by the Office, withdraws approval of an apprenticeship program, the Contractor will no longer be permitted to utilize apprentices at less than the applicable predetermined rate for the work performed until an acceptable program is approved.

(ii) Trainees. Except as provided in 29 CFR 5.16, trainees will not be permitted to work at less than the predetermined rate for the work performed unless they are employed pursuant to and individually registered in a program which has received prior approval, evidenced by formal certification by the U.S. Department of Labor, Employment and Training Administration. The ratio of trainees to journeymen on the job site shall not be greater than permitted under the plan approved by the Employment and Training Administration. Every trainee must be paid at not less than the rate specified in the approved program for the trainee's level of progress, expressed as a percentage of the journeyman hourly rate specified in the applicable wage determination. Trainees shall be paid fringe benefits in accordance with the provisions of the trainee program. If the trainee program does not mention fringe benefits, trainees shall be paid the full amount of fringe benefits listed on the wage determination unless the Administrator of the

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Wage and Hour Division determines that there is an apprenticeship program associated with the corresponding journeyman wage rate on the wage determination which provides for less than full fringe benefits for apprentices. Any employee listed on the payroll at a trainee rate who is not registered and participating in a training plan approved by the Employment and Training Administration shall be paid not less than the applicable wage rate on the wage determination for the classification of work actually performed. In addition, any trainee performing work on the job site in excess of the ratio permitted under the registered program shall be paid not less than the applicable wage rate on the wage determination for the work actually performed. In the event the Employment and Training Administration withdraws approval of a training program, the Contractor will no longer be permitted to utilize trainees at less than the applicable predetermined rate for the work performed until an acceptable program is approved.

(iii) Equal employment opportunity. The utilization of apprentices, trainees, and journeymen under this part shall be in conformity with the equal employment opportunity requirements of Executive Order 11246, as amended and 29 CFR part 30.

(5) Compliance with Copeland Act requirements. The Contractor shall comply with the requirements of 29 CFR part 3, which are incorporated by reference in this Contract.

(6) Contracts and Subcontracts. The Recipient, Subrecipient, the Recipient's, and Subrecipient's contractors and subcontractor shall insert in any Contracts the clauses contained herein in(a)(1) through (10) and such other clauses as the Department of Energy may by appropriate instructions require, and also a clause requiring the subcontractors to include these clauses in any lower tier subcontracts. The Recipient shall be responsible for the compliance by any subcontractor or lower tier subcontractor with all of the paragraphs in this clause.

(7) Contract termination: debarment. A breach of the Contract clauses in 29 CFR 5.5 may be grounds for termination of the Contract, and for debarment as a contractor and a subcontractor as provided in 29 CFR 5.12.

(8) Compliance with Davis-Bacon and Related Act requirements. All rulings and interpretations of the Davis-Bacon and Related Acts contained in 29 CFR parts 1, 3, and 5 are herein incorporated by reference in this Contract.

(9) Disputes concerning labor standards. Disputes arising out of the labor standards provisions of this Contract shall not be subject to the general disputes clause of this Contract. Such disputes shall be resolved in accordance with the procedures of the Department of Labor set forth in 29 CFR parts 5, 6, and 7. Disputes within the meaning of this clause include disputes between the Recipient, Subrecipient, the Contractor (or any of its subcontractors), and the contracting agency, the U.S. Department of Labor, or the employees or their representatives.

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(10) Certification of eligibility.

(i) By entering into this Contract, the Contractor certifies that neither it (nor he or she) nor any person or firm who has an interest in the Contractor's firm is a person or firm ineligible to be awarded Government contracts by virtue of section 3(a) of the Davis-Bacon Act or 29 CFR 5.12(a)(1).

(ii) No part of this Contract shall be subcontracted to any person or firm ineligible for award of a Government contract by virtue of section 3(a) of the Davis-Bacon Act or 29 CFR 5.12(a)(1).

(iii) The penalty for making false statements is prescribed in the U.S. Criminal Code, 18 U.S.C. 1001.

(b) Contract Work Hours and Safety Standards Act. As used in this paragraph, the terms laborers and mechanics include watchmen and guards.

(1) Overtime requirements. No Contractor or subcontractor contracting for any part of the Contract work which may require or involve the employment of laborers or mechanics shall require or permit any such laborer or mechanic in any workweek in which he or she is employed on such work to work in excess of forty hours in such workweek unless such laborer or mechanic receives compensation at a rate not less than one and one-half times the basic rate of pay for all hours worked in excess of forty hours in such workweek.

(2) Violation; liability for unpaid wages; liquidated damages. In the event of any violation of the clause set forth in paragraph (b)(1) of this section, the Contractor and any subcontractor responsible therefor shall be liable for the unpaid wages. In addition, such Contractor and subcontractor shall be liable to the United States (in the case of work done under contract for the District of Columbia or a territory, to such District or to such territory), for liquidated damages. Such liquidated damages shall be computed with respect to each individual laborer or mechanic, including watchmen and guards, employed in violation of the clause set forth in paragraph (b)(1) of this section, in the sum of $10 for each calendar day on which such individual was required or permitted to work in excess of the standard workweek of forty hours without payment of the overtime wages required by the clause set forth in paragraph (b)(1) of this section.

(3) Withholding for unpaid wages and liquidated damages. The Department of Energy or the Recipient or Subrecipient shall upon its own action or upon written request of an authorized representative of the Department of Labor withhold or cause to be withheld, from any moneys payable on account of work performed by the Contractor or subcontractor under any such contract or any other Federal contract with the same prime Contractor, or any other federally-assisted contract subject to the Contract Work Hours and Safety Standards Act, which is held by the same prime contractor, such sums as may be determined to be necessary to satisfy any liabilities of such Contractor or subcontractor for unpaid wages and liquidated damages as provided in the clause set forth in paragraph (b)(2) of this section.

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(4) Contracts and Subcontracts. The Recipient, Subrecipient, and Recipient's and Subrecipient's contractor or subcontractor shall insert in any Contracts, the clauses set forth in paragraph (b)(1) through (4) of this section and also a clause requiring the subcontractors to include these clauses in any lower tier subcontracts. The Recipient shall be responsible for compliance by any subcontractor or lower tier subcontractor with the clauses set forth in paragraphs (b)(1) through (4) of this section.

(5) The Contractor or subcontractor shall maintain payrolls and basic payroll records during the course of the work and shall preserve them for a period of three years from the completion of the Contract for all laborers and mechanics, including guards and watchmen, working on the Contract. Such records shall contain the name and address of each such employee, social security number, correct classifications, hourly rates of wages paid, daily and weekly number of hours worked, deductions made, and actual wages paid. The records to be maintained under this paragraph shall be made available by the Contractor or subcontractor for inspection, copying, or transcription by authorized representatives of the Department of Energy and the Department of Labor, and the Contractor or subcontractor will permit such representatives to interview employees during working hours on the job.

(c) Recipient Responsibilities for Davis Bacon Act

(1) On behalf of the Department of Energy (DOE), Recipient shall perform the following functions:

(i) Obtain, maintain, and monitor all Davis Bacon Act (DBA) certified payroll records submitted by the Subrecipients and Contractors at any tier under this Award;

(ii) Review all DBA certified payroll records for compliance with DBA requirements, including applicable DOL wage determinations;

(iii) Notify DOE of any non-compliance with DBA requirements by Subrecipients or Contractors at any tier, including any non-compliances identified as the result of reviews performed pursuant to paragraph (ii) above;

(iv) Address any Subrecipient and any Contractor DBA non-compliance issues; if DBA non-compliance issues cannot be resolved in a timely manner, forward complaints, summary of investigations and all relevant information to DOE;

(v) Provide DOE with detailed information regarding the resolution of any DBA non-compliance issues;

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(vi) Perform services in support of DOE investigations of complaints filed regarding noncompliance by Subrecipients and Contractors with DBA requirements;

(vii) Perform audit services as necessary to ensure compliance by Subrecipients and Contractors with DBA requirements and as requested by the Contracting Officer; and

(viii) Provide copies of all records upon request by DOE or DOL in a timely manner.

(d) Rates of Wages

The minimum wages to be paid laborers and mechanics under this award involved in performance of work at the project site, as determined by the Secretary of Labor to be prevailing for the corresponding classes of laborers and mechanics employed on projects of a character similar to the contract work in the pertinent locality, are found at http://www.wdol.gov/, by clicking on “Selecting DBA WDs”. The Wage Determination Number(s) and General Decision Number(s) specific to this award are found below. These wage rates are minimum rates and are not intended to represent the actual wage rates that the Contractor may have to pay.

CONSTRUCTION TYPE	WAGE DETERMINATION NUMBER	GENERAL DECISION NUMBER
Building	CA29, CO7, CA25, KS8	CA100029 03/19/2010 CA29 CO100007 03/12/2010 CO7 CA100025 03/12/2010 CA25 KS100008 03/19/2010 KS8
Highway	n/a	n/a
Residential	n/a	n/a

30. CONTINGENCY

(a) Contingency Requirement. A minimum amount of Contingency is required for awards selected under Funding Opportunity Announcement DE-FOA-0000096. “Contingency” is defined in the Appendix as: “a provision in the Project Management Plan to mitigate cost and/or schedule risk.” Contingency funds must be (a) liquid, (b) immediately available, and (c) unrestricted funds dedicated exclusively to the Project for the purpose of mitigating project performance baseline risk. Contingency funds may come from a variety of sources, as approved by the Contracting Officer on a case-by-case basis in accordance with the Appendix to these Special Terms and Conditions (Attachment 5).

(b) Minimum Amount of Contingency. Initial Contingency funds shall be not less than 25 percent of the Total Project Cost that begins with Budget Period 2, as more specifically described in Section B(2) of the Appendix to these Special Terms and Conditions (Attachment 5).

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(c) Contingency Not Counted Toward Cost Share or DOE Reimbursement. Contingency is in addition to the Total Project Cost and cannot count toward cost share or result in reimbursement by DOE above the share approved in the award.

(d) Appendix. All of the terms and conditions set forth in this provision shall be further subject to the requirements and clarifications of Attachment 5.

31. NATIONAL ENVIRONMENTAL POLICY ACT (NEPA) REQUIREMENTS

For this award, DOE has made a final NEPA determination for all activities under this award that are listed in the Statement of Project Objectives (SOPO) formally approved by DOE through incorporation into and attached to the award. You (Recipient) may proceed with the activities as described in the SOPO. This NEPA determination is specific to the project as described in the SOPO formally approved by DOE through incorporation into and attached to the award.

If you later add to or modify the activities in the above-referenced SOPO, you must submit the revised SOPO to the DOE Project Officer. Those additions or modifications are subject to review by the NEPA Compliance Officer and approval by the DOE's Contracting Officer. Recipients are restricted from taking any action using Federal funds, which would have an adverse effect on the environment or limit the choice of reasonable alternatives prior to DOE providing a final NEPA determination. Any new activities or modification of activities is subject to additional NEPA review and is not authorized for federal funding until DOE provides a NEPA determination on those additions or modifications. DOE may require the Recipient to submit additional information to support a revised NEPA determination. Should you move forward with activities that are not authorized for Federal funding by the DOE Contracting Officer in advance of the final NEPA determination, you are doing so at risk of not receiving Federal funding and such costs may not be recognized as allowable cost share.

32. SUBCONTRACT APPROVALS

a. At Risk Notice: The Recipient must obtain written approval by the Contracting Officer for reimbursement of costs associated with subcontractors/activities listed in paragraph b. below. No funds shall be expended on the subcontracts supporting the tasks identified in paragraph b. below unless DOE approval is provided. DOE does not guarantee or assume any obligation to reimburse costs incurred by the Recipient or subcontractor for these tasks, until approval is provided in writing by the Contracting Officer.

b. Contracting Officer approval as set out above is requested for the following:

Activity and SubcontractorsTotal Amount ($)

TBD - Product Testing        $20,000

TBD - Analysis            $15,000

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The DOE Contracting Officer may require additional information concerning these tasks prior to providing written approval.

c. Upon written approval by the Contracting Officer, the Recipient may then receive payment for the tasks identified in paragraph b. above for allowable costs incurred, or DOE will recognize costs incurred toward cost share requirements, if any, in accordance with the payment provisions contained in the Special Terms and Conditions of this agreement.

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EX-10.37

CONFIDENTIAL TREATMENT REQUESTED. CERTAIN PORTIONS OF THIS DOCUMENT HAVE BEEN OMITTED PURSUANT TO A REQUEST FOR CONFIDENTIAL TREATMENT AND, WHERE APPLICABLE, HAVE BEEN MARKED WITH AN ASTERISK TO DENOTE WHERE OMISSIONS HAVE BEEN MADE. THE CONFIDENTIAL MATERIAL HAS BEEN FILED SEPARATELY WITH THE SECURITIES AND EXCHANGE COMMISSION.

LEASE AGREEMENT

By this private lease agreement (hereinafter simply referred to as “Agreement”),

PARAÍSO BIONERGIA S.A., a corporation with head office at Rodovia Brotas/Torrinha, km 7.5, Fazenda Paraíso, in the City of Brotas, State of São Paulo, Corporate Taxpayer Enrollment Number CNPJ/MF No. 46.363.016/0001-60, herein represented in accordance with its Articles of Incorporation and hereinafter simply referred to as “Paraíso”, “Party”, or “Lessor”, and

AMYRIS BRASIL S.A., a corporation with head office in the City of Campinas, State of São Paulo, at Rua James Clerk Maxwell, 315, Techno Park, Corporate Taxpayer Enrollment Number CNPJ/MF No. 09.379.224.0001/20, herein represented in accordance with its Bylaws and hereinafter simply referred to as “Amyris”, “Party”, or “Lessee”,

WHEREAS:

(A) Amyris is a technology company focused on the research, development, production and sale of high-performance renewable chemicals, which produces certain renewable products based on the microbial technology developed by it to convert simple sugars into specific compounds by means of fermentation;

(B) Paraíso is a sugar, alcohol and power plant which produces sugarcane juice as a byproduct;

(C) Amyris and Paraíso executed, on the date hereof, an Agreement for the Supply of Sugarcane Juice and Other Utilities (“Supply Agreement”), which establishes the obligations and liabilities of the parties for full compliance with the obligations assumed thereunder;

(D) Paraíso is the lawful owner of a tract of land and some rights-of-way located in the City of Brotas, State of São Paulo, which are described in Exhibit I hereto (hereinafter referred to as “Real Property”);

(E) Pursuant to the provisions hereof, Paraíso wishes to deliver the Real Property to Amyris for construction of an industrial plant for sugarcane juice evaporation and fermentation (“Amyris Biorefinery”), which shall be operated and maintained by Amyris or by third parties engaged by Amyris;

(F) Except for the first perfected mortgage bond certificate exclusively in behalf of Banco do Brasil S.A., registered in [*] under [*] and the amendments to which are registered under [*], and for the second mortgage bond certificate in behalf of Banco Rabobank International Brasil S.A., the conditions of which are not breached hereby, the Real Property is free and clear of any options, rights of first refusal, attachments, debts, outstanding taxes and any other liens or encumbrances in any way limiting conduction of Amyris' activities, as contemplated herein, either of an environmental nature, imposed by zoning rules or of any other nature;

(G) Paraíso represents and warrants that this instrument does not breach any provision of the planned Agreement with Creditors contemplated in the Request for Homologation of Agreement with Creditors No. 095.01.2009.005156-00, in progress in the Court of the Judicial District of Brotas, State of São Paulo (“Plan”) ;

NOW, THEREFORE, the parties resolve to execute this Agreement, which shall be governed by the following clauses and conditions:

SECTION ONE - SUBJECT MATTER, TERM AND EFFECTIVENESS

1.1.    Paraíso hereby leases the Real Property to Amyris, which shall build and operate or engage third parties to build and operate the Amyris Biorefinery, pursuant to the provisions of law 8245/91.

1.2.    This Agreement shall be effective as of the date of execution hereof, and it shall remain valid and effective for fifteen (15) years as from the date of execution hereof.

1.3.    This Agreement shall be terminated in the event of early termination of the Supply Agreement, pursuant to the provisions of Subsections 8.1 and 8.3 thereof.

1.4.    The Parties acknowledge that Amyris shall return the Real Property to Paraíso upon termination of the Agreement, it being understood that Amyris may remove the machines and equipment installed therein, as agreed between the Parties in due course.

1.5.    The Parties acknowledge and agree that necessary improvements carried out by Amyris in the Real Property, which shall be understood as improvements required for the proper and actual use of the real property for the purposes for which it has been leased, shall be indemnified by Paraíso provided they are informed by Amyris to Paraíso in writing, at least five (5) business days in advance.

1.5.1.     The indemnification contemplated in Subsection 1.5 above shall be paid within at most ten (10) business days as of the day on which Amyris makes the necessary improvement and submits the respective proofs of payment of expenses, provided completion of such improvements has been informed to Paraíso.

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

1.6.    The Parties acknowledge and agree that valuable improvements, i.e., improvements for the purpose of increasing, improving or facilitating the use of the Real Property, which are made by Amyris with the prior consent of Paraíso and which, as agreed between the Parties, shall remain in the Real Property and shall not be removed, shall be indemnified at the end of the lease.

1.7.    Voluntary improvements and those exclusively related to the construction, installation, assembly, operation and maintenance of Amyris Biorefinery or, furthermore, any other improvement in addition to those mentioned in Subsections 1.5 and 1.6 above, shall not be indemnified by Paraíso, except as otherwise agreed between the Parties.

1.8.    The machines and equipment of Amyris Biorefinery, as agreed between the Parties from time to time, may be removed by Amyris upon termination hereof, provided such removal does not affect the structure and substance of the real property.

1.9.    At its sole discretion and expense, Amyris may inspect the Real Property on the date on which it is granted possession thereof, and it shall deliver a copy thereof to Paraíso, which shall not be bound to such inspection for any purpose.

SECTION TWO - PAYMENT

2.1.    Amyris shall pay Paraíso a monthly rent of twenty thousand Brazilian Reais (R$20,000.00) for the lease established herein.

2.2.    The amount contemplated in subsection 2.1 above shall be monthly paid by Amyris, by means of credit to checking account No. [*], held by Paraíso, subject to the bank hours in the city of Campinas, State of São Paulo, it being understood that the respective certificates of deposit shall serve as proof of payment and acquittance.

2.3.     Failure to pay any installment of the price on the maturity date shall subject Amyris to pay the outstanding installment adjusted in accordance with the Brazilian Extended Consumer Price Index -IPCA, as disclosed by the Brazilian Geography and Statistics Institute - IBGE, plus a default fine of two percent (2%) and default interest at the rate of one percent (1%) per month, calculated per day of delay.

Sole paragraph - Amyris shall be granted a tolerance of three (3) business days in the event it fails to make the payment on the agreed date, for any reason. After this period, the charges agreed in this Section shall retroact to the first day of delay in payment of the rent owed.

2.4.    Paraíso represents and warrants that the amount of the Brazilian Rural Land Tax - ITR levied on the Real Property is included in the price of the rent, it being understood that Paraíso shall pay the whole ITR levied on the farm where the Real Property is located, including the portion corresponding to the Real Property area. Paraíso shall exempt Amyris from any liability with regard to payment of the ITR levied on the Real Property.

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

SECTION THREE - OBLIGATIONS

3.1.    In addition to the other obligations assumed hereunder, the following are the obligations and liens of Paraíso during effectiveness hereof:

a) To ensure peaceable and uncontested possession of the Real Property to Amyris, continuity of Amyris Biorefinery's operations, protection against complaints, misfeasance and trespass by third parties, security and control of the access to the Real Property, prohibiting the entry of employees and third parties not involved in the operations of Amyris Biorefinery, and being liable to Amyris for any damage and/or loss caused to Amyris by the fault of Paraíso, as well as by the fault of its respective representatives and contractors;

b) Subject to the terms and conditions of the Supply Agreement, to provide or execute all documents that may be required for Amyris to obtain the permits and licenses required by law for conduction of the activities of Amyris Biorefinery, including those relating to the possible establishment of a branch on the leased land, pursuant to the provisions of article 1000 of Law 10406/02;

c) Neither to assign nor to transfer the use of the Real Property to third parties, wholly or in part;

d) Not to alienate, encumber or burden the Real Property without the prior written consent of Amyris, as well as to immediately cancel any attachment, seizure or encumbrance of any kind created by third parties on the Real Property, except for the first perfected mortgage bond certificate exclusively in behalf of Banco do Brasil S.A., registered in [*] under [*] and the amendments to which are registered under [*], and for the second mortgage bond certificate in behalf of Banco Rabobank International Brasil S.A., which have already been created;

e) Not to assign, transmit or transfer to Amyris, directly or indirectly, any of its obligations and liabilities resulting from ownership or possession of the Real Property;

f) To be liable to the governmental authorities and to any third party, without prejudice to the provisions of subsection 3.2(e) hereof, for all obligations relating to the Real Property, including, without limitation to, any contaminations or environmental liabilities, the creation, maintenance, regularization and/or recovery of legal reserves and/or permanent protection areas, licenses and other applicable environmental obligations, as well as for taxes and charges of any kind levied on the Real Property;

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

g) To allow Amyris to establish and maintain a branch in the Real Property's facilities as part of the subject matter hereof;

h) To allow Amyris to grant free access to and/or to assign, wholly or in part, the right of use of the Real Property to its representatives and contractors involved in the construction, operation and maintenance of Amyris Biorefinery;

i) To indemnify Amyris for the necessary improvements, pursuant to the terms and conditions of Subsections 1.5, 1.6 and 1.7 hereof.

3.2.    In addition to the other obligations assumed hereunder, the following are the obligations and liens of Amyris during effectiveness hereof:

a) To pay the rent in the form and within the term established herein;

b) To exercise care for the Real Property and to keep it in a perfect state of conservation and cleanliness;

c) Neither to assign nor to transfer the use of the Real Property to third parties without the prior and express approval of Paraíso;

d) To observe the determinations of the competent public authorities and to cause compliance with all applicable rules and determinations of federal, state and municipal authorities with regard to the use of the Real Property;

e) To observe the applicable environmental law, being liable for the damages provenly caused to the Real Property by the exclusive fault and/or negligence of Amyris and/or its subcontractors, during the period of installation of Amyris Biorefinery.

SECTION FOUR - OBLIGATION TO INDEMNIFY

4.1.    Each Party (hereinafter referred to as “Responsible Party”) assumes the obligation to fully and unconditionally indemnify the other Party (hereinafter referred to as “Aggrieved Party”), without any limitation with regard to the time and amount, for

(i) any and all damages or losses of any nature or amount, as well as mental anguish and any and all expenses relating to such damages or losses, including, without limitation to, taxes plus fines and interest, court costs, attorneys', consultants', accountants' or auditors' fees incurred by the Aggrieved Party as a result of the breach of or noncompliance with any of the duties or obligations of the Responsible Party contemplated herein; and

(ii) any and all losses and damages in any amount relating to liabilities or contingencies of any kind concerning Amyris Biorefinery and the generating event of which is a negligent or malicious action or failure to act of the Responsible Party, including, without limitation to, any labor, social security, tax, civil, commercial, environmental or regulatory liabilities or contingencies or any other liability relating to the Real Property.

(the losses and damages described in items “(i)” and “(ii)” above are hereinafter collectively referred to as “Losses”).

4.2.    Any and all amounts resulting from the provisions of Subsection 4.1 owed by one of the Parties to the other shall be paid within at most ten (10) days as from the date of receipt, by the Responsible Party, of the collection notice to be sent by the Aggrieved Party.

4.3.    In any of the events contemplated herein where (a) the Responsible Party is required to pay amounts owed by it or to reimburse the Aggrieved Party for these amounts, or (b) the Aggrieved Party is required to disburse the amounts owed by the Responsible Party or such disbursements are required for regular continuity of the obligations contemplated herein, upon receipt of a notice sent by the Aggrieved Party, the Responsible Party shall immediately credit the required funds, in cash, to a checking account to be timely informed by the Aggrieved Party for payment of such amounts.

SECTION FIVE - GENERAL PROVISIONS

5.1.    The provisions of the Supply Agreement and corresponding exhibits shall apply to this Agreement whenever applicable, especially with regard to conflict resolution.

5.2.    All notices sent hereunder shall be sent in writing and delivered personally against signature of a receipt by the other Party, which personal delivery may be substituted by facsimile transmission with proof of receipt, express mail with certified delivery or certified mail, return receipt requested, but always to the following addresses and to the attention of the following representatives of the parties:

If to Amyris:

Attn.: Roel Win Collier

Copy to: Odair Glavina

Rua James Clerk Maxwell, 315 Campinas/SP, CEP 13.088-900

Fax: [*]

If to Paraíso:

Dario Costa Gaeta

Copy to: Djalma Sebastião Fiori

Fax: [*]

5.3.    None of the Parties may assign, transfer or encumber its rights, interest or obligations hereunder without the prior written consent of the other Party.

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

5.4.    The terms or provisions hereof may be changed, amended, modified, cancelled or extinguished in writing, upon the mutual consent of the Parties.

5.5.    No forbearance of the parties with regard to the other Party's failure to comply with obligations or with the regular and timely exercise of its rights shall constitute a desistance of, amendment to, modification, waiver or novation of any of their rights herein established, contemplated and agreed.

5.6.    This Agreement and the obligations contemplated herein shall be governed and construed in accordance with the laws of Brazil.

5.7.    This Agreement is irrevocably and irreversibly executed and it is binding upon the Parties, the Intervening Parties and their successors on any account, pursuant to the provisions of the applicable law.

5.8.     The Parties acknowledge that the negotiation and execution hereof rigorously comply with the doctrines of honesty and good faith, which shall also be observed by the Parties in the exercise of their respective rights and for compliance with their obligations hereunder.

5.9.     Amyris may, at its sole discretion and expense, register this Agreement with the competent authorities.

5.10.     The Parties hereby agree to execute any and all applications, documents and agreements that are necessary or required for formalization of the obligations contemplated herein, including those relating to obtainment of the required permits for Amyris Biorefinery and establishment of Amyris' branch.

5.11.     This Agreement shall be governed, to the extent that it is silent, by the provisions of Law No. 8245/91, as amended.

IN WITNESS WHEREOF, the parties execute this private lease agreement in two (2) counterparts of equal contents and form, in the presence of the undersigned witnesses.

Campinas, March 18, 2011.

Lessor - PARAÍSO BIOENERGIA S.A.

/s/ Dario Costa Gaeta

Name: Dario Costa Gaeta

Title: Chief Executive Officer

/s/ Roel Win Collier

Name:

Title:

/s/ Fabio Schettino

Name: Fabio Schettino

Title: CFO

Lessee - AMYRIS BRASIL S.A.

_____________________________            ______________________________

Name:                            Name:

Title:                            Title:

Witnesses:

1.                            2.

/s/ Gabriel Mundim        /s/ Isadora C. Cohen        

Name: Gabriel Mundim                    Isadora C. Cohen

ID: [*]                            ID: [*]

CPF/MF: [*]                         CPF/MF: [*]

(This signature Page belongs to the Lease Agreement executed on March 18, 2011 between Amyris Brasil S.A. and Paraíso Bioenergia S.A.)

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

LEASE AGREEMENT

EXHIBIT I

DESCRIPTION OF THE REAL PROPERTY

Real Property Enrollment: No. 15.619 (part occupancy) of the Real Estate Registry Office and Related Offices of the Judicial District of Brotas, State of São Paulo, as per the copy attached hereto.

Real Property Description: Pursuant to the Specifications and plan attached hereto.

Map of Real Property - illegible

EX-10.38

CONFIDENTIAL TREATMENT REQUESTED. CERTAIN PORTIONS OF THIS DOCUMENT HAVE BEEN OMITTED PURSUANT TO A REQUEST FOR CONFIDENTIAL TREATMENT AND, WHERE APPLICABLE, HAVE BEEN MARKED WITH AN ASTERISK TO DENOTE WHERE OMISSIONS HAVE BEEN MADE. THE CONFIDENTIAL MATERIAL HAS BEEN FILED SEPARATELY WITH THE SECURITIES AND EXCHANGE COMMISSION.

ADDENDUM TO LEASE AGREEMENT

which between them form

PARAÍSO BIOENERGY SA liability company by shares, headquartered in Highway Brotas / Torrinha, km 7.5, PARAÍSO Farm, in the city of Brotas State of São Paulo, enrolled with the CNPJ / MF under n. º 46.363.016/0001- 60, herein represented in the form of its Constitutive Instruments, hereinafter simply called "PARAÍSO", "Party", or "Lessor", and

Amyris BRAZIL SA, a corporation, headquartered in Campinas, São Paulo, Rua James Clerk Maxwell, 315, Techno Park, duly enrolled with the CNPJ / MF under n. º 09.379.224.0001/20, herein represented pursuant to its Bylaws, hereinafter referred to as "Amyris," "Party," or "Lessee"

WHEREAS:

(A) The Parties signed on 18 March 2011 Lease Agreement ("Agreement") whereby it was agreed that the Lessee to Lessor cede a property located in the municipality of Sprouts, State of São Paulo, as described in in Annex I to that Agreement;

(B) The Agreement was signed in order to allow Lessor to build houses in the Biorefinery Amyris, all under the Supply Agreement Broth Cane Sugar and Other Utilities ("Supply Agreement"), entered into between Lessor and Lessee;

(C) The Parties agree that Amyris will enjoy a grace period of rent, which is due only from the start of operation of Biorefinery Amyris, notwithstanding the Contract is valid and in existence since his signature;

resolve the parties enter into this Addendum to Lease Agreement ("Amendment"), in accordance with the following terms and conditions:

SECTION ONE - DEFINITIONS

1.1 Unless expressly provided otherwise, the terms defined in this Amendment shall have the meanings assigned to them in the Agreement.

SECOND CLAUSE - WAITING PERIOD AND SECOND AMENDMENT OF CLAUSE OF THE CONTRACT

2.1 The Parties have resolved over the vesting period of the rent agreed upon, adding a sub-clause 2.2 below, renumbering the others:

"2.2 It is hereby agreed upon between the Parties agreed that the monthly rent hereunder shall only be payable by Lessor to Lessee from the moment the Biorefinery Amyris operates, without prejudice to the full validity and enforceability of this Agreement, from date of signature. "

2.2    In view of the above amendment agreed upon, the Second Clause of the Contract shall have the following wording:

"SECOND CLAUSE - PAYMENT

2.1 For the lease set forth herein, Amyris will pay the monthly rent of PARAÍSO U.S. $ 20,000.00 (twenty thousand dollars).

2.2 It is hereby agreed upon between the Parties agreed that the monthly rent hereunder shall only be payable by Lessor to Lessee from the moment the Biorefinery Amyris operates, without prejudice to the full validity and enforceability of this Agreement, from the date his signature.

2.3 The amount referred to in clause 2.1. above shall be paid monthly by Amyris, through bank deposit in current account No. [*], owned by PARAÍSO respected banking hours in Campinas - SP, using their deposit slips as proof of payment and discharge.

2.4 The non-payment of any portion of the price at maturity of Amyris will subject to payment of the installment due and unpaid, adjusted by the variation of the Consumer Price Index - IPCA, published by the Brazilian Institute of Geography and Statistics - IBGE plus late-payment penalty of 2% (two percent) and default interest of 1% (one percent) per month, pro rata.

§ - A tolerance of 3 (three) business days will be awarded to Amyris, if that, for whatever reason, can not make the payment on the date agreed upon. End of that period, the charges agreed this Clause retroacts the date of the first day of delay in the payment of rent due.

2.5 The PARAÍSO represents and warrants that the value of the Rural Land Tax - ITR levied on the property is included in the rent, and the PARAÍSO ITR collect the whole incident on the farm where the property is located, including the portion corresponding to the area Property. The PARAÍSO Amyris shall exempt from any liability regarding the payment of ITR levied on the property. "

THIRD CLAUSE - RETROACTIVITY THE EFFECTS OF NEW WRITING

3.1 The parties hereby declare and acknowledge that always had the intention that the rent agreed upon in the contract because it was only after the beginning of the entry of Amyris biorefinery in operation, and there is therefore any amounts payable by Lessee to Lessor, the Title of rent from the date of signing of this Agreement so far.

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

SECTION FOUR - OTHER PROVISIONS

4.1 They are kept fully valid and all other provisions not expressly modified by this Amendment.

SO BEING FAIR AND CONTRACTORS, sign this Addendum in two (2) copies of equal form and content, in the presence of the undersigned witnesses.

Campinas, April 28, 2011.

Lessor - PARAÍSO BIOENERGY S.A.

/s/ Dario Costa Gaeta            /s/ Djalma Sebastiao Fiore        

Dario Costa Gaeta                    Djalma Sebastiao Fiore

Director                         Director

Lessee - BRAZIL SA Amyris

/s/ Roel Win Collier            /s/ Fabio Abreu Schettino        

Roel Win Collier                    Fabio Abreu Schettino

Director                        Director

Witnesses:

1.                            2.

Name:                            Name:

RG:                            RG:

CPF/MF:                        CPF/MF:

EX-10.51

CONFIDENTIAL TREATMENT REQUESTED. CERTAIN PORTIONS OF THIS DOCUMENT HAVE BEEN OMITTED PURSUANT TO A REQUEST FOR CONFIDENTIAL TREATMENT AND, WHERE APPLICABLE, HAVE BEEN MARKED WITH AN ASTERISK TO DENOTE WHERE OMISSIONS HAVE BEEN MADE. THE CONFIDENTIAL MATERIAL HAS BEEN FILED SEPARATELY WITH THE SECURITIES AND EXCHANGE COMMISSION.

THIRD AMENDMENT TO THE PRIVATE ACT OF NON RESIDENTIAL

REALTY LEASE CONTRACT

By the present Third Amendment to the Private Act of Non Residential Realty Lease Contract (the “Third Amendment”) and in the best form of the law, the below designated parties (jointly, the “Parties”):

LESSORS: LÚCIO TOMASIELLO, Brazilian, single, over 18 years of age, businessman, bearer of identity card RG number [*], enrolled at CPF/MF under number [*], resident and domiciled in the City of Campinas, State of São Paulo, at [*]; and MAURÍCIO TOMASIELLO, Brazilian, single, over 18 years of age, businessman, bearer of identity card RG number [*], enrolled at CPF/MF under number [*], resident and domiciled in the City of Jundiaí, State of São Paulo, at [*].

LESSEE: AMYRIS BRASIL LTDA., private limited company with head office in the City of Campinas, State of São Paulo, at Rua James Clerk Maxwell, nº 315, CEP 13069--380, enrolled at CNPJ/MF under number 09.379.224/0001-20, in the present act represented under terms of its Articles of Incorporation.

WHEREAS, on 30 of March of 2008, the Parties signed the Private Act of Non Residential Realty Lease Contract (the “Contract”), regarding the realty lease, later amended on 05 of July of 2008 (the “First Amendment”),

WHEREAS, on 30 of October of 2008, the Parties signed the Second Amendment to Contract (the “Second Amendment”) prorogating the term of lease until 31 of May of 2013,

WHEREAS, the Parties are interested in (i) prorogating the lease Contract term for additional 36 (thirty six) months, (ii) altering clause 28, Contract caput, and still, (iii) determining the lease increase,

DECIDE the Parties to sign the present Third Amendment which shall be governed in accordance to the following terms and conditions:

CLAUSE FIRST - TERM OF LEASE

1.1    By the present Third Amendment, the Parties agree, jointly, in prorogating the Contract term for additional 36 (thirty six) months starting 01 of October of 2012. Thus, the final term of the referred Contract becomes 01 of October of 2015, with the possibility of being renewed for the same term after written agreement between the Parties.

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

CLAUSE SECOND - REALTY REINSTATEMENT

2.1    In face of modifications adjusted at clause 1.1 above, regarding the term of lease, and in face of the intention of modification of terms of reinstatement of herein leased realty, desire the Parties, jointly, to alter the wording of Clause 2^nd, caput, of the Contract, which begins effect with the following wording:

“2^nd) The Term of Lease is 36 (thirty six) months, starting on 01/Oct/2012, as long as fulfilled obligations determined at clauses 3^rd and 4^th below, and ending on 01/Oct/2015, date when definitely the LESSEE binds to reinstating the herein leased Realty in good conditions of use and conservation, safeguarded natural wear of Realty and that provided at clause 8^th, paragraph 4^th.”

CLAUSE THIRD - LEASE

3.1    Due to the prorogation of the Contract's term of lease, and after negotiations, the LESSEE shall pay the LESSORS, from the date of signature of the present Third Amendment, the amount of R$ 25,00 (twenty five Reais) per m² (square meter), calculated over the total constructed area, that is 1.368,09 m² (square meters), totaling thus the monthly amount of R$ 34.202,50 (thirty four thousand and two hundred and two Reais). Thus, Clause 5^th, Contract caput, by mutual agreement, has now the following wording:

“5ª) From the date of the Term of Initial Inspection, the LESSEE shall pay the LESSORS the monthly lease already determined in R$ 34.202,50 (thirty four thousand and two hundred and two Reais), with readjustments in accordance to the smallest periodicity allowed by Law in effect, with due date at the fifth of each month, following the owed month, by deposit in bank account [*] current account number [*], with deposit slip being suitable as receipt and acquittal. The monthly lease shall be annually indexed by the IGP-M variation measured by Fundação Getúlio Vargas, or, in the event of suppression by its legal substitute, which best reflects the period's inflation, at LESSORS discretion, adopting as base date, 01/Jun/2008.”

3.2    The Parties declare, under terms of clause 3.1, that the terms of payment shall be those determined at Contract.

CLAUSE FOURTH - OTHER PROVISIONS

4.1    Are ratified, in all their terms, further clauses and conditions at Contract, in the First Amendment and Second Amendment which have not been expressly altered in the present Third Amendment.

4.2    The Parties agree that the terms of the present Third Amendment prevail over the conditions foreseen in all annexes to the present Act.

And for being fair and agreed, the Parties sign the present Act in 3 (three) copies, with same content and form, in the presence of two (02) below signed witnesses.

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

Campinas, 01 of October of 2012.

/s/ Lúcio Tomasiello        /s/ Maurício Tomasiello        

LESSORS:LÚCIO TOMASIELLOMAURÍCIO TOMASIELLO

/s/ Paulo Diniz            /s/ Roel Win Collier        

LESSEE:             AMYRIS BRASIL LTDA.

Witnesses:

1.         2.

Name:                        Name:

RG:                        RG:

CPF/MF:                    CPF/MF:

EX-21.01

Exhibit 21.01

SUBSIDIARIES OF THE REGISTRANT

Subsidiaries	State or Other Jurisdiction of Incorporation or Organization
Amyris Fuels, LLC	Delaware
AB Technologies LLC	Delaware
Amyris Brasil Ltda.	Brazil
SMA Indústria Química S.A.	Brazil

EX-23.01

Exhibit 23.01

CONSENT OF INDEPENDENT REGISTERED PUBLIC ACCOUNTING FIRM

We hereby consent to the incorporation by reference in the Registration Statements on Form S-3 (No. 333-180005) and S-8 (Nos. 333-169715, 333-172514, and 333-180006) of Amyris, Inc. of our report dated March 28, 2013 relating to the consolidated financial statements, financial statement schedule and the effectiveness of internal control over financial reporting, which appears in this Form 10-K.

/s/    PricewaterhouseCoopers LLP

San Jose, California

March 28, 2013

EX-31.02

Exhibit 31.02

CERTIFICATION OF CHIEF FINANCIAL OFFICER

PURSUANT TO RULE 13a-14(c) and 15d-(14(a) OF THE SECURITIES EXCHANGE ACT OF 1934

I, Steven R. Mills, certify that:

1. I have reviewed this Annual Report on Form 10-K of Amyris, Inc.;

2. Based on my knowledge, this report does not contain any untrue statement of a material fact or omit to state a material fact necessary to make the statements made, in light of the circumstances under which such statements were made, not misleading with respect to the period covered by this report;

3. Based on my knowledge, the financial statements, and other financial information included in this report, fairly present in all material respects the financial condition, results of operations and cash flows of the registrant as of, and for, the periods presented in this report;

4. The registrant's other certifying officer and I are responsible for establishing and maintaining disclosure controls and procedures (as defined in Exchange Act Rules 13a-15(e) and 15d-15(e)) and internal control over financial reporting (as defined in Exchange Act Rules 13a-15(f) and 15d-15(f)) for the registrant and have:

a) Designed such disclosure controls and procedures, or caused such disclosure controls and procedures to be designed under our supervision, to ensure that material information relating to the registrant, including its consolidated subsidiaries, is made known to us by others within those entities, particularly during the period in which this report is being prepared;

b) Designed such internal control over financial reporting, or caused such internal control over financial reporting to be designed under our supervision, to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles;

c) Evaluated the effectiveness of the registrant's disclosure controls and procedures and presented in this report our conclusions about the effectiveness of the disclosure controls and procedures, as of the end of the period covered by this report based on such evaluation; and

d) Disclosed in this report any change in the registrant's internal control over financial reporting that occurred during the registrant's most recent fiscal quarter (the registrant's fourth fiscal quarter in the case of an annual report) that has materially affected, or is reasonably likely to materially affect, the registrant's internal control over financial reporting; and

5. The registrant's other certifying officer and I have disclosed, based on our most recent evaluation of internal control over financial reporting, to the registrant's auditors and the audit committee of the registrant's board of directors (or persons performing the equivalent functions):

a) All significant deficiencies and material weaknesses in the design or operation of internal control over financial reporting which are reasonably likely to adversely affect the registrant's ability to record, process, summarize and report financial information; and

b) Any fraud, whether or not material, that involves management or other employees who have a significant role in the registrant's internal control over financial reporting.

Date: March 28, 2013	/s/   STEVEN R. MILLS
	Steven R. Mills
	Chief Financial Officer

EX-31.31.01

Exhibit 31.01

CERTIFICATION OF CHIEF EXECUTIVE OFFICER

PURSUANT TO RULE 13a-14(c) and 15d-(14(a) OF THE SECURITIES EXCHANGE ACT OF 1934

I, John Melo, certify that:

1. I have reviewed this Annual Report on Form 10-K of Amyris, Inc.;

2. Based on my knowledge, this report does not contain any untrue statement of a material fact or omit to state a material fact necessary to make the statements made, in light of the circumstances under which such statements were made, not misleading with respect to the period covered by this report;

3. Based on my knowledge, the financial statements, and other financial information included in this report, fairly present in all material respects the financial condition, results of operations and cash flows of the registrant as of, and for, the periods presented in this report;

4. The registrant's other certifying officer and I are responsible for establishing and maintaining disclosure controls and procedures (as defined in Exchange Act Rules 13a-15(e) and 15d-15(e)) and internal control over financial reporting (as defined in Exchange Act Rules 13a-15(f) and 15d-15(f)) for the registrant and have:

a) Designed such disclosure controls and procedures, or caused such disclosure controls and procedures to be designed under our supervision, to ensure that material information relating to the registrant, including its consolidated subsidiaries, is made known to us by others within those entities, particularly during the period in which this report is being prepared;

b) Designed such internal control over financial reporting, or caused such internal control over financial reporting to be designed under our supervision, to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles;

c) Evaluated the effectiveness of the registrant's disclosure controls and procedures and presented in this report our conclusions about the effectiveness of the disclosure controls and procedures, as of the end of the period covered by this report based on such evaluation; and

d) Disclosed in this report any change in the registrant's internal control over financial reporting that occurred during the registrant's most recent fiscal quarter (the registrant's fourth fiscal quarter in the case of an annual report) that has materially affected, or is reasonably likely to materially affect, the registrant's internal control over financial reporting; and

5. The registrant's other certifying officer and I have disclosed, based on our most recent evaluation of internal control over financial reporting, to the registrant's auditors and the audit committee of the registrant's board of directors (or persons performing the equivalent functions):

a) All significant deficiencies and material weaknesses in the design or operation of internal control over financial reporting which are reasonably likely to adversely affect the registrant's ability to record, process, summarize and report financial information; and

b) Any fraud, whether or not material, that involves management or other employees who have a significant role in the registrant's internal control over financial reporting.

Date: March 28, 2013	/s/ JOHN MELO
	John Melo
	President and Chief Executive Officer

EX-32.01

Exhibit 32.01

Certification of CEO Furnished Pursuant to 18 U.S.C. Section 1350,

As Adopted Pursuant To

Section 906 of The Sarbanes-Oxley Act of 2002

In connection with the Annual Report of Amyris, Inc. (the “Company”) on Form 10-K for the year ended December 31, 2012, as filed with the Securities and Exchange Commission on the date hereof, I, John Melo, Chief Executive Officer of the Company, certify for the purposes of section 1350 of chapter 63 of title 18 of the United States Code, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002, that, to the best of my knowledge,

(i) the Annual Report of the Company on Form 10-K for the year ended December 31, 2012 (the “Report”), fully complies with the requirements of section 13(a) or 15(d) of the Securities Exchange Act of 1934, and

(ii) the information contained in the Report fairly presents, in all material respects, the financial condition and results of operations of the Company.

Date: March 28, 2013	/s/    JOHN MELO
	John Melo
	President and Chief Executive Officer
	(Principal Executive Officer)

EX-32.02

Exhibit 32.02

Certification of CFO Furnished Pursuant to 18 U.S.C. Section 1350,

As Adopted Pursuant To

Section 906 of The Sarbanes-Oxley Act of 2002

In connection with the Annual Report of Amyris, Inc. (the “Company”) on Form 10-K for the year ended December 31, 2012, as filed with the Securities and Exchange Commission on the date hereof, I, Steven R. Mills, Chief Financial Officer of the Company, certify for the purposes of section 1350 of chapter 63 of title 18 of the United States Code, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002, that, to the best of my knowledge,

(i) the Annual Report of the Company on Form 10-K for the year ended December 31, 2012 (the “Report”), fully complies with the requirements of section 13(a) or 15(d) of the Securities Exchange Act of 1934, and

(ii) the information contained in the Report fairly presents, in all material respects, the financial condition and results of operations of the Company.

Date: March 28, 2013	/s/   STEVEN R. MILLS
	Steven R. Mills
	Chief Financial Officer
	(Principal Financial Officer)

XML

Income Taxes (Tables)

12 Months Ended

Dec. 31, 2012

Income Tax Disclosure [Abstract]

Schedule of Income before Income Tax, Domestic and Foreign [Table Text Block]

The components of loss before income taxes and minority interests are as follows for the years ended December 31, 2012, 2011 and 2010 (in thousands):

	Years Ended December 31,
	2012			2011			2010
United States	$	(146,028	)	$	(140,153	)	$	(67,525	)
Foreign	(59,024		)	(38,806		)	(15,265		)
Loss before income taxes	$	(205,052	)	$	(178,959	)	$	(82,790	)

Schedule of Components of Income Tax Expense (Benefit) [Table Text Block]

The components of the provision for income taxes are as follows for the years ended December 31, 2012, 2011 and 2010 (in thousands):

	Years Ended December 31,
	2012		2011			2010
Current:
Federal	$	—	$	—		$	—
State	—		—			—
Foreign	981		727			—
Total current provision (benefit)	981		727			—
Deferred:
Federal	—		(150		)	—
State	—		(25		)	—
Foreign	—		—			—
Total deferred provision (benefit)	—		(175		)	—
Total provision for income taxes	$	981	$	552		$	—

Schedule of Effective Income Tax Rate Reconciliation [Table Text Block]

A reconciliation between the statutory federal income tax and the Company’s effective tax rates as a percentage of loss before income taxes is as follows:

	Years Ended December 31,
	2012		2011		2010
Statutory tax rate	(34.0	)%	(34.0	)%	(34.0	)%
State tax rate, net of federal benefit	(0.4	)%	(4.4	)%	(1.6	)%
Stock-based compensation	0.2	%	0.6	%	0.3	%
Federal R&D credit	—	%	(0.8	)%	(0.8	)%
Other	1.6	%	(0.7	)%	1.6	%
Foreign losses	(5.8	)%	(5.4	)%	—	%
Change in valuation allowance	38.8	%	45.0	%	34.5	%
Effective income tax rate	0.4	%	0.3	%	—	%

Schedule of Deferred Tax Assets and Liabilities [Table Text Block]

Temporary differences and carryforwards that gave rise to significant portions of deferred taxes are as follows (in thousands):

	December 31,
	2012			2011			2010
Net operating loss carryforwards	$	145,324		$	103,390		$	56,615
Fixed assets	—			—			340
Research and development credits	7,259			5,937			3,325
Foreign Tax Credit	1,782			801			—
Accruals and reserves	15,997			12,150			2,257
Stock-based compensation	15,882			11,351			4,316
Capitalized start-up costs	16,070			22,974			8,993
Capitalized research and development costs	26,850			—			—
Other	7,649			2,904			225
Total deferred tax assets	236,813			159,507			76,071
Fixed assets	(525		)	(2,742		)	—
Other	—			—			—
Total deferred tax liabilities	(525		)	(2,742		)	—
Net deferred tax asset prior to valuation allowance	236,288			156,765			76,071
Less: Valuation allowance	(236,288		)	(156,765		)	(76,071		)
Net deferred tax assets (liabilities)	$	—		$	—		$	—

Summary of Income Tax Contingencies [Table Text Block]

A reconciliation of the beginning and ending amounts of unrecognized tax benefits since the adoption of accounting guidance on uncertainty in income taxes is as follows:

Balance at December 31, 2010	1,734
Increases in tax positions for prior period	—
Increases in tax positions during current period	1,369
Balance at December 31, 2011	$	3,103
Increases in tax positions for prior period	82
Increases in tax positions during current period	733
Balance at December 31, 2012	$	3,918

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Fair Value Measurements Fair Value Using Significant Unobservable Inputs (Level 3) (Details) (Derivative Liability - Compound Embedded Derivatives [Member], USD $) In Thousands, unless otherwise specified	12 Months Ended
	Dec. 31, 2012
Derivative Liability - Compound Embedded Derivatives [Member]
Fair Value, Liabilities Measured on Recurring Basis, Unobservable Input Reconciliation, Calculation [Roll Forward]
Fair value, beginning of period	$ 0
Fair Value, Measurement with Unobservable Inputs Reconciliation, Liability, Transfers Into Level 3	11,025
Change in fair value recorded in other income (expense), net	(3,131)
Fair value, end of period	$ 7,894

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Summary of Significant Accounting Policies In-Process Research and Development (Details) (Draths Corporation [Member], USD $) In Thousands, unless otherwise specified	12 Months Ended
	Dec. 31, 2012	Oct. 06, 2011
Draths Corporation [Member]
Business Acquisition [Line Items]
In-process research and development		$ 8,560
Number of Years To Reach Viable Products, Maximum	3 years

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Debt Revolving Credit Facility (Details) (Revolving Credit Facility [Member], USD $) In Millions, unless otherwise specified	May 31, 2012	Apr. 30, 2012	Dec. 23, 2010
Line of Credit Facility [Line Items]
Line of Credit Facility, Maximum Borrowing Capacity			$ 10.0
Long-term Debt, Gross		7.7
Line of Credit Facility, Reduced Maximum Borrowing Capacity	2.3
Current Ratio That Must Be Maintained At End Of Quarter	1.3		2
Deposit Assets	15.0
Eurodollar Rate [Member]
Line of Credit Facility [Line Items]
Debt Instrument, Basis Spread on Variable Rate			3.00%
Bank Prime Rate [Member]
Line of Credit Facility [Line Items]
Debt Instrument, Basis Spread on Variable Rate			0.50%
Debt Instrument Basis Spread On Variable Default Rate			2.00%
Standby Letters of Credit [Member]
Line of Credit Facility [Line Items]
Line of Credit Facility, Maximum Borrowing Capacity			5.0
Line of Credit Facility, Reduced Maximum Borrowing Capacity	$ 2.3

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Fair Value of Financial Instruments, Derivative Disclosures (Details) (Not Designated as Hedging Instrument [Member], USD $) In Thousands, unless otherwise specified	12 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Future [Member] | Cost of products sold [Member]
Derivative [Line Items]
Derivative contracts, gain (loss)	$ (288)	$ (2,365)	$ (2,225)
Future [Member] | Regulated fixed price futures contracts, included as liability in accounts payable [Member]
Derivative [Line Items]
Quantity of Short Contracts (in contracts)	0	22
Fair Value	0	18
Future [Member] | Currency interest rate swap, included as net liability in other long term liability [Member]
Derivative [Line Items]
Quantity of Short Contracts (in contracts)	1	0
Fair Value	1,367	0
Currency interest rate swap [Member] | Other income (expense), net [Member]
Derivative [Line Items]
Derivative contracts, gain (loss)	$ (1,367)	$ 0	$ 0

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Noncontrolling Interest Redeemable Noncontrolling Interest (Details)	12 Months Ended							12 Months Ended	1 Months Ended
	Dec. 31, 2010 USD ($)	Dec. 31, 2010 Amyris Brasil S.A. Subsidiary [Member] USD ($)	Dec. 31, 2012 Amyris Brasil S.A. Subsidiary [Member] USD ($)	Dec. 31, 2011 Amyris Brasil S.A. Subsidiary [Member] USD ($)	May 31, 2010 Amyris Brasil S.A. Subsidiary [Member]	Mar. 31, 2010 Amyris Brasil S.A. Subsidiary [Member]	Dec. 31, 2009 Amyris Brasil S.A. Subsidiary [Member]	Dec. 31, 2010 Additional Paid-in Capital [Member] USD ($)	Sep. 30, 2010 Common Stock [Member] Amyris Brasil S.A. Subsidiary [Member]	May 31, 2010 Private Placement [Member] Amyris Brasil S.A. Subsidiary [Member] BRL	Mar. 31, 2010 Private Placement [Member] Amyris Brasil S.A. Subsidiary [Member] BRL	Dec. 31, 2009 Private Placement [Member] Amyris Brasil S.A. Subsidiary [Member] BRL
Redeemable Noncontrolling Interest [Line Items]
Sale of Stock, Number of Shares Issued in Transaction										1,111,111	853,333	1,111,111
Noncontrolling Interest, Incremental Ownership Percentage by Noncontrolling Owners					4.07%	3.40%	4.80%
Sale of Stock, Consideration Received on Transaction										10,000,000	3,000,000	10,000,000
Equity Instrument, Convertible, Conversion Ratio									0.28
Beneficial conversion feature on conversion of Amyis Brasil shares	(2,717,000)							(2,717,000)
Increase (Decrease) in Redeemable Noncontrolling Interest [Roll Forward]
Beginning Balance, redeemable noncontrolling interest		5,506,000	0	0
Proceeds from redeemable noncontrolling interest		7,041,000
Conversion of shares of Amyris Brasil S.A. subsidiary held by third parties into common stock	11,653,000	(11,870,000)						11,653,000
Foreign currency translation adjustment		217,000
Net loss		(894,000)
Ending Balance, redeemable noncontrolling interest		$ 0	$ 0	$ 0

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Subsequent Events (Details)	12 Months Ended			0 Months Ended	1 Months Ended		0 Months Ended																		0 Months Ended			0 Months Ended
	Dec. 31, 2012 USD ($)	Dec. 31, 2011 USD ($)	Dec. 31, 2010 USD ($)	Dec. 24, 2012 Private Placement [Member] USD ($)	May 31, 2012 Private Placement [Member] USD ($)	Feb. 29, 2012 Private Placement [Member] USD ($)	Mar. 27, 2013 Private Placement [Member] Subsequent Event [Member] USD ($)	Jan. 11, 2013 Private Placement [Member] Subsequent Event [Member] USD ($)	Jan. 23, 2013 Equity Incentive Plan, 2010 [Member] Subsequent Event [Member]	Jan. 23, 2013 Employee Stock Purchase Plan, 2010 [Member] Subsequent Event [Member]	Mar. 13, 2013 Firmenich SA Agreement [Member] Subsequent Event [Member] USD ($) payment	Mar. 18, 2013 ABC Brasil Agreement [Member] Subsequent Event [Member] USD ($)	Mar. 18, 2013 ABC Brasil Agreement [Member] Subsequent Event [Member] BRL	Mar. 13, 2013 Before Firmenich Receives $15 Million Dollars More Than The Company in Agregate [Member] Firmenich SA Agreement [Member] Subsequent Event [Member]	Mar. 13, 2013 Before Firmenich Receives $15 Million Dollars More Than The Company in Agregate [Member] Firmenich [Member] Firmenich SA Agreement [Member] Subsequent Event [Member]	Mar. 13, 2013 After Firmenich Received $15 Million Dollars More Than The Company in Agregate [Member] Firmenich SA Agreement [Member] Subsequent Event [Member]	Mar. 13, 2013 After Firmenich Received $15 Million Dollars More Than The Company in Agregate [Member] Firmenich [Member] Firmenich SA Agreement [Member] Subsequent Event [Member]	Mar. 20, 2013 Commitment Fulfilled [Member] Subsequent Event [Member] USD ($)	Dec. 24, 2012 Commitment Fulfilled [Member] Private Placement [Member] USD ($)	Mar. 24, 2013 May 15, 2013 [Member] Subsequent Event [Member] USD ($)	Mar. 24, 2013 June 15, 2013 [Member] Subsequent Event [Member] USD ($)	Jun. 30, 2011 Joint Venture with Cosan [Member] Corporate Joint Venture [Member]	Mar. 26, 2013 Joint Venture with Cosan [Member] Corporate Joint Venture [Member] Subsequent Event [Member]	Jun. 30, 2011 Joint Venture with Cosan [Member] Corporate Joint Venture [Member] Subsequent Event [Member]	Jul. 30, 2012 Unsecured Senior Convertible Promissory Notes [Member] USD ($)	Jul. 30, 2012 Unsecured Senior Convertible Promissory Notes [Member] Subsequent Event [Member] USD ($)	Jul. 30, 2012 Unsecured Senior Convertible Promissory Notes [Member] Select Whichever Greater At Consideration [Member] Subsequent Event [Member] USD ($)	Jul. 30, 2012 Unsecured Senior Convertible Promissory Notes [Member] July 2013 Convertible Notes [Member] Subsequent Event [Member] USD ($)
Subsequent Event [Line Items]
Share-based Compensation Arrangement by Share-based Payment Award, Number of Additional Shares Authorized									3,435,483	687,096
Share-based Compensation Arrangement by Share-based Payment Award, Number of Additional Shares Authorized, Percentage Increase of Common Stock, Shares, Outstanding									5.00%	1.00%
Common Stock, Shares, Outstanding	68,709,660	45,933,138
Proceeds from Private Placement Remaining Balance Settled								$ 15,000,000
Stock issued during period, shares							1,533,742	5,033,557
Stock Issued During Period, Price Per Share, New Issues				$ 2.98	$ 2.36	$ 5.78	$ 3.26
Proceeds from Issuance of Private Placement	84,682,000	0	0	37,200,000			5,000,000
Collaboration Agreement, Annual Funding											10,000,000
Collaboration Agreement, Annual Funding Period											3 years
Collaboration Agreement, Initial Payment											10,000,000
Revenue Recognition, Milestone Method, Potential Revenue to be Recognized											5,000,000
Collaboration Agreement, No Research and Development Commitments on Either Party Thereafter											6 years
Collaboration Agreement, Option to Mutually Agree for Additional Research and Development Commitments Thereafter Period of Agreement											6 years
Export Financing Agreement												2,500,000	5,000,000
Export Funding Agreement, Term												1 year	1 year
Future Proceeds from Convertible Debt																									21,700,000			30,000,000
Collaboration Agreement, Percentage Shares of Product Margins from Sales of Each Compound														30.00%	70.00%	50.00%	50.00%
Collaboration Agreement, Shares of Product Margins from Sales of Each Compound Threshold Amount Until New Percentage Share Distribution											15,000,000
Collaborator Agreement Performance Bonus, Number of Payment											1
Collaborator Agreement Performance Bonus											2,500,000.0
Debt Instrument, Convertible, Conversion Price																										$ 7.0682	$ 3.08
Debt Instrument, Closing Price Plus Incremental Rate																											$ 0.01
Collaboration Agreement, Funding Obligation Advanced Installments																				10,000,000	10,000,000
Commitment to purchase company common stock						$ 15,000,000												$ 5,000,000	$ 10,000,000
Equity Method Investment, Ownership Percentage																						50.00%	50.00%
Initial Term of Joint Venture																						20 years	20 years
Equity Method Investment, Ownership Percentage, Sale of Ownership Percentage																								50.00%

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Summary of Significant Accounting Policies Asset Retirement Obligation (Details) (USD $) In Thousands, unless otherwise specified	12 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Asset Retirement Obligations [Line Items]
Related amortization expense	$ 14,570	$ 11,077	$ 7,280
Asset Retirement Obligation, Roll Forward Analysis [Roll Forward]
Asset Retirement Obligation, Beginning Balance	1,129	984
Additions	0	166
Foreign currency impacts and other adjustments	(98)	(133)
Accretion expenses recorded during the period	91	112
Reversals	(1,122)
Asset Retirement Obligation, Ending Balance	0	1,129	984
Asset Retirement Obligation [Member]
Asset Retirement Obligations [Line Items]
Related amortization expense	$ 188	$ 193	$ 229

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Debt (Tables)

12 Months Ended

Dec. 31, 2012

Debt Disclosure [Abstract]

Schedule of Debt [Table Text Block]

Debt is comprised of the following (in thousands):

	December 31,
	2012			2011
Credit facilities	$	12,409		$	18,852
Notes payable	1,572			3,113
Convertible notes	25,000			—
Related party convertible notes	39,033			—
Loans payable	26,150			19,359
Total debt	104,164			41,324
Less: current portion	(3,325		)	(28,049		)
Long-term debt	$	100,839		$	13,275

Schedule of Long-term Debt Instruments [Table Text Block]

Future minimum payments under the debt agreements as of December 31, 2012 are as follows (in thousands):

Years ending December 31:	Related Party Convertible Debt			Convertible Debt			Notes Payable			Loans Payable			Credit Facility
2013	$	—		$	760		$	351		$	1,958		$	3,175
2014	—			760			379			2,970			2,926
2015	—			765			379			4,456			2,774
2016	—			760			381			4,286			2,623
2017	51,627			25,125			384			4,110			2,393
Thereafter	—			—			154			16,426			612
Total future minimum payments	51,627			28,170			2,028			34,206			14,503
Less: amount representing interest	(12,594		)	(3,170		)	(456		)	(8,056		)	(2,094		)
Present value of minimum debt payments	39,033			25,000			1,572			26,150			12,409
Less: current portion	—			—			(311		)	(556		)	(2,458		)
Noncurrent portion of debt	$	39,033		$	25,000		$	1,261		$	25,594		$	9,951

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Noncontrolling Interest Variable Interest Entity (Details) (USD $)	12 Months Ended			1 Months Ended
	Dec. 31, 2012 consolidated_VIE	Dec. 31, 2012 Variable Interest Entity, Primary Beneficiary [Member] consolidated_VIE	Dec. 31, 2011 Variable Interest Entity, Primary Beneficiary [Member]	Jan. 31, 2011 Glycotech Agreement [Member]	Jan. 31, 2011 Glycotech Agreement [Member] Variable Interest Entity, Primary Beneficiary [Member]	Dec. 31, 2012 Glycotech Agreement [Member] Variable Interest Entity, Primary Beneficiary [Member]
Variable Interest Entity [Line Items]
Period of Initial Term of Collaboration Agreement				2 years
Additional Year Periods of Collaboration Agreement				1 year
Variable Interest Entity, Financial or other support					100.00%
Variable Interest Entity Number of Entities (in VIEs)	2	2
Variable Interest Entity, Consolidated, Carrying Amount, Property and Equipment		$ 24,700,000
Variable Interest Entity, Consolidated, Carrying Amount, Other Assets		4,500,000
Variable Interest Entity, Consolidated, Carrying Amount, Current Assets		400,000
Variable Interest Entity, Consolidated, Carrying Amount, Accounts Payable And Accrued Liabilities		300,000
Variable Interest Entity, Consolidated, Carrying Amount, Loan Obligations						100,000
Assets		29,564,000	22,094,000
Liabilities		$ 355,000	$ 2,873,000

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Debt Convertible Notes (Details) (Unsecured Senior Convertible Promissory Notes [Member], USD $)	Jul. 30, 2012	Feb. 29, 2012 Fidelity [Member]
Debt Instrument [Line Items]
Debt Instrument, Face Amount	$ 105,000,000	$ 25,000,000
Debt Instrument, Interest Rate, Stated Percentage	1.50%	3.00%
Debt Instrument, Convertible, Conversion Price		$ 7.0682
Debt Instrument, Convertible, Common Stock, Shares		3,536,968
Percentage of Principal Amount of Notes, Required to Be Repaid In An Acquisition		101.00%
Debt Instrument, Debt Convenant, Outstanding Debt, Maximum	200,000,000.0	200,000,000.0
Debt Instrument, Debt Convenant, Percentage of Consolidated Total Assets, Maximum	50.00%	50.00%
Debt Instrument, Debt Convenant, Outstanding Secured Debt, Maximum	$ 125,000,000.0	$ 125,000,000
Debt Instrument, Debt Convenant, Secured Debt, Percentage of Consolidated Total Assets, Maximum	30.00%	30.00%

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Stock-Based Compensation Plans - Restricted Stock Units and Restricted Stock Activity (Details) (Restricted Stock Units (RSUs) [Member], USD $)	12 Months Ended
	Dec. 31, 2012	Dec. 31, 2011
Restricted Stock Units (RSUs) [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Nonvested, Number	2,550,799	375,189
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Nonvested, Weighted Average Grant Date Fair Value	$ 7.92	$ 29.84
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Outstanding, Weighted Average Remaining Contractual Term	1 year 3 months	1 year 4 months 10 days
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Grants in Period	2,966,900
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Grants in Period, Weighted Average Grant Date Fair Value	$ 3.45
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Vested in Period	(415,792)
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Vested in Period, Weighted Average Grant Date Fair Value	$ 13.47
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Forfeited in Period	(375,498)
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Forfeited in Period, Weighted Average Grant Date Fair Value	$ 10.28
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Expected to Vest	2,237,365
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Expected to Vest, Weighted Average Grant Date Fair Value	$ 7.92
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Vested and Expected to Vest , Weighted Average Remaining Contractual Term	1 year 2 months 1 day

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Balance Sheet Components Short Term Investments (Details) (USD $) In Thousands, unless otherwise specified	Dec. 31, 2012	Dec. 31, 2011
Schedule of Available-for-sale Securities [Line Items]
Short-Term Investments, Amortized Cost	$ 97	$ 7,889
Short-Term Investments, Unrealized Gain (Loss)	0	0
Short-Term Investments, Fair Value	97	7,889
Certificates of Deposit [Member]
Schedule of Available-for-sale Securities [Line Items]
Short-Term Investments, Amortized Cost	97	7,889
Short-Term Investments, Unrealized Gain (Loss)	0	0
Short-Term Investments, Fair Value	$ 97	$ 7,889

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Debt Letters of Credit (Details) (USD $)	Dec. 31, 2012	Jun. 30, 2012	Dec. 31, 2011	Sep. 30, 2012 Financial Institution [Member] Cash Advances [Member]	Oct. 31, 2009 Financial Institution [Member] Cash Advances [Member]	Oct. 31, 2009 Financial Institution [Member] Letter of Credit [Member]	Oct. 31, 2009 Maximum [Member] Financial Institution [Member]	Oct. 31, 2009 Bank Prime Rate [Member] Financial Institution [Member]	Oct. 31, 2009 Bank Cost Of Funds [Member] Financial Institution [Member]	Dec. 31, 2012 Credit Agreement [Member] Financial Institution [Member]	Dec. 31, 2011 Credit Agreement [Member] Financial Institution [Member]
Line of Credit Facility [Line Items]
Line of Credit Facility, Maximum Borrowing Capacity					$ 20,000,000	$ 5,700,000	$ 20,000,000
Debt Instrument, Basis Spread on Variable Rate								1.00%	3.50%
Line of Credit Facility, Amount Outstanding				0
Letters of Credit Outstanding, Amount		1,000,000								0	5,000,000
Restricted cash	$ 955,000		$ 0

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Stockholders' Equity Common Stock Warrants (Details) (USD $) In Thousands, except Share data, unless otherwise specified	12 Months Ended											12 Months Ended		33 Months Ended	12 Months Ended			1 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2012 Common Stock [Member]	Dec. 31, 2011 Common Stock [Member]	Sep. 30, 2010 Common Stock [Member]	Dec. 31, 2012 Common Stock [Member] Exercise Price Per Share $24.88 [Member]	Dec. 31, 2011 Common Stock [Member] Exercise Price Per Share $24.88 [Member]	Dec. 31, 2012 Common Stock [Member] Exercise Price Per Share $25.26 [Member]	Dec. 31, 2011 Common Stock [Member] Exercise Price Per Share $25.26 [Member]	Dec. 31, 2012 Common Stock [Member] Exercise Price Per Share $10.67 [Member]	Dec. 31, 2011 Common Stock [Member] Exercise Price Per Share $10.67 [Member]	Dec. 31, 2012 Common Stock Subject To Warrants [Member]	Dec. 31, 2011 Common Stock Subject To Warrants [Member]	Sep. 30, 2010 Warrants In Connection With Placement Agent Fees [Member] Common Stock [Member]	Dec. 31, 2012 Warrants In Connection With Capital Lease Arrangement [Member] Common Stock [Member] Y	Dec. 31, 2011 Warrants In Connection With Capital Lease Arrangement [Member] Common Stock [Member]	Sep. 30, 2010 IPO [Member]	Sep. 30, 2010 IPO [Member] Common Stock [Member]
Class of Warrant or Right [Line Items]
Class of Warrant or Right, Outstanding														182,405
Class of Warrant or Right, Number of Securities Called by Warrants or Rights					195,604
Warrants and Rights Outstanding																$ 193	$ 2,300
Class of Warrant or Right, Exercise Price of Warrants or Rights						24.88		25.26		10.67						10.67
Contractual term (in years)															10
Risk-free interest rate															2.00%
Expected volatility															86.00%
Expected dividend yield															0.00%
Class of Warrant or Right, Outstanding			21,087	26,223		0	2,884	0	2,252	21,087	21,087
Warrants Exercised	0	190,468
Stock issued during period, shares												0	77,087					5,300,000

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Significant Agreements (Research and Development Activities - Total Collaboration Agreement) (Details) (USD $)	0 Months Ended	12 Months Ended					1 Months Ended				1 Months Ended	12 Months Ended		12 Months Ended	0 Months Ended									0 Months Ended	1 Months Ended			0 Months Ended
	Jul. 30, 2012	Dec. 31, 2010	Dec. 31, 2012		Dec. 31, 2011		Jun. 30, 2010 Total Gas And Power USA Biotech Agreement [Member] Y	Dec. 31, 2012 Total Gas And Power USA Biotech Agreement [Member]	Dec. 31, 2011 Total Gas And Power USA Biotech Agreement [Member]	Jun. 30, 2010 Standstill Agreements [Member] Y	Jun. 30, 2010 Series D Preferred Stock [Member]	Dec. 31, 2010 Series D Preferred Stock [Member]	Sep. 30, 2010 IPO [Member]	Dec. 31, 2010 Additional Paid-in Capital [Member]	Jul. 30, 2012 July 2012 Funding Period [Member]	Jul. 30, 2012 September 20102 Funding Period [Member]	Jul. 30, 2012 July 2013 Funding Period [Member]	Jul. 30, 2012 July 2014 Funding Period [Member]	Jul. 30, 2012 January 2015 Funding Period [Member]	Jul. 13, 2012 Convertible Notes Payable [Member]	Jul. 13, 2012 Fuels JV [Member]	Jul. 13, 2012 Minimum [Member] Convertible Notes Payable [Member]	Jul. 13, 2012 Maximum [Member] Convertible Notes Payable [Member]	Jul. 30, 2012 November 2011 Amendment Collaborator Agreement [Member] Total Gas And Power USA Biotech Agreement [Member]	Jun. 30, 2010 November 2011 Amendment Collaborator Agreement [Member] Total Gas And Power USA Biotech Agreement [Member]	Dec. 24, 2012 Unsecured Senior Convertible Promissory Notes [Member]	Dec. 24, 2012 Private Placement [Member]	Dec. 24, 2012 Private Placement [Member] Unsecured Senior Convertible Promissory Notes [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Research and Development Arrangement Funding From Collaborator to Offset Costs Incurred							$ 50,000,000																		$ 50,000,000
Period To Achieve Profits Equal To Funding Provided							3
Period of Initial Term of Collaboration Agreement							12 years
Additional Year Periods of Collaboration Agreement							3 years
Stock issued during period, shares											7,101,548	7,101,548
Proceeds from Issuance of Preferred Stock and Preference Stock											133,000,000
Stock Issued During Period, Price Per Share, New Issues											$ 18.75
Stock Issued During Period, Fair Value Per Share, New Issues											$ 22.68
Other Deferred Costs, Gross							27,900,000
Accumulated Amortization of Other Deferred Costs								27,900,000	9,100,000
Offering price per share													$ 16.00
Beneficial Conversion Feature Charge on Conversion of Subsidiary Stock or Preferred to Common Stock		(39,292,000)												(39,292,000)
Collaborator Investor Percentage Ownership of Voting Securities							10.00%
Collaborator Negotiating Period							15 days
Collaborator Negotiation Period In the Event of Unsolicited Offer to be Acquired							5 days
Collaborator Additional Restricted Negotiation Period							10 days
Collaborator Agreement Period Not to Acquire Shares of Series D Preferred										3
Collaborator Agreement Not to Acquire Percentage										20.00%
Collaborator Agreement Not to Acquire During Third Year Percentage										30.00%
Collaborator Agreement Option to Acquire Equal Amount of Shares Plus Additional										1
Proceeds from Convertible Debt															15,000,000	15,000,000	30,000,000	10,850,000	10,850,000
Funding Period, Period after Completion to Decide to Proceed with Program	30 days
Debt Instrument Percent of Principal to Remain Outstanding After Agreement Termination																				70.00%
Debt Instrument Percent of Principal to be Canceled Upon Agreement Termination																				30.00%
Equity Method Investment, Ownership Percentage																					50.00%
Equity Method Investment Partner Ownership Percentage																					50.00%
Period Subsequent to Conversion of Debt Company Required to Register Shares																				30 days
Equity Or Debt Offering Amount Paid Through Cancellation Of Previous Debt																				30,000,000
Period Prior To Conversion Of Debt Company Required To Register Eligible Shares																				20 days
Period Subsequent To Filing Registration Statement Required To Be Effective																						70 days	100 days
Contingently repayable advance from related party collaborator			0	[1]	31,922,000	[1]																		46,500,000
Research And Development Advances from Collaborator No Longer Contingently Repayable And Recorded As Contract To Perform Services																								23,300,000
Research and Development Service Contract																								23,200,000
Research And Development Reduced Capitalized Deferred Charge Asset																								14,400,000
Revenue from Related Parties																								8,900,000
Extinguishment of Debt, Amount																												5,000,000
Convertible Debt, Amount Outstanding																										$ 53,300,000
Debt Instrument, Convertible, Common Stock, Shares																											1,677,852
Debt Instrument, Convertible, Conversion Price																											$ 2.98

[1] The contingently repayable advance from related party collaborator as of December 31, 2011 relates to the collaboration agreement between the Company and Total.

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Stock-Based Compensation Plans - (Details) (USD $) In Thousands, except Share data, unless otherwise specified	12 Months Ended
	Dec. 31, 2012 Y	Dec. 31, 2010	Sep. 28, 2010	Jun. 30, 2010
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Share-based Compensation Arrangement by Share-based Payment Award, Options, Period Available to Grant	10
Employee Service Share-based Compensation, Tax Benefit from Compensation Expense	0
Tax Benefit from Stock Options Exercised	0
2010 ESPP [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Share-based Compensation Arrangement by Share-based Payment Award, Options, Exercises in Period	579,167
Equity Incentive Plan, 2010 [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Common Stock Additional Capital Shares Reserved for Issuance		803,944
Shares Available For Issuance Percentage Of Total Outstanding Shares		5.00%
Share-based Compensation Arrangement by Share-based Payment Award, Number of Shares Authorized			30,000,000
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding, Number	5,708,475
Share-based Compensation Arrangement by Share-based Payment Award, Options, Period Available to Grant	10
Share-based Compensation Arrangement by Share-based Payment Award, Minimum Percent of Execrise Price to Fair Market Value On Grant Date	100.00%
Share-based Compensation Arrangement by Share-based Payment Award, Minimum Percent of Shareholder Triggering Higher Exercise Price	10.00%
Share-based Compensation Arrangement by Share-based Payment Award, Minimum Percent of Execrise Price to Fair Market Value On Grant Date Of Ten Percent Or Greater Shareholder Of Company	110.00%
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding, Weighted Average Exercise Price	9.84
Share-based Compensation Arrangement by Share-based Payment Award, Number of Shares Available for Grant	1,059,715
Equity Incentive Plan, 2010 [Member] | Maximum [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Share-based Compensation Arrangement by Share-based Payment Award, Award Vesting Period	5 years
Equity Incentive Plan, 2010 [Member] | Minimum [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Share-based Compensation Arrangement by Share-based Payment Award, Award Vesting Period	4 years
Stock Options And Stock Issuance Plans, 2005 [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding, Number	3,178,117
Share-based Compensation Arrangement by Share-based Payment Award, Options, Period Available to Grant	10
Share-based Compensation Arrangement by Share-based Payment Award, Minimum Percent of Execrise Price to Fair Market Value On Grant Date	100.00%
Share-based Compensation Arrangement by Share-based Payment Award, Minimum Percent of Shareholder Triggering Higher Exercise Price	10.00%
Share-based Compensation Arrangement by Share-based Payment Award, Minimum Percent of Execrise Price to Fair Market Value On Grant Date Of Ten Percent Or Greater Shareholder Of Company	110.00%
Share-based Compensation Arrangement by Share-based Payment Award, Award Vesting Period	5 years
Common Stock, Capital Shares Reserved for Future Issuance	0
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding, Weighted Average Exercise Price	7.79
Employee Stock Purchase Plan, 2010 [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Common Stock Additional Capital Shares Reserved for Issuance	459,325
Shares Available For Issuance Percentage Of Total Outstanding Shares		1.00%
Share-based Compensation Arrangement by Share-based Payment Award, Number of Shares Authorized				10,000,000
Common Stock, Capital Shares Reserved for Future Issuance	897,799
Share based Compensation Arrangement by Share-based Payment Award Purchase Price Percentage			85.00%
Share-based Compensation Arrangement by Share-based Payment Award, Number of Shares Available for Grant	186,700		168,627
Share Based Compensation, Period For Which Annual Increases Occur For Shares Reserved For Future Issuances	8

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Joint Ventures (Details)	12 Months Ended							12 Months Ended
	Dec. 31, 2012 USD ($)	Dec. 31, 2011 USD ($)	Dec. 31, 2010 USD ($)	Apr. 14, 2010 SMA Industria Quimica S.A. [Member] Corporate Joint Venture [Member] Y members	Dec. 31, 2012 SMA Industria Quimica S.A. [Member] Corporate Joint Venture [Member] Maximum [Member] USD ($)	Dec. 31, 2012 SMA Industria Quimica S.A. [Member] Corporate Joint Venture [Member] Maximum [Member] BRL	Jun. 30, 2011 Joint Venture with Cosan [Member] Corporate Joint Venture [Member] Y	Dec. 31, 2012 Novvi LLC [Member] Corporate Joint Venture [Member] Limited Liability Company [Member] USD ($)	Dec. 31, 2011 Novvi LLC [Member] Corporate Joint Venture [Member] Limited Liability Company [Member] USD ($)	Dec. 31, 2010 Novvi LLC [Member] Corporate Joint Venture [Member] Limited Liability Company [Member] USD ($)
Schedule of Equity Method Investments [Line Items]
Initial Term of Joint Venture				20 years			20 years
Equity Method Investment Number of Members of Executive Committee				3
Equity Method Investment Number of Company Appointed Members of Executive Committee				2
Equity Method Investment Number of Members of Executive Committee that are Senior Executive				1
Equity Method Investment Number of Members of Board of Directors				4
Equity Method Investment Number of Members of Board of Directors Appointed by Each Venture				2
Due from the other venture to the Company					$ 30,200,000	61,800,000
Equity Method Investment Period Company is required to Purchase Output of SMA				4
Equity Method Investment, Ownership Percentage				50.00%			50.00%
Initial Term of Shareholders' Agreement							10
Equity Method Investment Ownership Percentage Required							10.00%
Revenues	$ 73,694,000	$ 146,991,000	$ 80,311,000					$ 900,000	$ 3,600,000	$ 0

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Debt BNDES Credit Facility (Details) (BNDES Credit Facility [Member], BNDES [Member]) In Millions, unless otherwise specified	1 Months Ended			1 Months Ended
	Dec. 31, 2011 BRL Monthly_installment	Dec. 31, 2012 USD ($)	Dec. 31, 2012 BRL	Dec. 31, 2011 Maximum [Member] BRL	Dec. 31, 2012 Maximum [Member] USD ($)
Line of Credit Facility [Line Items]
Line of Credit Facility, Maximum Borrowing Capacity				22.4	$ 11.0
Line of Credit Facility, Initial Tranche				19.1
Line of Credit Facility, Additional Tranche, Available Upon Delivery of Additional Guarantees				3.3
Period Credit Line Is Available				12 months
Line of Credit Facility Number of Monthly Payments (in monthly installment)	60
Debt Instrument, Interest Rate, Stated Percentage	7.00%
Line of Credit Facility, Unused Capacity, Commitment Fee Percentage	0.10%
Collateral Provided By Company, Certain Equipment and Other Tangible Assets, Amount	24.9	12.2
Line of Credit Facility, Bank Guarantee, Percentage	10.00%
Line of Credit Facility, Second Tranche Floor	19.1
Line of Credit Facility, Bank Guarantee, Percentage, Second Tranche	90.00%
Guarantor Obligations, Liquidation Proceeds, Percentage	130.00%
Line of Credit Facility, Amount Outstanding		$ 9.3	19.1

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Reporting Segments

12 Months Ended

Dec. 31, 2012

Segment Reporting [Abstract]

Reporting Segments

Reporting Segments

The chief operating decision maker for the Company is the chief executive officer. The chief executive officer reviews financial information presented on a consolidated basis, accompanied by information about revenue by geographic region, for purposes of allocating resources and evaluating financial performance. The Company has one business activity comprised of research and development and sales of fuels and farnesene-derived products and there are no segment managers who are held accountable for operations, operating results or plans for levels or components below the consolidated unit level. Accordingly, the Company has determined that it has a single reportable segment and operating unit structure.

Revenues by geography are based on the location of the customer. The following tables set forth revenue and long-lived assets by geographic area (in thousands):

Revenues

	Years Ended December 31,
	2012		2011		2010
United States	$	49,111	$	141,098	$	80,311
Brazil	3,786		141		—
Europe	16,461		5,695		—
Asia	4,336		57		—
Total	$	73,694	$	146,991	$	80,311

Long-Lived Assets

	December 31,
	2012		2011
United States	$	70,273	$	76,108
Brazil	90,982		48,240
Europe	1,866		3,753
Total	$	163,121	$	128,101

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Summary of Significant Accounting Policies Comprehensive Income (Loss) (Details) (USD $) In Thousands, unless otherwise specified	Dec. 31, 2012	Dec. 31, 2011
Accounting Policies [Abstract]
Foreign currency translation adjustment, net of tax	$ (12,807)	$ (5,924)
Total accumulated other comprehensive loss	$ (12,807)	$ (5,924)

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Summary of Significant Accounting Policies Principles of Consolidations (Details)	12 Months Ended
	Dec. 31, 2012 consolidated_VIE
Accounting Policies [Abstract]
Variable Interest Entity Number of Entities (in VIEs)	2

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Debt Loans Payable (Details)			1 Months Ended			1 Months Ended										1 Months Ended
	Dec. 31, 2012 USD ($)	Dec. 31, 2011 USD ($)	Jul. 31, 2012 Banco Pine S.A Loan Agreement June 2012 [Member] Bridge Loan [Member] BRL	Dec. 31, 2012 Banco Pine S.A Loan Agreement June 2012 [Member] Bridge Loan [Member] USD ($)	Jun. 30, 2012 Banco Pine S.A Loan Agreement June 2012 [Member] Bridge Loan [Member] BRL	Jul. 31, 2012 Banco Pine December 2011 Loan Agreement [Member] Bridge Loan [Member] BRL	Dec. 31, 2012 Banco Pine December 2011 Loan Agreement [Member] Bridge Loan [Member] USD ($)	Dec. 31, 2011 Banco Pine December 2011 Loan Agreement [Member] Bridge Loan [Member] BRL	Dec. 31, 2012 Pine and Nossa Caixa Loan Agreement [Member] USD ($)	Jul. 13, 2012 Pine and Nossa Caixa Loan Agreement [Member] BRL	Jul. 13, 2012 Banco Pine July 2012 Loan Agreement [Member] BRL	Jul. 13, 2012 Nossa Caixa Loan Agreement [Member] BRL	Dec. 31, 2012 Loans Payable [Member] USD ($)	Oct. 31, 2012 Loans Payable [Member] USD ($) Monthly_installment	Dec. 31, 2011 Loans Payable [Member] USD ($)	Dec. 31, 2009 Loans Payable Lessor Emeryville Plant [Member] USD ($)	Dec. 31, 2012 Loans Payable Lessor Emeryville Plant [Member] USD ($)	Dec. 31, 2011 Loans Payable Lessor Emeryville Plant [Member] USD ($)	Dec. 31, 2012 Notes Payable to Banks [Member] USD ($)	Dec. 31, 2011 Notes Payable to Banks [Member] USD ($)	Dec. 31, 2012 Interest Rate Swap [Member] Banco Pine July 2012 Loan Agreement [Member] USD ($)	Jun. 30, 2012 Interest Rate Swap [Member] Banco Pine July 2012 Loan Agreement [Member] BRL
Debt Instrument [Line Items]
Debt Instrument, Face Amount				$ 25,400,000	52,000,000		$ 17,100,000	35,000,000	$ 25,400,000	52,000,000	22,000,000	30,000,000		$ 600,000		$ 250,000
Debt Instrument, Interest Rate, Stated Percentage					5.50%			12.30%		5.50%				3.24%		10.00%
Repayment Period																96 months
Long-term Debt	104,164,000	41,324,000											26,150,000		19,359,000		177,000	204,000	1,572,000	3,113,000
Debt Instrument, Interest Rate, Monthly Stated Percentage					0.4472%
Debt Instrument, Interest Rate, Percentage of Brazilian Interbank Lending Rate								119.20%
Notional Amount of Interest Rate Derivatives																					10,800,000	22,000,000
Derivative, Fixed Interest Rate																						3.94%
Collateral Provided By Company, Certain Equipment and Other Tangible Assets, Amount									33,300,000	68,000,000
Debt Instrument, Period of Interest Only Quarterly Payments										2 years
Repayments of Debt			52,000,000			35,000,000
Number Of Equal Monthly Installments														9
Loans Payable to Bank													$ 400,000

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Income Taxes (Details) (USD $) In Thousands, unless otherwise specified	12 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Income Tax Disclosure [Abstract]
Income Tax Expense (Benefit), Continuing Operations	$ 981	$ 552	$ 0
Current Foreign Tax Expense (Benefit)	981	727	0
Deferred Income Tax Expense (Benefit)	$ 0	$ (175)	$ 0

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Stock-Based Compensation Plans (Tables)

12 Months Ended

Dec. 31, 2012

Share-based Compensation Arrangement by Share-based Payment Award [Line Items]

Schedule of Employee Service Share-based Compensation, Allocation of Recognized Period Costs [Table Text Block]

Stock-based compensation expense related to options and restricted stock units granted to employees and nonemployees was allocated to research and development expense and sales, general and administrative expense as follows (in thousands):

	Years Ended December 31,
	2012		2011		2010
Research and development	$	6,451	$	6,345	$	2,161
Sales, general and administrative	21,022		19,147		8,271
Total stock-based compensation expense	$	27,473	$	25,492	$	10,432

Schedule of Share-based Compensation, Restricted Stock and Restricted Stock Units Activity [Table Text Block]

The Company’s restricted stock units and restricted stock activity and related information for the year ended December 31, 2012 was as follows:

	RSUs		Weighted Average Grant-Date Fair Value		Weighted Average Remaining Contractual Life (Years)
Outstanding - December 31, 2011	375,189		$	29.84	1.4
Awarded	2,966,900		$	3.45	—
Vested	(415,792	)	$	13.47	—
Forfeited	(375,498	)	$	10.28	—
Outstanding - December 31, 2012	2,550,799		$	7.92	1.3
Expected to vest after December 31, 2012	2,237,365		$	7.92	1.2

Schedule of Share-based Compensation, Stock Options and Stock Appreciation Rights Award Activity [Table Text Block]

The Company’s stock option activity and related information for the year ended December 31, 2012 was as follows:

		Number Outstanding		Weighted - Average Exercise Price		Weighted - Average Remaining Contractual Life (Years)	Aggregate Intrinsic Value
							(in thousands)
Outstanding - December 31, 2011		8,377,016		$	14.05	7.9	$	29,127
	Options granted	3,592,593		$	3.49
	Options exercised	(866,203	)	$	0.72
	Options cancelled	(2,156,814	)	$	15.78
Outstanding - December 31, 2012		8,946,592		$	9.07	7.5	$	954
Vested and expected to vest after December 31, 2012		8,281,330		$	9.18	7.3	$	893
Exercisable at December 31, 2012		4,134,023		$	9.94	5.8	$	575

Schedule of Share-based Compensation, Shares Authorized under Stock Option Plans, by Exercise Price Range [Table Text Block]

The following table summarizes information about stock options outstanding as of December 31, 2012:

	Options Outstanding				Options Exercisable
Exercise Price	Number of Options	Weighted - Average Remaining Contractual Life (Years)	Weighted Average Exercise Price		Number of Options	Weighted Average Exercise Price
$0.10—$2.76	1,129,158	8.1	$	2.31	279,345	$	1.06
$3.04—$3.55	768,990	9.7	$	3.12	10,936	$	3.13
$3.86—$3.86	1,424,649	8.9	$	3.86	296,482	$	3.86
$3.93—$3.93	1,198,288	3.9	$	3.93	1,152,673	$	3.93
$4.06—$9.32	1,351,331	6.8	$	6.37	799,576	$	6.38
$10.44—$14.28	326,936	7.2	$	12.61	190,964	$	13.51
$16.00—$16.00	1,174,667	8.0	$	16.00	531,966	$	16.00
$16.50—$20.41	959,303	7.0	$	18.72	552,878	$	18.77
$24.20—$27.13	533,270	7.5	$	26.32	272,539	$	26.15
$30.17—$30.17	80,000	8.2	$	30.17	46,664	$	30.17
$0.10—$30.17	8,946,592	7.5	$	9.07	4,134,023	$	9.94

Employee Share Based Compensation [Member]

Share-based Compensation Arrangement by Share-based Payment Award [Line Items]

Schedule of Share-based Payment Award, Stock Options, Valuation Assumptions [Table Text Block]

Stock-based compensation cost for RSUs is measured based on the closing fair market value of the Company's common stock on the date of grant. Stock-based compensation cost for stock options and employee stock purchase plan rights is estimated at the grant date and offering date, respectively, based on the fair-value using the Black-Scholes option pricing model. The fair value of employee stock options is being amortized on a straight-line basis over the requisite service period of the awards. The fair value of employee stock options was estimated using the following weighted-average assumptions:

	Years Ended December 31,
	2012		2011		2010
Expected dividend yield	—	%	—	%	—	%
Risk-free interest rate	1.1	%	2.3	%	2.5	%
Expected term (in years)	6.0		5.8		6.0
Expected volatility	77	%	86	%	96	%

Schedule of Employee Service Share-based Compensation, Allocation of Recognized Period Costs [Table Text Block]

Compensation expense was recorded for stock-based awards granted to employees based on the grant date estimated fair value (in thousands):

	Years Ended December 31,
	2012		2011		2010
Research and development	$	6,442	$	6,306	$	2,086
Sales, general and administrative	20,887		18,288		5,696
Total stock-based compensation expense	$	27,329	$	24,594	$	7,782

Non Employee Share Based Compensation [Member]

Share-based Compensation Arrangement by Share-based Payment Award [Line Items]

Schedule of Share-based Payment Award, Stock Options, Valuation Assumptions [Table Text Block]

The fair value of nonemployee stock options was estimated using the following weighted-average assumptions:

	Years Ended December 31,
	2012		2011		2010
Expected dividend yield	—	%	—	%	—	%
Risk-free interest rate	1.4	%	2.1	%	3.2	%
Expected term (in years)	7.0		7.8		8.6
Expected volatility	77	%	86	%	95	%

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Summary of Significant Accounting Policies Antidilutive Securities Excluded from Computation of Earnings Per Share (Details)	12 Months Ended
	Dec. 31, 2012		Dec. 31, 2011		Dec. 31, 2010
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive Securities Excluded from Computation of Earnings Per Share, Amount	21,888,920		8,786,357		7,503,637
Period-end stock options to purchase common stock [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive Securities Excluded from Computation of Earnings Per Share, Amount	8,946,592		8,377,016		7,274,637
Convertible promissory notes [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive Securities Excluded from Computation of Earnings Per Share, Amount	10,370,391		0		0
Period-end common stock subject to repurchase [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive Securities Excluded from Computation of Earnings Per Share, Amount	51		7,929		33,396
Period-end common stock warrants [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive Securities Excluded from Computation of Earnings Per Share, Amount	21,087	[1]	26,223	[1]	195,604	[1]
Warrants Issued			21,087
Stock Warrants issued in connection with the issuance of convertible preferred stock			5,136
Period-end restricted stock units [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive Securities Excluded from Computation of Earnings Per Share, Amount	2,550,799		375,189		0

[1] The common stock warrants at December 31, 2011 includes 21,087 warrants issued in 2011 and 5,136 common stock warrants converted from preferred stock warrants computed on an as converted basis using the conversion ratios in effect as of September 30, 2010, the date of the IPO Closing. The common stock warrants at December 31, 2010 were converted from preferred stock warrants computed on an as converted basis using the conversion ratios in effect as of September 30, 2010.

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Commitments and Contingencies Guarantor Arrangements/Purchase Obligations and Other Matters (Details)	12 Months Ended			1 Months Ended	12 Months Ended	0 Months Ended
	Dec. 31, 2012 USD ($)	Dec. 31, 2012 BRL	Dec. 31, 2012 FINEP Credit Facility [Member] disbursements	Nov. 30, 2010 FINEP Credit Facility [Member] Chattel Mortgage [Member] BRL disbursements	Dec. 31, 2012 FINEP Credit Facility [Member] Chattel Mortgage [Member] USD ($)	Nov. 15, 2011 Performance Guarantee [Member]	Dec. 31, 2012 Performance Guarantee [Member] Payment Guarantee [Member] USD ($)	Nov. 15, 2011 Performance Guarantee [Member] Payment Guarantee [Member] BRL	Dec. 31, 2012 BNDES Credit Facility [Member] BNDES [Member] USD ($)	Dec. 31, 2011 BNDES Credit Facility [Member] BNDES [Member] BRL	Jul. 13, 2012 Banco Pine July 2012 Loan Agreement [Member] BRL	Jul. 13, 2012 Nossa Caixa Loan Agreement [Member] BRL	Dec. 31, 2012 Pine and Nossa Caixa Loan Agreement [Member] USD ($)	Jul. 13, 2012 Pine and Nossa Caixa Loan Agreement [Member] BRL
Commitments and Contingencies Disclosure [Abstract]
Purchase Obligation	$ 53,100,000
Contractual Obligation	52,700,000
Loss on Purchase Commitments	13,900,000
Loss Contingency, Accrual Carrying Value	1,200,000	2,500,000
Loss Contingencies [Line Items]
Guaranty Liabilities				3,300,000	1,600,000
Line of Credit Facility, Maximum Borrowing Capacity				6,400,000	3,100,000
Research and Development Asset Acquired Other than Through Business Combination, Fair Value Acquired				6,000,000	2,900,000
Disbursements Received After Compliance with Certain Terms and Conditions (in disbursements)			3	4
Collateral Provided By Company, Certain Equipment and Other Tangible Assets, Amount									12,200,000	24,900,000			33,300,000	68,000,000
Debt Instrument, Face Amount											22,000,000	30,000,000	25,400,000	52,000,000
Period Required For Restricted Cash						3 months
Restricted Cash and Cash Equivalents							$ 100,000	200,000

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Balance Sheet Components Other Assets (Details) (USD $) In Thousands, unless otherwise specified	Dec. 31, 2012		Dec. 31, 2011
Balance Sheet Components [Abstract]
Deferred charge asset	$ 0	[1]	$ 18,792	[1]
Deposits on property and equipment, including taxes	2,363		17,455
Advances to contract manufacturers, net of current portion	2,222	[2]	2,866	[2]
Recoverable taxes on purchased property and equipment	13,597	[3]	2,075	[3]
Other	1,930		1,813
Total other assets	$ 20,112		$ 43,001

[1] The deferred charge asset relates to the collaboration agreement between the Company and Total (see Note 9)

[2] At December 31, 2012 and 2011, $2.2 million and $2.9 million, respectively, relates to the non-current unamortized portion of equipment costs funded by the Company to a contract manufacturer. The related amortization is being offset against purchases of inventory

[3] At December 31, 2012 and December 31, 2011, $13.6 million and $2.1 million, respectively, are recoverable taxes from the Brazilian government.

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Summary of Significant Accounting Policies Property, Plant, and Equipment, net (Details) (USD $) In Millions, unless otherwise specified	12 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Property, Plant and Equipment [Line Items]
Capitalized software additions	$ 1.4	$ 1.1	$ 1.3
Amortization expense	0.7	0.4	0.3
Unamortized cost of capitalized software	2.6
Capitalized Computer Software, Impairments	0.9
Asset impairment charges	$ 6.4	$ 0	$ 0
Buildings [Member]
Property, Plant and Equipment [Line Items]
Property, Plant and Equipment, Useful Life	15 years
Furniture and office equipment [Member]
Property, Plant and Equipment [Line Items]
Property, Plant and Equipment, Useful Life	5 years
Vehicles [Member]
Property, Plant and Equipment [Line Items]
Property, Plant and Equipment, Useful Life	5 years
Minimum [Member] | Machinery and equipment [Member]
Property, Plant and Equipment [Line Items]
Property, Plant and Equipment, Useful Life	7 years
Minimum [Member] | Computer and software [Member]
Property, Plant and Equipment [Line Items]
Property, Plant and Equipment, Useful Life	3 years
Minimum [Member] | Software [Member]
Property, Plant and Equipment [Line Items]
Property, Plant and Equipment, Useful Life	3 years
Maximum [Member] | Machinery and equipment [Member]
Property, Plant and Equipment [Line Items]
Property, Plant and Equipment, Useful Life	15 years
Maximum [Member] | Computer and software [Member]
Property, Plant and Equipment [Line Items]
Property, Plant and Equipment, Useful Life	5 years
Maximum [Member] | Software [Member]
Property, Plant and Equipment [Line Items]
Property, Plant and Equipment, Useful Life	5 years

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The Company

12 Months Ended

Dec. 31, 2012

The Company [Abstract]

The Company

The Company

Amyris, Inc. (the “Company”) was incorporated in California on July 17, 2003 and reincorporated in Delaware on June 10, 2010 for the purpose of leveraging breakthroughs in synthetic biology to develop and provide renewable compounds for a variety of markets. The Company is currently building and applying its industrial synthetic biology platform to provide alternatives to select petroleum-sourced products used in specialty chemical and transportation fuel markets worldwide. The Company's first commercialization efforts have been focused on a renewable hydrocarbon molecule called farnesene (Biofene®), which forms the basis for a wide range of products varying from specialty chemical applications to transportation fuels, such as diesel. While the Company's platform is able to use a wide variety of feedstocks, the Company is focused initially on Brazilian sugarcane. In addition, the Company has entered into various contract manufacturing agreements to support commercial production. The Company has established two principal operating subsidiaries, Amyris Brasil Ltda. (formerly Amyris Brasil S.A., “Amyris Brasil”) for production in Brazil, and Amyris Fuels, LLC ("Amyris Fuels"). Nearly all of the Company's revenues to date have come from the sale of ethanol and reformulated ethanol-blended gasoline with substantially all of the remaining revenues coming from collaborations, government grants and sales of renewable products. In the third quarter of 2012, the Company transitioned out of the ethanol and reformulated ethanol-blended gasoline business. The Company does not expect to be able to replace much of the revenue lost in the near term as a result of this transition, particularly in 2013 while it continues its efforts to establish a renewable products business.

Beginning in March 2012, the Company initiated a plan to shift a portion of its production capacity from contract manufacturing facilities to a Company-owned plant that was then under construction. As a result, the Company evaluated its contract manufacturing agreements and recorded a loss of $30.4 million related to adverse purchase commitments, $10.0 million related to the write-off of facility modification costs and $5.5 million related to Company-owned equipment at contract manufacturing facilities in the year ended December 31, 2012. The Company regularly monitors its plan related to production capacity, sales requirements and related cost structure. Changes to this plan may result in additional losses and impairment charges.

The Company's renewable products business strategy is to focus on direct commercialization of higher-value, lower-volume markets while moving lower-margin, higher-volume commodity products into joint venture arrangements with established industry partners. To commercialize its products, the Company must be successful in using its technology to manufacture its products at commercial scale and on an economically viable basis (i.e., low per unit production costs). The Company is building its experience producing renewable products at commercial scale. The Company's prospects are subject to risks, expenses and uncertainties frequently encountered by companies in this stage of development.

The Company expects to fund its operations for the foreseeable future with cash and investments currently on hand, with cash inflows from collaboration and grant funding, cash contributions from product sales, and with new debt and equity financing. The Company's planned 2013 working capital needs and its planned operating and capital expenditures for 2013 are dependent on significant inflows of cash from existing collaboration partners, as well as additional funding from new collaborations, equity or debt offerings, credit facilities or loans, or combinations of these sources. The Company will continue to need to fund its research and development and related activities and to provide working capital to fund production, storage, distribution and other aspects of its business. The Company's operating plan contemplates capital expenditures of approximately $10.0 million in 2013 and the Company expects to continue to incur costs in connection with its existing contract manufacturing arrangements. During 2012, the Company completed multiple debt and equity financings, raising aggregate cash proceeds of $193.6 million. (See Note 6 - “Debt” and Note 11 - “Stockholders' Equity”). The Company's most recent financing of R$5.0 million reais (approximately US$2.5 million) was completed in March 2013. (See Note 18 - “Subsequent Events”).

Liquidity

The Company has incurred significant losses in each year since its inception and believes that it will continue to incur losses and negative cash flow from operations into at least 2014. As of December 31, 2012, the Company had an accumulated deficit of $586.3 million and had cash, cash equivalents and short term investments of $30.7 million. The Company has significant outstanding debt and contractual obligations related to purchase commitments, as well as capital and operating leases. As of December 31, 2012, the Company's debt totaled $104.2 million, of which $3.3 million matures within the next twelve months. In addition, the Company's debt agreements contain various covenants, including restrictions on business that could cause the Company to be at risk of defaults. Please refer to Note 5 “Commitments and Contingencies” and Note 6 “Debt” for further details regarding the Company's obligations and commitments.

As of December 31, 2012, the Company had cash, cash equivalents and short-term investments of $30.7 million. In March 2013, the Company signed a collaboration agreement that included a funding component, and obtained a commitment letter from an existing stockholder with respect to additional convertible note funding (see Note 18 - “Subsequent Events”), and the Company expects to use amounts received under these arrangements to fund its operations. Furthermore, the Company is expecting additional funding in 2013 from collaborations, equity or debt offerings, or combinations of these sources. The Company's operating plan contemplates securing a portion of this additional funding in the second quarter of 2013. However, as of the date of this filing, the Company has not yet secured this additional funding. There can be no assurance that financing will be available on commercially acceptable terms or at all.

If the Company is unable to raise additional financing, or if other expected sources of funding are delayed or not received, the Company would take the following actions as early as the second quarter of 2013 to support its liquidity needs through the remainder of 2013 and into 2014:

• Effect significant headcount reductions in the U.S. and in Brazil, particularly with respect to both general and administrative employees and other employees not connected to critical or contracted activities.

• Shift its focus to existing products and customers with significantly reduced investment in new product and commercial development efforts.

• Reduce its expenditures for third party contractors, including consultants, professional advisors and other vendors.

• Suspend operations at its pilot plants and demonstration facilities.

• Reduce or delay uncommitted capital expenditures, including non-essential lab equipment and information technology projects.

The contingency cash plan contemplating these actions is designed to save the Company an estimated $35 million to $40 million over the next twelve months. Implementing this plan could have a material negative impact on the Company's ability to continue its business as currently contemplated, including, without limitation, delays or failures in its ability to:

• Achieve planned production levels;

• Develop and commercialize products within planned timelines or at planned scales; and

• Continue other core activities.

Furthermore, any inability to scale-back operations as necessary, and any unexpected liquidity needs, could create pressure to implement more severe measures. Such measures could have a material adverse effect on the Company's ability to meet contractual requirements, including obligations to maintain manufacturing operations, and increase the severity of the consequences described above.

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Balance Sheet Components Accrued and Other Current Liabilities (Details) (USD $) In Thousands, unless otherwise specified	Dec. 31, 2012	Dec. 31, 2011
Balance Sheet Components [Abstract]
Professional services	$ 824	$ 4,384
Accrued vacation	2,673	2,761
Payroll and related expenses	5,809	6,343
Construction in progress	0	4,992
Tax-related liabilities	851	2,180
Deferred rent, current portion	1,448	1,274
Contractual obligations to contract manufacturers	9,952	0
Customer advances	970	3,667
Other	1,883	5,381
Total accrued and other current liabilities	$ 24,410	$ 30,982

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Summary of Significant Accounting Policies Concentration of Credit Risk (Details) (Customer Concentration Risk [Member])	12 Months Ended
	Dec. 31, 2011 Customer A. [Member] Accounts Receivable [Member]	Dec. 31, 2012 Customer A. [Member] Revenues [Member]	Dec. 31, 2011 Customer A. [Member] Revenues [Member]	Dec. 31, 2011 Customer B. [Member] Accounts Receivable [Member]	Dec. 31, 2012 Customer C. [Member] Accounts Receivable [Member]	Dec. 31, 2012 Customer D. [Member] Accounts Receivable [Member]	Dec. 31, 2010 Customer D. [Member] Revenues [Member]	Dec. 31, 2012 Customer E. [Member] Accounts Receivable [Member]	Dec. 31, 2010 Customer F. [Member] Revenues [Member]	Dec. 31, 2011 Customer G [Member] Revenues [Member]	Dec. 31, 2010 Customer G [Member] Revenues [Member]	Dec. 31, 2012 Customer H. [Member] Revenues [Member]	Dec. 31, 2010 Customer I. [Member] Revenues [Member]
Concentration Risk [Line Items]
Concentration Risk, Percentage	20.00%	13.00%	11.00%	10.00%	44.00%	22.00%	12.00%	14.00%	10.00%	14.00%	23.00%	13.00%	10.00%

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Summary of Significant Accounting Policies (Tables)

12 Months Ended

Dec. 31, 2012

Accounting Policies [Abstract]

Schedules of Concentration of Risk, by Risk Factor [Table Text Block]

Concentration of Credit Risk

Financial instruments that potentially subject the Company to a concentration of credit risk consist primarily of cash and cash equivalents and accounts receivable. The Company places its cash equivalents and investments with high credit quality financial institutions and, by policy, limits the amount of credit exposure with any one financial institution. Deposits held with banks may exceed the amount of insurance provided on such deposits. The Company has not experienced any losses on its deposits of cash and cash equivalents and short-term investments.

The Company performs ongoing credit evaluation of its customers, does not require collateral, and maintains allowances for potential credit losses on customer accounts when deemed necessary.

Customers representing 10% or greater of accounts receivable were as follows:

	December 31,
Customers	2012		2011
Customer A	*		20	%
Customer B	*		10	%
Customer C	44	%	**
Customer D	22	%	**
Customer E	14	%	**

______________ 

 * No outstanding balance

** Less than 10%

Customers representing 10% or greater of revenues were as follows:

	Years Ended December 31,
Customers	2012		2011		2010
Customer A	13	%	11	%	**
Customer D	**		**		12	%
Customer F	**		**		10	%
Customer G	**		14	%	23	%
Customer H	13	%	*		*
Customer I	**		*		10	%

______________

 * Not a customer

** Less than 10%

Schedule of Asset Retirement Obligations [Table Text Block]

The change in the asset retirement obligation is summarized below (in thousands):

Balance at December 31, 2010	$	984
Additions	166
Foreign currency impacts and other adjustments	(133		)
Accretion expenses recorded during the period	112
Balance at December 31, 2011	$	1,129
Additions	—
Foreign currency impacts and other adjustments	(98		)
Accretion expenses recorded during the period	91
Reversals	(1,122		)
Balance at December 31, 2012	$	—

Property, Plant and Equipment [Table Text Block]

Depreciation and amortization periods for the Company’s property, plant and equipment are as follows:

Machinery and equipment	7-15 years
Buildings	15 years
Computers and software	3-5 years
Furniture and office equipment	5 years
Vehicles	5 years

Property, plant and equipment, net is comprised of the following (in thousands):

	December 31,
	2012			2011
Leasehold improvements	$	39,290		$	40,011
Machinery and equipment	105,162			59,657
Computers and software	8,232			6,491
Furniture and office equipment	2,467			2,223
Buildings	5,888			—
Vehicles	575			596
Construction in progress	45,372			45,318
	$	206,986		154,296
Less: accumulated depreciation and amortization	(43,865		)	(26,195		)
Property, plant and equipment, net	$	163,121		$	128,101

Schedule of Accumulated Other Comprehensive Income (Loss) [Table Text Block]

The components of accumulated other comprehensive loss are as follows (in thousands):

	December 31,
	2012			2011
Foreign currency translation adjustment, net of tax	$	(12,807	)	$	(5,924	)
Total accumulated other comprehensive loss	$	(12,807	)	$	(5,924	)

Schedule of Calculation of Numerator and Denominator in Earnings Per Share [Table Text Block]

The following table presents the calculation of basic and diluted net loss per share of common stock attributable to Amyris, Inc. common stockholders (in thousands, except share and per share amounts):

	Years Ended December 31,
	2012			2011			2010
Numerator:
Net loss attributable to Amyris, Inc. common stockholders	$	(205,139	)	$	(178,870	)	$	(123,879	)
Denominator:
Weighted-average shares of common stock outstanding used in computing net loss per share of common stock, basic and diluted	56,717,869			44,799,056			14,840,253
Net loss per share attributable to common stockholders, basic and diluted	$	(3.62	)	$	(3.99	)	$	(8.35	)

Schedule of Antidilutive Securities Excluded from Computation of Earnings Per Share [Table Text Block]

The following outstanding shares of potentially dilutive securities were excluded from the computation of diluted net loss per share of common stock for the periods presented because including them would have been anti-dilutive:

	Years Ended December 31,
	2012	2011	2010
Period-end stock options to purchase common stock	8,946,592	8,377,016	7,274,637
Convertible promissory notes	10,370,391	—	—
Period-end common stock subject to repurchase	51	7,929	33,396
Period-end common stock warrants*	21,087	26,223	195,604
Period-end restricted stock units	2,550,799	375,189	—
Total	21,888,920	8,786,357	7,503,637

______________ 

• The common stock warrants at December 31, 2011 includes 21,087 warrants issued in 2011 and 5,136 common stock warrants converted from preferred stock warrants computed on an as converted basis using the conversion ratios in effect as of September 30, 2010, the date of the IPO Closing. The common stock warrants at December 31, 2010 were converted from preferred stock warrants computed on an as converted basis using the conversion ratios in effect as of September 30, 2010.

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Summary of Significant Accounting Policies (Policies)

12 Months Ended

Dec. 31, 2012

Accounting Policies [Abstract]

Basis of Accounting [Text Block]

Basis of Presentation

The accompanying consolidated financial statements have been prepared in accordance with the accounting principles generally accepted in the United States of America (“GAAP”) and with the instructions for Form 10-K and Regulations S-X statements. The consolidated financial statements include the accounts of the Company and its consolidated subsidiaries. All intercompany accounts and transactions have been eliminated in consolidation.

Principles of Consolidations [Policy Text Block]

Principles of Consolidations

The Company has interests in joint venture entities that are variable interest entities (“VIEs”). Determining whether to consolidate a variable interest entity requires judgment in assessing (i) whether an entity is a VIE and (ii) if the Company is the entity’s primary beneficiary and thus required to consolidate the entity. To determine if the Company is the primary beneficiary of a VIE, the Company evaluates whether it has (i) the power to direct the activities that most significantly impact the VIE’s economic performance and (ii) the obligation to absorb losses or the right to receive benefits of the VIE that could potentially be significant to the VIE. The Company’s evaluation includes identification of significant activities and an assessment of its ability to direct those activities based on governance provisions and arrangements to provide or receive product and process technology, product supply, operations services, equity funding and financing and other applicable agreements and circumstances. The Company’s assessment of whether it is the primary beneficiary of its VIEs requires significant assumptions and judgment.

The consolidated financial statements of the Company include the accounts of Amyris, Inc., its subsidiaries and two consolidated VIEs with respect to which the Company is considered the primary beneficiary, after elimination of intercompany accounts and transactions. Disclosure regarding the Company’s participation in the VIEs is included in Note 8.

Use of Estimates [Policy Text Block]

Use of Estimates

In preparing the consolidated financial statements, management must make estimates and assumptions that affect the reported amounts of assets and liabilities and disclosure of contingent assets and liabilities as of the date of the consolidated financial statements and the reported amounts of revenue and expenses during the reporting period. Actual results could differ from those estimates.

Concentration Of Credit Risk [Policy Text Block]

Customers representing 10% or greater of accounts receivable were as follows:

	December 31,
Customers	2012		2011
Customer A	*		20	%
Customer B	*		10	%
Customer C	44	%	**
Customer D	22	%	**
Customer E	14	%	**

______________ 

 * No outstanding balance

** Less than 10%

Customers representing 10% or greater of revenues were as follows:

	Years Ended December 31,
Customers	2012		2011		2010
Customer A	13	%	11	%	**
Customer D	**		**		12	%
Customer F	**		**		10	%
Customer G	**		14	%	23	%
Customer H	13	%	*		*
Customer I	**		*		10	%

______________

 * Not a customer

** Less than 10%

Fair Value of Financial Instruments, Policy [Policy Text Block]

Fair Value of Financial Instruments

The Company measures certain financial assets and liabilities at fair value based on the exchange price that would be received for an asset or paid to transfer a liability (an exit price) in the principal or most advantageous market for the asset or liability in an orderly transaction between market participants. Where available, fair value is based on or derived from observable market prices or other observable inputs. Where observable prices or inputs are not available, valuation models are applied. These valuation techniques involve some level of management estimation and judgment, the degree of which is dependent on the price transparency for the instruments or market and the instruments’ complexity.

The carrying amounts of certain financial instruments, such as cash equivalents, accounts receivable, accounts payable and accrued liabilities, approximate fair value due to their relatively short maturities, and low market interest rates if applicable. The fair values of the notes payable, loan payable, convertible notes and credit facility are based on the present value of expected future cash flows and assumptions about current interest rates and the creditworthiness of the Company.

The Company estimates the fair value of its embedded derivative related to Total senior unsecured convertible notes using a Black-Scholes valuation model that combines expected cash outflows with market-based assumptions regarding risk-adjusted yields, stock price volatility, probability of a change of control and the trading information of the Company's common stock into which the notes are convertible. The Company will continue to mark the bifurcated compound derivative to market due to the conversion price not being indexed to the Company's own stock because of the feature requiring the Company to redeem foregone interest upon conversion by the holder. The change in the fair value of the bifurcated compound derivative is primarily related to the change in price of the underlying common stock and is reflected in the Company's consolidated statements of operations as “other income (expense)”.

Cash and Cash Equivalents, Policy [Policy Text Block]

Cash and Cash Equivalents

All highly liquid investments purchased with an original maturity date of 90 days or less at the date of purchase are considered to be cash equivalents. Cash and cash equivalents consist of money market funds and certificates of deposit.

Receivables, Policy [Policy Text Block]

Accounts Receivable

The Company maintains an allowance for doubtful accounts receivable for estimated losses resulting from the inability of its customers to make required payments. The Company determines this allowance based on specific doubtful account identification and management judgment on estimated exposure. The Company writes off accounts receivable against the allowance when it determines a balance is uncollectible and no longer actively pursues collection of the receivable. 

Investments [Policy Text Block]

Investments

Investments with original maturities greater than 90 days that mature less than one year from the consolidated balance sheet date are classified as short-term investments. The Company classifies investments as short-term or long-term based upon whether such assets are reasonably expected to be realized in cash or sold or consumed during the normal cycle of business. The Company invests its excess cash balances primarily in certificates of deposit. Certificates of deposits that have maturities greater than 90 days that mature less than one year from the consolidated balance sheet date are classified as short term investments. The Company classifies all of its investments as available-for-sale and records such assets at estimated fair value in the consolidated balance sheets, with unrealized gains and losses, if any, reported as a component of accumulated other comprehensive income (loss) in stockholders’ equity. Debt securities are adjusted for amortization of premiums and accretion of discounts and such amortization and accretion are reported as a component of interest income. Realized gains and losses and declines in value that are considered to be other-than-temporary are recognized in the statements of operations. The cost of securities sold is determined on the specific identification method. There were no significant realized gains or losses from sales of debt securities during the years ended December 31, 2012, 2011 and 2010. As of December 31, 2012 and 2011, the Company did not have any other-than-temporary declines in the fair value of its debt securities.

Restricted Cash and Cash Equivalents, Policy [Policy Text Block]

Restricted Cash

Cash accounts that are restricted to withdrawal or usage are presented as restricted cash. As ofDecember 31, 2012 and 2011, the Company had $955,000 and zero, respectively, of restricted cash held by a bank in a certificate of deposit as collateral under a facility lease.

Inventories [Policy Text Block]

Inventories

Inventories, which consist of farnesene-derived products, as well as ethanol and reformulated ethanol-blended gasoline, are stated at the lower of cost or market and categorized as finished goods, work-in-process or raw material inventories. During the quarter ended September 30, 2012, the Company sold its remaining inventory of ethanol and reformulated ethanol-blended gasoline as it transitioned out of this business. The Company evaluates the recoverability of its inventories based on assumptions about expected demand and net realizable value. If the Company determines that the cost of inventories exceeds its estimated net realizable value, the Company records a write-down equal to the difference between the cost of inventories and the estimated net realizable value. If actual net realizable values are less favorable than those projected by management, additional inventory write-downs may be required that could negatively impact the Company's operating results. If actual net realizable values are more favorable, the Company may have favorable operating results when products that have been previously written down are sold in the normal course of business. The Company also evaluates the terms of its agreements with its suppliers and establishes accruals for estimated losses on adverse purchase commitments as necessary, applying the same lower of cost or market approach that is used to value inventory. Cost is computed on a first-in, first-out basis. Inventory costs include transportation costs incurred in bringing the inventory to its existing location.

Derivative Instruments [Policy Text Block]

Derivative Instruments

The Company makes limited use of derivative instruments, which includes currency interest rate swap agreements to manage the Company's exposure to foreign currency exchange rate fluctuations and interest rate fluctuations related to the Company's Banco Pine S.A. loan (discussed below under Note 6). Through the third quarter of 2012, the Company held futures positions on the New York Mercantile Exchange and the CME/Chicago Board of Trade to mitigate the risks related to the price volatility of ethanol and reformulated ethanol-blended gasoline but, as of September 30, 2012, the Company had transitioned out of that business and no longer held such derivative instruments. The Company does not engage in speculative derivative activities, and the purpose of its activity in derivative commodity instruments is to manage the financial risk posed by physical transactions and inventory. Changes in the fair value of the derivative contracts are recognized currently in the consolidated statements of operations.

Asset Retirement Obligations, Policy [Policy Text Block]

Asset Retirement Obligations

The fair value of an asset retirement obligation is recognized in the period in which it is incurred if a reasonable estimate of fair value can be made. In addition, asset retirement cost is added to the carrying amount of the associated asset and this additional carrying amount is amortized over the life of the asset. The Company’s asset retirement obligations were associated with its commitment to return property subject to an operating lease in Brazil to its original condition upon lease termination. In October 2012, this operating lease was amended which included an amendment to the terms of restitution of the property under lease. As a result of this amendment, the Company no longer has asset retirement obligations and therefore reversed the previously accrued liabilities.

As of December 31, 2012 and 2011, the Company had asset retirement obligations of zero and $1.1 million, respectively. The related leasehold improvements are being amortized to depreciation expense over the term of the lease or the useful life of the assets, whichever is shorter. Related amortization expense was $188,000, $193,000 and $229,000 for the years ended December 31, 2012, 2011 and 2010, respectively.

The change in the asset retirement obligation is summarized below (in thousands):

Balance at December 31, 2010	$	984
Additions	166
Foreign currency impacts and other adjustments	(133		)
Accretion expenses recorded during the period	112
Balance at December 31, 2011	$	1,129
Additions	—
Foreign currency impacts and other adjustments	(98		)
Accretion expenses recorded during the period	91
Reversals	(1,122		)
Balance at December 31, 2012	$	—

Property, Plant and Equipment, net [Policy Text Block]

Property, Plant and Equipment, net

Property, plant and equipment, net are stated at cost less accumulated depreciation and amortization. Depreciation and amortization is computed using the straight-line method over the estimated useful lives of the related assets. Maintenance and repairs are charged to expense as incurred, and improvements and betterments are capitalized. When assets are retired or otherwise disposed of, the cost and accumulated depreciation are removed from the balance sheet and any resulting gain or loss is reflected in operations in the period realized.

Depreciation and amortization periods for the Company’s property, plant and equipment are as follows:

Machinery and equipment	7-15 years
Buildings	15 years
Computers and software	3-5 years
Furniture and office equipment	5 years
Vehicles	5 years

Buildings and leasehold improvements are amortized on a straight-line basis over the terms of the lease, or the useful life of the assets, whichever is shorter.

Computers and software includes internal-use software that is acquired to meet the Company’s needs. Amortization commences when the software is ready for its intended use and the amortization period is the estimated useful life of the software, generally 3 to 5 years. Capitalized costs primarily include contract labor and payroll costs of the individuals dedicated to the installation of internal-use software. Capitalized software additions totaled approximately $1.4 million, $1.1 million, and $1.3 million for the years ended December 31, 2012, 2011 and 2010, respectively, related to software costs pertaining to the installation of new financial reporting systems. For the years ended December 31, 2012, 2011 and 2010, $0.7 million, $0.4 million and $0.3 million, respectively, of amortization expense was recorded and as of December 31, 2012 the total unamortized cost of capitalized software was $2.6 million. During the year ended December 31, 2012, the Company wrote-off capitalized software with a net book value of $0.9 million.

Impairment of Long-Lived Assets [Policy Text Block]

Impairment of Long-Lived Assets

Long-lived assets to be held and used are reviewed for impairment whenever events or changes in circumstances indicate that the carrying amount of an asset may not be recoverable or the estimated useful life is no longer appropriate. If indicators of impairment exist and the undiscounted projected cash flows associated with such assets are less than the carrying amount of the asset, an impairment loss is recorded to write the asset down to their estimated fair values. Fair value is estimated based on discounted future cash flows. There were $6.4 million, zero and zero, respectively, of impairment charges recorded during the years ended December 31, 2012, 2011 and 2010, respectively. The impairment charges of $6.4 million in 2012 included the write-off of capitalized software with a net book value of $0.9 million

Valuation of Goodwill and Intangible Assets [Policy Text Block]

Goodwill and Intangible Assets

Goodwill represents the excess of the cost over the fair value of net assets acquired from our business combinations. Intangible assets are comprised primarily of in-process research and development ("IPR&D"). The Company makes significant judgments in relation to the valuation of goodwill and intangible assets resulting from business combinations.

There are several methods that can be used to determine the estimated fair value of the IPR&D acquired in a business combination. We used the "income method," which applies a probability weighting that considers the risk of development and commercialization, to the estimated future net cash flows that are derived from projected sales revenues and estimated costs. These projections are based on factors such as relevant market size, pricing of similar products, and expected industry trends. The estimated future net cash flows are then discounted to the present value using an appropriate discount rate. These assets are treated as indefinite-lived intangible assets until completion or abandonment of the projects, at which time the assets will be amortized over the remaining useful life or written off, as appropriate.

Goodwill and intangible assets with indefinite lives are assessed for impairment using fair value measurement techniques on an annual basis or more frequently if facts and circumstance warrant such a review. When required, a comparison of fair value to the carrying amount of assets is performed to determine the amount of any impairment.

The Company evaluates its intangible assets with finite lives for indications of impairment whenever events or changes in circumstances indicate that the carrying value may not be recoverable. Intangible assets consist of purchased licenses and permits and are amortized on a straight-line basis over their estimated useful lives. Amortization of intangible assets was $0.4 million, $0.4 million and zero for the years ended December 31, 2012, 2011 and 2010, respectively. Factors that could trigger an impairment review include significant under-performance relative to expected historical or projected future operating results, significant changes in the manner of our use of the acquired assets or the strategy for our overall business or significant negative industry or economic trends. If this evaluation indicates that the value of the intangible asset may be impaired, we make an assessment of the recoverability of the net carrying value of the asset over its remaining useful life. If this assessment indicates that the intangible asset is not recoverable, based on the estimated undiscounted future cash flows of the technology over the remaining amortization period, we reduce the net carrying value of the related intangible asset to fair value and may adjust the remaining amortization period. Any such impairment charge could be significant and could have a material adverse effect on our reported financial results. The Company has not recognized any impairment charges on our intangible assets through December 31, 2012.

In-Process Research and Development [Policy Text Block]

In-Process Research and Development

During 2011, the Company recorded IPR&D of $8.6 million related to the acquisition of Draths. Amounts recorded as IPR&D will begin being amortized upon first sales of the product over the estimated useful life of the technology. In accordance with authoritative guidance, as the technology has not yet been proven, the amortization of the acquired IPR&D has not begun. The Company estimates that it could take up to three years before it will have viable products resulting from the acquired technology.

Revenue Recognition [Policy Text Block]

Revenue Recognition

The Company recognizes revenue from the sale of farnesene-derived products, delivery of research and development services, and from governmental grants. Through the third quarter of 2012, the Company also sold ethanol and reformulated ethanol-blended gasoline under short-term agreements at prevailing market prices. As of September 30, 2012, the Company had transitioned out of that business. Revenue is recognized when all of the following criteria are met: persuasive evidence of an arrangement exists, delivery has occurred or services have been rendered, the fee is fixed or determinable, and collectibility is reasonably assured.

If sales arrangements contain multiple elements, the Company evaluates whether the components of each arrangement represent separate units of accounting.

Product Sales

Beginning in the second quarter of 2011, the Company began to sell farnesene-derived products, which were produced by contracted third parties. Through the third quarter of 2012, the Company also sold ethanol and reformulated ethanol-blended gasoline under short-term agreements at prevailing market prices. As of September 30, 2012, the Company had transitioned out of that business.Ethanol and reformulated ethanol-blended gasoline sales consisted of sales to customers through purchases from third-party suppliers in which the Company took physical control of the ethanol and reformulated ethanol-blended gasoline and accepted risk of loss. The Company's renewable product sales do not include rights of return. Returns are only accepted if the product does not meet product specifications and such nonconformity is communicated to the Company within a set number of days of delivery. Commencing April 1, 2012, the Company began offering a two year standard warranty provision for squalane products sold after March 31, 2012, if the products do not meet Company-established criteria as set forth in the Company's trade terms. The Company bases its return reserve on a combination of historical rate of return for the Company's squalane products and historical returns for companies in the cosmetics industry since the Company did not have a full two years of historical return data. Revenues are recognized, net of discounts and allowances, once passage of title and risk of loss has occurred and contractually specified acceptance criteria have been met, provided all other revenue recognition criteria have also been met.

Grants and Collaborative Revenue

Revenue from collaborative research services is recognized as the services are performed consistent with the performance requirements of the contract. In cases where the planned levels of research services fluctuate over the research term, the Company recognizes revenue using the proportionate performance method based upon actual efforts to date relative to the amount of expected effort to be incurred by the Company. When up-front payments are received and the planned levels of research services do not fluctuate over the research term, revenue is recorded on a ratable basis over the arrangement term, up to the amount of cash received. When up-front payments are received and the planned levels of research services fluctuate over the research term, revenue is recorded using the proportionate performance method, up to the amount of cash received. Where arrangements include milestones that are determined to be substantive and at risk at the inception of the arrangement, revenue is recognized upon achievement of the milestone and is limited to those amounts whereby collectibility is reasonably assured.

Government grants are agreements that generally provide cost reimbursement for certain types of expenditures in return for research and development activities over a contractually defined period. Revenues from government grants are recognized in the period during which the related costs are incurred, provided that the conditions under which the government grants were provided have been met and only perfunctory obligations are outstanding. Under the Defense Advanced Research Projects Agency (DARPA) contract signed in June 2012, the Company will receive funding based on achievement of program milestones. Accordingly, the Company will recognize revenue using the proportionate performance method based upon actual efforts to date relative to the amount of expected effort to be incurred, up to the amount of verified payable milestones.

Cost of Product Sales [Policy Text Block]

Cost of Products Sold

Starting in the second quarter of 2011, cost of products sold includes production costs of farnesene-derived products, which include cost of raw materials, amounts paid to contract manufacturers and period costs including inventory write-downs resulting from applying lower-of-cost-or-market inventory valuation. Cost of farnesene-derived products sold also includes certain costs related to the scale-up in production of such products. Through the third quarter of 2012, cost of products sold consisted primarily of cost of purchased ethanol and reformulated ethanol-blended gasoline, terminal fees paid for storage and handling, transportation costs between terminals and changes in the fair value of derivative commodity instruments. The Company transitioned out of its ethanol and gasoline business in the quarter ended September 30, 2012.

Shipping and handling costs charged to customers are recorded as revenues. Shipping costs are included in cost of products sold. Such charges were not significant in any of the periods presented.

Costs of Start-Up Actvities [Policy Text Block]

Costs of Start-Up Activities

Start-up activities are defined as those one-time activities related to opening a new facility, introducing a new product or service, conducting business in a new territory, conducting business with a new class of customer or beneficiary, initiating a new process in an existing facility, commencing some new operation or activities related to organizing a new entity. All the costs associated with start-up activities related to a potential facility are expensed and recorded within selling, general and administrative expenses until the facility is considered viable by management, at which time costs would be considered for capitalization based on authoritative accounting literature.

Research and Development [Policy Text Block]

Research and Development

Research and development costs are expensed as incurred and include costs associated with research performed pursuant to collaborative agreements and government grants. Research and development costs consist of direct and indirect internal costs related to specific projects as well as fees paid to others that conduct certain research activities on the Company’s behalf.

Income Taxes [Policy Text Block]

Income Taxes

The Company accounts for income taxes under the asset and liability method, which requires, among other things, that deferred income taxes be provided for temporary differences between the tax basis of the Company’s assets and liabilities and their financial statement reported amounts. In addition, deferred tax assets are recorded for the future benefit of utilizing net operating losses and research and development credit carryforwards. A valuation allowance is provided against deferred tax assets unless it is more likely than not that they will be realized.

The Company recognizes and measures uncertain tax positions in accordance with Income Taxes subtopic 05-6 of ASC 740, which prescribes a recognition threshold and measurement process for recording uncertain tax positions taken, or expected to be taken in a tax return, in the consolidated financial statements. Additionally, the guidance also prescribes treatment for the derecognition, classification, accounting in interim periods and disclosure requirements for uncertain tax positions. The Company accrues for the estimated amount of taxes for uncertain tax positions if it is more likely than not that the Company would be required to pay such additional taxes. An uncertain tax position will not be recognized if it has a less than 50% likelihood of being sustained.

Currency Translation [Policy Text Block]

Currency Translation

The Brazilian real is the functional currency of the Company’s wholly-owned subsidiary in Brazil and of the Company’s joint venture with Usina São Martinho. Accordingly, asset and liability accounts of those operations are translated into United States dollars using the current exchange rate in effect at the balance sheet date and equity accounts are translated into United States dollars using historical rates. The revenues and expenses are translated using the exchange rates in effect when the transactions occur. Gains and losses from foreign currency translation adjustments are included as a component of accumulated other comprehensive income (loss) in the consolidated balance sheets.

Stock-Based Compensation [Policy Text Block]

Stock-Based Compensation

The Company accounts for stock-based compensation arrangements with employees using a fair value method which requires the recognition of compensation expense for costs related to all stock-based payments including stock options. The fair value method requires the Company to estimate the fair value of stock-based payment awards on the date of grant using an option pricing model. The Company uses the Black-Scholes option pricing model to estimate the fair value of options granted, which is expensed on a straight-line basis over the vesting period. The Company accounts for restricted stock unit awards issued to employees based on the fair market value of the Company’s common stock.

The Company accounts for stock options issued to nonemployees based on the estimated fair value of the awards using the Black-Scholes option pricing model. The Company accounts for restricted stock units issued to nonemployees based on the fair market value of the Company’s common stock. The measurement of stock-based compensation is subject to periodic adjustments as the underlying equity instruments vest, and the resulting change in value, if any, is recognized in the Company’s consolidated statements of operations during the period the related services are rendered.

Comprehensive Income, Policy [Policy Text Block]

Comprehensive Income (Loss)

Comprehensive income (loss) represents all changes in stockholders’ equity except those resulting from investments or contributions by stockholders. The Company’s foreign currency translation adjustments represent the components of comprehensive income (loss) excluded from the Company’s net loss and have been disclosed in the consolidated statements of comprehensive loss for all periods presented.

Net Loss Attributable to Common Stockholders and Net Loss per Share [Policy Text Block]

Net Loss Attributable to Common Stockholders and Net Loss per Share

The Company computes net loss per share in accordance with ASC 260, “Earnings per Share.” Basic net loss per share of common stock is computed by dividing the Company’s net loss attributable to Amyris, Inc. common stockholders by the weighted-average number of shares of common stock outstanding during the period. Diluted net loss per share of common stock is computed by giving effect to all potentially dilutive securities, including stock options, restricted stock units, common stock warrants, using the treasury stock method or the as converted method, as applicable. For all periods presented, basic net loss per share was the same as diluted net loss per share because the inclusion of all potentially dilutive securities outstanding was anti-dilutive. As such, the numerator and the denominator used in computing both basic and diluted net loss are the same for each period presented.

The following table presents the calculation of basic and diluted net loss per share of common stock attributable to Amyris, Inc. common stockholders (in thousands, except share and per share amounts):

	Years Ended December 31,
	2012			2011			2010
Numerator:
Net loss attributable to Amyris, Inc. common stockholders	$	(205,139	)	$	(178,870	)	$	(123,879	)
Denominator:
Weighted-average shares of common stock outstanding used in computing net loss per share of common stock, basic and diluted	56,717,869			44,799,056			14,840,253
Net loss per share attributable to common stockholders, basic and diluted	$	(3.62	)	$	(3.99	)	$	(8.35	)

The following outstanding shares of potentially dilutive securities were excluded from the computation of diluted net loss per share of common stock for the periods presented because including them would have been anti-dilutive:

	Years Ended December 31,
	2012	2011	2010
Period-end stock options to purchase common stock	8,946,592	8,377,016	7,274,637
Convertible promissory notes	10,370,391	—	—
Period-end common stock subject to repurchase	51	7,929	33,396
Period-end common stock warrants*	21,087	26,223	195,604
Period-end restricted stock units	2,550,799	375,189	—
Total	21,888,920	8,786,357	7,503,637

______________ 

• The common stock warrants at December 31, 2011 includes 21,087 warrants issued in 2011 and 5,136 common stock warrants converted from preferred stock warrants computed on an as converted basis using the conversion ratios in effect as of September 30, 2010, the date of the IPO Closing. The common stock warrants at December 31, 2010 were converted from preferred stock warrants computed on an as converted basis using the conversion ratios in effect as of September 30, 2010.

New Accounting Pronouncements, Policy [Policy Text Block]

Recent Accounting Pronouncements

In December 2011, the International Accounting Standards Board ("IASB") and the FASB issued common disclosure requirements that are intended to enhance comparability between financial statements prepared on the basis of U.S. GAAP and those prepared in accordance with IFRS. In January 2013, the FASB issued an accounting standard update to limit the scope of the new balance sheet offsetting disclosures to derivative instruments, repurchase agreements, and securities lending transactions to the extent that they are offset in the financial statement or subject to an enforceable master netting arrangement or similar arrangement. While this guidance does not change existing offsetting criteria in U.S. GAAP or the permitted balance sheet presentation for items meeting the criteria, it requires an entity to disclose both net and gross information about assets and liabilities that have been offset and the related arrangements. Required disclosures under this new guidance should be provided retrospectively for all comparative periods presented. This new guidance is effective for fiscal years beginning on or after January 1, 2013, and interim periods within those years, which would be the Company's first quarter of fiscal 2013. The adoption of this guidance will require expanded disclosure in the Company's consolidated financial statements but will not impact financial results.

In July 2012, the FASB issued an amended accounting standard update to simplify how entities test indefinite-lived intangible assets for impairment which improve consistency in impairment testing requirements among long-lived asset categories. The amended guidance permits an assessment of qualitative factors to determine whether it is more likely than not that the fair value of an indefinite-lived intangible asset is less than its carrying value. For assets in which this assessment concludes it is more likely than not that the fair value is more than its carrying value, then the amended guidance eliminates the requirement to perform quantitative impairment testing as outlined in the previously issued standards. The amended guidance is effective for fiscal years beginning after September 15, 2012; however, early adoption is permitted. The Company does not expect this amended guidance to have an impact on the Company's financial results.

In February 2013, in connection with the accounting standard related to the presentation of the Statement of Comprehensive Income, the FASB issued an accounting standard update to improve the reporting of reclassifications out of accumulated other comprehensive income of various components. This guidance requires companies to present either parenthetically on the face of the financial statements or in the notes, significant amounts reclassified from each component of accumulated other comprehensive income and the income statement line items affected by the reclassification. This standard is effective for interim periods and fiscal years beginning after December 15, 2012, which would be the Company's first quarter of fiscal 2013. The adoption of this guidance will require expanded disclosure in the Company's consolidated financial statements but will not impact financial results.

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Income Taxes - Effective Tax Rate Reconciliation (Details)	12 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Income Tax Disclosure [Abstract]
Statutory tax rate	(34.00%)	(34.00%)	(34.00%)
State tax rate, net of federal benefit	(0.40%)	(4.40%)	(1.60%)
Stock-based compensation	0.20%	0.60%	0.30%
Federal R&D credit	0.00%	(0.80%)	(0.80%)
Other	1.60%	(0.70%)	1.60%
Foreign losses	(5.80%)	(5.40%)	0.00%
Change in valuation allowance	38.80%	45.00%	34.50%
Effective income tax rate	0.40%	0.30%	0.00%

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Fair Value of Financial Instruments Fair Value of Financial Instruments, Textuals (Details)	Jul. 13, 2012 Banco Pine July 2012 Loan Agreement [Member] BRL	Dec. 31, 2012 Bridge Loan [Member] Banco Pine S.A Loan Agreement June 2012 [Member] USD ($)	Jun. 30, 2012 Bridge Loan [Member] Banco Pine S.A Loan Agreement June 2012 [Member] BRL	Dec. 31, 2012 Interest Rate Swap [Member] Banco Pine July 2012 Loan Agreement [Member] USD ($)	Jun. 30, 2012 Interest Rate Swap [Member] Banco Pine July 2012 Loan Agreement [Member] BRL	Dec. 31, 2012 Derivative Liability - Compound Embedded Derivatives [Member] USD ($)	Dec. 31, 2011 Derivative Liability - Compound Embedded Derivatives [Member] USD ($)
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Debt Instrument, Face Amount	22,000,000	$ 25,400,000	52,000,000
Notional Amount of Interest Rate Derivatives				10,800,000	22,000,000
Derivative, Fixed Interest Rate					3.94%
Fair Value, Measurement with Unobservable Inputs Reconciliations, Recurring Basis, Liability Value						$ 7,894,000	$ 0

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Summary of Significant Accounting Policies Cash and Cash Equivalents (Details) (Maximum [Member])	12 Months Ended
	Dec. 31, 2012 days
Maximum [Member]
Certificates of Deposit, Maturities	90

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Fair Value of Financial Instruments (Tables)

12 Months Ended

Dec. 31, 2012

Fair Value Disclosures [Abstract]

Schedule of Fair Value, Assets and Liabilities Measured on Recurring Basis [Table Text Block]

The Company’s financial assets and financial liabilities as of December 31, 2011 are presented below at fair value and were classified within the fair value hierarchy as follows (in thousands):

	Quoted Prices in Active Markets for Identical Assets (Level 1)		Other Observable Inputs (Level 2)		Significant Unobservable Inputs (Level 3)		Balance as of December 31, 2011
Financial Assets
Money market funds	$	57,127	$	—	$	—	$	57,127
Certificates of Deposit	27,384		—		—		27,384
Total financial assets	$	84,511	$	—	$	—	$	84,511
Financial Liabilities
Derivative liabilities	$	18	$	—	$	—	$	18
Total financial liabilities	$	18	$	—	$	—	$	18

As of December 31, 2012, the Company’s financial assets and financial liabilities are presented below at fair value and were classified within the fair value hierarchy as follows (in thousands):

	Level 1		Level 2		Level 3		Balance as of December 31, 2012
Financial Assets
Money market funds	$	15,847	$	—	$	—	$	15,847
Certificates of deposit	757		—		—		757
Total financial assets	$	16,604	$	—	$	—	$	16,604
Financial Liabilities
Notes payable	$	—	$	1,676	$	—	$	1,676
Loans payable	—		20,707		—		20,707
Credit facilities	—		11,503		—		11,503
Convertible notes	—		—		62,522		62,522
Compound embedded derivative liability	—		—		7,894		7,894
Currency interest rate swap derivative liability	—		1,367		—		1,367
Total financial liabilities	$	—	$	35,253	$	70,416	$	105,669

Fair Value, Liabilities Measured on Recurring Basis, Unobservable Input Reconciliation [Table Text Block]

The following table provides a reconciliation of the beginning and ending balances for the compound embedded derivative liability measured at fair value using significant unobservable inputs (Level 3) (in thousands):

	Compound Embedded Derivative Liability
Balance at December 31, 2011	$	—
Transfers in to Level 3	11,025
Total (gain) losses included in other income (expense), net	(3,131		)
Balance at December 31, 2012	$	7,894

Schedule of Derivative Instruments in Statement of Financial Position, Fair Value [Table Text Block]

Derivative instruments measured at fair value as of December 31, 2012 and 2011, and their classification on the consolidated balance sheets and consolidated statements of operations, are presented in the following tables (in thousands except contract amounts):

	Asset/Liability as of
	December 31, 2012			December 31, 2011
Type of Derivative Contract	Quantity of Short Contracts	Fair Value		Quantity of Short Contracts	Fair Value
Regulated fixed price futures contracts, included as liability in accounts payable	—	$	—	22	$	18
Currency interest rate swap, included as net liability in other long term liability	1	$	1,367	—	$	—

Schedule of Derivative Instruments, Gain (Loss) in Statement of Financial Performance [Table Text Block]

	Income Statement Classification	Years Ended December 31,
Type of Derivative Contract		2012			2011			2010
		Gain (Loss) Recognized
Regulated fixed price futures contracts	Cost of products sold	$	(288	)	$	(2,365	)	$	(2,225	)
Currency interest rate swap	Other income (expense), net	$	(1,367	)	$	—		$	—

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Balance Sheet Components (Tables)

12 Months Ended

Dec. 31, 2012

Balance Sheet Components [Abstract]

Available-for-sale Securities [Table Text Block]

The following table summarizes the Company’s investments as of December 31, 2012 (in thousands):

	December 31, 2012
	Amortized Cost		Unrealized Gain (Loss)		Fair Value
Short-Term Investments
Certificates of Deposit	$	97	$	—	$	97
Total short-term investments	$	97	$	—	$	97

The following table summarizes the Company’s investments as of December 31, 2011 (in thousands):

	December 31, 2011
	Amortized Cost		Unrealized Gain (Loss)		Fair Value
Short-Term Investments
Certificates of Deposit	$	7,889	$	—	$	7,889
Total short-term investments	$	7,889	$	—	$	7,889

Schedule of Inventory, Current [Table Text Block]

Inventories, net is comprised of the following (in thousands):

	December 31,
	2012		2011
Raw materials	$	1,574	$	2,191
Work-in-process	1,771		1,237
Finished goods	2,689		5,642
Inventories, net	$	6,034	$	9,070

Schedule of Prepaid and Other Current Assets [Table Text Block]

Prepaid and other current assets is comprised of the following (in thousands):

	December 31,
	2012		2011
Advances to contract manufacturers(1)	$	784	$	10,748
Manufacturing catalysts	1,895		3,929
Recoverable VAT and other taxes	4,167		2,193
Other	2,079		3,003
Prepaid and other current assets	$	8,925	$	19,873

⁽¹⁾  At December 31, 2012 and 2011, the amount of $784,000 and $748,000, respectively, relates to the current unamortized portion of equipment costs funded by the Company to a contract manufacturer. The related amortization is being offset against purchases of inventory.

Property, Plant and Equipment [Table Text Block]

Depreciation and amortization periods for the Company’s property, plant and equipment are as follows:

Machinery and equipment	7-15 years
Buildings	15 years
Computers and software	3-5 years
Furniture and office equipment	5 years
Vehicles	5 years

Property, plant and equipment, net is comprised of the following (in thousands):

	December 31,
	2012			2011
Leasehold improvements	$	39,290		$	40,011
Machinery and equipment	105,162			59,657
Computers and software	8,232			6,491
Furniture and office equipment	2,467			2,223
Buildings	5,888			—
Vehicles	575			596
Construction in progress	45,372			45,318
	$	206,986		154,296
Less: accumulated depreciation and amortization	(43,865		)	(26,195		)
Property, plant and equipment, net	$	163,121		$	128,101

Schedule of Other Assets, Noncurrent [Table Text Block]

Other assets are comprised of the following (in thousands):

	December 31,
	2012		2011
Deferred charge asset(1)	$	—	$	18,792
Deposits on property and equipment, including taxes	2,363		17,455
Advances to contract manufacturers, net of current portion(2)	2,222		2,866
Recoverable taxes on purchased property, plant and equipment(3)	13,597		2,075
Other	1,930		1,813
Total other assets	$	20,112	$	43,001

______________ 

⁽¹⁾  The deferred charge asset relates to the collaboration agreement between the Company and Total (see Note 9).

⁽²⁾  At December 31, 2012 and 2011, $2.2 million and $2.9 million, respectively, relates to the non-current unamortized portion of equipment costs funded by the Company to a contract manufacturer. The related amortization is being offset against purchases of inventory.

⁽³⁾  At December 31, 2012 and December 31, 2011, $13.6 million and $2.1 million, respectively, are recoverable taxes from the Brazilian government.

Schedule Of Accrued And Other Current Liabilities [Table Text Block]

Accrued and other current liabilities are comprised of the following (in thousands):

	December 31,
	2012		2011
Professional services	$	824	$	4,384
Accrued vacation	2,673		2,761
Payroll and related expenses	5,809		6,343
Construction in progress	—		4,992
Tax-related liabilities	851		2,180
Deferred rent, current portion	1,448		1,274
Contractual obligations to contract manufacturers	9,952		—
Customer advances	970		3,667
Other	1,883		5,381
Total accrued and other current liabilities	$	24,410	$	30,982

Schedule of Other Liabilities, Noncurrent [Table Text Block]

Other liabilities are comprised of the following (in thousands):

	December 31,
	2012		2011
Contingently repayable advance from related party collaborator(1)	$	—	$	31,922
Bonus payable to contract manufacturer, non-current	—		2,500
Contractual obligations to contract manufacturers, non-current	4,000		—
Fair market value of swap obligations	1,367		—
Asset retirement obligations	—		1,129
Fair value of compound embedded derivative liability(2)	7,894		—
Other	2,672		1,534
Total other liabilities	$	15,933	$	37,085

______________ 

⁽¹⁾  The contingently repayable advance from related party collaborator as of December 31, 2011 relates to the collaboration agreement between the Company and Total.

⁽²⁾  The compound embedded derivative liability represents the fair value of the equity conversion feature and a "make-whole" feature of the outstanding senior unsecured convertible promissory notes issued to Total.

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Consolidated Statements of Cash Flows (USD $) In Thousands, unless otherwise specified	12 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Operating activities
Net loss	$ (206,033)	$ (179,511)	$ (82,790)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization	14,570	11,077	7,280
Loss on disposal of property, plant and equipment	370	52	205
Stock-based compensation	27,473	25,492	10,432
Amortization of premium on investments	0	630	1,557
Amortization of debt discount	1,758	0	0
Provision for doubtful accounts	236	245	0
Loss on purchase commitments and write off of production assets	45,854	0	0
Change in fair value of convertible preferred stock warrant liability	0	0	(929)
Change in fair value of derivative instruments	(1,764)	0	0
Restructuring and asset impairment (income) charges	0	0	(2,061)
Other noncash expenses	159	40	116
Changes in assets and liabilities:
Accounts receivable	2,837	(1,975)	(3,565)
Inventories, net	2,919	(5,327)	(1,708)
Prepaid expenses and other assets	11,239	(17,250)	1,133
Accounts payable	(11,811)	15,648	3,478
Accrued and other long-term liabilities and restructuring	(35,754)	53,894	664
Deferred revenue	(1,648)	5,542	1,316
Deferred rent	(1,277)	(1,053)	295
Net cash used in operating activities	(150,872)	(92,496)	(64,577)
Investing activities
Purchase of short-term investments	(8,334)	(67,556)	(189,486)
Maturities of short-term investments	0	105,000	100,711
Sales of short-term investments	16,503	68,106	28,374
Purchase of long-term investments	0	0	(7,998)
Change in restricted cash	(955)	0	4,506
Payments for business acquisitions	0	(2,934)	0
Acquisition of cash in noncontrolling interest	0	344	0
Investment in unconsolidated joint venture	0	(83)	0
Purchase of property, plant and equipment, net of disposals	(56,832)	(81,917)	(10,906)
Deposits on property, plant and equipment	(26)	(15,107)	(4,606)
Net cash provided by (used in) investing activities	(49,644)	5,853	(79,405)
Financing activities
Proceeds from issuance of convertible preferred stock, net	0	0	184,360
Proceeds from issuance of common stock, net of repurchases	891	8,445	231
Proceeds from issuance of common stock in private placements, net of issuance costs	84,682	0	0
Proceeds from equipment financing	0	3,000	1,445
Principal payments on capital leases	(3,727)	(2,835)	(2,728)
Proceeds from debt	78,904	37,957	0
Proceeds from debt issued to related party	30,000	0	0
Principal payments on debt	(52,633)	(5,018)	(9,722)
Proceeds from issuance of common stock in initial public offering, net	0	(497)	86,032
Proceeds from sale of noncontrolling interest	0	0	7,069
Net cash provided by financing activities	138,117	41,052	266,687
Effect of exchange rate changes on cash and cash equivalents	(2,712)	(1,766)	1,167
Net increase (decrease) in cash and cash equivalents	(65,111)	(47,357)	123,872
Cash and cash equivalents at beginning of period	95,703	143,060	19,188
Cash and cash equivalents at end of period	30,592	95,703	143,060
Supplemental disclosures of cash flow information:
Cash paid for interest	3,399	1,412	1,378
Cash paid for income taxes, net of refunds	0	0	0
Supplemental disclosures of noncash investing and financing activities:
Acquisitions of property, plant and equipment under accounts payable, accrued liabilities and notes payable	2,538	3,177	8,278
Financing of equipment	0	3,420	0
Warrants issued in connection with equipment financing	0	193	0
Financing of insurance premium under notes payable	0	0	101
Change in unrealized gain (loss) on investments	0	(5)	3
Change in unrealized gain (loss) on foreign currency	(6,366)	(7,905)	(623)
Asset retirement obligation	0	174	115
Warrants issued in connection with the issuance of convertible preferred stock	0	0	507
Accrued deferred offering costs	0	0	496
Financing of rent payments under notes payable	0	0	239
Deferred charge asset related to the issuance of Series D preferred stock	0	0	27,909
Issuance of common stock upon exercise of warrants	0	3,554	0
Issuance of common stock related to business acquisition	0	7,000	0
Conversion of convertible preferred stock to common stock	0	0	391,411
Conversion of preferred stock warrants to common stock warrants	0	0	2,318
Conversion of shares of Amyris Brasil S.A. held by third parties into Amyris, Inc. common stock	0	0	11,653
Conversion of other liability to related party debt	(23,300)	0	0
Conversion of related party debt to common stock	5,000	0	0
Deemed dividend related to a beneficial conversion feature	0	0	42,009
Transfer of property, plant and equipment to current assets	0	886	0
Transfer of long term deposits to property, plant and equipment	12,218	50	0
Acquisition of net assets in noncontrolling interest	0	25	0
Reclassification of long-term investments to short-term investments	$ 0	$ 0	$ 7,998

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Commitments and Contingencies (Tables)

12 Months Ended

Dec. 31, 2012

Commitments and Contingencies Disclosure [Abstract]

Schedule of Future Minimum Payments Under Sale Leaseback Transactions [Table Text Block]

Future minimum payments under this sales/leaseback agreement as of December 31, 2012 are as follows (in thousands):

Years ending December 31:	Sales/Leaseback
2013	$	1,098
2014	1,007
2015	289
2016	—
2017	—
Thereafter	—
Total future minimum lease payments	2,394
Less: amount representing interest	(168		)
Present value of minimum lease payments	2,226
Less: current portion	(982		)
Long-term portion	$	1,244

Schedule of Future Minimum Lease Payments for Capital Leases [Table Text Block]

Future minimum payments under capital leases, including the sales/leaseback, as of December 31, 2012 are as follows (in thousands):

Years ending December 31:	Capital Leases
2013	$	1,489
2014	1,007
2015	289
2016	—
2017	—
Thereafter	—
Total future minimum lease payments	2,785
Less: amount representing interest	(175		)
Present value of minimum lease payments	2,610
Less: current portion	(1,366		)
Long-term portion	$	1,244

Schedule of Future Minimum Rental Payments for Operating Leases [Table Text Block]

Future minimum payments under operating leases as of December 31, 2012, are as follows (in thousands):

Years ending December 31:	Operating Leases - Facilities		Operating Leases - Land		Total Operating Leases
2013	$	6,463	$	161	$	6,624
2014	6,610		162		6,772
2015	6,738		162		6,900
2016	6,729		162		6,891
2017	6,598		162		6,760
Thereafter	2,786		1,556		4,342
Total future minimum lease payments	$	35,924	$	2,365	$	38,289

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Significant Agreements (Manufacturing Agreements) (Details) (USD $)	3 Months Ended				12 Months Ended					5 Months Ended	12 Months Ended				1 Months Ended
	Dec. 31, 2012		Sep. 30, 2012	Mar. 31, 2012	Dec. 31, 2012		Dec. 31, 2011		Dec. 31, 2010	Dec. 31, 2011 Albemarle Agreement [Member]	Dec. 31, 2012 Albemarle Agreement [Member]	Dec. 31, 2011 Albemarle Agreement [Member] payment	Feb. 24, 2012 Albemarle Agreement [Member]	Jul. 31, 2011 Albemarle Agreement [Member]	Dec. 31, 2011 Soliance Termination of Collaboration Agreement [Member]	Aug. 31, 2011 Nikko Chemicals Agreement [Member]	Dec. 31, 2012 Payable 2014 [Member] Albemarle Agreement [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Reimbursement Expenditure					$ 13,800,000
(Gain) Loss On Facility Modifications And Fixed Purchase Commitments				31,200,000
Facility Modification Costs Written Off				10,000,000
Loss On Fixed Purchase Commitments				21,200,000
Loss on purchase commitments and write off of production assets	7,800,000		1,400,000		45,854,000		0		0
Production Assets Written Off				5,500,000
Deposits Assets, Current	784,000				784,000		748,000
Deposits Assets, Noncurrent	2,222,000	[1]			2,222,000	[1]	2,866,000	[1]
Agreed Reimbursement to Collaborator for Capital Expenditures														10,000,000
Collaborator Agreement Performance Bonus										5,000,000
Collaborator Agreement Alternate Performance Bonus										2,000,000
Collaborator Agreement Performance Bonus, Number of Payment												2
Payment for Collaborator Agreement Performance Bonus											2,500,000
Collaborator Agreement Performance Bonus, Second Required Payment											2,500,000
Agreement With Collaborator, Obligation To Pay Fixed Costs											3,500,000		7,500,000				4,000,000
Agreement With Collaborator, Obligation To Pay Fixed Costs, Agreed Quarterly Payment													$ 2,000,000
Collaborator Agreement, Commission Percentage Paid to Collaborator At Termination															10.00%
Period of Initial Term of Collaboration Agreement																2 years

[1] At December 31, 2012 and 2011, $2.2 million and $2.9 million, respectively, relates to the non-current unamortized portion of equipment costs funded by the Company to a contract manufacturer. The related amortization is being offset against purchases of inventory

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Reporting Segments (Tables)

12 Months Ended

Dec. 31, 2012

Segment Reporting [Abstract]

Schedule of Revenue from External Customers and Long-Lived Assets, by Geographical Areas [Table Text Block]

Revenues by geography are based on the location of the customer. The following tables set forth revenue and long-lived assets by geographic area (in thousands):

Revenues

	Years Ended December 31,
	2012		2011		2010
United States	$	49,111	$	141,098	$	80,311
Brazil	3,786		141		—
Europe	16,461		5,695		—
Asia	4,336		57		—
Total	$	73,694	$	146,991	$	80,311

Long-Lived Assets

	December 31,
	2012		2011
United States	$	70,273	$	76,108
Brazil	90,982		48,240
Europe	1,866		3,753
Total	$	163,121	$	128,101

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Fair Value of Financial Instruments, Hierarchy (Details) (Fair Value, Measurements, Recurring [Member], USD $) In Thousands, unless otherwise specified	Dec. 31, 2012	Dec. 31, 2011
Quoted Prices in Active Markets for Identical Assets (Level 1) [Member]
Financial Assets [Abstract]
Money market funds	$ 15,847	$ 57,127
Certificates of deposit	757	27,384
Total financial assets	16,604	84,511
Financial Liabilities [Abstract]
Notes payable	0
Loans payable	0
Credit facilities	0
Convertible notes	0
Compound embedded derivative liability	0
Currency interest rate swap derivative liability	0
Derivative liabilities		18
Total financial liabilities	0	18
Other Observable Inputs (Level 2) [Member]
Financial Assets [Abstract]
Money market funds	0	0
Certificates of deposit	0	0
Total financial assets	0	0
Financial Liabilities [Abstract]
Notes payable	1,676
Loans payable	20,707
Credit facilities	11,503
Convertible notes	0
Compound embedded derivative liability	0
Currency interest rate swap derivative liability	1,367
Derivative liabilities		0
Total financial liabilities	35,253	0
Significant Unobservable Inputs (Level 3) [Member]
Financial Assets [Abstract]
Money market funds	0	0
Certificates of deposit	0	0
Total financial assets	0	0
Financial Liabilities [Abstract]
Notes payable	0
Loans payable	0
Credit facilities	0
Convertible notes	62,522
Compound embedded derivative liability	7,894
Currency interest rate swap derivative liability	0
Derivative liabilities		0
Total financial liabilities	70,416	0
Balance as of December 31 [Member]
Financial Assets [Abstract]
Money market funds	15,847	57,127
Certificates of deposit	757	27,384
Total financial assets	16,604	84,511
Financial Liabilities [Abstract]
Notes payable	1,676
Loans payable	20,707
Credit facilities	11,503
Convertible notes	62,522
Compound embedded derivative liability	7,894
Currency interest rate swap derivative liability	1,367
Derivative liabilities		18
Total financial liabilities	$ 105,669	$ 18

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Debt Notes Payable (Details) (USD $)				6 Months Ended		1 Months Ended
	Dec. 31, 2012 Notes Payable, Other Payables-Lessor [Member]	Dec. 31, 2011 Notes Payable, Other Payables-Lessor [Member]	Oct. 31, 2008 Notes Payable, Other Payables-Lessor [Member]	Oct. 31, 2008 Notes Payable, Other Payables-Lessor [Member] Minimum [Member]	Oct. 31, 2008 Notes Payable, Other Payables-Lessor [Member] Maximum [Member]	Jun. 30, 2011 Notes Payable Other Payables Operating Lease [Member] Monthly_installment	Dec. 31, 2012 Notes Payable Other Payables Operating Lease [Member]	Dec. 31, 2011 Notes Payable Other Payables Operating Lease [Member]
Debt Instrument [Line Items]
Debt Instrument, Face Amount			$ 3,300,000.0			$ 1,500,000.0
Debt Instrument, Interest Rate, Stated Percentage			9.50%
Repayment Period				55 months	120 months
Notes payable outstanding	1,600,000	2,000,000					0	1,100,000
Number Of Equal Monthly Installments						24
Debt Instrument, Periodic Payment						$ 63,000

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Consolidated Balance Sheets (USD $) In Thousands, unless otherwise specified	Dec. 31, 2012	Dec. 31, 2011
Current assets:
Cash and cash equivalents	$ 30,592	$ 95,703
Short-term investments	97	7,889
Accounts receivable, net of allowance of $481 and $245, respectively	3,846	6,936
Inventories, net	6,034	9,070
Prepaid expenses and other current assets	8,925	19,873
Total current assets	49,494	139,471
Property, plant and equipment, net	163,121	128,101
Restricted cash	955	0
Other assets	20,112	43,001
Goodwill and Intangible assets	9,152	9,538
Total assets	242,834	320,111
Current liabilities:
Accounts payable	15,392	26,379
Deferred revenue	1,333	3,139
Accrued and other current liabilities	24,410	30,982
Capital lease obligation, current portion	1,366	3,717
Debt, current portion	3,325	28,049
Total current liabilities	45,826	92,266
Capital lease obligation, net of current portion	1,244	2,619
Long-term debt, net of current portion	61,806	13,275
Related party debt	39,033	0
Deferred rent, net of current portion	8,508	9,957
Deferred revenue, net of current portion	4,255	4,097
Other liabilities	15,933	37,085
Total liabilities	176,605	159,299
Commitments and contingencies (Note 5)
Stockholders' equity:
Preferred stock - $0.0001 par value, 5,000,000 shares authorized, none issued and outstanding	0	0
Common stock - $0.0001 par value, 100,000,000 shares authorized as of December 31, 2012 and 2011; 68,709,660 and 45,933,138 shares issued and outstanding as of December 31, 2012 and 2011, respectively	7	5
Additional paid-in capital	666,233	548,159
Accumulated other comprehensive loss	(12,807)	(5,924)
Accumulated deficit	(586,327)	(381,188)
Total Amyris, Inc. stockholders’ equity	67,106	161,052
Noncontrolling interest	(877)	(240)
Total stockholders' equity	66,229	160,812
Total liabilities and stockholders' equity	$ 242,834	$ 320,111

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Summary of Significant Accounting Policies Investments (Details) (USD $) In Thousands, unless otherwise specified			12 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2012 Minimum [Member] days	Dec. 31, 2012 Maximum [Member] years
Accounting Policies [Abstract]
Restricted cash	$ 955	$ 0
Schedule of Investments [Line Items]
Investment Maturity Period, Cash and Cash Equivalents				90 days
Investments Original Maturities			90
Investments Maturity Period				1

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Restructuring Accrued Restructuring (Details) (USD $) In Thousands, unless otherwise specified	12 Months Ended
	Dec. 31, 2010
Restructuring Reserve [Roll Forward]
Accrued restructuring, beginning of period	$ 5,078
Cash payments	(906)
Accretion expense	395
Reversal of restructuring liability	(4,567)
Accrued restructuring, end of period	0
Exit Costs [Member]
Restructuring Reserve [Roll Forward]
Accrued restructuring, beginning of period	5,078
Cash payments	(906)
Accretion expense	395
Reversal of restructuring liability	(2,061)
Accrued restructuring, end of period	2,506
Deferred Rent [Member]
Restructuring Reserve [Roll Forward]
Accrued restructuring, beginning of period	0
Cash payments	0
Accretion expense	0
Reversal of restructuring liability	(2,506)
Accrued restructuring, end of period	$ (2,506)

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Consolidated Statements of Convertible Preferred Stock, Redeemable Noncontrolling Interest and Equity (Deficit) (USD $) In Thousands, except Share data, unless otherwise specified	Total	Amyris Brasil S.A. [Member]	Convertible Preferred Stock [Member]	Series C Preferred Stock [Member]	Series C-1 Preferred Stock [Member]	Series D Preferred Stock [Member]	Convertible Preferred Stock Warrants [Member]	Common Stock [Member]	Additional Paid-in Capital [Member]	Accumulated Deficit [Member]	Accumulated Other Comprehensive Income (Loss) [Member]	Noncontrolling Interest [Member]
Beginning Balance, redeemable noncontrolling interest at Dec. 31, 2009		$ 5,506
Beginning Balance, value at Dec. 31, 2009	(113,745)							1	5,366	(120,448)	1,336	0
Beginning Balance, convertible preferred stock, value at Dec. 31, 2009			179,651
Beginning Balance, shares at Dec. 31, 2009								5,114,205
Beginning Balance, convertible preferred stock, shares at Dec. 31, 2009			18,365,222
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Stock issued during period				3,683	47,779	160,805
Stock issued during period, shares				295,981	2,724,766	7,101,548
Issuance of warrants in connection with issuance of convertible preferred stock							(507)
Issuance of common stock upon exercise of stock options, net of restricted stock, value	277								277
Issuance of common stock upon exercise of stock options, net of restricted stock, shares								60,883
Issuance of common stock warrants in connection with equipment financing	0
Shares issued from restricted stock unit settlement, shares								176,272
Repurchase of common stock, shares								(10,367)
Stock-based compensation	10,432								10,432
Proceeds from redeemable noncontrolling interest		7,041
Proceeds from noncontrolling interest	28											28
Common stock issuance in public offering, net of issuance costs (Note 11), value	85,534								85,534
Common stock issuance in public offering, net of issuance costs (Note 11), shares								6,095,000
Conversion of convertible preferred stock to common stock	391,411		(391,411)					3	391,408
Conversion of convertible preferred stock to common stock, shares			(28,487,517)					31,550,277
Conversion of convertible preferred stock warrants to common stock warrants	2,318								2,318
Conversion of shares of Amyris Brasil S.A. shares into common stock	11,653	(11,870)							11,653
Conversion of shares of Amyris Brasil S.A. shares into common stock, shares								861,155
Beneficial conversion feature on conversion of subsidiary stock or convertible preferred stock	39,292								39,292
Deemed dividend related to the beneficial conversion feature	(39,292)								(39,292)
Beneficial conversion feature on conversion of Amyis Brasil shares	2,717								2,717
Deemed Dividend Related to the Beneficial Conversion Feature of AB shares	(2,717)								(2,717)
Redeemable noncontrolling Interest, foreign currency translation Adjustment		217
Redeemable noncontrolling interest, net Ioss		(894)
Components of comprehensive income (loss)
Change in unrealized loss on investments	2										2
Foreign currency translation adjustment, net of tax	1,534										1,534
Net loss	(81,896)									(81,870)		(26)
Ending Balance, value at Dec. 31, 2010	307,548							4	506,988	(202,318)	2,872	2
Ending Balance, convertible preferred stock, value at Dec. 31, 2010			0
Ending Balance, redeemable noncontrolling interest at Dec. 31, 2010		0
Ending Balance, shares at Dec. 31, 2010								43,847,425
Ending Balance, convertible preferred stock, shares at Dec. 31, 2010			0
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Issuance of common stock upon exercise of stock options, net of restricted stock, value	8,492							1	8,491
Issuance of common stock upon exercise of stock options, net of restricted stock, shares								1,641,439
Issuance of common stock upon net exercise of warrants, shares								77,087
Issuance of common stock warrants in connection with equipment financing	193								193
Issuance of common stock in connection with Draths business acquisition, value	7,000								7,000
Issuance of common stock in connection with Draths business acquisition, shares								362,319
Shares issued from restricted stock unit settlement, shares								6,005
Repurchase of common stock, value	(5)								(5)
Repurchase of common stock, shares								(1,137)
Stock-based compensation	25,492								25,492			0
Proceeds from noncontrolling interest												369
Conversion of convertible preferred stock warrants to common stock warrants	0
Fair value of assets and liabilities assigned to noncontrolling interest	369											369
Components of comprehensive income (loss)
Change in unrealized loss on investments	(5)										(5)
Foreign currency translation adjustment, net of tax	(8,761)										(8,791)	30
Net loss	(179,511)									(178,870)		(641)
Ending Balance, value at Dec. 31, 2011	160,812							5	548,159	(381,188)	(5,924)	(240)
Ending Balance, convertible preferred stock, value at Dec. 31, 2011			0
Ending Balance, redeemable noncontrolling interest at Dec. 31, 2011		0
Ending Balance, shares at Dec. 31, 2011	45,933,138							45,933,138
Ending Balance, convertible preferred stock, shares at Dec. 31, 2011			0
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Stock issued during period	89,682							2	89,680
Stock issued during period, shares								21,040,717
Issuance of common stock upon exercise of stock options, net of restricted stock, value	1,509								1,509
Issuance of common stock upon exercise of stock options, net of restricted stock, shares								1,441,676
Issuance of common stock warrants in connection with equipment financing	0
Recovery of shares from Draths escrow								(5,402)
Shares issued from restricted stock unit settlement, value	(588)								(588)
Shares issued from restricted stock unit settlement, shares								299,584
Repurchase of common stock, shares								(53)
Stock-based compensation	27,473								27,473
Proceeds from noncontrolling interest												0
Conversion of convertible preferred stock warrants to common stock warrants	0
Components of comprehensive income (loss)
Change in unrealized loss on investments	0
Foreign currency translation adjustment, net of tax	(6,626)										(6,883)	257
Net loss	(206,033)									(205,139)		(894)
Ending Balance, value at Dec. 31, 2012	66,229							7	666,233	(586,327)	(12,807)	(877)
Ending Balance, convertible preferred stock, value at Dec. 31, 2012			0
Ending Balance, redeemable noncontrolling interest at Dec. 31, 2012		$ 0
Ending Balance, shares at Dec. 31, 2012	68,709,660							68,709,660
Ending Balance, convertible preferred stock, shares at Dec. 31, 2012			0

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Related Party Transactions (Details) (USD $)	12 Months Ended									0 Months Ended	3 Months Ended	12 Months Ended		0 Months Ended		1 Months Ended		0 Months Ended		1 Months Ended				0 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010	Dec. 31, 2012 Co-founder and Advisor [Member]	Dec. 31, 2011 Co-founder and Advisor [Member]	Dec. 31, 2010 Co-founder and Advisor [Member]	Dec. 31, 2008 Non Employee Share Based Compensation [Member] Director [Member] directors	Oct. 06, 2011 Draths Corporation [Member]	Dec. 31, 2008 Draths Corporation [Member] Director [Member] board_members	Oct. 06, 2011 Draths Corporation [Member] Common Stock [Member]	Jun. 30, 2012 Draths Corporation [Member] Common Stock [Member]	Dec. 31, 2012 Common Stock [Member]	Dec. 31, 2011 Common Stock [Member]	Oct. 06, 2011 Common Stock [Member] Draths Corporation [Member]	Dec. 24, 2012 Private Placement [Member]	May 31, 2012 Private Placement [Member]	Feb. 29, 2012 Private Placement [Member]	Dec. 24, 2012 Private Placement [Member] Common Stock [Member]	Feb. 23, 2012 Private Placement [Member] Common Stock [Member]	May 31, 2012 Private Placement [Member] Common Stock [Member]	Feb. 29, 2012 Private Placement [Member] Common Stock [Member]	Dec. 24, 2012 Private Placement [Member]	Dec. 24, 2012 Convertible Notes Payable [Member] Private Placement [Member]	Mar. 27, 2013 Subsequent Event [Member] Private Placement [Member]	Jan. 11, 2013 Subsequent Event [Member] Private Placement [Member]	Dec. 24, 2012 Commitment Fulfilled [Member] Private Placement [Member]	Mar. 20, 2013 Commitment Fulfilled [Member] Subsequent Event [Member]
Related Party Transaction [Line Items]
Expenses paid to the advisor				$ 0	$ 2,500	$ 23,000
Equity Method Investment Number of Members of Board of Directors							1		1
Issuance of common stock in connection with Draths business acquisition, shares													362,319	362,319
Business Acquisition, Equity Interest Issued and Held in Escrow, Number of Shares										41,408
Cash paid to Draths								2,934,000
Shares Received From Escrow											5,402
Initial public offering, shares of common stock												21,040,717						14,177,849		1,736,100	10,160,325			1,533,742	5,033,557
Stock Issued During Period, Price Per Share, New Issues															$ 2.98	$ 2.36	$ 5.78							$ 3.26
Stock Issued During Period, Value, New Issues	89,682,000											2,000				4,100,000	58,700,000
Related Party Transaction, Percentage of Existing Common Stock at Time of Transaction																			5.00%
Debt Instrument, Convertible, Common Stock, Shares																						1,677,852
Proceeds from Issuance of Private Placement	84,682,000	0	0												37,200,000									5,000,000
Proceeds from Issuance of Private Placement Remaining Balance to be Settled																									15,000,000
Contractual Obligation	52,700,000
Commitment to purchase company common stock																	$ 15,000,000									$ 10,000,000	$ 5,000,000
Extinguishment of Debt, Common Stock, Shares																							1,677,852.00

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Balance Sheet Components Prepaid and Other Current Assets (Details) (USD $) In Thousands, unless otherwise specified	Dec. 31, 2012		Dec. 31, 2011
Balance Sheet Components [Abstract]
Advances to contract manufacturers	$ 784	[1]	$ 10,748
Manufacturing catalysts	1,895		3,929
Recoverable VAT and other taxes	4,167		2,193
Other	2,079		3,003
Prepaid and other current assets	8,925		19,873
Deposits Assets, Current	$ 784		$ 748

[1] At December 31, 2012 and 2011, the amount of $784,000 and $748,000, respectively, relates to the current unamortized portion of equipment costs funded by the Company to a contract manufacturer. The related amortization is being offset against purchases of inventory.

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Income Taxes - Components of Benefit (Provision) (Details) (USD $) In Thousands, unless otherwise specified	12 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Current:
Federal	$ 0	$ 0	$ 0
State	0	0	0
Foreign	981	727	0
Total current provision (benefit)	981	727	0
Deferred:
Federal	0	(150)	0
State	0	(25)	0
Foreign	0	0	0
Total deferred provision (benefit)	0	(175)	0
Total provision for income taxes	$ 981	$ 552	$ 0

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Draths Corporation Acquisition (Tables)

12 Months Ended

Dec. 31, 2012

Draths Corporation Acquistion [Abstract]

Schedule of Purchase Price Allocation [Table Text Block]

The components of the purchase price allocation for Draths are as follows:

Purchase Consideration:
(in thousands)
Fair value of common stock issued to Draths	$	7,000
Cash paid to Draths	2,934
Total purchase consideration	$	9,934

Allocation of Purchase Price:
(in thousands)
Property and Equipment	$	713
Other	101
In-process research and development	8,560
Goodwill	560
Total purchase consideration	$	9,934

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Commitments and Contingencies Capital Leases Textuals (Details) (USD $)	12 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Capital Leased Assets [Line Items]
Capital Leases, Income Statement, Interest Expense	$ 382,000	$ 559,000	$ 821,000
Computer Equipment [Member]
Capital Leased Assets [Line Items]
Capital Leased Assets, Gross	0	0	1,400,000
Capital Lease Obligations	400,000	3,100,000
Incremental Borrowing Rate Capital Lease	9.50%
Machinery and equipment [Member]
Capital Leased Assets [Line Items]
Capital Leased Assets, Gross	3,000,000
Capital Lease Obligations	2,200,000	3,400,000
Incremental Borrowing Rate Capital Lease	6.50%
Sale Leaseback Transaction, Unrealized Loss	$ 1,300,000

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Related Party Transactions

12 Months Ended

Dec. 31, 2012

Related Party Transactions [Abstract]

Related Party Transactions

Related Party Transactions

The Company has entered into a license agreement with University of California, Berkeley. A co-founder and advisor to the Company is a professor at the University of California, Berkeley. The Company paid the advisor zero, $2,500 and $23,000, during the years ended December 31, 2012, 2011 and 2010, respectively.

During 2008, the Company entered into an agreement with a venture capital group to provide strategic advisory services to Amyris and its then majority owned subsidiary, Amyris Brasil. One of the venture capital group's former directors is also a member of the Company’s Board of Directors. Under the agreement, the Company issued options to the venture capital group, which vest and become exercisable based on the service of the former director of the group on the Company's Board of Directors.

In June 2010, the Company entered into agreements with Total relating to the Company’s Series D preferred stock and collaboration for the research, development, production and commercialization of chemical and/or fuel products (see Note 9).

In October 2011, the Company completed a business combination with Draths. In connection with the acquisition, the Company issued 362,319 shares of the Company's common stock, of which 41,408 shares were held in escrow and paid $2.9 million in cash. In the quarter ended June 30, 2012, the Company recovered 5,402 shares of common stock from the escrow in connection with certain Draths indemnification obligations under the purchase agreement. One of the Company's Board of Directors was also on the board of Draths.

In November 2011, the Company and Total entered into an amendment to their Technology License, Development, Research and Collaboration Agreement (see Note 4).

In February 2012, the Company completed a private placement of 10,160,325 shares of its common stock at a price of $5.78 per share for aggregate proceeds of $58.7 million pursuant to a securities purchase agreement, among the Company and existing certain investors, including Total and Maxwell (Mauritius) Pte Ltd, each a beneficial owner of more than 5% of the Company's existing common stock at the time of the transaction. In addition, members of the Company's Board of Directors and certain parties related to such directors participated in the offering.

In May 2012, the Company completed a private placement of 1,736,100 shares of it's common stock at a price of $2.36 per share for aggregate proceeds of $4.1 million pursuant to a series of Common Stock Purchase Agreements, among the Company and members of the Company's Board of Directors and certain parties related to such directors.

In July 2012, the Company entered into various agreements with Total relating to the Program (see Note 9).

In December 2012, the Company completed a private placement of its common stock for the issuance of 14,177,849 shares it's common stock at a price of $2.98 per share for aggregate proceeds of $37.2 million and the cancellation of $5.0 million worth of outstanding senior unsecured convertible promissory notes previously issued by the Company (see Note 6). Shares totaling 1,677,852 were issued to Total in exchange for this cancellation. Net cash received as of December 31, 2012 was $22.2 million and the remaining $15.0 million of proceeds were settled in January 2013.

In connection with the December 2012 private placement, the Company entered into a Letter of Agreement, dated December 24, 2012 with Biolding, an existing investor. Under the letter agreement, the Company acknowledged that Biolding's initial investment of $10.0 million under the Purchase Agreement represented partial satisfaction of Biolding's preexisting contractual obligation to fund $15.0 million by March 31, 2013 upon satisfaction by the Company of criteria associated with the commissioning of the Company's production plant in Brotas. Pursuant to the letter agreement, Biolding would invest the remaining $5.0 million no later than March 31, 2013 following satisfaction of the criteria. A member of the Company's Board of Directors is affiliated with Biolding.

In connection with the February 2012 and December 2012 private placement, Naxyris SA and TPG Biotechnology Partners II, L.P., each a beneficial owner of more than 5% of the Company's outstanding common stock at the time of the December 2012 offering, purchased shares in the December 2012 offering; in addition, Naxyris SA's Board designee (pursuant to the February 2012 agreement), was serving on the Company's Board of Directors at the time of both the February 2012 and the December 2012 offerings, and a partner of TPG Biotech, an affiliate of TPG Biotechnology Partners II, L.P., was serving on the Company's Board of Directors at the time of the December 2012 offering.

Foris Ventures LLC and Sualk Capital Ltd, entities affiliated with two of the Company's existing Board of Directors, purchased shares of the Company's common stock in both the February 2012 and December 2012 offerings; in addition, Sualk Capital Ltd's Board designee (pursuant to the February 2012 agreement), was serving on the Company's Board of Directors at the time of the December 2012 offering.

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Stockholders' Equity (Tables)

12 Months Ended

Dec. 31, 2012

Stockholders' Equity Note [Abstract]

Schedule of Stockholders' Equity Note, Warrants or Rights [Table Text Block]

As of December 31, 2012 and 2011, the Company had the following unexercised common stock warrants:

		Exercise Price per Share		Shares as of
Underlying Stock	Expiration Date			December 31, 2012	December 31, 2011
Common Stock	1/31/2018	$	24.88	—	2,884
Common Stock	9/23/2018	$	25.26	—	2,252
Common Stock	12/23/2021	$	10.67	21,087	21,087
Total				21,087	26,223

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Income Taxes - Components of Income Loss (Details) (USD $) In Thousands, unless otherwise specified	12 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Income Tax Disclosure [Abstract]
United States	$ (146,028)	$ (140,153)	$ (67,525)
Foreign	(59,024)	(38,806)	(15,265)
Loss before income taxes	$ (205,052)	$ (178,959)	$ (82,790)

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Income Taxes

12 Months Ended

Dec. 31, 2012

Income Tax Disclosure [Abstract]

Income Taxes

Income Taxes

For the years ended December 31, 2012, 2011 and 2010, the Company recorded a provision for income taxes of $981,000, $552,000 and zero, respectively. The provision for income taxes for the year ended December 31, 2012 consisted of an accrual of Brazilian withholding tax on an intercompany interest liability. The provision for incomes taxes for the year ended December 31, 2011 consisted of $727,000 for the accrual of Brazilian withholding tax on an intercompany interest liability, partially offset by a $175,000 benefit from income taxes resulting from valuation allowance adjustments due to an increase in currency translation adjustments classified as other comprehensive losses. Other than the above mentioned provision for income tax, no additional provision for income taxes has been made, net of the valuation allowance, due to cumulative losses since the commencement of operations.

The components of loss before income taxes and minority interests are as follows for the years ended December 31, 2012, 2011 and 2010 (in thousands):

	Years Ended December 31,
	2012			2011			2010
United States	$	(146,028	)	$	(140,153	)	$	(67,525	)
Foreign	(59,024		)	(38,806		)	(15,265		)
Loss before income taxes	$	(205,052	)	$	(178,959	)	$	(82,790	)

The components of the provision for income taxes are as follows for the years ended December 31, 2012, 2011 and 2010 (in thousands):

	Years Ended December 31,
	2012		2011			2010
Current:
Federal	$	—	$	—		$	—
State	—		—			—
Foreign	981		727			—
Total current provision (benefit)	981		727			—
Deferred:
Federal	—		(150		)	—
State	—		(25		)	—
Foreign	—		—			—
Total deferred provision (benefit)	—		(175		)	—
Total provision for income taxes	$	981	$	552		$	—

A reconciliation between the statutory federal income tax and the Company’s effective tax rates as a percentage of loss before income taxes is as follows:

	Years Ended December 31,
	2012		2011		2010
Statutory tax rate	(34.0	)%	(34.0	)%	(34.0	)%
State tax rate, net of federal benefit	(0.4	)%	(4.4	)%	(1.6	)%
Stock-based compensation	0.2	%	0.6	%	0.3	%
Federal R&D credit	—	%	(0.8	)%	(0.8	)%
Other	1.6	%	(0.7	)%	1.6	%
Foreign losses	(5.8	)%	(5.4	)%	—	%
Change in valuation allowance	38.8	%	45.0	%	34.5	%
Effective income tax rate	0.4	%	0.3	%	—	%

Temporary differences and carryforwards that gave rise to significant portions of deferred taxes are as follows (in thousands):

	December 31,
	2012			2011			2010
Net operating loss carryforwards	$	145,324		$	103,390		$	56,615
Fixed assets	—			—			340
Research and development credits	7,259			5,937			3,325
Foreign Tax Credit	1,782			801			—
Accruals and reserves	15,997			12,150			2,257
Stock-based compensation	15,882			11,351			4,316
Capitalized start-up costs	16,070			22,974			8,993
Capitalized research and development costs	26,850			—			—
Other	7,649			2,904			225
Total deferred tax assets	236,813			159,507			76,071
Fixed assets	(525		)	(2,742		)	—
Other	—			—			—
Total deferred tax liabilities	(525		)	(2,742		)	—
Net deferred tax asset prior to valuation allowance	236,288			156,765			76,071
Less: Valuation allowance	(236,288		)	(156,765		)	(76,071		)
Net deferred tax assets (liabilities)	$	—		$	—		$	—

Recognition of deferred tax assets is appropriate when realization of such assets is more likely than not. Based upon the weight of available evidence, especially the uncertainties surrounding the realization of deferred tax assets through future taxable income, the Company believes it is not yet more likely than not that the net deferred tax assets will be fully realizable. Accordingly, the Company has provided a full valuation allowance against its net deferred tax assets as of December 31, 2012. The valuation allowance increased $79.5 million, $80.7 million, and $28.3 million, during the years ended December 31, 2012, 2011 and 2010, respectively.

As of December 31, 2012, the Company had federal and state net operating loss carryforwards of approximately $373.7 million and $202.4 million , respectively, available to reduce future taxable income, if any. Approximately $25.7 million and $12.7 million of the federal and state net operating loss carryforwards, respectively, resulted from exercises of employee stock options and vesting of restricted stock units and have not been included in the Company’s gross deferred tax assets. In accordance with ASC 718, such unrealized tax benefits of approximately $9.5 million will be accounted for as a credit to additional paid-in capital if and when realized through a reduction in income taxes payable.

The Company also has federal research and development credits of $5.1 million and foreign tax credit carryforwards of $1.8 million, and California research and development credit carryforwards of $7.9 million, respectively, at December 31, 2012. The American Taxpayer Relief Act of 2012 (the "Act") was enacted on January 2, 2013. The Act retroactively reinstates the federal research and development credit from January 1, 2012, through December 31, 2013. The benefit of the reinstated credit is not expected to impact the income statement in the period of enactment, which is the first quarter of 2013 as the research and development credit carryforwards are offset by a full valuation allowance.

The Tax Reform Act of 1986 and similar state provisions limit the use of net operating loss and credit carryforwards in certain situations where equity transactions result in a change of ownership as defined by Internal Revenue Code Section 382. In the event the Company has experienced an ownership change, as defined, utilization of its federal and state net operating loss and credit carryforwards could be limited. If not utilized, the federal net operating loss carryforward begins expiring in 2025, and the California net operating loss carryforward begins expiring in 2015. The federal foreign tax credits and research and development credit carryforwards will expire starting in 2020 and in 2024; respectively, if not utilized. The California tax credits can be carried forward indefinitely.

Effective January 1, 2007, the Company adopted the accounting guidance on uncertainties in income taxes. A reconciliation of the beginning and ending amounts of unrecognized tax benefits since the adoption of accounting guidance on uncertainty in income taxes is as follows:

Balance at December 31, 2010	1,734
Increases in tax positions for prior period	—
Increases in tax positions during current period	1,369
Balance at December 31, 2011	$	3,103
Increases in tax positions for prior period	82
Increases in tax positions during current period	733
Balance at December 31, 2012	$	3,918

The Company’s policy is to include interest and penalties related to unrecognized tax benefits within the provision for taxes. The Company determined that no accrual for interest and penalties was required as of December 31, 2012.

As of December 31, 2012, the Company’s total unrecognized tax benefits were $3.9 million, of which none of the tax benefits, if recognized, would affect the effective income tax rate due to the valuation allowance that currently offsets deferred tax assets. The Company does not anticipate the total amount of unrecognized income tax benefits will significantly increase or decrease in the next 12 months.

The Company’s primary tax jurisdiction is the United States. For United States federal and state tax purposes, tax years 2003 and forward remain open and subject to tax examination by the appropriate federal or state taxing authorities. Brazil tax years 2008 through the current remain open and subject to examination.

The Company is currently under audit by the US Internal Revenue Service for tax year 2008. As of December 31, 2012, the Company has received a Form 4549-A, Income Tax Discrepancy Adjustments (Examination No Change Report) which concluded that there were no adjustments resulting from the audit by the US Internal Revenue Service for the tax year 2008.  As of December 31, 2012, the Company has not yet received the Area Director's final approval of the report.

XML

Debt (Details) (USD $) In Thousands, unless otherwise specified	Dec. 31, 2012	Dec. 31, 2011
Debt Instrument [Line Items]
Total debt	$ 104,164	$ 41,324
Less: current portion	(3,325)	(28,049)
Long-term debt	100,839	13,275
Convertible Debt [Member]
Debt Instrument [Line Items]
Total debt	25,000	0
Years ending December 31: [Abstract]
2013	760
2014	760
2015	765
2016	760
2017	25,125
Thereafter	0
Total future minimum payments	28,170
Less: amount representing interest	(3,170)
Present value of minimum debt payments	25,000
Less: current portion	0
Noncurrent portion of debt	25,000
Related Party Convertible Notes [Member]
Debt Instrument [Line Items]
Total debt	39,033	0
Years ending December 31: [Abstract]
2013	0
2014	0
2015	0
2016	0
2017	51,627
Thereafter	0
Total future minimum payments	51,627
Less: amount representing interest	(12,594)
Present value of minimum debt payments	39,033
Less: current portion	0
Noncurrent portion of debt	39,033
Notes Payable [Member]
Debt Instrument [Line Items]
Total debt	1,572	3,113
Years ending December 31: [Abstract]
2013	351
2014	379
2015	379
2016	381
2017	384
Thereafter	154
Total future minimum payments	2,028
Less: amount representing interest	(456)
Present value of minimum debt payments	1,572
Less: current portion	(311)
Noncurrent portion of debt	1,261
Loans Payable [Member]
Debt Instrument [Line Items]
Total debt	26,150	19,359
Years ending December 31: [Abstract]
2013	1,958
2014	2,970
2015	4,456
2016	4,286
2017	4,110
Thereafter	16,426
Total future minimum payments	34,206
Less: amount representing interest	(8,056)
Present value of minimum debt payments	26,150
Less: current portion	(556)
Noncurrent portion of debt	25,594
Credit Facility [Member]
Debt Instrument [Line Items]
Total debt	12,409	18,852
Years ending December 31: [Abstract]
2013	3,175
2014	2,926
2015	2,774
2016	2,623
2017	2,393
Thereafter	612
Total future minimum payments	14,503
Less: amount representing interest	(2,094)
Present value of minimum debt payments	12,409
Less: current portion	(2,458)
Noncurrent portion of debt	$ 9,951

XML

Consolidated Statements of Convertible Preferred Stock, Redeemable Noncontrolling Interest and Equity (Deficit) (Parentheticals) (USD $) In Thousands, except Per Share data, unless otherwise specified	12 Months Ended
	Dec. 31, 2012	Dec. 31, 2010
Preferred stock, par value	$ 0.0001
Deferred charge asset related to issuance of Series D preferred stock	$ 0	$ 27,909
Series C Preferred Stock [Member]
Preferred stock, par value		$ 12.46
Stock issuance costs		5
Series C-1 Preferred Stock [Member]
Preferred stock, par value		$ 17.56
Stock issuance costs		68
Series D Preferred Stock [Member]
Preferred stock, par value		$ 18.75
Deferred charge asset related to issuance of Series D preferred stock		27,909
Stock issuance costs		258
Common Stock [Member]
Stock issuance costs	$ 392

XML

Consolidated Balance Sheets (Parentheticals) (USD $) In Thousands, except Share data, unless otherwise specified	Dec. 31, 2012	Dec. 31, 2011
Allowance for Doubtful Accounts	$ 481	$ 245
Stockholders' Equity:
Preferred stock, par value	$ 0.0001	$ 0.0001
Preferred stock, shares authorized	5,000,000	5,000,000
Preferred stock, shares issued	0	0
Preferred stock, shares outstanding	0	0
Common stock, par value	$ 0.0001	$ 0.0001
Common stock, shares authorized	100,000,000	100,000,000
Common stock, shares issued	68,709,660	45,933,138
Common Stock, Shares, Outstanding	68,709,660	45,933,138

XML

Significant Agreements

12 Months Ended

Dec. 31, 2012

Significant Agreements [Abstract]

Significant Agreements

Significant Agreements

Research and Development Activities

Total Collaboration Agreement

In June 2010, the Company entered into a technology license, development, research and collaboration agreement (“collaboration agreement”) with Total Gas & Power USA Biotech, Inc., an affiliate of Total S.A. (Total S.A. and its relevant affiliates, collectively, “Total”). The collaboration agreement sets forth the terms for the research, development, production and commercialization of certain to-be-determined chemical and/or fuel products made through the use of the Company’s synthetic biology platform. The collaboration agreement establishes a multiphased process through which projects are identified, screened, studied for feasibility, and ultimately selected as a project for development of an identified lead compound using an identified microbial strain. Under the terms of the collaboration agreement, Total will fund up to the first $50.0 million in research and development costs for the selected projects; thereafter the parties will share such costs equally. Amyris has agreed to dedicate the laboratory resources needed for collaboration projects. Total also plans to second employees at Amyris to work on the projects. Once a development project has commenced, the parties are obligated to work together exclusively to develop the lead compound during the project development phase. After a development project is completed, the Company and Total expect to form one or more joint ventures to commercialize any products that are developed, with costs and profits to be shared on an equal basis, provided that if Total has not achieved profits from sales of a joint venture product equal to the amount of funding it provided for development plus an agreed upon rate of return within three years of commencing sales, then Total will be entitled to receive all profits from sales until this rate of return has been achieved. Each party has certain rights to independently produce commercial quantities of these products under certain circumstances, subject to paying royalties to the other party. Total has the right of first negotiation with respect to exclusive commercialization arrangements that the Company would propose to enter into with certain third parties, as well as the right to purchase any of the Company’s products on terms no less favorable than those offered to or received by the Company from third parties in any market where Total or its affiliates have a significant market position.

The collaboration agreement has an initial term of twelve years and is renewable by mutual agreement by the parties for additional three year periods. Neither the Company nor Total has the right to terminate the agreement voluntarily. The Company and Total each have the right to terminate the agreement in the event the other party commits a material breach, is the subject of certain bankruptcy proceedings or challenges a patent licensed to it under the collaboration agreement. Total also has the right to terminate the collaboration agreement in the event the Company undergoes a sale or change of control to certain entities. If the Company terminates the collaboration agreement due to a breach, bankruptcy or patent challenge by Total, all licenses the Company has granted to Total terminate except licenses related to products for which Total has made a material investment and licenses related to products with respect to which binding commercialization arrangements have been approved, which will survive subject, in most cases, to the payment of certain royalties by Total to the Company. Similarly, if Total terminates the collaboration agreement due to a breach, bankruptcy or patent challenge by the Company, all licenses Total has granted to the Company terminate except licenses related to products for which the Company has made a material investment, certain grant-back licenses and licenses related to products with respect to which binding commercialization arrangements have been approved, which will survive subject, in most cases, to the payment of certain royalties to Total by the Company. On expiration of the collaboration agreement, or in the event the collaboration agreement is terminated for a reason other than a breach, bankruptcy or patent challenge by one party, licenses applicable to activities outside the collaboration generally continue with respect to intellectual property existing at the time of expiration or termination subject, in most cases, to royalty payments. There are circumstances under which certain of the licenses granted to Total will survive on a perpetual, royalty-free basis after expiration or termination of the collaboration agreement. Generally these involve licenses to use the Company’s synthetic biology technology and core metabolic pathway for purposes of either independently developing further improvements to marketed collaboration technologies or products or the processes for producing them within a specified scope agreed to by the Company and Total prior to the time of expiration or termination, or independently developing early stage commercializing products developed from collaboration compounds that met certain performance criteria prior to the time the agreement expired or was terminated and commercializing products related to such compounds. After the collaboration agreement expires, the Company may be obligated to provide Total with ongoing access to Amyris laboratory facilities to enable Total to complete research and development activities that commenced prior to termination.

In June 2010, concurrent with the collaboration agreement, the Company issued 7,101,548 shares of Series D preferred stock to Total for aggregate proceeds of approximately $133.0 million at a per share price of $18.75, which was lower than the per share fair value of common stock as determined by management and the Board of Directors. Due to the fact the collaboration agreement and the issuance of shares to Total occurred concurrently, the terms of both the collaboration agreement and the issuance of preferred stock were evaluated to determine whether their separately stated pricing was equal to the fair value of services and preferred stock. The Company determined that the fair value of Series D preferred stock was $22.68 at the time of issuance, and therefore, the Company measured the preferred stock initially at its fair value with a corresponding reduction in the consideration for the services under the collaboration agreement. As revenue from the collaboration agreement will be generated over a period of time based on the performance requirements, the Company recorded the difference between the fair value and consideration received for the Series D preferred stock of $27.9 million as a Deferred Charge Asset within Other Assets on the balance sheet at the time of issuance which will be recognized as a reduction to revenue in proportion to the total estimated revenue under the collaboration agreement. As of December 31, 2012 and 2011, the Company has recognized a cumulative reduction of $27.9 million and $9.1 million, respectively, against the deferred charge asset.

As a result of recording the Series D preferred stock at its fair value, the effective conversion price was greater than the fair value of common stock as determined by management and the Board of Directors. Therefore, no beneficial conversion feature was recorded at the time of issuance. The Company further determined that the conversion option with a contingent reduction in the conversion price upon a qualified IPO was a potential contingent beneficial feature and, as a result, the Company calculated the intrinsic value of such conversion option upon occurrence of the qualified IPO. The Company determined that a contingent beneficial conversion feature existed and the Company recorded a charge within the equity section of its balance sheet, which impacted earnings per share for the year ended December 31, 2010, based upon the price at which shares were offered to the public in the IPO in relation to the adjustment provisions provided for the Series D preferred stock. Based on the IPO price of $16.00 per share, the charge to net loss attributable to Amyris’ common stockholders was $39.3 million.

In connection with Total’s equity investment, the Company agreed to appoint a person designated by Total to serve as a member of the Company’s Board of Directors in the class subject to the latest reelection date, and to use reasonable efforts, consistent with the Board of Directors’ fiduciary duties, to cause the director designated by Total to be re-nominated by the Board of Directors in the future. These membership rights terminate upon the earlier of Total holding less than half of the shares of common stock originally issuable upon conversion of the Series D preferred stock or a sale of the Company.

The Company also agreed with Total that, so long as Total holds at least 10% of the Company’s voting securities, the Company will notify Total if the Company’s Board of Directors seeks to cause the sale of the Company or if the Company receives an offer to be acquired. In the event of such decision or offer, the Company must provide Total with all information given to an offering party and certain other information, and Total will have an exclusive negotiating period of fifteen business days in the event the Board of Directors authorizes the Company to solicit offers to buy the Company, or five business days in the event that the Company receives an unsolicited offer to be acquired. This exclusive negotiation period will be followed by an additional restricted negotiation period of ten business days, during which the Company will be obligated to negotiate with Total and will be prohibited from entering into an agreement with any other potential acquirer. Total has also entered into a standstill agreement pursuant to which it agreed for a period of three years not to acquire in excess of the greater of 20% of the number of shares of Series D preferred stock purchased by Total (during the initial two years) or 30% (during the third year) of the Company’s common stock without the prior consent of our Board of Directors, except that, among other things, if another person acquires more than Total’s then current holdings of the Company’s common stock, then Total may acquire up to that amount plus one share.

In November 2011, the Company and Total entered into an amendment of the collaboration agreement as described above in Note 4 under "Other Liabilities".

In July 2012, the Company entered into an amendment of its collaboration agreement with Total and related agreements. Under such July agreements, the scope of the collaboration initially contemplated by the parties under the November 2011 amendment described in Note 4, was expanded to encompass certain joint venture products for use in diesel and jet fuel on a worldwide basis and to provide a new structure for the research and development program and formation of the joint venture (the “Fuels JV”) to commercialize the products encompassed by the diesel and jet fuel research and development program (the “Program”).

Under the new agreements, the Company controls operations and execution of the Program subject to strategic and ultimate decision-making authority by a management committee composed of Company and Total representatives, and Total participates in the ultimate Fuels JV, or receives rights to recover its investment if, at a series of decision points, it decides not to proceed with the project. The agreements contemplate that the parties would grant exclusive manufacturing and commercial licenses to the Fuels JV for the Fuels JV products when the Fuels JV is formed (subject to requirements for the Company to grant the license to Total in the event the Fuels JV is not formed because of a deadlock, followed by an election by the Company to sell to Total the assets it otherwise would have contributed to the Fuels JV, or earlier under certain circumstances), and that the Company would retain the right to make and sell products other than the Fuels JV products. Under the agreements, the Fuels JV licenses would be consistent with the principle that development, production and commercialization of the Fuels JV products in Brazil will remain with the Company unless Total elects, after formation of the Fuels JV, to have such business contributed to the Fuels JV. The agreements also provide that certain Fuels JV non-exclusive products that were contemplated by the November 2011 amendment to the collaboration agreement are no longer to be included in the Fuels JV, but that the parties will explore potential development and commercialization of such products at a later date.

The agreements contemplate that the research and development efforts under the Program may extend through 2016, with a series of “Go/No Go” decisions by Total through such date tied to funding by Total. Each funding tranche involves the issuance of senior unsecured convertible promissory notes by the Company to Total (see Note 6). The agreements provided for cash funding by Total of $15.0 million in July 2012 and an additional $15.0 million in September 2012. (Such funding occurred in July and September as contemplated by the agreements.) Further, Total will fund $30.0 million by July 2013, and, if it chooses to proceed with the Program, fund an additional $10.85 million in July 2014 and $10.85 million in January 2015. Thirty days following the earlier of the completion of the research and development program or December 31, 2016, Total has a final opportunity to decide whether or not to proceed with the Program.

At either of the decision points tied to the funding described above (in July 2013 or July 2014), if Total decides not to continue to fund the Program (or, at any funding date does not provide funding based on (i) the Company's failure to satisfy a closing condition under the purchase agreement for the notes, or (ii) Total's breach of the purchase agreement), the notes previously issued under the purchase agreement would remain outstanding and become payable by the Company at the maturity date in March 2017, the Program and associated agreements would terminate, all Company rights granted for use in farnesene-based diesel and farnesene-based jet fuel would revert to the Company, and no Fuels JV would be formed to commercialize the Fuels JV products.

In the final “Go/No Go” decision described above, Total may elect to (i) go forward with the full Program (diesel and jet fuel) (a “Go” decision), (ii) not continue its participation in the full Program, or (iii) go forward only with the jet fuel component of the Program, with the following outcomes:

• For a “Go” decision by Total with respect to the whole Program, the parties would form the Fuels JV and the notes would be canceled.

• For a “No-Go” decision by Total with respect to the whole Program, the consequences would be as described in the paragraph above regarding a decision by Total not to continue to fund the Program.

• For a decision by Total to proceed with the jet fuel component of the Program and not the diesel component of the Program, 70% of the principal amount outstanding under the notes would remain outstanding and become payable by the Company and 30% of the outstanding principal of such notes would be canceled, the diesel product would no longer be included in the collaboration, the Fuels JV would not receive rights to products for use in diesel fuels, and the Fuels JV would be formed by the parties to commercialize products for use in jet fuels.

The agreements contemplate that the parties will finalize the structure for the Fuels JV in the future as set forth in the agreements and that the Fuels JV, if and when it is formed, would, subject to the conditions described below and absent other agreement, be owned equally (50%/50%) by the Company and Total. Under the agreements, the parties will, prior to the projected completion date, enter into a shareholders' agreement governing the Fuels JV, agree on the budget and business plan for the Fuels JV, and form the Fuels JV. In addition, following a final “Go” decision, the parties would enter into the Fuels JV license agreements, contribution agreements and other agreements required to establish the Fuels JV and enable it to operate.

Within thirty days prior to the final “Go” decision, Total may declare a “deadlock” if the parties fail to come to agreement on various matters relating to the formation of the Fuels JV, at which point Total may (i) elect to declare a “No-Go” decision, which has the consequences described above, or (ii) initiate a process whereby the fair value of the proposed Fuels JV would be determined and the Company would then have the option to: (i) elect to sell to Total the assets that the Company would have been required to contribute to the Fuels JV for an amount equal to 50% of such fair value; (ii) proceed with the formation of the Fuels JV (accepting Total's position with respect to the funding requirement of the Fuels JV) and becoming a 50% owner of the Fuels JV; or (iii) proceed with the formation of the Fuels JV (accepting Total's position with respect to the funding requirements of the Fuels JV), and then sell all or a portion of its 50% interest in the Fuels JV to Total for a price equal to the fair value multiplied by the percentage ownership of the Fuels JV sold to Total.

The agreements provide that the Company would initially retain its ability to develop its diesel and jet fuel business in Brazil, and that Total has an option to require the Company to contribute its Brazil diesel and jet fuel business to the Fuels JV at a price determined pursuant to the agreements. Such option terminates if the Fuels JV is not formed or if Total subsequently buys out the Company's Fuels JV contribution. Furthermore, the option is limited to the jet fuel business if Total opts out of the diesel component of the Program as described above.

Under the agreements, Total has a right to participate in future equity or convertible debt financings of the Company through December 31, 2013 to preserve its pro rata ownership of the Company and thereafter in limited circumstances. The purchase price for the first $30 million of purchases under this pro rata right would be paid by cancellation of outstanding notes held by Total.

In connection with the purchase agreement and sale of the Notes, the Company entered into a registration rights agreement. Under such agreement, the Company is obligated to file a registration statement on Form S-3 with the SEC registering the resale of all of the shares of the Company's common stock issuable upon conversion of the notes within twenty days prior to the maturity date of the notes or within 30 days following optional conversion. In addition, the Company is obligated to have the registration statement declared effective within 70-100 days following the filing depending on whether the Company receives comments from the SEC. If the registration statement filing is delayed or the registration statement is not declared effective within the foregoing time frames, the Company is required to make certain monthly payments to the Total.

As a result, $46.5 million of payments received from Total that had been recorded as an advance from the collaborator were no longer contingently repayable. Of this amount, $23.3 million was treated as a repayment by the Company and included as part of the senior unsecured convertible promissory note issued to Total in July 2012 and the remaining $23.2 million was recorded as a contract to perform research and development services, which was offset by the reduction of the capitalized deferred charge asset of $14.4 million resulting in the Company recording revenue from a related party of $8.9 million.

In December 2012, Total elected to participate in a private placement of the Company's common stock by exchanging approximately $5.0 million of its $53.3 million in senior unsecured convertible promissory notes into 1,677,852 shares of the Company's common stock at $2.98 per share. As such, $5.0 million of the outstanding $53.3 million in senior unsecured convertible debt was cancelled.

M&G Finanziaria Collaboration Agreement

In June 2010, the Company entered into a collaboration agreement with M&G Finanziaria S.R.L. (“M&G”) to incorporate Biofene as an ingredient in M&G's polyethylene terephthalate, or PET, resins to be incorporated into containers for food, beverages and other products. In April 2011, Amyris and M&G entered into an Amended and Restated Collaboration Agreement to amend certain portions of the original agreement entered into in June 2010 and adding Chemtex Italia S.R.L. and Chemtex International Inc. (both wholly owned subsidiaries of M&G) to the collaboration agreement. Under the terms of the amended agreement, the Company and Chemtex International Inc. will share the costs incurred associated with the PET collaboration on a 50/50 basis. In addition, the amended agreement expanded the collaboration arrangement between the Company and M&G to include a Cellulosic feasibility study with each party bearing its own costs associated with such feasibility study. The collaboration agreement also establishes the terms under which M&G may purchase Biofene from the Company upon successful completion of product integration.

Firmenich Collaboration and Joint Development Agreements

In November 2010, the Company entered into collaboration and joint development agreements with Firmenich SA (“Firmenich”), a flavors and fragrances company based in Geneva, Switzerland. Under the agreements, Firmenich will fund technical development at the Company to produce an ingredient for the flavors and fragrances market. The Company will manufacture the ingredient and Firmenich will market it, and the parties will share in any resulting economic value. The agreement also grants exclusive worldwide flavors and fragrances commercialization rights to Firmenich for the ingredient. In addition, Firmenich has an option to collaborate with the Company to develop a second ingredient. In July 2011, the Company and Firmenich expanded their collaboration agreement to include a third ingredient. The collaboration and joint development agreements will continue in effect unit the later of the expiration or termination of the development agreements or the supply agreements. The Company is also eligible to receive potential total payments of $6.0 million upon the achievement of certain performance milestones towards which the Company will be required to make a contributory performance. These milestones are accounted for under the guidance in the FASB accounting standard update related to revenue recognition under the milestone method. The Company concluded that these milestone payments are substantive.

For the years ended December 31, 2012 and 2011, the Company recorded $4.8 million and $5.2 million, respectively, of revenue from the collaboration agreement with Firmenich. Included in these collaboration revenues were the first milestone payment of $2.0 million which was recognized as revenue during the year ended December 31, 2011 and the second milestone payment of $2.0 million which was recognized as revenue during the year ended December 31, 2012.

In March 2013, the Company and Firmenich entered into a collaboration agreement as described in Note 18-"Subsequent Events."

Michelin Collaboration Agreement

In September 2011, the Company entered into a collaboration agreement with Manufacture Francaise des Pneumatiques Michelin (“Michelin”). Under the terms of the collaboration agreement, the Company and Michelin will collaborate on the development, production and worldwide commercialization of isoprene or isoprenol, generally for tire applications, using the Company's technology. Under the agreement, Michelin has agreed to pay an upfront payment to the Company of $5.0 million, subject to a reimbursement provision under which the Company would have to repay $1.0 million if it fails to achieve specified future technical milestones. The agreement provides that, subject to achievement of technical milestones, Michelin can notify the Company of its desired date for initial delivery, and the parties will either collaborate to establish a production facility or use an existing Company facility for production. The agreement also includes a term sheet for a supply agreement that would be negotiated at the time the decision regarding production facilities is made. The agreement has an initial term that will expire upon the earlier of 42 months from the effective date and the completion of a development work plan. As of December 31, 2012, the Company recorded the upfront payment of $5.0 million from Michelin as deferred revenue.

Manufacturing Agreements

In 2010 and 2011, the Company entered into contract manufacturing agreements with various contract manufacturing partners to utilize their manufacturing facilities to produce Amyris products.

Under the terms of these contract manufacturing agreements, the Company provided necessary equipment for the manufacturing of its products, over which the Company retained ownership. The Company also reimbursed the contract manufacturers for an aggregate of $13.8 million in expenditures related to the modification of their facilities. The Company recorded facility modification costs as Other Assets on the balance sheet and amortized them as an offset against purchases of inventory. Certain of these contract manufacturing agreements also impose fixed purchase commitments on the Company, regardless of the production volumes.

Beginning in March 2012, the Company initiated a plan to shift a portion of its production capacity from contract manufacturing facilities to a Company-owned plant that was then under construction. As a result, the Company evaluated its contract manufacturing agreements and recorded a loss of $31.2 million related to the write-off of $10.0 million in facility modification costs and the recognition of $21.2 million of fixed purchase commitments in the three months ended March 31, 2012. The Company recognized an additional charge of $1.4 million and $7.8 million, respectively, in the third and fourth quarters of 2012 associated with loss on fixed purchase commitments. The Company computed the loss on facility modification costs and fixed purchase commitments using the same lower of cost or market approach that is used to value inventory. The computation of the loss on fixed purchase commitments is subject to several estimates, including cost to complete and the ultimate selling price of any Company products manufactured at the relevant production facilities, and is therefore inherently uncertain. The Company also recorded a loss on write-off of production assets of $5.5 million related to Amyris-owned production equipment at contract manufacturing facilities in the quarter ended March 31, 2012. Total loss on purchase commitments and write-off of production assets for the year ended December 31, 2012 was $45.9 million. The Company will continue to evaluate the potential for losses in future periods based on updated production and sales price assumptions.

Tate & Lyle

In November 2010, the Company entered into a contract manufacturing agreement with Tate & Lyle Ingredients Americas, Inc. (“Tate & Lyle”), an affiliate of Tate & Lyle PLC. Tate & Lyle commenced production operations in the fourth quarter of 2011. At December 31, 2012 and 2011, the Company has recorded $0.8 million and $0.7 million, respectively, in prepaid and other current assets and $2.2 million and $2.9 million, respectively, in other noncurrent assets pertaining to the unamortized portion of equipment costs funded by the Company to Tate & Lyle (see Note 4). The related amortization is being offset against purchases of inventory from this contract manufacturer.

Paraíso Bioenergia

In March 2011, the Company entered into a supply agreement with Paraíso Bioenergia, a renewable energy company producing sugar, ethanol and electricity headquartered in São Paulo State, Brazil. Under the agreement, the Company will construct fermentation and separation capacity to produce its products and Paraíso Bioenergia will supply sugar cane juice and other utilities. The Company will retain the full economic benefits enabled by the sale of Amyris renewable products over the lower of sugar or ethanol alternatives. In conjunction with the supply agreement, the Company also entered into an operating lease on a real property owned by Paraíso Bioenergia. The real property is being used by the Company for its production site in Brotas (see Note 5).

Per the terms of the supply agreement, in the event that Paraíso is presented with an offer to sell or decides to sell the real property, the Company has the right of first refusal to acquire it. If the Company fails to exercise its right of first refusal the purchaser of the real property will need to comply with the specific obligations of Paraíso Bioenergia to the Company under the lease agreement.

Albemarle

In July 2011, the Company entered into a contract manufacturing agreement with Albemarle Corporation ("Albemarle"), which will provide toll manufacturing services at its facility in Orangeburg, South Carolina. Under this agreement, Albemarle will manufacture lubricant base oils from Biofene, which will be owned and distributed by the Company or a Company-designated commercial partner. The initial term of this agreement is from July 31, 2011 through December 31, 2012. Albemarle is required to modify its facility, including installation and qualification of equipment and instruments necessary to perform the toll manufacturing services under the agreement. The Company reimbursed Albemarle $10.0 million for all capital expenditures related to the facility modification, which was accounted for as a prepaid asset. All equipment or facility modifications acquired or made by Albemarle will be owned by Albemarle, subject to Albemarle's obligation to transfer title to, and ownership of, certain assets to the Company within 30 days after termination of the agreement, at the Company's discretion and sole expense. In March 2012, the Company recorded a loss of $10.0 million related to the write-off of the facility modification costs, described above.

In addition, the Company will pay a one-time, non-refundable performance bonus of $5.0 million if Albemarle delivers to the Company certain quantity of the lubricant base stock by December 31, 2011 or $2.0 million if Albemarle delivers the same quantity by January 31, 2012. Based on Albermarle's performance as of December 31, 2011, the Company concluded that Albermarle had earned the bonus which is payable in two payments. The Company paid Albemarle $2.5 million during the year ended December 31, 2012 and recorded a liability of $2.5 million as of December 31, 2012 for the second payment which is payable on March 31, 2013.

In February 2012, the Company entered into an amended and restated agreement with Albemarle, which superseded the original contract manufacturing agreement with Albemarle.  The term of the new agreement continues through December 31, 2019.  The agreement includes certain obligations for the Company to pay fixed costs totaling $7.5 million, of which $3.5 million and $4.0 million are payable in 2012 and 2014, respectively. In the three months ended March 31, 2012, the Company recorded a corresponding loss related to these fixed purchase commitments, as described above. In addition, fixed costs of $2.0 million per quarter are payable in 2013 if the Company exercises its option to have product manufactured in the facility in 2013.  The agreement also includes variable pricing during the contract term.

Supply Agreements

The Company has also entered into agreements to sell Biofene and its derivatives directly to various potential customers, including M&G for use in plastics, Kuraray Co., Ltd. ("Kuraray") for use in the production of polymers, Firmenich and Givaudan SA. ("Givaudan") for ingredients for the flavors and fragrances market, and Method Products, Inc. ("Method") for use in home and personal care products.

Soliance Agreements

In June 2010, the Company entered into an agreement with Soliance for the development and commercialization of Biofene-based squalane for use as an ingredient in cosmetics products. In December 2011, the Company and Soliance entered into an agreement and release to terminate the collaboration agreement and any other obligations with respect to the proposed joint venture. As part of the termination agreement the parties agreed that for a period commencing October 1, 2011 and ending on December 31, 2013, Soliance will be paid a commission of 10.0% of amounts received by the Company from Nikko Chemicals Co., Ltd. (“Nikko") on quantities of squalane sold by the Company to Nikko with respect to Nikko's committed minimum purchase obligation pursuant to a distribution agreement with Nikko. Concurrently with the execution of such termination agreement, the parties executed a distribution agreement, pursuant to which the Company appointed Soliance as its exclusive distributor to distribute the Company's squalane in the cosmetic market in the approved territory.

Nikko Chemicals

In August 2011, the Company entered into an agreement with Nikko, a private limited company in Japan, for the sales of renewable squalane to Nikko (commencing in September 2011 and continuing for two years through the end of December 2013).

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Reporting Segments (Details) (USD $) In Thousands, unless otherwise specified	12 Months Ended
	Dec. 31, 2012 businessactivities segmentmanagers	Dec. 31, 2011	Dec. 31, 2010
Revenues from External Customers and Long-Lived Assets [Line Items]
Segment Reporting, Number of Business Activities	1
Segment Reporting, Number of Segment Managers Held Accountable	0
Revenues	$ 73,694	$ 146,991	$ 80,311
Long-Lived Assets	163,121	128,101
United States [Member]
Revenues from External Customers and Long-Lived Assets [Line Items]
Revenues	49,111	141,098	80,311
Long-Lived Assets	70,273	76,108
Brazil [Member]
Revenues from External Customers and Long-Lived Assets [Line Items]
Revenues	3,786	141	0
Long-Lived Assets	90,982	48,240
Europe [Member]
Revenues from External Customers and Long-Lived Assets [Line Items]
Revenues	16,461	5,695	0
Long-Lived Assets	1,866	3,753
Japan [Member]
Revenues from External Customers and Long-Lived Assets [Line Items]
Revenues	$ 4,336	$ 57	$ 0

XML

Employee Benefit Plan (Details)	Dec. 31, 2012
Compensation and Retirement Disclosure [Abstract]
401K Voluntary Contributions, Percentage of Eligible Compensation	90.00%

XML

Stock-Based Compensation Plans - Employee Stock-Based Compensation (Details) (USD $)	12 Months Ended																									1 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010	Dec. 31, 2012 Restricted Stock Units (RSUs) [Member]	Dec. 31, 2012 Research and Development Expense [Member]	Dec. 31, 2011 Research and Development Expense [Member]	Dec. 31, 2010 Research and Development Expense [Member]	Dec. 31, 2012 Sales General and Administrative Expense [Member]	Dec. 31, 2011 Sales General and Administrative Expense [Member]	Dec. 31, 2010 Sales General and Administrative Expense [Member]	Dec. 31, 2012 Employee Share Based Compensation [Member]	Dec. 31, 2011 Employee Share Based Compensation [Member]	Dec. 31, 2010 Employee Share Based Compensation [Member]	Dec. 31, 2012 Employee Share Based Compensation [Member] Restricted Stock Units (RSUs) [Member]	Dec. 31, 2011 Employee Share Based Compensation [Member] Restricted Stock Units (RSUs) [Member]	Dec. 31, 2010 Employee Share Based Compensation [Member] Restricted Stock Units (RSUs) [Member]	Dec. 31, 2012 Employee Share Based Compensation [Member] Employee Stock Purchase Plan, 2010 [Member]	Dec. 31, 2011 Employee Share Based Compensation [Member] Employee Stock Purchase Plan, 2010 [Member]	Dec. 31, 2010 Employee Share Based Compensation [Member] Employee Stock Purchase Plan, 2010 [Member]	Dec. 31, 2012 Employee Share Based Compensation [Member] Research and Development Expense [Member]	Dec. 31, 2011 Employee Share Based Compensation [Member] Research and Development Expense [Member]	Dec. 31, 2010 Employee Share Based Compensation [Member] Research and Development Expense [Member]	Dec. 31, 2012 Employee Share Based Compensation [Member] Sales General and Administrative Expense [Member]	Dec. 31, 2011 Employee Share Based Compensation [Member] Sales General and Administrative Expense [Member]	Dec. 31, 2010 Employee Share Based Compensation [Member] Sales General and Administrative Expense [Member]	Aug. 31, 2012 Chief Executive Officer [Member] Board of Directors and Their Affiliates [Member] Employee Share Based Compensation [Member]	Jun. 30, 2012 Amyris US [Member] Employee Share Based Compensation [Member]	Jun. 30, 2012 IPO [Member] Employee Share Based Compensation [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Share-based Compensation Arrangement by Share-based Payment Award, Options, Grants in Period, Gross											3,589,593	2,677,249	2,918,440
Share-based Compensation Arrangement by Share-based Payment Award, Options, Grants in Period, Weighted Average Grant Date Fair Value											$ 2.28	$ 18.41	$ 11.84
Employee Service Share-based Compensation, Nonvested Awards, Total Compensation Cost Not yet Recognized											$ 51,200,000	$ 54,700,000		$ 7,800,000	$ 6,000,000
Employee Service Share-based Compensation, Nonvested Awards, Total Compensation Cost Not yet Recognized, Period for Recognition											2 years 10 months 24 days
Share-based Compensation Arrangement by Share-based Payment Award, Options, Exercises in Period																										668,730
Share-based Compensation Arrangement by Share-based Payment Award, Options, Exercised in Period, Private Sale Per Share to Related Party																										$ 3.70
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Grants in Period				2,966,900										2,956,900	352,301	0
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other Than Options, Grants in Period, Weighted Average Fair Value														$ 3.46	$ 29.85
Share-based Compensation Arrangement by Share-based Payment Award, Plan Modification, Compensation Cost											907,000
Share-based Compensation Arrangement by Share-based Payment Award, Accelerated Vesting of Options											825,523
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding, Weighted Average Exercise Price																											$ 24.00	$ 16.00
Allocated Share-based Compensation Expense	$ 27,473,000	$ 25,492,000	$ 10,432,000		$ 6,451,000	$ 6,345,000	$ 2,161,000	$ 21,022,000	$ 19,147,000	$ 8,271,000	$ 27,329,000	$ 24,594,000	$ 7,782,000	$ 6,300,000	$ 3,600,000		$ 800,000	$ 1,900,000	$ 500,000	$ 6,442,000	$ 6,306,000	$ 2,086,000	$ 20,887,000	$ 18,288,000	$ 5,696,000	$ 388,000
Expected dividend yield											0.00%	0.00%	0.00%
Risk-free interest rate											1.10%	2.30%	2.50%
Expected term (in years)											6 years	5 years 9 months 18 days	6 years
Expected volatility											77.00%	86.00%	96.00%

XML

Document and Entity Information (USD $) In Millions, except Share data, unless otherwise specified	12 Months Ended
	Dec. 31, 2012	Mar. 01, 2013	Jun. 29, 2012
Document Information [Line Items]
Entity Registrant Name	AMYRIS, INC.
Entity Central Index Key	0001365916
Current Fiscal Year End Date	--12-31
Entity Filer Category	Accelerated Filer
Document Type	10-K
Document Period End Date	Dec. 31, 2012
Document Fiscal Year Focus	2012
Document Fiscal Period Focus	FY
Amendment Flag	false
Entity Common Stock, Shares Outstanding		73,876,289
Entity Well-known Seasoned Issuer	No
Entity Voluntary Filers	No
Entity Current Reporting Status	Yes
Entity Public Float			$ 154.3

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Draths Corporation Acquisition

12 Months Ended

Dec. 31, 2012

Draths Corporation Acquistion [Abstract]

Draths Corporation Acquisition

Draths Corporation Acquisition

On October 6, 2011 (the Closing Date), the Company completed an acquisition of certain assets from Draths related to production of renewable chemicals. The acquisition was accounted for as a business combination. In connection with the acquisition, the Company issued 362,319 shares of common stock, of which 41,408 shares were held in escrow and paid $2.9 million in cash. In the quarter ended June 30, 2012, the Company recovered 5,402 shares of common stock from the escrow in connection with certain Draths indemnification obligations under the purchase agreement.

The components of the purchase price allocation for Draths are as follows:

Purchase Consideration:
(in thousands)
Fair value of common stock issued to Draths	$	7,000
Cash paid to Draths	2,934
Total purchase consideration	$	9,934

Allocation of Purchase Price:
(in thousands)
Property and Equipment	$	713
Other	101
In-process research and development	8,560
Goodwill	560
Total purchase consideration	$	9,934

The Company has allocated $8.6 million of the purchase price of Draths to acquired IPR&D. This amount represents management's valuation of the fair value of assets acquired at the date of the acquisition. Management used the income approach to determine the estimated fair values of acquired IPR&D, applying a risk adjusted discount rate of 30% to the development project's cash flows. The discounted cash flow model applies probability weighting factors, based on estimates of successful product development and commercialization, to estimated future net cash flows resulting from projected revenues and related costs. These success rates take into account the stages of completion and the risks surrounding successful development and commercialization of the underlying products such as estimates of revenues and operating profits related to the IPR&D considering its stage of development; the time and resources needed to complete the development; the life of the potential commercialized product and associated risks, including the inherent difficulties and uncertainties in developing a product.

Goodwill totaling $0.6 million represents the excess of the purchase price over the fair value of tangible and identifiable intangible assets acquired and is due primarily to synergies expected from combining the new genetic pathway with the Company's existing platform to accelerate development to get the technology to market sooner leading to increased market penetration from future products and customers.

The Draths business acquisition is a taxable transaction. For federal and state tax purposes, the above in-process research and development and goodwill is amortized over a 15-year period. The Company has determined that there are no significant differences in the tax basis of assets and the basis for financial reporting purposes. In addition, the business combination did not have any impact on the Company's deferred tax balance, net of the full valuation allowance, or to uncertain tax positions, at the acquisition date.

The Company applies the applicable accounting principles set forth in the U.S. Financial Accounting Standards Board's Accounting Standards Codification to its intangible assets (including goodwill), which prohibits the amortization of intangible assets with indefinite useful lives and requires that these assets be reviewed for impairment at least annually. There are several methods that can be used to determine the estimated fair value of the IPR&D acquired in a business combination. The Company utilized the "income method," which applies a probability weighting that considers the risk of development and commercialization, to the estimated future net cash flows that are derived from projected sales revenues and estimated costs. These projections are based on factors such as relevant market size, pricing of similar products, and expected industry trends. The estimated future net cash flows are then discounted to the present value using an appropriate discount rate. These assets are treated as indefinite-lived intangible assets until completion or abandonment of the projects, at which time the assets will be amortized over the remaining useful life or written off, as appropriate.If the carrying amount of the assets is greater than the measures of fair value, impairment is considered to have occurred and a write-down of the asset is recorded. Any finding that the value of its intangible assets has been impaired would require the Company to write-down the impaired portion, which could reduce the value of its assets and reduce its net income for the year in which the related impairment charges occur.

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Noncontrolling Interest Noncontrolling Interest (Details) (USD $) In Thousands, unless otherwise specified	12 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Stockholders' Equity Attributable to Noncontrolling Interest [Roll Forward]
Beginning Balance	$ (240)
Addition to noncontrolling interest			28
Foreign currency translation adjustment,	(6,626)	(8,761)	1,534
Loss attributable to noncontrolling interest	894	641	920
Ending Balance	(877)	(240)
Noncontrolling Interest [Member]
Stockholders' Equity Attributable to Noncontrolling Interest [Roll Forward]
Beginning Balance	(240)	2
Addition to noncontrolling interest	0	369	28
Foreign currency translation adjustment,	257	30
Loss attributable to noncontrolling interest	(894)	(641)
Ending Balance	$ (877)	$ (240)	$ 2

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Stock-Based Compensation Plans - Common Stock Subject to Repurchase and Stock-Based Compensation Expense (Details) (USD $)	12 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Employee Service Share-based Compensation, Allocation of Recognized Period Costs [Line Items]
Allocated Share-based Compensation Expense	$ 27,473,000	$ 25,492,000	$ 10,432,000
Research and Development Expense [Member]
Employee Service Share-based Compensation, Allocation of Recognized Period Costs [Line Items]
Allocated Share-based Compensation Expense	6,451,000	6,345,000	2,161,000
Sales General and Administrative Expense [Member]
Employee Service Share-based Compensation, Allocation of Recognized Period Costs [Line Items]
Allocated Share-based Compensation Expense	21,022,000	19,147,000	8,271,000
Stock Options [Member]
Employee Service Share-based Compensation, Allocation of Recognized Period Costs [Line Items]
Deferred Compensation Share-based Arrangements, Liability, Current	$ 197	$ 30,000
Share-based Compensation Arrangement by Share-based Payment Award, Options, Exercises in Period, Nonvested	51	7,929

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Consolidated Statements of Operations (USD $) In Thousands, except Share data, unless otherwise specified	12 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Revenues
Product sales	$ 49,638	$ 129,837	$ 68,664
Grants and collaborations revenue	24,056	17,154	11,647
Total revenues	73,694	146,991	80,311
Cost and operating expenses
Cost of product sales	77,314	155,615	70,515
Loss on purchase commitments and write off of production assets	45,854	0	0
Research and development	73,630	87,317	55,249
Sales, general and administrative	78,718	83,231	40,393
Restructuring and asset impairment (income) charges	0	0	(2,061)
Total cost and operating expenses	275,516	326,163	164,096
Loss from operations	(201,822)	(179,172)	(83,785)
Other income (expense):
Interest income	1,472	1,542	1,540
Interest expense	(4,926)	(1,543)	(1,443)
Other income, net	224	214	898
Total other income (expense)	(3,230)	213	995
Loss before income taxes	(205,052)	(178,959)	(82,790)
Provision for income taxes	(981)	(552)	0
Net loss	(206,033)	(179,511)	(82,790)
Net loss attributable to noncontrolling interest	894	641	920
Net loss attributable to Amyris, Inc.	(205,139)	(178,870)	(81,870)
Deemed dividend related to a beneficial conversion feature	0	0	(42,009)
Net loss attributable to Amyris, Inc. common stockholders	$ (205,139)	$ (178,870)	$ (123,879)
Net loss per share attributable to common stockholders, basic and diluted	$ (3.62)	$ (3.99)	$ (8.35)
Weighted-average shares of common stock outstanding used in computing net loss per share of common stock, basic and diluted	56,717,869	44,799,056	14,840,253

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Balance Sheet Components

12 Months Ended

Dec. 31, 2012

Balance Sheet Components [Abstract]

Balance Sheet Components

Balance Sheet Components

Investments

The following table summarizes the Company’s investments as of December 31, 2012 (in thousands):

	December 31, 2012
	Amortized Cost		Unrealized Gain (Loss)		Fair Value
Short-Term Investments
Certificates of Deposit	$	97	$	—	$	97
Total short-term investments	$	97	$	—	$	97

The following table summarizes the Company’s investments as of December 31, 2011 (in thousands):

	December 31, 2011
	Amortized Cost		Unrealized Gain (Loss)		Fair Value
Short-Term Investments
Certificates of Deposit	$	7,889	$	—	$	7,889
Total short-term investments	$	7,889	$	—	$	7,889

Inventories

Inventories, net is comprised of the following (in thousands):

	December 31,
	2012		2011
Raw materials	$	1,574	$	2,191
Work-in-process	1,771		1,237
Finished goods	2,689		5,642
Inventories, net	$	6,034	$	9,070

Prepaid and Other Current Assets

Prepaid and other current assets is comprised of the following (in thousands):

	December 31,
	2012		2011
Advances to contract manufacturers(1)	$	784	$	10,748
Manufacturing catalysts	1,895		3,929
Recoverable VAT and other taxes	4,167		2,193
Other	2,079		3,003
Prepaid and other current assets	$	8,925	$	19,873

⁽¹⁾  At December 31, 2012 and 2011, the amount of $784,000 and $748,000, respectively, relates to the current unamortized portion of equipment costs funded by the Company to a contract manufacturer. The related amortization is being offset against purchases of inventory.

Property, Plant and Equipment, net

Property, plant and equipment, net is comprised of the following (in thousands):

	December 31,
	2012			2011
Leasehold improvements	$	39,290		$	40,011
Machinery and equipment	105,162			59,657
Computers and software	8,232			6,491
Furniture and office equipment	2,467			2,223
Buildings	5,888			—
Vehicles	575			596
Construction in progress	45,372			45,318
	$	206,986		154,296
Less: accumulated depreciation and amortization	(43,865		)	(26,195		)
Property, plant and equipment, net	$	163,121		$	128,101

Property, plant and equipment, net includes $9.1 million and $13.7 million of machinery and equipment and furniture and office equipment under capital leases as of December 31, 2012 and 2011, respectively. Accumulated amortization of assets under capital leases totaled $4.1 million and $4.7 million as of December 31, 2012 and 2011, respectively.

Depreciation and amortization expense, including amortization of assets under capital leases, was $14.2 million, $10.7 million and $7.3 million for the years ended December 31, 2012, 2011 and 2010, respectively.

The Company capitalizes interest costs incurred to construct plant and equipment. The capitalized interest is recorded as part of the depreciable cost of the asset to which it relates to and is amortized over the asset's estimated useful life. Interest cost capitalized as of December 31, 2012 and 2011was $0.6 million and zero, respectively.

Other Assets

Other assets are comprised of the following (in thousands):

	December 31,
	2012		2011
Deferred charge asset(1)	$	—	$	18,792
Deposits on property and equipment, including taxes	2,363		17,455
Advances to contract manufacturers, net of current portion(2)	2,222		2,866
Recoverable taxes on purchased property, plant and equipment(3)	13,597		2,075
Other	1,930		1,813
Total other assets	$	20,112	$	43,001

______________ 

⁽¹⁾  The deferred charge asset relates to the collaboration agreement between the Company and Total (see Note 9).

⁽²⁾  At December 31, 2012 and 2011, $2.2 million and $2.9 million, respectively, relates to the non-current unamortized portion of equipment costs funded by the Company to a contract manufacturer. The related amortization is being offset against purchases of inventory.

⁽³⁾  At December 31, 2012 and December 31, 2011, $13.6 million and $2.1 million, respectively, are recoverable taxes from the Brazilian government.

Accrued and Other Current Liabilities

Accrued and other current liabilities are comprised of the following (in thousands):

	December 31,
	2012		2011
Professional services	$	824	$	4,384
Accrued vacation	2,673		2,761
Payroll and related expenses	5,809		6,343
Construction in progress	—		4,992
Tax-related liabilities	851		2,180
Deferred rent, current portion	1,448		1,274
Contractual obligations to contract manufacturers	9,952		—
Customer advances	970		3,667
Other	1,883		5,381
Total accrued and other current liabilities	$	24,410	$	30,982

Other Liabilities

Other liabilities are comprised of the following (in thousands):

	December 31,
	2012		2011
Contingently repayable advance from related party collaborator(1)	$	—	$	31,922
Bonus payable to contract manufacturer, non-current	—		2,500
Contractual obligations to contract manufacturers, non-current	4,000		—
Fair market value of swap obligations	1,367		—
Asset retirement obligations	—		1,129
Fair value of compound embedded derivative liability(2)	7,894		—
Other	2,672		1,534
Total other liabilities	$	15,933	$	37,085

______________ 

⁽¹⁾  The contingently repayable advance from related party collaborator as of December 31, 2011 relates to the collaboration agreement between the Company and Total.

⁽²⁾  The compound embedded derivative liability represents the fair value of the equity conversion feature and a "make-whole" feature of the outstanding senior unsecured convertible promissory notes issued to Total.

In November 2011, the Company and Total entered into an amendment of their Technology License, Development, Research and Collaboration Agreement (the "Amendment”). The Amendment provided for an exclusive strategic collaboration for the development of renewable diesel products and contemplated that the parties would establish a joint venture (the “JV”) for the production and commercialization of such renewable diesel products on an exclusive, worldwide basis. In addition, the Amendment contemplated providing the JV with the right to produce and commercialize certain other chemical products on a non-exclusive basis. The amendment further provided that definitive agreements to form the JV had to be in place by March 31, 2012 or such other date as agreed to by the parties or the renewable diesel program, including any further collaboration payments by Total related to the renewable diesel program, would terminate. In the second quarter of 2012, the parties extended the deadline to June 30, 2012, and, through June 30, 2012 the parties were engaged in discussions regarding the structure of future payments related to the program, until the amendment was superseded by a further amendment in July 2012 (as discussed in Note 9).

Pursuant to the Amendment, Total agreed to fund the following amounts: (i) the first $30 million in research and development costs related to the renewable diesel program which have been incurred since August 1, 2011, which amount would be in addition to the $50 million in research and development funding contemplated by the Collaboration Agreement, and (ii) for any research and development costs incurred following the JV formation date that were not covered by the initial $30 million, an additional $10 million in 2012 and up to an additional $10 million in 2013, which amounts would be considered part of the $50 million contemplated by the Collaboration Agreement. In addition to these payments, Total further agreed to fund 50% of all remaining research and development costs for the renewable diesel program under the Amendment.

Under the Amendment,Total had an option for a period of 90 days following the completion of the renewable diesel program on December 31, 2013 (or any other date as determined by the management committee to achieve the end-project milestone), to notify the Company that it did not wish to pursue production or commercialization of renewable diesel under the Amendment. If Total exercised this right, all of Total's intellectual property rights that were developed during the renewable diesel program would terminate and would be assigned to the Company, and the Company would be obligated to pay Total specified royalties based on the Company's net income in consideration of the benefits the Company derived from the technology and intellectual property developed during the renewable diesel development project. Such royalty payments would commence on the royalty notification date and end on the date when the Company had paid Total an aggregate amount equal to $150 million. Such royalty payments would be equal to (20%) of the Company and Company-affiliate (i) net income on a yearly basis derived from licenses or sales of intellectual property developed under the collaboration other than to the extent such licenses or sales relate to the use of such intellectual property for the non-exclusive JV products, and (ii) net income of the Company on a consolidated basis other than that derived from the jet fuel development program with Total or from the non-exclusive JV products.

In addition, under the Amendment, if the Company sold all or substantially all of its renewable diesel business prior to the time the aggregate royalty amount has been paid, the Company would be required to pay Total fifty percent (50%) of the net proceeds from such sale up to the then-remaining unpaid amount of the aggregate royalty amount. Net income was to be calculated in accordance with generally accepted accounting principles consistently applied by the Company and in the event that the foregoing net income was negative for a given fiscal quarter, the Company would not be required to pay any royalty for such fiscal quarter). Beginning on the sixth year from the royalty notification date, the aforementioned royalty would be additionally derived from the non-exclusive JV products.

The Company concluded that there was a significant amount of risk associated with the development of these products and therefore the arrangement is within the scope of ASC 730-20 Research and Development. The Company also determined that until Total exercised its royalty option under the Amendment, it would be uncertain that financial risk involved with research and development was transferred from the Company to Total. Accordingly, the funds received from Total for the diesel product research and development activities were recorded as a contingently repayable advance from the collaborator as part of other liabilities in the Company's consolidated balance sheets. Depending on the resolution of Total's royalty option contingency, the Company will record this arrangement as a contract to perform research and development services or as an obligation to repay the funds.

In July 2012, the Company entered into a further amendment of the collaboration agreement with Total that expanded Total's investment in the biofene collaboration, incorporated the development of certain joint venture products for use in diesel and jet fuel into the scope of the collaboration, and changed the structure of the funding from Total to include a convertible debt mechanism (see Note 9). As a part of the July 2012 amendment agreements, Total's royalty option contingency related to diesel was removed and the jet fuel collaboration was combined with the expanded biofene collaboration. As a result, $46.5 million of payments received from Total that had been recorded as an advance from the collaborator were no longer contingently repayable. Of this amount, $23.3 million was treated as a repayment by the Company and included as part of the senior unsecured convertible promissory note issued to Total in July 2012 and the remaining $23.2 million was recorded as a contract to perform research and development services, which was offset by the reduction of the capitalized deferred charge asset of $14.4 million resulting in the Company recording revenue from a related party of $8.9 million.

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Fair Value of Financial Instruments

12 Months Ended

Dec. 31, 2012

Fair Value Disclosures [Abstract]

Fair Value of Financial Instruments

Fair Value of Financial Instruments

The inputs to the valuation techniques used to measure fair value are classified into the following categories:

Level 1: Quoted market prices in active markets for identical assets or liabilities.

Level 2: Observable market-based inputs or unobservable inputs that are corroborated by market data.

Level 3: Unobservable inputs that are not corroborated by market data.

As of December 31, 2012, the Company’s financial assets and financial liabilities are presented below at fair value and were classified within the fair value hierarchy as follows (in thousands):

	Level 1		Level 2		Level 3		Balance as of December 31, 2012
Financial Assets
Money market funds	$	15,847	$	—	$	—	$	15,847
Certificates of deposit	757		—		—		757
Total financial assets	$	16,604	$	—	$	—	$	16,604
Financial Liabilities
Notes payable	$	—	$	1,676	$	—	$	1,676
Loans payable	—		20,707		—		20,707
Credit facilities	—		11,503		—		11,503
Convertible notes	—		—		62,522		62,522
Compound embedded derivative liability	—		—		7,894		7,894
Currency interest rate swap derivative liability	—		1,367		—		1,367
Total financial liabilities	$	—	$	35,253	$	70,416	$	105,669

The Company’s assessment of the significance of a particular input to the fair value measurement in its entirety requires management to make judgments and consider factors specific to the asset or liability. The fair values of money market funds are based on fair values of identical assets. The fair values of the notes payable, loan payable, convertible notes, credit facility and currency interest rate swaps are based on the present value of expected future cash flows and assumptions about current interest rates and the creditworthiness of the Company. Market risk associated with our fixed and variable rate long-term debt relates to the potential reduction in fair value and negative impact to future earnings, respectively, from an increase in interest rates.

The following table provides a reconciliation of the beginning and ending balances for the compound embedded derivative liability measured at fair value using significant unobservable inputs (Level 3) (in thousands):

	Compound Embedded Derivative Liability
Balance at December 31, 2011	$	—
Transfers in to Level 3	11,025
Total (gain) losses included in other income (expense), net	(3,131		)
Balance at December 31, 2012	$	7,894

The compound embedded derivative liability, which is included in other liabilities, represents the value of the equity conversion option and a "make-whole" provision of outstanding senior unsecured convertible promissory notes issued to Total Gas & Power USA SAS (see Note 6). There is no current observable market for this type of derivative and, as such, the Company determined the value of the embedded derivative using a Black-Scholes valuation model that combines expected cash outflows with market-based assumptions regarding risk-adjusted yields, stock price volatility, probability of a change of control and the trading information of the Company's common stock into which the notes are convertible. The Company marks the embedded derivative to market due to the conversion price not being indexed to the Company's own stock. Except for the "make-whole interest" provision included in the conversion option, which is only required to be settled in cash upon a change of control at the noteholder's option, the embedded derivative will be settled in either cash or shares. As of December 31, 2012, the Company had enough common shares to settle the conversion option in shares.

The Company’s financial assets and financial liabilities as of December 31, 2011 are presented below at fair value and were classified within the fair value hierarchy as follows (in thousands):

	Quoted Prices in Active Markets for Identical Assets (Level 1)		Other Observable Inputs (Level 2)		Significant Unobservable Inputs (Level 3)		Balance as of December 31, 2011
Financial Assets
Money market funds	$	57,127	$	—	$	—	$	57,127
Certificates of Deposit	27,384		—		—		27,384
Total financial assets	$	84,511	$	—	$	—	$	84,511
Financial Liabilities
Derivative liabilities	$	18	$	—	$	—	$	18
Total financial liabilities	$	18	$	—	$	—	$	18

Derivative Instruments

The Company’s derivative instruments included Chicago Board of Trade (CBOT) ethanol futures and Reformulated Blendstock for Oxygenate Blending (RBOB) gasoline futures. All derivative commodity instruments were recorded at fair value on the consolidated balance sheets. None of the Company’s derivative instruments were designated as a hedging instrument. Changes in the fair value of these non-designated hedging instruments were recognized in cost of products sold in the consolidated statements of operations. As of December 31, 2012, the Company had no outstanding derivative commodity instruments resulting from the Company's transition out of of its ethanol and gasoline business in the quarter ended September 30, 2012.

In June 2012, the Company entered into a loan agreement with Banco Pine S.A. under which the bank provided the Company with a short term loan of R$52.0 million (approximately US$25.4 million based on the exchange rate as of December 31, 2012) (the “Bridge Loan”). At the time of the Bridge Loan, the Company also entered into a currency interest rate swap arrangement with Banco Pine with respect to the repayment of R$22.0 million (approximately US$10.8 million based on the exchange rate of as of December 31, 2012). The swap arrangement exchanges the principal and interest payments under the Banco Pine loan of R$22.0 million entered into in July 2012 for alternative principal and interest payments that are subject to adjustment based on fluctuations in the foreign exchange rate between the U.S. dollar and Brazilian real. The swap has a fixed interest rate of 3.94%. Changes in the fair value of the swap are recognized in other income (expense), net in the consolidated statements of operations.

As of December 31, 2012, the Company recognized compound embedded derivative liability of $7.9 million which was included in other liabilities and represents the value of the equity conversion option and a "make-whole" provision of outstanding senior unsecured convertible promissory notes issued to Total Gas & Power USA SAS (see Note 6).

Derivative instruments measured at fair value as of December 31, 2012 and 2011, and their classification on the consolidated balance sheets and consolidated statements of operations, are presented in the following tables (in thousands except contract amounts):

	Asset/Liability as of
	December 31, 2012			December 31, 2011
Type of Derivative Contract	Quantity of Short Contracts	Fair Value		Quantity of Short Contracts	Fair Value
Regulated fixed price futures contracts, included as liability in accounts payable	—	$	—	22	$	18
Currency interest rate swap, included as net liability in other long term liability	1	$	1,367	—	$	—

	Income Statement Classification	Years Ended December 31,
Type of Derivative Contract		2012			2011			2010
		Gain (Loss) Recognized
Regulated fixed price futures contracts	Cost of products sold	$	(288	)	$	(2,365	)	$	(2,225	)
Currency interest rate swap	Other income (expense), net	$	(1,367	)	$	—		$	—

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Restructuring

12 Months Ended

Dec. 31, 2012

Restructuring and Related Activities [Abstract]

Restructuring

Restructuring

In June 2009, the Company initiated a restructuring plan to reduce its cost structure. The restructuring plan resulted in the consolidation of the Company’s headquarter facility located in Emeryville, California, which is under an operating lease. The Company ceased using a certain part of this headquarter facility in August 2009. The Company recorded approximately $5.4 million of restructuring charges associated with the facility lease costs after the operations ceased. In addition, as a result of the consolidation of the headquarter facility, the Company recorded approximately $3.1 million related to asset impairments and reversed $2.7 million related to deferred rent associated with the leased facility. In September 2010, the Company’s Board of Directors approved the Company’s plan to reoccupy the part of its headquarter facility which was previously the subject of the 2009 restructuring. This reoccupied space was used to meet the Company’s expansion requirements. As a result, the Company reversed approximately $4.6 million of its restructuring liability and recognized an income from restructuring of $2.1 million during the year ended December 31, 2010.

The following table summarizes the liability and utilization by cost type associated with the restructuring (in thousands):

	Exit Costs			Deferred Rent			Total
Accrued restructuring as of December 31, 2009	$	5,078		$	—		$	5,078
Cash payments	(906		)	—			(906		)
Accretion expense	395			—			395
Reversal of restructuring liability	(2,061		)	(2,506		)	(4,567		)
Accrued restructuring as of December 31, 2010	$	2,506		$	(2,506	)	$	—

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Stockholders' Equity

12 Months Ended

Dec. 31, 2012

Stockholders' Equity Note [Abstract]

Stockholders' Equity

Stockholders’ Equity

Private Placement

In February 2012, the Company completed a private placement of its common stock of 10,160,325 shares of it's common stock at a price of $5.78 per share for aggregate proceeds of $58.7 million. In connection with this private placement, the Company entered into an agreement with an investor to purchase additional shares of the Company's Common Stock for an additional $15.0 million by March 2013 upon satisfaction by the Company of criteria associated with the commissioning of the Company's production plant in Brotas. This was partially satisfied by the investor through its $10.0 million investment under the private placement in December 2012. Additionally, such agreement granted certain investors Board designation rights and certain rights of first investment with respect to future issuances of the Company's securities.

In May 2012, the Company also completed a private placement of its common stock for the issuance of 1,736,100 shares of it's common stock at a price of $2.36 per share for aggregate proceeds of $4.1 million.

In December 2012, the Company completed a private placement of its common stock for the issuance of 14,177,849 shares of its common stock at a price of $2.98 per share for aggregate proceeds of $37.2 million and the cancellation of $5.0 million worth of outstanding senior unsecured convertible promissory notes previously issued by the Company. Shares totaling 1,677,852 were issued to Total in exchange for this cancellation. Net cash received as of December 31, 2012 was $22.2 million and the remaining $15.0 million of proceeds was settled in January 2013. In connection with this private placement, the Company entered into a Letter of Agreement, dated December 24, 2012 with an investor under which the Company acknowledged that the investor's initial investment of $10.0 million in December 2012 represented partial satisfaction of the investor's preexisting contractual obligation to fund $15.0 million by March 31, 2013 upon satisfaction by the Company of criteria associated with the commissioning of the Company's production plant in Brotas.

Initial Public Offering

On September 30, 2010, the Company closed its initial public offering (“IPO”) of 5,300,000 shares of common stock at an offering price of $16.00 per share, resulting in net proceeds to the Company of approximately $73.7 million, after deducting underwriting discounts of $5.9 million and offering costs of $5.2 million. Upon the closing of the IPO, the Company’s outstanding shares of convertible preferred stock were automatically converted into 31,550,277 shares of common stock and the outstanding convertible preferred stock warrants were automatically converted into common stock warrants to purchase a total of 195,604 shares of common stock and shares of Amyris Brasil held by third party investors were automatically converted into 861,155 shares of common stock.

In connection with the IPO, the Company granted the underwriters the right to purchase up to an additional 795,000 shares of common stock to cover over-allotments. In October 2010, the underwriters exercised such right to purchase 795,000 shares and the Company received approximately $11.8 million of proceeds, net of underwriter’s discount.

Common Stock

Pursuant to the Company’s amended and restated certificate of incorporation, the Company is authorized to issue 100,000,000 shares of common stock. Holders of the Company’s common stock are entitled to dividends as and when declared by the Board of Directors, subject to the rights of holders of all classes of stock outstanding having priority rights as to dividends. There have been no dividends declared to date. The holder of each share of common stock is entitled to one vote.

Preferred Stock

Pursuant to the Company’s amended and restated certificate of incorporation, the Company is authorized to issue 5,000,000 shares of preferred stock. The Board of Directors has the authority, without action by its stockholders, to designate and issue shares of preferred stock in one or more series and to fix the rights, preferences, privileges and restrictions thereof. Prior to the closing of the Company’s IPO, the Company had four series of convertible preferred stock outstanding, including Series D preferred stock issued to Total (see Note 9). As of December 31, 2012 and December 31, 2011, the Company had zero convertible preferred stock outstanding.

Common Stock Warrants

During the period from January 1, 2008 to September 30, 2010, the Company issued 182,405 warrants in connection with placement agent fees associated with its preferred stock issuance, capital and operating lease agreements and consulting services. Upon the closing of the Company’s IPO on September 30, 2010, these outstanding convertible preferred stock warrants were automatically converted into common stock warrants to purchase 195,604 shares of common stock. In addition, the fair value of the convertible preferred stock warrants as of September 30, 2010, estimated to be $2.3 million using the Black-Scholes option pricing model, was reclassified to additional paid in capital.

In December 2011, in connection with a capital lease agreement, the Company issued warrants to purchase 21,087 shares of the Company's common stock at an exercise price of $10.67 per share. The Company estimated the fair value of these warrants as of the issuance date to be $193,000 and recorded these warrants as other assets and were amortized subsequently over the term of the lease. The fair value was based on the contractual term of the warrants of 10 years, risk free interest rate of 2.0%, expected volatility of 86% and zero expected dividend yield. The warrants remain unexercised and outstanding as of December 31, 2012.

Each of these warrants includes a cashless exercise provision which permits the holder of the warrant to elect to exercise the warrant without paying the cash exercise price, and receive a number of shares determined by multiplying (i) the number of shares for which the warrant is being exercised by (ii) the difference between the fair market value of the stock on the date of exercise and the warrant exercise price, and dividing such by (iii) the fair market value of the stock on the date of exercise. During the years ended December 31, 2012 and 2011, warrants were exercised with respect to zero and 190,468 shares, respectively through the cashless exercise provision and zero and 77,087 shares of common stock were issued after deducting the shares to cover the cashless exercises.

As of December 31, 2012 and 2011, the Company had the following unexercised common stock warrants:

		Exercise Price per Share		Shares as of
Underlying Stock	Expiration Date			December 31, 2012	December 31, 2011
Common Stock	1/31/2018	$	24.88	—	2,884
Common Stock	9/23/2018	$	25.26	—	2,252
Common Stock	12/23/2021	$	10.67	21,087	21,087
Total				21,087	26,223

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Draths Corporation Acquisition (Details) (USD $) In Thousands, except Share data, unless otherwise specified	0 Months Ended		12 Months Ended	0 Months Ended
	Oct. 06, 2011 Draths Corporation [Member]	Oct. 06, 2011 Income Approach Valuation Technique [Member] Draths Corporation [Member]	Dec. 31, 2011 Common Stock [Member]	Oct. 06, 2011 Common Stock [Member] Draths Corporation [Member]
Business Acquisition [Line Items]
Issuance of common stock in connection with Draths business acquisition, shares			362,319	362,319
Fair Value Inputs, Discount Rate		30.00%
Finite-Lived Intangible Asset, Useful Life	15 years
Purchase Consideration:
Fair value of common stock issued to Draths	$ 7,000
Cash paid to Draths	2,934
Allocation of Purchase Price:
Property and Equipment	713
Other	101
In-process research and development	8,560
Goodwill	560
Total purchase consideration	$ 9,934

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Joint Ventures

12 Months Ended

Dec. 31, 2012

Equity Method Investments and Joint Ventures [Abstract]

Joint Ventures

Joint Ventures

SMA Indústria Química S.A.

On April 14, 2010, the Company established SMA, a joint venture with Usina São Martinho, to build the first facility in Brazil fully dedicated to the production of Amyris renewable products. The new company is located at the Usina São Martinho mill in Pradópolis, São Paulo state. SMA has a 20 year initial term.

 SMA is managed by a three member executive committee, of which the Company appoints two members, one of whom is the plant manager who is the most senior executive responsible for managing the construction and operation of the facility. SMA is governed by a four member board of directors, of which the Company and Usina São Martinho each appoint two members. The board of directors has certain protective rights which include final approval of the engineering designs and project work plan developed and recommended by the executive committee.

The joint venture agreements require the Company to fund the construction costs of the new facility and Usina São Martinho would reimburse the Company up to RS$61.8 million (approximately US$30.2 million based on the exchange rate as of December 31, 2012) of the construction costs after SMA commences production. Post commercialization, the Company would market and distribute Amyris renewable products and Usina São Martinho would sell feedstock and provide certain other services to SMA. The cost of the feedstock to SMA would be a price that is based on the average return that Usina São Martinho could receive from the production of its current products, sugar and ethanol. The Company would be required to purchase the output of SMA for the first four years at a price that guarantees the return of Usina São Martinho’s investment plus a fixed interest rate. After this four year period, the price would be set to guarantee a break-even price to SMA plus an agreed upon return.

Under the terms of the joint venture agreements, if the Company becomes controlled, directly or indirectly, by a competitor of Usina São Martinho, then Usina São Martinho has the right to acquire the Company’s interest in SMA. If Usina São Martinho becomes controlled, directly or indirectly, by a competitor of the Company, then the Company has the right to sell its interest in SMA to Usina São Martinho. In either case, the purchase price shall be determined in accordance with the joint venture agreements, and the Company would continue to have the obligation to acquire products produced by SMA for the remainder of the term of the supply agreement then in effect even though the Company would no longer be involved in SMA’s management.

Amyris has a 50% ownership interest in SMA. The Company has identified SMA as a VIE. The Company is the primary beneficiary and consequently consolidates SMA’s operations in its financial statements.

Joint Venture with Cosan

In June 2011, the Company entered into joint venture agreements with Cosan Combustíveis e Lubrificantes S.A. and Cosan S.A. Industria e Comércio (such Cosan entities, collectively or individually, “Cosan”), related to the formation of a joint venture (the “Novvi JV”), to focus on the worldwide development, production and commercialization of base oils made from Biofene for the automotive, commercial and industrial lubricants markets (the "Original JV Agreement"). The parties originally envisioned operating their joint venture through Novvi S.A., a Brazilian entity jointly owned by Cosan and Amyris Brasil.

Under the Original JV Agreement and related agreements (including a Shareholders' Agreement and Joint Venture Implementation Agreement), the Company and Cosan each owned 50% of the Novvi JV and each party would share equally in any costs and any profits ultimately realized by the JV. The joint venture agreement had an initial term of 20 years from the date of the Original JV Agreement, subject to earlier termination by mutual written consent or by a non-defaulting party in the event of specified defaults by the other party (including breach by a party of any material obligations under the joint venture agreements). The Shareholders' Agreement had an initial term of 10 years from the date of the agreement, subject to earlier termination if either the Company or Cosan ceases to own at least 10% of the voting stock of the Novvi JV.

The Company identified Novvi S.A. as a VIE. The power to direct activities, which most significantly impact the economic success of the joint venture, is equally shared between the Company and Cosan who are not related parties. Accordingly, the Company is not the primary beneficiary and therefore accounts for its investment in the JV entity using the equity method. The Company periodically reviews its consolidation analysis on an ongoing basis. As of December 31, 2012, the carrying amounts of the unconsolidated JV entity's assets and liabilities were not material to the Company's consolidated financial statements.

In September 2011, a U.S. JV entity, Novvi LLC, was formed. Novvi LLC is jointly owned by the Company and Cosan US, Inc. ("Cosan US"). For the years ended December 31, 2012, 2011 and 2010, the Company recorded $0.9 million, $3.6 million and zero, respectively, of revenue from the research and development activities that it has performed on behalf of the joint venture.

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Balance Sheet Components Property, Plant and Equipment, net (Details) (USD $)	12 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Property, Plant and Equipment [Line Items]
Property, Plant and Equipment, Gross	$ 206,986,000	$ 154,296,000
Less: accumulated depreciation and amortization	43,865,000	26,195,000
Property, plant and equipment, net	163,121,000	128,101,000
Depreciation and amortization	14,570,000	11,077,000	7,280,000
Interest Costs Capitalized	600,000	0
Capital Lease Obligations [Member]
Property, Plant and Equipment [Line Items]
Less: accumulated depreciation and amortization	4,100,000	4,700,000
Leasehold improvements [Member]
Property, Plant and Equipment [Line Items]
Property, Plant and Equipment, Gross	39,290,000	40,011,000
Machinery and equipment [Member]
Property, Plant and Equipment [Line Items]
Property, Plant and Equipment, Gross	105,162,000	59,657,000
Computer and software [Member]
Property, Plant and Equipment [Line Items]
Property, Plant and Equipment, Gross	8,232,000	6,491,000
Furniture and office equipment [Member]
Property, Plant and Equipment [Line Items]
Property, Plant and Equipment, Gross	2,467,000	2,223,000
Buildings [Member]
Property, Plant and Equipment [Line Items]
Property, Plant and Equipment, Gross	5,888,000	0
Vehicles [Member]
Property, Plant and Equipment [Line Items]
Property, Plant and Equipment, Gross	575,000	596,000
Construction in progress [Member]
Property, Plant and Equipment [Line Items]
Property, Plant and Equipment, Gross	45,372,000	45,318,000
Machinery and Equipment and Furniture and Office Equipment Under Capital Lease [Member] | Capital Lease Obligations [Member]
Property, Plant and Equipment [Line Items]
Property, Plant and Equipment, Gross	9,100,000	13,700,000
Property Plant and Equipment Including Capital Leases [Member]
Property, Plant and Equipment [Line Items]
Depreciation and amortization	$ 14,200,000	$ 10,700,000	$ 7,300,000

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Commitments and Contingencies

12 Months Ended

Dec. 31, 2012

Commitments and Contingencies Disclosure [Abstract]

Commitments and Contingencies

Commitments and Contingencies

Capital Leases

In March 2008, the Company executed an equipment financing agreement intended to cover certain qualifying research and laboratory hardware and software. In January 2009, the agreement was amended to increase the financing amount. During the years ended December 31, 2012, 2011 and 2010, the Company financed certain purchases of hardware equipment and software of approximately zero, zero and $1.4 million, respectively. Pursuant to the equipment financing agreement, the Company financed the equipment with the transactions representing capital leases. Accordingly, fixed assets and capital lease liabilities were recorded at the present values of the future lease payments of $0.4 million and $3.1 million at December 31, 2012 and 2011. The incremental borrowing rates used to determine the present values of the future lease payments was 9.5%. The capital lease obligations expire at various dates, with the latest maturity in March 2013. In connection with the agreement entered into in 2008, the Company issued a warrant to purchase shares of the Company's convertible preferred stock (see Note 11).

In December 2011, the Company executed an equipment financing agreement for $3.0 million for certain qualifying manufacturing and laboratory equipment. Pursuant to the equipment financing agreement, the Company financed the equipment with transactions representing capital leases. This sales/leaseback transaction resulted in a $1.3 million unrealized loss which is being amortized over the life of the assets under lease. Accordingly, a capital lease liability was recorded at the present value of the future lease payments of $2.2 million and $3.4 million during the years ended December 31, 2012 and 2011, respectively. The incremental borrowing rate used to determine the present values of the future lease payments was 6.5%. The lease obligations expire on January 1, 2015. In connection with the capital lease entered into in 2011, the Company issued a warrant to purchase shares of the Company's common stock (see Note 11). Future minimum payments under this sales/leaseback agreement as of December 31, 2012 are as follows (in thousands):

Years ending December 31:	Sales/Leaseback
2013	$	1,098
2014	1,007
2015	289
2016	—
2017	—
Thereafter	—
Total future minimum lease payments	2,394
Less: amount representing interest	(168		)
Present value of minimum lease payments	2,226
Less: current portion	(982		)
Long-term portion	$	1,244

The Company recorded interest expense in connection with its capital leases of $382,000, $559,000 and $821,000 for the years ended December 31, 2012, 2011 and 2010, respectively. Future minimum payments under capital leases, including the sales/leaseback, as of December 31, 2012 are as follows (in thousands):

Years ending December 31:	Capital Leases
2013	$	1,489
2014	1,007
2015	289
2016	—
2017	—
Thereafter	—
Total future minimum lease payments	2,785
Less: amount representing interest	(175		)
Present value of minimum lease payments	2,610
Less: current portion	(1,366		)
Long-term portion	$	1,244

Operating Leases

The Company has noncancelable operating lease agreements for office, research and development, and manufacturing space in the United States that expire at various dates, with the latest expiration in May 2018 with an estimated annual rent payment of approximately $6.2 million. In addition, the Company leases facilities in Brazil pursuant to noncancelable operating leases that expire at various dates, with the latest expiration in November 2016 and with an estimated annual rent payment of approximately $0.6 million.

In 2007, the Company entered into an operating lease for its headquarters in Emeryville, California, with a term of ten years commencing in May 2008. As part of the operating lease agreement, the Company received a tenant improvements allowance of $11.4 million. The Company recorded the allowance as deferred rent and associated expenditures as leasehold improvements that are being amortized over the shorter of their estimated useful life or the term of the lease. In connection with the operating lease, the Company elected to defer a portion of the monthly base rent due under the lease and entered into notes payable agreements with the lessor for the purchase of certain tenant improvements. In October 2010, the Company amended its lease agreement with the lessor of its headquarters, to lease up to approximately 22,000 square feet of research and development and office space. In return for the removal of the early termination clause in its amended lease agreement, the Company received approximately $1.0 million from the lessor in December 2010.

The Company recognizes rent expense on a straight-line basis over the noncancelable lease term and records the difference between cash rent payments and the recognition of rent expense as a deferred rent liability. Where leases contain escalation clauses, rent abatements, and/or concessions, such as rent holidays and landlord or tenant incentives or allowances, the Company applies them in the determination of straight-line rent expense over the lease term. Rent expense was $4.9 million, $4.8 million and $3.3 million, respectively, for the years ended December 31, 2012, 2011 and 2010, respectively.

In January 2011, the Company entered into a right of first refusal agreement with respect to a facility and site in Leland, North Carolina leased by Glycotech covering a two year period commencing in January 2011. Under the right of first refusal agreement, the lessor agrees not to sell the facility and site leased by Glycotech during the term of the production service agreement. If the lessor is presented with an offer to sell, or decides to sell, an adjacent parcel, the Company has a right of first refusal to acquire the adjacent parcel or leased property.

In February 2011, the Company commenced payment of rent related to an operating lease on real property owned by Usina São Martinho in Brazil. In conjunction with a joint venture agreement (see Note 7) with the same entity, the real property will be used by the joint venture entity, SMA Indústria Química S.A. (“SMA”), for the construction of a production facility. This lease has a term of 20 years commencing in February 2011 with an estimated annual rent payment of approximately $46,000.

In February 2011, the Company entered into an operating lease for certain equipment owned by GEA Engenharia de Processos e Sistemas Industriais Ltda (“GEA”) in Brazil. The equipment under this lease was used by the Company in its production activities in Brazil. This lease had a term of one year commencing in March 2011 and was terminated in June 2012 and the equipment was returned to GEA.

In March 2011, the Company entered into an operating lease on real property owned by Paraíso Bioenergia S.A. (“Paraíso Bioenergia”) in Brazil. In conjunction with a supply agreement (see Note 9) with the same entity, the real property is being used by the Company for its Biofene production plant in Brotas. This lease has a term of 15 years commencing in March 2011 with an estimated annual rent payment of approximately $116,000.

In August 2011, the Company notified the lessor of its leased office facilities in Brazil of the Company's termination of its existing lease effective November 30, 2011. At the same time, the Company entered into an operating lease for new office facilities in Campinas, Brazil. The new lease has a term of 5 years commencing in November 2011 with an estimated annual rent payment of approximately $367,000.

In October 2012, an operating lease associated with the Company's pilot plant in Brazil was amended. As a result of this amendment, the Company's operating lease was extended and the new expiration is October 2015 and included an amendment to the terms of restitution of the property under lease. As a result of this amendment, the Company no longer has asset retirement obligations and therefore reversed the previously accrued liabilities.

Future minimum payments under operating leases as of December 31, 2012, are as follows (in thousands):

Years ending December 31:	Operating Leases - Facilities		Operating Leases - Land		Total Operating Leases
2013	$	6,463	$	161	$	6,624
2014	6,610		162		6,772
2015	6,738		162		6,900
2016	6,729		162		6,891
2017	6,598		162		6,760
Thereafter	2,786		1,556		4,342
Total future minimum lease payments	$	35,924	$	2,365	$	38,289

Guarantor Arrangements

The Company has agreements whereby it indemnifies its officers and directors for certain events or occurrences while the officer or director is, or was, serving at the Company’s request in such capacity. The term of the indemnification period is for the officer or director’s lifetime. The maximum potential amount of future payments the Company could be required to make under these indemnification agreements is unlimited; however, the Company has a director and officer insurance policy that limits its exposure and enables the Company to recover a portion of any future amounts paid. As a result of its insurance policy coverage, the Company believes the estimated fair value of these indemnification agreements is minimal. Accordingly, the Company had no liabilities recorded for these agreements as of December 31, 2012 and 2011.

The Company has a facility (“FINEP Credit Facility”) with a financial institution to finance a research and development project on sugarcane-based biodiesel (see Note 6). The FINEP Credit Facility provides for loans of up to an aggregate principal amount of R$6.4 million (approximately US$3.1 million based on the exchange rate as of December 31, 2012) which is guaranteed by a chattel mortgage on certain equipment of the Company. The Company's total acquisition cost for the equipment under this guarantee is approximately R$6.0 million (approximately US$2.9 million based on the exchange rate as of December 31, 2012). Through December 31, 2012, the Company received all four disbursements after compliance with certain terms and conditions under the FINEP Credit Facility as described in more detail in Note 6. After the release of the first disbursement and prior to any subsequent drawdown from the FINEP Credit Facility, the Company provided bank letters of guarantee of R$3.3 million (approximately US$1.6 million based on the exchange rate as of December 31, 2012) through Banco ABC Brasil S.A. As of December 31, 2012, all available credit under this facility was fully drawn.

The Company has a credit facility (“BNDES Credit Facility”) with a financial institution to finance a production site in Brazil. This credit facility is collateralized by a first priority security interest in certain of the Company's equipment and other tangible assets totaling R$24.9 million (approximately US$12.2 million based on the exchange rate at December 31, 2012). The Company is a parent guarantor for the payment of the outstanding balance under the BNDES Credit Facility. Additionally, the Company is required to provide a bank guarantee under the BNDES Credit Facility.

The Company has signed loan agreements and a security agreement where the Company pledged certain farnesene production assets as collateral (the fiduciary conveyance of movable goods) with each of Nossa Caixa and Banco Pine. Under the loan agreements, Banco Pine, agreed to lend R$22.0 million and Nossa Caixa agreed to lend R$30.0 million as financing for capital expenditures relating to the Company's production facility in Brotas. The Company's total acquisition cost for the farnesene production assets pledged as collateral under these agreements is approximately R$68.0 million (approximately US$33.3 million based on the exchange rate as of December 31, 2012). The Company is a also a parent guarantor for the payment of the outstanding balance under these loan agreements. 

Under an operating lease agreement for its office facilities in Brazil, which commenced on November 15, 2011, the Company is required to maintain restricted cash or letters of credit equal to 3 months of rent of approximately R$0.2 million (approximately US$0.1 million based on the exchange rate as of December 31, 2012) in the aggregate as a guarantee that the Company will meet its performance obligations under such operating lease agreement.

Purchase Obligations

As of December 31, 2012, the Company had $53.1 million in purchase obligations which included $52.7 million in non-cancelable contractual obligations and construction commitments, of which $13.9 million have been accrued as loss on purchase commitments.

Other Matters

Certain conditions may exist as of the date the financial statements are issued, which may result in a loss to the Company but which will only be resolved when one or more future events occur or fail to occur. The Company's management assesses such contingent liabilities, and such assessment inherently involves an exercise of judgment. In assessing loss contingencies related to legal proceedings that are pending against and by the Company or unasserted claims that may result in such proceedings, the Company's management evaluates the perceived merits of any legal proceedings or unasserted claims as well as the perceived merits of the amount of relief sought or expected to be sought.

If the assessment of a contingency indicates that it is probable that a material loss has been incurred and the amount of the liability can be estimated, then the estimated liability would be accrued in the Company's financial statements. If the assessment indicates that a potential material loss contingency is not probable but is reasonably possible, or is probable but cannot be estimated, then the nature of the contingent liability, together with an estimate of the range of possible loss if determinable and material would be disclosed. Loss contingencies considered to be remote by management are generally not disclosed unless they involve guarantees, in which case the guarantee would be disclosed.

The Company is subject to disputes and claims that arise or have arisen in the ordinary course of business and that have not resulted in legal proceedings or have not been fully adjudicated. For example, as of December 31, 2012, the Company had accrued approximately R$2.5 million (approximately US$1.2 million based on the exchange rate as of December 31, 2012) for losses it deemed to be probable arising from a potential claim relating to a contract manufacturing arrangement. Such matters that may arise in the ordinary course of business are subject to many uncertainties and outcomes are not predictable with assurance. Therefore, if one or more of these legal disputes or claims resulted in settlements or legal proceedings that were resolved against the Company for amounts in excess of management’s expectations, the Company’s consolidated financial statements for the relevant reporting period could be materially adversely affected.

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Debt

12 Months Ended

Dec. 31, 2012

Debt Disclosure [Abstract]

Debt

Debt

Debt is comprised of the following (in thousands):

	December 31,
	2012			2011
Credit facilities	$	12,409		$	18,852
Notes payable	1,572			3,113
Convertible notes	25,000			—
Related party convertible notes	39,033			—
Loans payable	26,150			19,359
Total debt	104,164			41,324
Less: current portion	(3,325		)	(28,049		)
Long-term debt	$	100,839		$	13,275

FINEP Credit Facility

In November 2010, the Company entered into a credit facility with Financiadora de Estudos e Projetos (“FINEP”), a state-owned company subordinated to the Brazilian Ministry of Science and Technology. This FINEP Credit Facility was extended to partially fund expenses related to the Company’s research and development project on sugarcane-based biodiesel (“FINEP Project”) and provides for loans of up to an aggregate principal amount of R$6.4 million (approximately US$3.1 million based on the exchange rate as of December 31, 2012) which is secured by a chattel mortgage on certain equipment of the Company as well as by bank letters of guarantee. Through December 31, 2012, the Company received all four disbursements after compliance with certain terms and conditions under the FINEP Credit Facility. The first disbursement of approximately R$1.8 million (approximately US$0.9 million based on the exchange rate as of December 31, 2012) was received in February 2011. The remaining balance totaling approximately R$4.6 million (approximately US$2.2 million based on exchange rate as December 31, 2012) was received in December 2012 in three equal disbursements of approximately R$1.6 million (approximately US$0.8 million based on exchange rate as of December 31, 2012). As of December 31, 2012, all available credit under this facility was fully drawn.

Interest on loans drawn under this credit facility is fixed at 5% per annum. In case of default under or non-compliance with the terms of the agreement, the interest on loans will be dependent on the long-term interest rate as published by the Central Bank of Brazil (“TJLP”). If the TJLP at the time of default is greater than 6%, then the interest will be 5% plus a TJLP adjustment factor, otherwise the interest will be at 11% per annum. In addition, a fine of up to 10% shall apply to the amount of any obligation in default. Interest on late balances will be 1% interest per month, levied on the overdue amount. Payment of the outstanding loan balance is being made in 81 monthly installments, which commenced in July 2012 and extends through March 2019. Interest on loans drawn and other charges are paid on a monthly basis and commenced in March 2011. As of December 31, 2012, the total outstanding loan balance under this credit facility was R$6.4 million (approximately US$3.1 million based on exchange rate as of December 31, 2012).

The FINEP Credit Facility contains the following significant terms and conditions:

• The Company would share with FINEP the costs associated with the FINEP Project. At a minimum, the Company would contribute from its own funds approximately R$14.5 million (approximately US$7.1 million based on the exchange rate as of December 31, 2012) of which R$11.1 million was to be contributed prior to the release of the second disbursement. As of December 31, 2012, all four disbursements were completed and for its part, the Company has fulfilled all of its cost sharing obligations;

• After the release of the first disbursement, prior to any subsequent drawdown from the FINEP Credit Facility, the Company was required to provide bank letters of guarantee of up to R$3.3 million in aggregate (approximately US$1.6 million based on the exchange rate as of December 31, 2012). On December 17, 2012 and prior to release of the second disbursement on December 26, 2012, the Company obtained the required bank letter of guarantees from Banco ABC Brasil, S.A.

• Amounts released from the FINEP Credit Facility must be completely used by the Company towards the FINEP Project within 30 months after the contract execution.

Revolving Credit Facility

In December 2010, the Company established a revolving credit facility with a financial institution that provided for loans and standby letters of credit of up to an aggregate principal amount of $10.0 million with a sublimit of $5.0 million on standby letters of credit. Interest on loans drawn under this revolving credit facility was equal to (i) the Eurodollar Rate plus 3.0%; or (ii) the Prime Rate plus 0.5%. In case of default or non-compliance with the terms of the agreement, the interest on loans was Prime Rate plus 2.0%. The credit facility was collateralized by a first priority security interest in certain of the Company's present and future assets. In April 2012, the Company repaid $7.7 million of its outstanding loans under the Credit Facility. In May 2012, the Company entered into a letter agreement with the bank amending the credit facility agreement to reduce the committed amount under the credit facility from $10.0 million to approximately $2.3 million, and the letters of credit sublimit from $5.0 million to approximately $2.3 million. The amendment also modified the current ratio covenant to require a ratio of current assets to current liabilities of at least $1.3:1 (as compared to 2:1 in the Credit Facility), and required the Company to maintain unrestricted cash of at least $15.0 million in its account with the Bank. In June 2012, the credit facility was terminated and, as of December 31, 2012, no loans or letters of credit were outstanding.

BNDES Credit Facility

In December 2011, the Company entered into a credit facility ("BNDES Credit Facility”) in the amount of R$22.4 million (approximately US$11.0 million based on the exchange rate at December 31, 2012) with Banco Nacional de Desenvolvimento Econômico e Social ('BNDES”), a government owned bank headquartered in Brazil. This BNDES facility was extended as project financing for a production site in Brazil. The credit line is divided into an initial tranche for up to approximately R$19.1 million reais and an additional tranche of approximately R$3.3 million that becomes available upon delivery of additional guarantees. The credit line is available for 12 months from the date of the Credit Facility, subject to extension by the lender.

The principal of the loans under the BNDES Credit Facility is required to be repaid in 60 monthly installments, with the first installment due in January 2013 and the last due in December 2017. Interest will be due initially on a quarterly basis with the first installment due in March 2012. From and after January 2013, interest payments will be due on a monthly basis together with principal payments. The loaned amounts carry interest of 7% per annum. Additionally, there is a credit reserve charge of 0.1% on the unused balance from each credit installment from the day immediately after it is made available through its date of use, when it is paid.

The BNDES Credit Facility is denominated in Brazilian reais. The BNDES Credit Facility is collateralized by a first priority security interest in certain of the Company's equipment and other tangible assets totaling R$24.9 million (approximately US$12.2 million based on the exchange rate as of December 31, 2012). The Company is a parent guarantor for the payment of the outstanding balance under the BNDES Credit Facility. Additionally, the Company is required to provide a bank guarantee equal to 10.0% of the total approved amount (R$22.4 million in total debt) available under this Credit Facility. For advances of the second tranche (above R$19.1 million), the Company is required to provide additional bank guarantees equal to 90.0% of each such advance, plus additional Company guarantees equal to at least 130.0% of such advance. The BNDES Credit Facility contains customary events of default, including payment failures, failure to satisfy other obligations under this credit facility or related documents, defaults in respect of other indebtedness, bankruptcy, insolvency and inability to pay debts when due, material judgments, and changes in control of Amyris Brasil. If any event of default occurs, the Lender may terminate its commitments and declare immediately due all borrowings under the facility. As of December 31, 2012 the Company had R$19.1 million (approximately US$9.3 million based on the exchange rate as of December 31, 2012) in outstanding advances under the BNDES Credit Facility.

Notes Payable

During the period between May 2008 and October 2008, the Company entered into notes payable agreements with the lessor of its headquarters under which it borrowed a total of $3.3 million for the purchase of tenant improvements, bearing an interest rate of 9.5% per annum and to be repaid over a period of 55 to 120 months. As of December 31, 2012 and 2011, a principal amount of $1.6 million and $2.0 million, respectively, was outstanding under these notes payable.

In connection with the operating lease for its headquarters (see Note 5) in Emeryville, California, the Company elected to defer a portion of it's monthly base rent due under the lease. In June 2011, a deferred rent obligation of $1.5 million resulting from this election became due and payable in 24 equal monthly installments of approximately $63,000. As such, the Company reclassified this obligation from Other Liabilities to Notes Payable. In June 2012, the Company paid off the outstanding notes payable balance. As of December 31, 2012 and 2011, a principal amount of zero and $1.1 million, respectively, was outstanding under this note payable.

Convertible Notes

In February 2012, the Company completed the sale of senior unsecured convertible promissory notes in an aggregate principal amount of $25.0 million pursuant to a Securities Purchase Agreement, between the Company and certain investment funds affiliated with Fidelity Investments Institutional Services Company, Inc. The offering consisted of the sale of 3.0% senior unsecured convertible promissory notes with a March 1, 2017 maturity date and an initial conversion price equal to $7.0682 per share of the Company's common stock, subject to adjustment for proportional adjustments to outstanding common stock and anti-dilution provisions in case of dividends and distributions. As of December 31, 2012, the notes were convertible into an aggregate of up to 3,536,968 shares of common stock. The note holders have a right to require repayment of 101% of the principal amount of the notes in an acquisition of the Company, and the notes provide for payment of unpaid interest on conversion following such an acquisition if the note holders do not require such repayment.  The securities purchase agreement and notes include covenants regarding payment of interest, maintaining the Company's listing status, limitations on debt, maintenance of corporate existence, and filing of SEC reports. The notes include standard events of default resulting in acceleration of indebtedness, including failure to pay, bankruptcy and insolvency, cross-defaults, material adverse effect clauses and breaches of the covenants in the securities purchase agreement and notes, with default interest rates and associated cure periods applicable to the covenant regarding SEC reporting. Furthermore, the senior unsecured convertible notes include restrictions on the amount of debt the Company is permitted to incur. The Company's total outstanding debt at any time can not exceed the greater of $200.0 million or 50% of its consolidated total assets and its secured debt cannot exceed the greater of $125 million or 30% of its consolidated total assets.

Related Party Convertible Notes

In July 30, 2012, the Company entered into a further amendment of the collaboration agreement with Total that expanded Total's investment in the biofene collaboration, incorporated the development of certain joint venture products for use in diesel and jet fuel into the scope of the collaboration, and changed the structure of the funding from Total to include a convertible debt mechanism (see Note 9).

The purchase agreement for the notes related to the funding from Total provides for the sale of an aggregate of $105.0 million in notes as follows:

• As part of an initial closing under the purchase agreement (which initial closing was completed in two installments), (i) on July 30, 2012, the Company sold a 1.5% Senior Unsecured Convertible Note Due 2017 to Total in the face amount of $38.3 million, including $15.0 million in new funds and $23.3 million in previously-provided diesel research and development funding by Total, and (ii) on September 14, 2012, the Company sold another note (in the same form) for $15.0 million in new funds from Total.

• The purchase agreement provides that additional notes may be sold in subsequent closings in July 2013 (for cash proceeds to the Company of $30.0 million) and July 2014 (for cash proceeds to the Company of $21.7 million, which would be settled in an initial installment of $10.85 million payable at such closing and a second installment of $10.85 million payable in January 2015).

The notes each have a March 1, 2017 maturity date and an initial conversion price equal to $7.0682 per share of the Company's common stock. The notes bear interest of 1.5% per annum (with a default rate of 2.5%), accruing from the date of funding and payable at maturity or on conversion or a change of control where Total exercises the right to require the Company to repay the notes. Accrued interest is canceled if the notes are canceled based on a “Go” decision.

The notes become convertible into the Company's common stock (i) within 10 trading days prior to maturity (if they are not canceled as described above prior to their maturity date), (ii) on a change of control of the Company, (iii) if Total is no longer the largest stockholder of the Company following a “No-Go” decision (subject to a six-month lock-up with respect to any shares of common stock issued upon conversion), and (iv) on a default by the Company. If Total makes a final “Go” decision, then the notes will be exchanged by Total for equity interests in the Fuels JV, after which the notes will not be convertible and any obligation to pay principal or interest on the notes will be extinguished. If Total makes a “No-Go” decision, outstanding notes will remain outstanding and become payable at maturity.

In connection with the Private Placement that occurred on December 24, 2012, Total elected to participate in the Private Placement by exchanging approximately $5.0 million of its $53.3 million in senior unsecured convertible promissory notes into 1,677,852 of the Company's common stock at $2.98 per share. As such, $5.0 million of the outstanding $53.3 million in senior unsecured convertible promissory notes was cancelled. The cancellation of the debt was treated as an extinguishment of debt in accordance with the guidance outlined in AS 470-50.

The conversion price of the notes is subject to adjustment for proportional adjustments to outstanding common stock and under anti-dilution provisions in case of certain dividends and distributions. Total has a right to require repayment of 101% of the principal amount of the notes in the event of a change of control of the Company and the notes provide for payment of unpaid interest on conversion following such a change of control if Total does not require such repayment. The purchase agreement and notes include covenants regarding payment of interest, maintenance of the Company's listing status, limitations on debt, maintenance of corporate existence, and filing of SEC reports. The notes include standard events of default resulting in acceleration of indebtedness, including failure to pay, bankruptcy and insolvency, cross-defaults, and breaches of the covenants in the purchase agreement and notes, with added default interest rates and associated cure periods applicable to the covenant regarding SEC reporting. Furthermore, the senior unsecured convertible notes include restrictions on the amount of debt the Company is permitted to incur. The Company's total outstanding debt at any time can not exceed the greater of $200.0 million or 50% of its consolidated total assets and its secured debt cannot exceed the greater of $125.0 million or 30% of its consolidated total assets.

Loans Payable

In December 2009, the Company entered into a loans payable agreement with the lessor of its Emeryville pilot plant under which it borrowed a total of $250,000, bearing an interest rate of 10.0% per annum and to be repaid over a period of 96 months. As of December 31, 2012 and 2011, a principal amount of $177,000 and $204,000, respectively, was outstanding under the loan.

In December 2011, the Company entered into a loan agreement with Banco Pine under which Banco Pine provided the Company with a short term loan of R$35.0 million (approximately US$17.1 million based on the exchange rate as of December 31, 2012). Such loan was an advance on an anticipated July 2012 financing from Nossa Caixa Desenvolvimento, ("Nossa Caixa"), the Sao Paulo State development bank, and Banco Pine, under which Banco Pine and Nossa Caxia would provide the Company with loans of up to approximately R$52.0 million (approximately US$25.4 million based on the exchange rate as of December 31, 2012) as financing for capital expenditures relating to the Company's manufacturing facility in Brotas. The interest rate for the loan was 119.2% of the Brazilian interbank lending rate (approximately 12.3% on an annualized basis). The principal and interest due on the principal under the loan agreement, as amended, matured and was repaid on August 15, 2012.

In June 2012, the Company entered into a separate loan agreement with Banco Pine under which Banco Pine provided the Company with a short-term bridge loan of R$52.0 million (approximately US$25.4 million based on the exchange rate as of December 31, 2012). The bridge loan was an additional advance on the anticipated Banco Pine and Nossa Caixa financing described above. The interest rate for the bridge loan was 0.4472% monthly (approximately 5.5% on an annualized basis). The principal and interest due under the bridge loan matured and were required to be repaid on September 19, 2012, subject to extension by Banco Pine. The bridge loan was in addition to the R$35.0 million short term loan to the Company described above. At the time of this bridge loan, the Company entered into a currency interest rate swap arrangement with the lender for R$22.0 million (approximately US$10.8 million based on the exchange rate as of December 31, 2012). The interest rate swap arrangement exchanged the principal and interest payments under the Banco Pine loan of R$22.0 million entered into in July 2012 for alternative principal and interest payments that were subject to adjustment based on fluctuations in the foreign exchange rate between the U.S. dollar and Brazilian real. The swap had a fixed interest rate of 3.94%.

In July 2012, the Company entered into a Note of Bank Credit and a Fiduciary Conveyance of Movable Goods agreements with each of Nossa Caixa and Banco Pine. Under these agreements, the Company's total acquisition cost for the farnesene production assets pledged as collateral is approximately R$68.0 million (approximately US$33.3 million based on the exchange rate as of December 31, 2012). The Company is a also a parent guarantor for the payment of the outstanding balance under these loan agreements.

Under such instruments, the Company could borrow an aggregate of R$52.0 million (approximately US$25.4 million based on the exchange rate as of December 31, 2012) as financing for capital expenditures relating to the Company's manufacturing facility in Brotas.  Under the loan agreements, Banco Pine, agreed to lend R$22.0 million and Nossa Caixa agreed to lend R$30.0 million.  The funds for the loans are provided by Banco Nacional de Desenvolvimento Econômico e Social ("BNDES"), but are guaranteed by the lenders. The loans have a final maturity date of July 15, 2022 and bear a fixed interest rate of 5.5% per year.  For the first two years that the loans are outstanding, the Company is required to pay interest only on a quarterly basis.  After August 15, 2014, the Company is required to pay equal monthly installments of both principal and interest for the remainder of the term of the loans. In July 2012, the Company repaid the outstanding bridge loans of R$52.0 million and R$35.0 million from Banco Pine.

In October 2012, the Company entered into a loans payable agreement with a lender under which it borrowed $0.6 million to pay the insurance premiums of certain schedule of policies. The loan is payable in nine monthly installments of principal and interest. Interest accrues at a rate of 3.24% per annum. As of December 31, 2012, the outstanding unpaid loan balance was $0.4 million.

Letters of Credit

In November 2008, the Company entered into the Credit Agreement with a financial institution to finance the purchase and sale of fuel and for working capital requirements, as needed. In October 2009, the agreement was amended to decrease the maximum amount that the Company may borrow under such facility. The Credit Agreement, as amended, provided, as of March 31, 2012, for an aggregate maximum availability up to the lower of $20.0 million and the borrowing base as defined in the agreement, and was subject to a sub-limit of $5.7 million for the issuance of letters of credit and a sub-limit of $20.0 million for short-term cash advances for product purchases. The Credit Agreement was collateralized by a first priority security interest in certain of the Company’s present and future assets. The Company was a parent guarantor for the payment of the outstanding balance under the Credit Agreement. Outstanding advances bore an interest rate at the Company’s option of the bank’s prime rate plus 1.0% or the bank’s cost of funds plus 3.5%. In April 2012, the Company, entered into an Amendment to the credit agreement, effective as of April 14, 2012 to extend the maturity date pending the Company's transition out of its ethanol and reformulated ethanol-blended gasoline business, and its plan to repay all amounts remaining outstanding under the Credit Agreement, and terminate the Credit Agreement as of the new maturity date. As of December 31, 2012, the Credit Agreement was terminated. As of December 31, 2012 and 2011, the Company had no outstanding advances and had zero and $5.0 million, respectively, in outstanding letters of credit under the Credit Agreement.

In June 2012, the Company entered into a letter of credit agreement for $1.0 million under which it provided a letter of credit to the landlord for its headquarters in Emeryville, California in order to cover the security deposit on the lease. The letter of credit is secured by a certificate of deposit. Accordingly, the Company recorded $1.0 million as restricted cash as of December 31, 2012.

Future minimum payments under the debt agreements as of December 31, 2012 are as follows (in thousands):

Years ending December 31:	Related Party Convertible Debt			Convertible Debt			Notes Payable			Loans Payable			Credit Facility
2013	$	—		$	760		$	351		$	1,958		$	3,175
2014	—			760			379			2,970			2,926
2015	—			765			379			4,456			2,774
2016	—			760			381			4,286			2,623
2017	51,627			25,125			384			4,110			2,393
Thereafter	—			—			154			16,426			612
Total future minimum payments	51,627			28,170			2,028			34,206			14,503
Less: amount representing interest	(12,594		)	(3,170		)	(456		)	(8,056		)	(2,094		)
Present value of minimum debt payments	39,033			25,000			1,572			26,150			12,409
Less: current portion	—			—			(311		)	(556		)	(2,458		)
Noncurrent portion of debt	$	39,033		$	25,000		$	1,261		$	25,594		$	9,951

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Noncontrolling Interest

12 Months Ended

Dec. 31, 2012

Noncontrolling Interest [Abstract]

Noncontrolling Interest

Noncontrolling Interest

Redeemable Noncontrolling Interest

In December 2009, Amyris Brasil sold 1,111,111 of its shares representing a 4.8% interest in Amyris Brasil for R$10.0 million. The redeemable noncontrolling interest was reported in the mezzanine equity section of the consolidated balance sheet because the Company was then subject to a contingent put option under which it could have been required to repurchase an interest in Amyris Brasil from the noncontrolling interest holder.

In March 2010, Amyris Brasil sold an additional 853,333 shares of its stock, an incremental 3.4% interest, for R$3.0 million. In May 2010, Amyris Brasil sold an additional 1,111,111 shares of its stock, an incremental 4.07% interest, for R$10.0 million.

Under the terms of the agreements with these Amyris Brasil investors, the Company had the right to require the investors to convert their shares of Amyris Brasil into shares of the Company's common stock at a 1:0.28 conversion ratio. On September 30, 2010, in connection with the Company’s IPO, shares of Amyris Brasil held by these investors were converted into 861,155 shares of the Company’s common stock. The remaining noncontrolling interest as of September 30, 2010 was converted to common stock and additional paid-in capital.

At the closing of the IPO, the Company recorded a one-time beneficial conversion feature charge of $2.7 million associated with the conversion of the shares of Amyris Brasil held by investors into shares of Amyris, Inc. common stock, which impacted earnings per share for the year ended December 31, 2010.

The following table provides a roll forward of the redeemable noncontrolling interest (in thousands):

Balance as of December 31, 2009	$	5,506
Proceeds from redeemable noncontrolling interest	7,041
Conversion of shares of Amyris Brasil S.A. subsidiary held by third parties into common stock	(11,870		)
Foreign currency translation adjustment	217
Net loss	(894		)
Balance as of December 31, 2010	$	—

Noncontrolling Interest

SMA Indústria Química

The joint venture, SMA (see Note 7), is a VIE pursuant to the accounting guidance for consolidating VIEs because the amount of total equity investment at risk is not sufficient to permit SMA to finance its activities without additional subordinated financial support, as well as because the related commercialization agreement provides a substantive minimum price guarantee. Under the terms of the joint venture agreement, Amyris directs the design and construction activities, as well as production and distribution. In addition, Amyris has the obligation to fund the design and construction activities until commercialization is achieved. Subsequent to the construction phase, both parties equally fund SMA for the term of the joint venture. Based on those factors, the Company was determined to have the power to direct the activities that most significantly impact SMA’s economic performance and the obligation to absorb losses and the right to receive benefits. Accordingly, the financial results of SMA are included in the Company’s consolidated financial statements and amounts pertaining to Usina São Martinho’s interest in SMA are reported as noncontrolling interests in subsidiaries.

Glycotech

In January 2011, the Company entered into a production service agreement with Glycotech, whereby Glycotech is to provide process development and production services for the manufacturing of various Company products at its leased facility in Leland, North Carolina. The Company products to be manufactured by Glycotech will be owned and distributed by the Company. Pursuant to the terms of the agreement, the Company is required to pay the manufacturing and operating costs of the Glycotech facility which is dedicated solely to the manufacture of Amyris products. The initial term of the agreement is for a two year period commencing on February 1, 2011 and will renew automatically for successive one-year terms, unless terminated by the Company. On the same date as the production service agreement, the Company also entered into a right of first refusal agreement with the lessor of the facility and site leased by Glycotech covering a two year period commencing in January 2011. Per the terms of the right of first refusal agreement, the lessor agreed not to sell the facility and site leased by Glycotech during the term of the production service agreement. In the event that the lessor is presented with an offer to sell or decides to sell an adjacent parcel, the Company has the right of first refusal to acquire it.

The Company has determined that the arrangement with Glycotech qualifies as a VIE. The Company determined that it is the primary beneficiary of this arrangement since it has the power through the management committee over which it has majority control to direct the activities that most significantly impact Glycotech's economic performance. In addition, the Company is required to fund 100% of Glycotech's actual operating costs for providing services each month while the facility is in operation under the production service agreement. Accordingly, the Company consolidates the financial results of Glycotech. As of December 31, 2012, the carrying amounts of the consolidated VIE's assets and liabilities were not material to the Company's consolidated financial statements.

The table below reflects the carrying amount of the assets and liabilities of the two consolidated VIEs for which the Company is the primary beneficiary. The assets include $24.7 million in property, plant and equipment and $4.5 million in other assets, and $0.4 million in current assets. The liabilities include $0.3 million in accounts payable and accrued current liabilities and $0.1 million in loan obligations by Glycotech to its shareholders that are non-recourse to the Company. The creditors of each consolidated VIE have recourse only to the assets of that VIE.

	December 31,
(In thousands)	2012		2011
Assets	$	29,564	$	22,094
Liabilities	$	355	$	2,873

The change in noncontrolling interest for the years ended December 31, 2012 and 2011 is summarized below (in thousands):

	2012			2011
Balance at January 1	$	(240	)	$	2
Addition to noncontrolling interest	—			369
Foreign currency translation adjustment	257			30
Loss attributable to noncontrolling interest	(894		)	(641		)
Balance at December 31	$	(877	)	$	(240	)

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Commitments and Contingencies (Details) (USD $) In Thousands, unless otherwise specified	Dec. 31, 2012	Dec. 31, 2011
Present Value of Future Minimum Lease Payments, Sale Leaseback Transactions [Abstract]
2013	$ 1,098
2014	1,007
2015	289
2016	0
2017	0
Thereafter	0
Total future minimum lease payments	2,394
Less: amount representing interest	(168)
Present value of minimum lease payments	2,226
Less: current portion	(982)
Long-term portion	1,244
Capital Leases, Future Minimum Payments Due [Abstract]
2013	1,489
2014	1,007
2015	289
2016	0
2017	0
Thereafter	0
Total future minimum lease payments	2,785
Less: amount representing interest	(175)
Present value of minimum lease payments	2,610
Less: current portion	(1,366)	(3,717)
Long-term portion	1,244	2,619
Operating Leases, Future Minimum Payments Due, Fiscal Year Maturity [Abstract]
2013	6,624
2014	6,772
2015	6,900
2016	6,891
2017	6,760
Thereafter	4,342
Total future minimum lease payments	38,289
Operating Leases - Facilities [Member]
Operating Leases, Future Minimum Payments Due, Fiscal Year Maturity [Abstract]
2013	6,463
2014	6,610
2015	6,738
2016	6,729
2017	6,598
Thereafter	2,786
Total future minimum lease payments	35,924
Operating Leases - Land [Member]
Operating Leases, Future Minimum Payments Due, Fiscal Year Maturity [Abstract]
2013	161
2014	162
2015	162
2016	162
2017	162
Thereafter	1,556
Total future minimum lease payments	$ 2,365

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Stockholders' Equity (Details) (USD $)	12 Months Ended					0 Months Ended	1 Months Ended		0 Months Ended	1 Months Ended
	Dec. 31, 2012 votes	Dec. 31, 2011	Dec. 31, 2010	Sep. 30, 2010	Sep. 30, 2010 Convertible Preferred Stock [Member] series	Dec. 24, 2012 Private Placement [Member]	May 31, 2012 Private Placement [Member]	Feb. 29, 2012 Private Placement [Member]	Dec. 24, 2012 Private Placement [Member] Common Stock [Member]	May 31, 2012 Private Placement [Member] Common Stock [Member]	Feb. 29, 2012 Private Placement [Member] Common Stock [Member]	Oct. 31, 2010 IPO [Member]	Sep. 30, 2010 IPO [Member]	Sep. 30, 2010 IPO [Member] Common Stock [Member]	Dec. 24, 2012 Convertible Notes Payable [Member] Private Placement [Member]	Dec. 24, 2012 Commitment Fulfilled [Member] Private Placement [Member]
Class of Stock [Line Items]
Stock issued during period, shares									14,177,849	1,736,100	10,160,325			5,300,000
Stock Issued During Period, Price Per Share, New Issues						$ 2.98	$ 2.36	$ 5.78
Stock Issued During Period, Value, New Issues	$ 89,682,000						$ 4,100,000	$ 58,700,000
Proceeds from Issuance of Private Placement, First Payment Received						22,200,000
Extinguishment of Debt, Common Stock, Shares															1,677,852.00
Proceeds from Issuance of Private Placement	84,682,000	0	0			37,200,000
Commitment to purchase company common stock								15,000,000								10,000,000
Offering price per share													$ 16.00
Proceeds from Issuance Initial Public Offering													73,700,000
Underwriting Discounts													(5,900,000)
Offering Costs													(5,200,000)
Convertible preferred stock shares converted into common stock shares													31,550,277
Conversion Of Preferred Stock Warrant To Common Stock Warrant Shares													195,604
Conversion of Stock, Shares Issued													861,155
Number of Additional Shares Sold to Underwriters Pursuant To Over Allotment Option												795,000
Proceeds from Issuance or Sale of Equity												$ 11,800,000
Common stock, shares authorized	100,000,000	100,000,000		100,000,000
Common Stock, Number of Votes Entitled to Holder of each share	1
Preferred stock, shares authorized	5,000,000	5,000,000		5,000,000
Number of Series Of Stock Outstanding					4
Preferred stock, shares outstanding	0	0

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Commitments and Contingencies Operating Lease Textuals (Details) (USD $)	12 Months Ended			1 Months Ended			12 Months Ended	1 Months Ended	12 Months Ended	1 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010	May 31, 2008 Building Operating Lease [Member]	Dec. 31, 2010 Building Operating Lease [Member]	Oct. 31, 2010 Building Operating Lease [Member] sqft	Dec. 31, 2012 Building Operating Lease [Member] Amyris US [Member]	Aug. 31, 2011 Building Operating Lease [Member] Amyris Brasil S.A. Subsidiary [Member]	Dec. 31, 2012 Building Operating Lease [Member] Amyris Brasil S.A. Subsidiary [Member]	Feb. 28, 2011 Land and Land Improvements Operating Leases [Member] Corporate Joint Venture [Member] SMA Industria Quimica S.A. [Member]	Jan. 31, 2011 Right of First Refusal Glycotech [Member] Glycotech [Member]	Feb. 28, 2011 Gea [Member] Equipment [Member]	Mar. 31, 2011 Paraiso Bioenergia Sa Agreement [Member] Land and Land Improvements Operating Leases [Member]
Operating Leased Assets [Line Items]
Estimated Annual Rent Expense Operating Leases							$ 6,200,000	$ 367,000	$ 600,000	$ 46,000			$ 116,000
Incentive from Lessor				11,400,000
Square Footage of Real Estate Property						22,000
Cash Received From Lessor Amended Lease Agreement Operating Lease					1,000,000
Operating Leases, Rent Expense	$ 4,900,000	$ 4,800,000	$ 3,300,000
Commencement Period of Agreement											2 years
Period of Lease Term				10 years				5 years		20 years		1 year	15 years

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Income Taxes - Uncertain Tax Benefits (Details) (USD $)	12 Months Ended
	Dec. 31, 2012	Dec. 31, 2011
Reconciliation of Unrecognized Tax Benefits, Excluding Amounts Pertaining to Examined Tax Returns [Roll Forward]
Beginning balance	$ 3,103,000	$ 1,734,000
Increases in tax positions for prior period	82,000	0
Increases in tax position during current period	733,000	1,369,000
Ending balance	3,918,000	3,103,000
Unrecognized Tax Benefits that Would Impact Effective Tax Rate	$ 0

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Balance Sheet Components Other Liabilities (Details) (USD $)					1 Months Ended	0 Months Ended		1 Months Ended
	Dec. 31, 2012		Dec. 31, 2011		Jun. 30, 2010 Total Gas And Power USA Biotech Agreement [Member]	Jul. 30, 2012 November 2011 Amendment Collaborator Agreement [Member] Total Gas And Power USA Biotech Agreement [Member]	Nov. 30, 2011 November 2011 Amendment Collaborator Agreement [Member] Total Gas And Power USA Biotech Agreement [Member]	Jun. 30, 2010 November 2011 Amendment Collaborator Agreement [Member] Total Gas And Power USA Biotech Agreement [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Research and Development Arrangement, Funding From Collaborator to Offset Costs Incurred, First Additional Amount							$ 30,000,000
Research and Development Arrangement Funding From Collaborator to Offset Costs Incurred					50,000,000			50,000,000
Research and Development Arrangement Funding From Collaborator to Offset Costs Incurred, Second Additional Amount							10,000,000
Research and Development Arrangement Funding From Collaborator to Offset Costs Incurred, Third Additional Amount							10,000,000
Agreement to Fund, Percentage of All Remaining Research and Development Costs							50.00%
Collaborator Agreement Notification Period from the Completion of Renewable Diesel Program							90 days
Aggregate Amount of Payments Paid In Order to End Royalty Obligation							150,000,000
Research and Development Arrangement, Royalty, Percentage of Net Income Paid to Collaborator							20.00%
Research and Development Arrangement, Royalty, Percentage of Net Proceeds From Sale, Up To Remaining Unpaid Amount							50.00%
Research And Development Advances from Collaborator No Longer Contingently Repayable And Recorded As Contract To Perform Services						23,300,000
Research and Development Service Contract						23,200,000
Research And Development Reduced Capitalized Deferred Charge Asset						14,400,000
Revenue from Related Parties						8,900,000
Other Liabilities, Noncurrent [Abstract]
Contingently repayable advance from related party collaborator	0	[1]	31,922,000	[1]		46,500,000
Bonus payable to contract manufacturer, non-current	0		2,500,000
Contractual obligations to contract manufacturers, non-current	4,000,000		0
Fair market value of swap obligations	1,367,000		0
Asset retirement obligations	0		1,129,000
Fair value of compound embedded derivative liability	7,894,000	[2]	0	[2]
Other	2,672,000		1,534,000
Total other liabilities	$ 15,933,000		$ 37,085,000

[1] The contingently repayable advance from related party collaborator as of December 31, 2011 relates to the collaboration agreement between the Company and Total.

[2] The compound embedded derivative liability represents the fair value of the equity conversion feature and a "make-whole" feature of the outstanding senior unsecured convertible promissory notes issued to Total.

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Stock-Based Compensation Plans - Nonemployee Stock-Based Compensation (Details) (USD $) In Thousands, except Share data, unless otherwise specified	12 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Stock Options [Member] | Non Employee Share Based Compensation [Member]
Share-based Goods and Nonemployee Services Transaction [Line Items]
Share-based Compensation Arrangement by Share-based Payment Award, Options, Grants in Period, Gross	3,000	15,000	101,000
Share-based Compensation Arrangement by Share-based Payment Award, Compensation Cost	$ 86	$ 797	$ 834
Expected dividend yield	0.00%	0.00%	0.00%
Risk-free interest rate	1.40%	2.10%	3.20%
Expected term (in years)	7 years 0 months 4 days	7 years 9 months 29 days	8 years 7 months 6 days
Expected volatility	77.00%	86.00%	95.00%
Restricted Stock Units (RSUs) [Member]
Share-based Goods and Nonemployee Services Transaction [Line Items]
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Grants in Period	2,966,900
Restricted Stock Units (RSUs) [Member] | Non Employee Share Based Compensation [Member]
Share-based Goods and Nonemployee Services Transaction [Line Items]
Share-based Compensation Arrangement by Share-based Payment Award, Compensation Cost	$ 58	$ 101	$ 1,800
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Grants in Period	10,000	32,855	126,272

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Noncontrolling Interest (Tables)

12 Months Ended

Dec. 31, 2012

Noncontrolling Interest [Abstract]

Redeemable Noncontrolling Interest [Table Text Block]

The following table provides a roll forward of the redeemable noncontrolling interest (in thousands):

Balance as of December 31, 2009	$	5,506
Proceeds from redeemable noncontrolling interest	7,041
Conversion of shares of Amyris Brasil S.A. subsidiary held by third parties into common stock	(11,870		)
Foreign currency translation adjustment	217
Net loss	(894		)
Balance as of December 31, 2010	$	—

Schedule of Variable Interest Entities [Table Text Block]

The table below reflects the carrying amount of the assets and liabilities of the two consolidated VIEs for which the Company is the primary beneficiary. The assets include $24.7 million in property, plant and equipment and $4.5 million in other assets, and $0.4 million in current assets. The liabilities include $0.3 million in accounts payable and accrued current liabilities and $0.1 million in loan obligations by Glycotech to its shareholders that are non-recourse to the Company. The creditors of each consolidated VIE have recourse only to the assets of that VIE.

	December 31,
(In thousands)	2012		2011
Assets	$	29,564	$	22,094
Liabilities	$	355	$	2,873

Noncontrolling Interest [Table Text Block]

The change in noncontrolling interest for the years ended December 31, 2012 and 2011 is summarized below (in thousands):

	2012			2011
Balance at January 1	$	(240	)	$	2
Addition to noncontrolling interest	—			369
Foreign currency translation adjustment	257			30
Loss attributable to noncontrolling interest	(894		)	(641		)
Balance at December 31	$	(877	)	$	(240	)

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Summary of Significant Accounting Policies Basic and Diluted Net Loss Per Share (Details) (USD $) In Thousands, except Share data, unless otherwise specified	12 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Numerator:
Net loss attributable to Amyris, Inc. common stockholders	$ (205,139)	$ (178,870)	$ (123,879)
Denominator:
Weighted-average shares of common stock outstanding used in computing net loss per share of common stock, basic and diluted	56,717,869	44,799,056	14,840,253
Net loss per share attributable to common stockholders, basic and diluted	$ (3.62)	$ (3.99)	$ (8.35)

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Employee Benefit Plan

12 Months Ended

Dec. 31, 2012

Compensation and Retirement Disclosure [Abstract]

Employee Benefit Plan

Employee Benefit Plan

The Company established a 401(k) Plan to provide tax deferred salary deductions for all eligible employees. Participants may make voluntary contributions to the 401(k) Plan up to 90% of their eligible compensation, limited by certain Internal Revenue Service restrictions. The Company does not match employee contributions.

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Subsequent Events

12 Months Ended

Dec. 31, 2012

Subsequent Events [Abstract]

Subsequent Events

Subsequent Events

Evergreen Shares for 2010 Equity Plan and 2010 ESPP

On January 23, 2013, the Company's Board of Directors approved the additional shares which will be available for issuance under the 2010 Equity Plan and the 2010 ESPP. These shares represent an automatic increase in the number of shares available for issuance under the 2010 Equity Plan and the 2010 ESPP of 3,435,483 and 687,096, respectively, equal to 5% and 1%, respectively of 68,709,660 shares, the total outstanding shares of the Company’s common stock as of December 31, 2012. This automatic increase was effective as of January 1, 2013. Shares available for issuance under the 2010 Equity Plan and 2010 ESPP were initially registered on a registration statement on Form S-8 filed with the Securities and Exchange Commission on October 1, 2010 (Registration No. 333-169715). The Company intends to file a registration statement on Form S-8 with respect to a portion of the shares added by the automatic increase on January 1, 2013 following the filing of its annual report on Form 10-K.

Proceeds from December 2012 Private Placement

On January 11, 2013, the Company received the remaining $15.0 million of proceeds from the private placement offering that closed in December 2012. Consequently, the Company issued 5,033,557 shares of the Company's common stock to an investor on that date.

Firmenich Agreement

On March 13, 2013, the Company entered into a Master Collaboration Agreement (the “Agreement”) with Firmenich to establish a collaboration for the development and commercialization of multiple renewable flavors and fragrances ("F&F") compounds. Under this Agreement, except for rights granted under preexisting collaboration relationships, the Company is granting Firmenich exclusive access for such compounds to specified Company intellectual property for the development and commercialization of F&F products in exchange for research and development funding and a profit sharing arrangement. The Agreement supersedes and expands a prior collaboration agreement between the Company and Firmenich as described in Note 9.

The Agreement provides annual, up-front funding to the Company by Firmenich of $10.0 million for each of the first three years of the collaboration. The initial payment of $10.0 million was received by the Company on March 27, 2013. The Agreement contemplates additional funding by Firmenich on a discretionary basis and up to $5.0 million in milestone payments from Firmenich to the Company. In addition, the Agreement contemplates that the parties will mutually agree on a supply price for each compound and share product margins from sales of each compound on a 70/30 basis (70% for Firmenich) until Firmenich receives $15.0 million more than the Company in the aggregate, after which the parties will share 50/50 in the product margins on all compounds. The Company also agreed to pay a one-time success bonus of up to $2.5 million to Firmenich for outperforming certain commercialization targets.

The Agreement does not impose any specific research and development commitments on either party after year six, but if the parties mutually agree to perform development after year six, the Agreement provides that the parties will fund it equally.

Under the Agreement, the parties jointly select target compounds, subject to final approval of compound specifications by Firmenich. During the development phase, the Company is required to provide labor, intellectual property and technology infrastructure and Firmenich is required to contribute downstream polishing expertise and market access. The Agreement provides that the Company will own research and development and strain engineering intellectual property, and Firmenich will own blending and, if applicable, chemical conversion intellectual property. Under certain circumstances such as the Company's insolvency, Firmenich gains expanded access to the Company's intellectual property. Following development of F&F compounds under the Agreement, the Agreement contemplates that Company will manufacture the initial target molecules for the compounds and Firmenich will perform any required downstream polishing and distribution, sales and marketing.

Export Financing with ABC Brasil

On March 18, 2013, the Company entered into an export financing agreement with Banco ABC Brasil S.A. (ABC Bank) for approximately US$2.5 million (approximately R$5.0 million based on exchange rate as of March 18, 2013) for a 1 year-term to fund exports through March 2014.

Letter Agreement with Total

As of March 24, 2013, the Company entered into a letter agreement with Total under which Total agreed to waive its right to cease its participation in our fuels collaboration at the July 2013 decision point referenced above under Note 9 - “Significant Agreements,” and committed to proceed with the July 2013 funding tranche of $30.0 million (subject to the Company's satisfaction of the relevant closing conditions for such funding in the securities purchase agreement).  As consideration for this waiver and commitment, the Company agreed to:

• Reduce the conversion price for the senior unsecured convertible promissory notes to be issued in connection with such funding from $7.0682 per share to a price per share equal to the greater of (i) the consolidated closing bid price of the Company's common stock on the date of the letter agreement, plus $0.01, and (ii) $3.08 per share, provided that the conversion price will not be reduced by more than the maximum possible amount permitted under the NASDAQ rules such that the new conversion price would require the Company to obtain stockholder consent; and

• Grant Total a senior security interest in the Company's intellectual property, subject to certain exclusions and subject to release by Total when the Company and Total enter into final documentation regarding the establishment of the Fuels JV.

In addition to the waiver by Total described above, Total also agreed that, at the Company's request and contingent upon the Company meeting its obligations described above, it would pay advance installments of the amounts otherwise payable at the July 2013 closing.  Specifically, if the Company requests such advance installments, subject to certain closing conditions and delivery of certifications regarding the Company's cash levels, Total is obligated to fund $10.0 million no later than May 15, 2013, and an additional $10.0 million no later than June 15, 2013, with the remainder funding on the original July 2013 closing date.

Biolding Follow-on Investment

On March 27, 2013, the Company completed a private placement of its common stock to Biolding for the issuance of 1,533,742 of its common stock at a price of $3.26 per share aggregate proceeds of approximately $5.0 million. This private placement represented the final tranche of Biolding's preexisting contractual obligation to fund $15.0 million upon satisfaction by the Company of certain criteria associated with the commissioning of a production plant in Brazil.

Joint Venture with Cosan

As of March 26, 2013, the Company and Cosan US, Inc. (“Cosan US”) entered into agreements to (i) expand their base oils joint venture to also include additives and lubricants and (ii) operate their joint venture exclusively through Novvi LLC. Specifically, the parties entered into an Amended and Restated Operating Agreement for Novvi LLC, which sets forth the governance procedures for Novvi LLC and the joint venture and the parties initial contribution, which for the Company are the licenses granted under the IP License Agreement. The Company also entered into an IP License Agreement with Novvi LLC under which the Company granted Novvi LLC (i) an exclusive (subject to certain limited exceptions for the Company), worldwide, royalty-free license to develop, produce and commercialize base oils, additives, and lubricants derived from Biofene for use in the automotive, commercial and industrial lubricants markets and (ii) a non-exclusive, royalty-free license, subject to certain conditions, to manufacture Biofene solely for its own products. In addition, both the Company and Cosan US granted Novvi LLC certain rights of first refusal with respect to alternative base oil and additive technologies that may be acquired by the Company or Cosan US during the term of the IP License Agreement. Under these agreements, the Company and Cosan US will each own 50% of Novvi LLC, and each party will share equally in any costs and any profits ultimately realized by the joint venture. The IP License Agreement has an initial term of 20 years from the date of the agreement, subject to standard early termination provisions such as uncured material breach or a party's insolvency.

In conjunction with the execution of the documents above, the Company, Amyris Brasil and Cosan are also entering into a termination of the Original JV Agreement.  In addition, Amyris Brasil agreed to sell, for a nominal amount, its 50% interest in the Novvi S.A. entity, a now-dormant company, to Cosan.  Following consummation of such sale, the Shareholders' Agreement between Amyris Brasil and Cosan with regard to Novvi S.A. will automatically terminate pursuant to its terms.

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Restructuring (Details) (USD $)	12 Months Ended	1 Months Ended		12 Months Ended
	Dec. 31, 2010	Aug. 31, 2009 2009 Restructuring Cost Structure Reduction [Member]	Aug. 31, 2009 2009 Restructuring Cost Structure Reduction [Member] Operating Lease Expense [Member]	Dec. 31, 2010 Exit Costs [Member]
Restructuring charges	$ 395,000		$ 5,400,000	$ 395,000
Asset impairments		3,100,000
Reversal related to deferred rent		2,700,000
Restructuring Reserve, Accrual Adjustment	$ (4,567,000)			$ (2,061,000)

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Summary of Significant Accounting Policies Income Taxes (Details) (Maximum [Member])	Dec. 31, 2012
Maximum [Member]
Income Tax Contingency [Line Items]
Uncertain Tax Position Not Recognized	50.00%

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Schedule II Valuation and Qualifying Accounts (Details) (USD $) In Thousands, unless otherwise specified	12 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Valuation Allowance of Deferred Tax Assets [Member]
Income Tax Valuation Allowance:
Balance at Beginning Period	$ 156,765	$ 76,071	$ 47,799
Additions	79,523	80,694	28,272
Write-off/Adjustments		0	0
Balance at End of Period	236,288	156,765	76,071
Allowance for Doubtful Accounts [Member]
Income Tax Valuation Allowance:
Balance at Beginning Period	245	0	0
Additions	236	245	0
Write-off/Adjustments	0	0	0
Balance at End of Period	$ 481	$ 245	$ 0

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The Company (Details)	3 Months Ended	12 Months Ended				12 Months Ended
	Mar. 31, 2012 USD ($)	Dec. 31, 2012 USD ($) Operating_Subsidiaries	Dec. 31, 2011 USD ($)	Mar. 18, 2013 Subsequent Event [Member] ABC Brasil Agreement [Member] USD ($)	Mar. 18, 2013 Subsequent Event [Member] ABC Brasil Agreement [Member] BRL	Dec. 31, 2012 Minimum [Member] USD ($)	Dec. 31, 2012 Maximum [Member] USD ($)
Number of Operating Subsidiaries		2
Loss Related to Adverse Purchase Commitments		$ 30,400,000
Facility Modification Costs Written Off	10,000,000
Production Assets Written Off	5,500,000
Expected Capital Expenditures During Next Fiscal Year		10,000,000
Proceeds from Debt and Equity Financing		193,600,000
Export Financing Agreement				2,500,000	5,000,000
Retained Earnings (Accumulated Deficit)		(586,327,000)	(381,188,000)
Cash, Cash Equivalents, and Short-term Investments		30,700,000
Long-term Debt		104,164,000	41,324,000
Debt, current portion		3,325,000	28,049,000
Contingency Cash Plan Savings Estimate During Next Fiscal Year						$ 35,000,000	$ 40,000,000

XML

Consolidated Statements of Comprehensive Loss (USD $) In Thousands, unless otherwise specified	12 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Net loss	$ (206,033)	$ (179,511)	$ (82,790)
Change in unrealized loss on investments	0	(5)	2
Foreign currency translation adjustment, net of tax	(6,626)	(8,761)	1,751
Total comprehensive loss	(212,659)	(188,277)	(81,037)
Loss attributable to noncontrolling interest	894	641	920
Foreign currency translation adjustment attributable to noncontrolling interest	(257)	(30)	(217)
Comprehensive loss attributable to Amyris, Inc.	$ (212,022)	$ (187,666)	$ (80,334)

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Stock-Based Compensation Plans - Stock Option Activity (Details) (USD $) In Thousands, except Share data, unless otherwise specified	12 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Share-based Compensation Arrangement by Share-based Payment Award, Options, Exercises in Period, Total Intrinsic Value	$ 2,700	$ 28,700	$ 934
Stock Options [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding, Number, Beginning Balance	8,377,016
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding, Weighted Average Exercise Price, Beginning Balance	$ 14.05
Share-based Compensation Arrangement by Share-based Payment Award, Options, Grants in Period, Net of Forfeitures	3,592,593
Share-based Compensation Arrangements by Share-based Payment Award, Options, Grants in Period, Weighted Average Exercise Price	$ 3.49
Share-based Compensation Arrangement by Share-based Payment Award, Options, Exercises in Period	(866,203)
Share-based Compensation Arrangements by Share-based Payment Award, Options, Exercises in Period, Weighted Average Exercise Price	$ 0.72
Share-based Compensation Arrangement by Share-based Payment Award, Options, Forfeitures in Period	(2,156,814)
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding, Number, Ending Balance	8,946,592	8,377,016
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding, Weighted Average Exercise Price, Ending Balance	$ 9.07	$ 14.05
Share-based Compensation Arrangements by Share-based Payment Award, Options, Forfeitures in Period, Weighted Average Exercise Price	$ 15.78
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding, Weighted Average Remaining Contractual Term	7 years 5 months 16 days	7 years 10 months 17 days
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding, Intrinsic Value	954	29,127
Share-based Compensation Arrangement by Share-based Payment Award, Options, Vested and Expected to Vest, Outstanding, Number	8,281,330
Share-based Compensation Arrangement by Share-based Payment Award, Options, Vested and Expected to Vest, Outstanding, Weighted Average Exercise Price	$ 9.18
Share-based Compensation Arrangement by Share-based Payment Award, Options, Vested and Expected to Vest, Outstanding, Weighted Average Remaining Contractual Term	7 years 3 months 11 days
Share-based Compensation Arrangement by Share-based Payment Award, Options, Vested and Expected to Vest, Outstanding, Aggregate Intrinsic Value	893
Share-based Compensation Arrangement by Share-based Payment Award, Options, Exercisable, Number	4,134,023
Share-based Compensation Arrangement by Share-based Payment Award, Options, Exercisable, Weighted Average Exercise Price	$ 9.94
Share-based Compensation Arrangement by Share-based Payment Award, Options, Exercisable, Weighted Average Remaining Contractual Term	5 years 9 months 22 days
Share-based Compensation Arrangement by Share-based Payment Award, Options, Exercisable, Intrinsic Value	$ 575
Stock Options [Member] | $0.10—$2.76
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range, Lower Range Limit	$ 0.10
Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range, Upper Range Limit	$ 2.76
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding, Number, Ending Balance	1,129,158
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding, Weighted Average Exercise Price, Ending Balance	$ 2.31
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding, Weighted Average Remaining Contractual Term	8 years 1 month 13 days
Share-based Compensation Arrangement by Share-based Payment Award, Options, Exercisable, Number	279,345
Share-based Compensation Arrangement by Share-based Payment Award, Options, Exercisable, Weighted Average Exercise Price	$ 1.06
Stock Options [Member] | $3.04—$3.55
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range, Lower Range Limit	$ 3.04
Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range, Upper Range Limit	$ 3.55
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding, Number, Ending Balance	768,990
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding, Weighted Average Exercise Price, Ending Balance	$ 3.12
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding, Weighted Average Remaining Contractual Term	9 years 8 months 19 days
Share-based Compensation Arrangement by Share-based Payment Award, Options, Exercisable, Number	10,936
Share-based Compensation Arrangement by Share-based Payment Award, Options, Exercisable, Weighted Average Exercise Price	$ 3.13
Stock Options [Member] | $3.86—$3.86
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range, Lower Range Limit	$ 3.86
Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range, Upper Range Limit	$ 3.86
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding, Number, Ending Balance	1,424,649
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding, Weighted Average Exercise Price, Ending Balance	$ 3.86
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding, Weighted Average Remaining Contractual Term	8 years 10 months 10 days
Share-based Compensation Arrangement by Share-based Payment Award, Options, Exercisable, Number	296,482
Share-based Compensation Arrangement by Share-based Payment Award, Options, Exercisable, Weighted Average Exercise Price	$ 3.86
Stock Options [Member] | $3.93 to $3.93
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range, Lower Range Limit	$ 3.93
Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range, Upper Range Limit	$ 3.93
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding, Number, Ending Balance	1,198,288
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding, Weighted Average Exercise Price, Ending Balance	$ 3.93
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding, Weighted Average Remaining Contractual Term	3 years 10 months 10 days
Share-based Compensation Arrangement by Share-based Payment Award, Options, Exercisable, Number	1,152,673
Share-based Compensation Arrangement by Share-based Payment Award, Options, Exercisable, Weighted Average Exercise Price	$ 3.93
Stock Options [Member] | $4.06—$9.32
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range, Lower Range Limit	$ 4.06
Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range, Upper Range Limit	$ 9.32
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding, Number, Ending Balance	1,351,331
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding, Weighted Average Exercise Price, Ending Balance	$ 6.37
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding, Weighted Average Remaining Contractual Term	6 years 9 months 18 days
Share-based Compensation Arrangement by Share-based Payment Award, Options, Exercisable, Number	799,576
Share-based Compensation Arrangement by Share-based Payment Award, Options, Exercisable, Weighted Average Exercise Price	$ 6.38
Stock Options [Member] | $10.44—$14.28
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range, Lower Range Limit	$ 10.44
Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range, Upper Range Limit	$ 14.28
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding, Number, Ending Balance	326,936
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding, Weighted Average Exercise Price, Ending Balance	$ 12.61
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding, Weighted Average Remaining Contractual Term	7 years 2 months 9 days
Share-based Compensation Arrangement by Share-based Payment Award, Options, Exercisable, Number	190,964
Share-based Compensation Arrangement by Share-based Payment Award, Options, Exercisable, Weighted Average Exercise Price	$ 13.51
Stock Options [Member] | $16.00—$16.00
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range, Lower Range Limit	$ 16.00
Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range, Upper Range Limit	$ 16.00
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding, Number, Ending Balance	1,174,667
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding, Weighted Average Exercise Price, Ending Balance	$ 16.00
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding, Weighted Average Remaining Contractual Term	8 years 0 months 7 days
Share-based Compensation Arrangement by Share-based Payment Award, Options, Exercisable, Number	531,966
Share-based Compensation Arrangement by Share-based Payment Award, Options, Exercisable, Weighted Average Exercise Price	$ 16.00
Stock Options [Member] | $16.50—$20.41
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range, Lower Range Limit	$ 16.50
Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range, Upper Range Limit	$ 20.41
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding, Number, Ending Balance	959,303
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding, Weighted Average Exercise Price, Ending Balance	$ 18.72
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding, Weighted Average Remaining Contractual Term	7 years 0 months 18 days
Share-based Compensation Arrangement by Share-based Payment Award, Options, Exercisable, Number	552,878
Share-based Compensation Arrangement by Share-based Payment Award, Options, Exercisable, Weighted Average Exercise Price	$ 18.77
Stock Options [Member] | $24.20—$27.13
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range, Lower Range Limit	$ 24.20
Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range, Upper Range Limit	$ 27.13
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding, Number, Ending Balance	533,270
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding, Weighted Average Exercise Price, Ending Balance	$ 26.32
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding, Weighted Average Remaining Contractual Term	7 years 6 months 18 days
Share-based Compensation Arrangement by Share-based Payment Award, Options, Exercisable, Number	272,539
Share-based Compensation Arrangement by Share-based Payment Award, Options, Exercisable, Weighted Average Exercise Price	$ 26.15
Stock Options [Member] | $30.17 to $30.17
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range, Lower Range Limit	$ 30.17
Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range, Upper Range Limit	$ 30.17
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding, Number, Ending Balance	80,000
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding, Weighted Average Exercise Price, Ending Balance	$ 30.17
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding, Weighted Average Remaining Contractual Term	8 years 2 months 12 days
Share-based Compensation Arrangement by Share-based Payment Award, Options, Exercisable, Number	46,664
Share-based Compensation Arrangement by Share-based Payment Award, Options, Exercisable, Weighted Average Exercise Price	$ 30.17
Stock Options [Member] | $0.10 to $30.17
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range, Lower Range Limit	$ 0.10
Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range, Upper Range Limit	$ 30.17
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding, Number, Ending Balance	8,946,592
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding, Weighted Average Exercise Price, Ending Balance	$ 9.07
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding, Weighted Average Remaining Contractual Term	7 years 5 months 28 days
Share-based Compensation Arrangement by Share-based Payment Award, Options, Exercisable, Number	4,134,023
Share-based Compensation Arrangement by Share-based Payment Award, Options, Exercisable, Weighted Average Exercise Price	$ 9.94

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Summary of Significant Accounting Policies

12 Months Ended

Dec. 31, 2012

Accounting Policies [Abstract]

Summary of Significant Accounting Policies

Summary of Significant Accounting Policies

Basis of Presentation

The accompanying consolidated financial statements have been prepared in accordance with the accounting principles generally accepted in the United States of America (“GAAP”) and with the instructions for Form 10-K and Regulations S-X statements. The consolidated financial statements include the accounts of the Company and its consolidated subsidiaries. All intercompany accounts and transactions have been eliminated in consolidation.

Principles of Consolidations

The Company has interests in joint venture entities that are variable interest entities (“VIEs”). Determining whether to consolidate a variable interest entity requires judgment in assessing (i) whether an entity is a VIE and (ii) if the Company is the entity’s primary beneficiary and thus required to consolidate the entity. To determine if the Company is the primary beneficiary of a VIE, the Company evaluates whether it has (i) the power to direct the activities that most significantly impact the VIE’s economic performance and (ii) the obligation to absorb losses or the right to receive benefits of the VIE that could potentially be significant to the VIE. The Company’s evaluation includes identification of significant activities and an assessment of its ability to direct those activities based on governance provisions and arrangements to provide or receive product and process technology, product supply, operations services, equity funding and financing and other applicable agreements and circumstances. The Company’s assessment of whether it is the primary beneficiary of its VIEs requires significant assumptions and judgment.

The consolidated financial statements of the Company include the accounts of Amyris, Inc., its subsidiaries and two consolidated VIEs with respect to which the Company is considered the primary beneficiary, after elimination of intercompany accounts and transactions. Disclosure regarding the Company’s participation in the VIEs is included in Note 8.

Use of Estimates

In preparing the consolidated financial statements, management must make estimates and assumptions that affect the reported amounts of assets and liabilities and disclosure of contingent assets and liabilities as of the date of the consolidated financial statements and the reported amounts of revenue and expenses during the reporting period. Actual results could differ from those estimates.

Concentration of Credit Risk

Financial instruments that potentially subject the Company to a concentration of credit risk consist primarily of cash and cash equivalents and accounts receivable. The Company places its cash equivalents and investments with high credit quality financial institutions and, by policy, limits the amount of credit exposure with any one financial institution. Deposits held with banks may exceed the amount of insurance provided on such deposits. The Company has not experienced any losses on its deposits of cash and cash equivalents and short-term investments.

The Company performs ongoing credit evaluation of its customers, does not require collateral, and maintains allowances for potential credit losses on customer accounts when deemed necessary.

Customers representing 10% or greater of accounts receivable were as follows:

	December 31,
Customers	2012		2011
Customer A	*		20	%
Customer B	*		10	%
Customer C	44	%	**
Customer D	22	%	**
Customer E	14	%	**

______________ 

 * No outstanding balance

** Less than 10%

Customers representing 10% or greater of revenues were as follows:

	Years Ended December 31,
Customers	2012		2011		2010
Customer A	13	%	11	%	**
Customer D	**		**		12	%
Customer F	**		**		10	%
Customer G	**		14	%	23	%
Customer H	13	%	*		*
Customer I	**		*		10	%

______________

 * Not a customer

** Less than 10%

Fair Value of Financial Instruments

The Company measures certain financial assets and liabilities at fair value based on the exchange price that would be received for an asset or paid to transfer a liability (an exit price) in the principal or most advantageous market for the asset or liability in an orderly transaction between market participants. Where available, fair value is based on or derived from observable market prices or other observable inputs. Where observable prices or inputs are not available, valuation models are applied. These valuation techniques involve some level of management estimation and judgment, the degree of which is dependent on the price transparency for the instruments or market and the instruments’ complexity.

The carrying amounts of certain financial instruments, such as cash equivalents, accounts receivable, accounts payable and accrued liabilities, approximate fair value due to their relatively short maturities, and low market interest rates if applicable. The fair values of the notes payable, loan payable, convertible notes and credit facility are based on the present value of expected future cash flows and assumptions about current interest rates and the creditworthiness of the Company.

The Company estimates the fair value of its embedded derivative related to Total senior unsecured convertible notes using a Black-Scholes valuation model that combines expected cash outflows with market-based assumptions regarding risk-adjusted yields, stock price volatility, probability of a change of control and the trading information of the Company's common stock into which the notes are convertible. The Company will continue to mark the bifurcated compound derivative to market due to the conversion price not being indexed to the Company's own stock because of the feature requiring the Company to redeem foregone interest upon conversion by the holder. The change in the fair value of the bifurcated compound derivative is primarily related to the change in price of the underlying common stock and is reflected in the Company's consolidated statements of operations as “other income (expense)”.

Cash and Cash Equivalents

All highly liquid investments purchased with an original maturity date of 90 days or less at the date of purchase are considered to be cash equivalents. Cash and cash equivalents consist of money market funds and certificates of deposit.

Accounts Receivable

The Company maintains an allowance for doubtful accounts receivable for estimated losses resulting from the inability of its customers to make required payments. The Company determines this allowance based on specific doubtful account identification and management judgment on estimated exposure. The Company writes off accounts receivable against the allowance when it determines a balance is uncollectible and no longer actively pursues collection of the receivable. 

Investments

Investments with original maturities greater than 90 days that mature less than one year from the consolidated balance sheet date are classified as short-term investments. The Company classifies investments as short-term or long-term based upon whether such assets are reasonably expected to be realized in cash or sold or consumed during the normal cycle of business. The Company invests its excess cash balances primarily in certificates of deposit. Certificates of deposits that have maturities greater than 90 days that mature less than one year from the consolidated balance sheet date are classified as short term investments. The Company classifies all of its investments as available-for-sale and records such assets at estimated fair value in the consolidated balance sheets, with unrealized gains and losses, if any, reported as a component of accumulated other comprehensive income (loss) in stockholders’ equity. Debt securities are adjusted for amortization of premiums and accretion of discounts and such amortization and accretion are reported as a component of interest income. Realized gains and losses and declines in value that are considered to be other-than-temporary are recognized in the statements of operations. The cost of securities sold is determined on the specific identification method. There were no significant realized gains or losses from sales of debt securities during the years ended December 31, 2012, 2011 and 2010. As of December 31, 2012 and 2011, the Company did not have any other-than-temporary declines in the fair value of its debt securities.

Restricted Cash

Cash accounts that are restricted to withdrawal or usage are presented as restricted cash. As ofDecember 31, 2012 and 2011, the Company had $955,000 and zero, respectively, of restricted cash held by a bank in a certificate of deposit as collateral under a facility lease.

Inventories

Inventories, which consist of farnesene-derived products, as well as ethanol and reformulated ethanol-blended gasoline, are stated at the lower of cost or market and categorized as finished goods, work-in-process or raw material inventories. During the quarter ended September 30, 2012, the Company sold its remaining inventory of ethanol and reformulated ethanol-blended gasoline as it transitioned out of this business. The Company evaluates the recoverability of its inventories based on assumptions about expected demand and net realizable value. If the Company determines that the cost of inventories exceeds its estimated net realizable value, the Company records a write-down equal to the difference between the cost of inventories and the estimated net realizable value. If actual net realizable values are less favorable than those projected by management, additional inventory write-downs may be required that could negatively impact the Company's operating results. If actual net realizable values are more favorable, the Company may have favorable operating results when products that have been previously written down are sold in the normal course of business. The Company also evaluates the terms of its agreements with its suppliers and establishes accruals for estimated losses on adverse purchase commitments as necessary, applying the same lower of cost or market approach that is used to value inventory. Cost is computed on a first-in, first-out basis. Inventory costs include transportation costs incurred in bringing the inventory to its existing location.

Derivative Instruments

The Company makes limited use of derivative instruments, which includes currency interest rate swap agreements to manage the Company's exposure to foreign currency exchange rate fluctuations and interest rate fluctuations related to the Company's Banco Pine S.A. loan (discussed below under Note 6). Through the third quarter of 2012, the Company held futures positions on the New York Mercantile Exchange and the CME/Chicago Board of Trade to mitigate the risks related to the price volatility of ethanol and reformulated ethanol-blended gasoline but, as of September 30, 2012, the Company had transitioned out of that business and no longer held such derivative instruments. The Company does not engage in speculative derivative activities, and the purpose of its activity in derivative commodity instruments is to manage the financial risk posed by physical transactions and inventory. Changes in the fair value of the derivative contracts are recognized currently in the consolidated statements of operations.

Asset Retirement Obligations

The fair value of an asset retirement obligation is recognized in the period in which it is incurred if a reasonable estimate of fair value can be made. In addition, asset retirement cost is added to the carrying amount of the associated asset and this additional carrying amount is amortized over the life of the asset. The Company’s asset retirement obligations were associated with its commitment to return property subject to an operating lease in Brazil to its original condition upon lease termination. In October 2012, this operating lease was amended which included an amendment to the terms of restitution of the property under lease. As a result of this amendment, the Company no longer has asset retirement obligations and therefore reversed the previously accrued liabilities.

As of December 31, 2012 and 2011, the Company had asset retirement obligations of zero and $1.1 million, respectively. The related leasehold improvements are being amortized to depreciation expense over the term of the lease or the useful life of the assets, whichever is shorter. Related amortization expense was $188,000, $193,000 and $229,000 for the years ended December 31, 2012, 2011 and 2010, respectively.

The change in the asset retirement obligation is summarized below (in thousands):

Balance at December 31, 2010	$	984
Additions	166
Foreign currency impacts and other adjustments	(133		)
Accretion expenses recorded during the period	112
Balance at December 31, 2011	$	1,129
Additions	—
Foreign currency impacts and other adjustments	(98		)
Accretion expenses recorded during the period	91
Reversals	(1,122		)
Balance at December 31, 2012	$	—

Property, Plant and Equipment, net

Property, plant and equipment, net are stated at cost less accumulated depreciation and amortization. Depreciation and amortization is computed using the straight-line method over the estimated useful lives of the related assets. Maintenance and repairs are charged to expense as incurred, and improvements and betterments are capitalized. When assets are retired or otherwise disposed of, the cost and accumulated depreciation are removed from the balance sheet and any resulting gain or loss is reflected in operations in the period realized.

Depreciation and amortization periods for the Company’s property, plant and equipment are as follows:

Machinery and equipment	7-15 years
Buildings	15 years
Computers and software	3-5 years
Furniture and office equipment	5 years
Vehicles	5 years

Buildings and leasehold improvements are amortized on a straight-line basis over the terms of the lease, or the useful life of the assets, whichever is shorter.

Computers and software includes internal-use software that is acquired to meet the Company’s needs. Amortization commences when the software is ready for its intended use and the amortization period is the estimated useful life of the software, generally 3 to 5 years. Capitalized costs primarily include contract labor and payroll costs of the individuals dedicated to the installation of internal-use software. Capitalized software additions totaled approximately $1.4 million, $1.1 million, and $1.3 million for the years ended December 31, 2012, 2011 and 2010, respectively, related to software costs pertaining to the installation of new financial reporting systems. For the years ended December 31, 2012, 2011 and 2010, $0.7 million, $0.4 million and $0.3 million, respectively, of amortization expense was recorded and as of December 31, 2012 the total unamortized cost of capitalized software was $2.6 million. During the year ended December 31, 2012, the Company wrote-off capitalized software with a net book value of $0.9 million.

Impairment of Long-Lived Assets

Long-lived assets to be held and used are reviewed for impairment whenever events or changes in circumstances indicate that the carrying amount of an asset may not be recoverable or the estimated useful life is no longer appropriate. If indicators of impairment exist and the undiscounted projected cash flows associated with such assets are less than the carrying amount of the asset, an impairment loss is recorded to write the asset down to their estimated fair values. Fair value is estimated based on discounted future cash flows. There were $6.4 million, zero and zero, respectively, of impairment charges recorded during the years ended December 31, 2012, 2011 and 2010, respectively. The impairment charges of $6.4 million in 2012 included the write-off of capitalized software with a net book value of $0.9 million.

Goodwill and Intangible Assets

Goodwill represents the excess of the cost over the fair value of net assets acquired from our business combinations. Intangible assets are comprised primarily of in-process research and development ("IPR&D"). The Company makes significant judgments in relation to the valuation of goodwill and intangible assets resulting from business combinations.

There are several methods that can be used to determine the estimated fair value of the IPR&D acquired in a business combination. We used the "income method," which applies a probability weighting that considers the risk of development and commercialization, to the estimated future net cash flows that are derived from projected sales revenues and estimated costs. These projections are based on factors such as relevant market size, pricing of similar products, and expected industry trends. The estimated future net cash flows are then discounted to the present value using an appropriate discount rate. These assets are treated as indefinite-lived intangible assets until completion or abandonment of the projects, at which time the assets will be amortized over the remaining useful life or written off, as appropriate.

Goodwill and intangible assets with indefinite lives are assessed for impairment using fair value measurement techniques on an annual basis or more frequently if facts and circumstance warrant such a review. When required, a comparison of fair value to the carrying amount of assets is performed to determine the amount of any impairment.

The Company evaluates its intangible assets with finite lives for indications of impairment whenever events or changes in circumstances indicate that the carrying value may not be recoverable. Intangible assets consist of purchased licenses and permits and are amortized on a straight-line basis over their estimated useful lives. Amortization of intangible assets was $0.4 million, $0.4 million and zero for the years ended December 31, 2012, 2011 and 2010, respectively. Factors that could trigger an impairment review include significant under-performance relative to expected historical or projected future operating results, significant changes in the manner of our use of the acquired assets or the strategy for our overall business or significant negative industry or economic trends. If this evaluation indicates that the value of the intangible asset may be impaired, we make an assessment of the recoverability of the net carrying value of the asset over its remaining useful life. If this assessment indicates that the intangible asset is not recoverable, based on the estimated undiscounted future cash flows of the technology over the remaining amortization period, we reduce the net carrying value of the related intangible asset to fair value and may adjust the remaining amortization period. Any such impairment charge could be significant and could have a material adverse effect on our reported financial results. The Company has not recognized any impairment charges on our intangible assets through December 31, 2012.

In-Process Research and Development

During 2011, the Company recorded IPR&D of $8.6 million related to the acquisition of Draths. Amounts recorded as IPR&D will begin being amortized upon first sales of the product over the estimated useful life of the technology. In accordance with authoritative guidance, as the technology has not yet been proven, the amortization of the acquired IPR&D has not begun. The Company estimates that it could take up to three years before it will have viable products resulting from the acquired technology.

Noncontrolling Interest and Redeemable Noncontrolling Interest

Changes in noncontrolling interest ownership that do not result in a change of control and where there is a difference between fair value and carrying value are accounted for as equity transactions. On April 14, 2010, the Company entered into a joint venture with Usina São Martinho. The carrying value of the noncontrolling interest from this joint venture is recorded in the equity section of the consolidated balance sheets (see Note 8). On January 3, 2011, the Company entered into a production service agreement with Glycotech, Inc. ("Glycotech"). The Company has determined that the arrangement with Glycotech qualifies as a VIE. The Company determined that it is the primary beneficiary. The carrying value of the noncontrolling interest from this VIE is recorded in the equity section of the consolidated balance sheets (see Note 8).

Revenue Recognition

The Company recognizes revenue from the sale of farnesene-derived products, delivery of research and development services, and from governmental grants. Through the third quarter of 2012, the Company also sold ethanol and reformulated ethanol-blended gasoline under short-term agreements at prevailing market prices. As of September 30, 2012, the Company had transitioned out of that business. Revenue is recognized when all of the following criteria are met: persuasive evidence of an arrangement exists, delivery has occurred or services have been rendered, the fee is fixed or determinable, and collectibility is reasonably assured.

If sales arrangements contain multiple elements, the Company evaluates whether the components of each arrangement represent separate units of accounting.

Product Sales

Beginning in the second quarter of 2011, the Company began to sell farnesene-derived products, which were produced by contracted third parties. Through the third quarter of 2012, the Company also sold ethanol and reformulated ethanol-blended gasoline under short-term agreements at prevailing market prices. As of September 30, 2012, the Company had transitioned out of that business.Ethanol and reformulated ethanol-blended gasoline sales consisted of sales to customers through purchases from third-party suppliers in which the Company took physical control of the ethanol and reformulated ethanol-blended gasoline and accepted risk of loss. The Company's renewable product sales do not include rights of return. Returns are only accepted if the product does not meet product specifications and such nonconformity is communicated to the Company within a set number of days of delivery. Commencing April 1, 2012, the Company began offering a two year standard warranty provision for squalane products sold after March 31, 2012, if the products do not meet Company-established criteria as set forth in the Company's trade terms. The Company bases its return reserve on a combination of historical rate of return for the Company's squalane products and historical returns for companies in the cosmetics industry since the Company did not have a full two years of historical return data. Revenues are recognized, net of discounts and allowances, once passage of title and risk of loss has occurred and contractually specified acceptance criteria have been met, provided all other revenue recognition criteria have also been met.

Grants and Collaborative Revenue

Revenue from collaborative research services is recognized as the services are performed consistent with the performance requirements of the contract. In cases where the planned levels of research services fluctuate over the research term, the Company recognizes revenue using the proportionate performance method based upon actual efforts to date relative to the amount of expected effort to be incurred by the Company. When up-front payments are received and the planned levels of research services do not fluctuate over the research term, revenue is recorded on a ratable basis over the arrangement term, up to the amount of cash received. When up-front payments are received and the planned levels of research services fluctuate over the research term, revenue is recorded using the proportionate performance method, up to the amount of cash received. Where arrangements include milestones that are determined to be substantive and at risk at the inception of the arrangement, revenue is recognized upon achievement of the milestone and is limited to those amounts whereby collectibility is reasonably assured.

Government grants are agreements that generally provide cost reimbursement for certain types of expenditures in return for research and development activities over a contractually defined period. Revenues from government grants are recognized in the period during which the related costs are incurred, provided that the conditions under which the government grants were provided have been met and only perfunctory obligations are outstanding. Under the Defense Advanced Research Projects Agency (DARPA) contract signed in June 2012, the Company will receive funding based on achievement of program milestones. Accordingly, the Company will recognize revenue using the proportionate performance method based upon actual efforts to date relative to the amount of expected effort to be incurred, up to the amount of verified payable milestones.

Cost of Products Sold

Starting in the second quarter of 2011, cost of products sold includes production costs of farnesene-derived products, which include cost of raw materials, amounts paid to contract manufacturers and period costs including inventory write-downs resulting from applying lower-of-cost-or-market inventory valuation. Cost of farnesene-derived products sold also includes certain costs related to the scale-up in production of such products. Through the third quarter of 2012, cost of products sold consisted primarily of cost of purchased ethanol and reformulated ethanol-blended gasoline, terminal fees paid for storage and handling, transportation costs between terminals and changes in the fair value of derivative commodity instruments. The Company transitioned out of its ethanol and gasoline business in the quarter ended September 30, 2012.

Shipping and handling costs charged to customers are recorded as revenues. Shipping costs are included in cost of products sold. Such charges were not significant in any of the periods presented.

Costs of Start-Up Activities

Start-up activities are defined as those one-time activities related to opening a new facility, introducing a new product or service, conducting business in a new territory, conducting business with a new class of customer or beneficiary, initiating a new process in an existing facility, commencing some new operation or activities related to organizing a new entity. All the costs associated with start-up activities related to a potential facility are expensed and recorded within selling, general and administrative expenses until the facility is considered viable by management, at which time costs would be considered for capitalization based on authoritative accounting literature.

Research and Development

Research and development costs are expensed as incurred and include costs associated with research performed pursuant to collaborative agreements and government grants. Research and development costs consist of direct and indirect internal costs related to specific projects as well as fees paid to others that conduct certain research activities on the Company’s behalf.

Income Taxes

The Company accounts for income taxes under the asset and liability method, which requires, among other things, that deferred income taxes be provided for temporary differences between the tax basis of the Company’s assets and liabilities and their financial statement reported amounts. In addition, deferred tax assets are recorded for the future benefit of utilizing net operating losses and research and development credit carryforwards. A valuation allowance is provided against deferred tax assets unless it is more likely than not that they will be realized.

The Company recognizes and measures uncertain tax positions in accordance with Income Taxes subtopic 05-6 of ASC 740, which prescribes a recognition threshold and measurement process for recording uncertain tax positions taken, or expected to be taken in a tax return, in the consolidated financial statements. Additionally, the guidance also prescribes treatment for the derecognition, classification, accounting in interim periods and disclosure requirements for uncertain tax positions. The Company accrues for the estimated amount of taxes for uncertain tax positions if it is more likely than not that the Company would be required to pay such additional taxes. An uncertain tax position will not be recognized if it has a less than 50% likelihood of being sustained.

Currency Translation

The Brazilian real is the functional currency of the Company’s wholly-owned subsidiary in Brazil and of the Company’s joint venture with Usina São Martinho. Accordingly, asset and liability accounts of those operations are translated into United States dollars using the current exchange rate in effect at the balance sheet date and equity accounts are translated into United States dollars using historical rates. The revenues and expenses are translated using the exchange rates in effect when the transactions occur. Gains and losses from foreign currency translation adjustments are included as a component of accumulated other comprehensive income (loss) in the consolidated balance sheets.

Stock-Based Compensation

The Company accounts for stock-based compensation arrangements with employees using a fair value method which requires the recognition of compensation expense for costs related to all stock-based payments including stock options. The fair value method requires the Company to estimate the fair value of stock-based payment awards on the date of grant using an option pricing model. The Company uses the Black-Scholes option pricing model to estimate the fair value of options granted, which is expensed on a straight-line basis over the vesting period. The Company accounts for restricted stock unit awards issued to employees based on the fair market value of the Company’s common stock.

The Company accounts for stock options issued to nonemployees based on the estimated fair value of the awards using the Black-Scholes option pricing model. The Company accounts for restricted stock units issued to nonemployees based on the fair market value of the Company’s common stock. The measurement of stock-based compensation is subject to periodic adjustments as the underlying equity instruments vest, and the resulting change in value, if any, is recognized in the Company’s consolidated statements of operations during the period the related services are rendered.

Comprehensive Income (Loss)

Comprehensive income (loss) represents all changes in stockholders’ equity except those resulting from investments or contributions by stockholders. The Company’s foreign currency translation adjustments represent the components of comprehensive income (loss) excluded from the Company’s net loss and have been disclosed in the consolidated statements of comprehensive loss for all periods presented.

The components of accumulated other comprehensive loss are as follows (in thousands):

	December 31,
	2012			2011
Foreign currency translation adjustment, net of tax	$	(12,807	)	$	(5,924	)
Total accumulated other comprehensive loss	$	(12,807	)	$	(5,924	)

Net Loss Attributable to Common Stockholders and Net Loss per Share

The Company computes net loss per share in accordance with ASC 260, “Earnings per Share.” Basic net loss per share of common stock is computed by dividing the Company’s net loss attributable to Amyris, Inc. common stockholders by the weighted-average number of shares of common stock outstanding during the period. Diluted net loss per share of common stock is computed by giving effect to all potentially dilutive securities, including stock options, restricted stock units, common stock warrants, using the treasury stock method or the as converted method, as applicable. For all periods presented, basic net loss per share was the same as diluted net loss per share because the inclusion of all potentially dilutive securities outstanding was anti-dilutive. As such, the numerator and the denominator used in computing both basic and diluted net loss are the same for each period presented.

The following table presents the calculation of basic and diluted net loss per share of common stock attributable to Amyris, Inc. common stockholders (in thousands, except share and per share amounts):

	Years Ended December 31,
	2012			2011			2010
Numerator:
Net loss attributable to Amyris, Inc. common stockholders	$	(205,139	)	$	(178,870	)	$	(123,879	)
Denominator:
Weighted-average shares of common stock outstanding used in computing net loss per share of common stock, basic and diluted	56,717,869			44,799,056			14,840,253
Net loss per share attributable to common stockholders, basic and diluted	$	(3.62	)	$	(3.99	)	$	(8.35	)

The following outstanding shares of potentially dilutive securities were excluded from the computation of diluted net loss per share of common stock for the periods presented because including them would have been anti-dilutive:

	Years Ended December 31,
	2012	2011	2010
Period-end stock options to purchase common stock	8,946,592	8,377,016	7,274,637
Convertible promissory notes	10,370,391	—	—
Period-end common stock subject to repurchase	51	7,929	33,396
Period-end common stock warrants*	21,087	26,223	195,604
Period-end restricted stock units	2,550,799	375,189	—
Total	21,888,920	8,786,357	7,503,637

______________ 

• The common stock warrants at December 31, 2011 includes 21,087 warrants issued in 2011 and 5,136 common stock warrants converted from preferred stock warrants computed on an as converted basis using the conversion ratios in effect as of September 30, 2010, the date of the IPO Closing. The common stock warrants at December 31, 2010 were converted from preferred stock warrants computed on an as converted basis using the conversion ratios in effect as of September 30, 2010.

Recent Accounting Pronouncements

In December 2011, the International Accounting Standards Board ("IASB") and the FASB issued common disclosure requirements that are intended to enhance comparability between financial statements prepared on the basis of U.S. GAAP and those prepared in accordance with IFRS. In January 2013, the FASB issued an accounting standard update to limit the scope of the new balance sheet offsetting disclosures to derivative instruments, repurchase agreements, and securities lending transactions to the extent that they are offset in the financial statement or subject to an enforceable master netting arrangement or similar arrangement. While this guidance does not change existing offsetting criteria in U.S. GAAP or the permitted balance sheet presentation for items meeting the criteria, it requires an entity to disclose both net and gross information about assets and liabilities that have been offset and the related arrangements. Required disclosures under this new guidance should be provided retrospectively for all comparative periods presented. This new guidance is effective for fiscal years beginning on or after January 1, 2013, and interim periods within those years, which would be the Company's first quarter of fiscal 2013. The adoption of this guidance will require expanded disclosure in the Company's consolidated financial statements but will not impact financial results.

In July 2012, the FASB issued an amended accounting standard update to simplify how entities test indefinite-lived intangible assets for impairment which improve consistency in impairment testing requirements among long-lived asset categories. The amended guidance permits an assessment of qualitative factors to determine whether it is more likely than not that the fair value of an indefinite-lived intangible asset is less than its carrying value. For assets in which this assessment concludes it is more likely than not that the fair value is more than its carrying value, then the amended guidance eliminates the requirement to perform quantitative impairment testing as outlined in the previously issued standards. The amended guidance is effective for fiscal years beginning after September 15, 2012; however, early adoption is permitted. The Company does not expect this amended guidance to have an impact on the Company's financial results.

In February 2013, in connection with the accounting standard related to the presentation of the Statement of Comprehensive Income, the FASB issued an accounting standard update to improve the reporting of reclassifications out of accumulated other comprehensive income of various components. This guidance requires companies to present either parenthetically on the face of the financial statements or in the notes, significant amounts reclassified from each component of accumulated other comprehensive income and the income statement line items affected by the reclassification. This standard is effective for interim periods and fiscal years beginning after December 15, 2012, which would be the Company's first quarter of fiscal 2013. The adoption of this guidance will require expanded disclosure in the Company's consolidated financial statements but will not impact financial results.

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Balance Sheet Components Inventory (Details) (USD $) In Thousands, unless otherwise specified	Dec. 31, 2012	Dec. 31, 2011
Balance Sheet Components [Abstract]
Raw materials	$ 1,574	$ 2,191
Work-in-process	1,771	1,237
Finished goods	2,689	5,642
Inventories, net	$ 6,034	$ 9,070

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Significant Agreements ((Research and Development Activities - Other Agreements) (Details) (USD $) In Millions, unless otherwise specified	1 Months Ended		12 Months Ended		1 Months Ended
	Apr. 30, 2011 M and G Finanziaria SRL Agreement [Member]	Nov. 30, 2010 Firmenich SA Agreement [Member]	Dec. 31, 2012 Firmenich SA Agreement [Member]	Dec. 31, 2011 Firmenich SA Agreement [Member]	Sep. 30, 2011 Michelin Agreement [Member]	Dec. 31, 2012 Michelin Agreement [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaborator Agreement, Costs Incurred, Company Responsible Percentage	50.00%
Collaborator Agreement, Costs Incurred, Collaborator Responsible Percentage	50.00%
Potential Future Payments From Collaborators		$ 6.0
Revenue Reognized, Including Portion Related to Milestone Method			4.8	5.2
Revenue Recognition, Milestone Method, Revenue Recognized			2.0	2.0
Proceeds from Collaborators					5.0
Amount of Repayment For Failure to Achieve Milestones					1.0
Collaborator Agreement Notification Period from the Completion of Renewable Diesel Program					42 months
Deferred Revenue						$ 5.0

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Debt FINEP Credit Facility (Details) In Millions, unless otherwise specified	0 Months Ended	1 Months Ended		2 Months Ended	12 Months Ended
	Nov. 30, 2010 FINEP Credit Facility [Member] Monthly_installment	Dec. 31, 2012 FINEP Credit Facility [Member] USD ($) disbursements	Dec. 31, 2012 FINEP Credit Facility [Member] BRL disbursements	Dec. 31, 2011 FINEP Credit Facility [Member] BRL	Dec. 31, 2012 FINEP Credit Facility [Member] USD ($) disbursements	Dec. 31, 2012 FINEP Credit Facility [Member] BRL disbursements	Dec. 31, 2012 Chattel Mortgage [Member] FINEP Credit Facility [Member] USD ($)	Dec. 31, 2012 Chattel Mortgage [Member] FINEP Credit Facility [Member] BRL	Nov. 30, 2010 Chattel Mortgage [Member] FINEP Credit Facility [Member] BRL disbursements	Nov. 30, 2010 Minimum [Member] FINEP Credit Facility [Member]	Dec. 31, 2012 FINEP Project [Member] USD ($)	Nov. 30, 2010 FINEP Project [Member] BRL
Line of Credit Facility [Line Items]
Line of Credit Facility, Maximum Borrowing Capacity							$ 3.1		6.4
Disbursements Received After Compliance with Certain Terms and Conditions (in disbursements)		3	3		3	3			4
Line of Credit Facility, First Disbursement of Loan				1.8	0.9
Line of Credit Facility, Remaining Balance Received from Disbursements					2.2	4.6
Line of Credit Facility, Additional Loan Disbursements		0.8	1.6
Debt Instrument, Interest Rate, Stated Percentage	5.00%
Long-term Debt, Percentage Bearing Fixed Interest, Percentage Rate										6.00%
Debt Instrument, Basis Spread on Variable Rate	5.00%
Long-term Debt, Percentage Bearing Variable Interest, Percentage Rate	11.00%
Debt Instrument Debt Default Fine Percentage	10.00%
Debt Instrument Interest On Late Balance Percentage Per Month	1.00%
Line of Credit Facility Number of Monthly Payments (in monthly installment)	81
Line of Credit Facility, Amount Outstanding							3.1	6.4
Research and Development Project, Amount To Be Contributed From Company Funds											7.1	14.5
Research and Development Project Amount To Be Contributed From Company Prior To Release Of Second Tranche												11.1
Guaranty Liabilities							$ 1.6		3.3
Period Of Time Amounts Released Must Be Used	30 months

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Schedule II Valuation and Qualifying Accounts

12 Months Ended

Dec. 31, 2012

Valuation and Qualifying Accounts [Abstract]

Schedule II Valuation and Qualifying Accounts

	Balance at Beginning of Period		Additions		Write-off/ Adjustments		Balance at End of Period
Deferred Tax Assets Valuation Allowance:
Year ended December 31, 2012	$	156,765	$	79,523	$	—	$	236,288
Year ended December 31, 2011	$	76,071	$	80,694	$	—	$	156,765
Year ended December 31, 2010	$	47,799	$	28,272	$	—	$	76,071

	Balance at Beginning of Period		Additions		Write-off/ Adjustments		Balance at End of Period
Allowance for Doubtful Accounts:
Year ended December 31, 2012	$	245	$	236	$	—	$	481
Year ended December 31, 2011	$	—	$	245	$	—	$	245
Year ended December 31, 2010	$	—	$	—	$	—	$	—

Schedules not listed above are omitted because they are not required, they are not applicable or the information is already included in the consolidated financial statements or notes thereto.

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Debt Related Party Convertible Notes (Details) (USD $)	12 Months Ended			0 Months Ended		0 Months Ended			0 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010	Jul. 30, 2012 Unsecured Senior Convertible Promissory Notes [Member]	Dec. 24, 2012 Unsecured Senior Convertible Promissory Notes [Member]	Jul. 30, 2012 Unsecured Senior Convertible Promissory Notes [Member] Unsecured Senior Convertible Notes 1.5% Due 2017 [Member]	Sep. 14, 2012 Unsecured Senior Convertible Promissory Notes [Member] Unsecured Senior Convertible Notes 1.5% Due 2017 [Member]	Dec. 24, 2012 Private Placement [Member]	Dec. 24, 2012 Private Placement [Member] Unsecured Senior Convertible Promissory Notes [Member]	Jul. 30, 2012 Initial Installment [Member] Unsecured Senior Convertible Promissory Notes [Member] July 2014 Convertible Notes [Member]	Jul. 30, 2012 Second Installment [Member] Unsecured Senior Convertible Promissory Notes [Member] January 2015 Convertible Notes [Member]
Debt Instrument [Line Items]
Debt Instrument, Face Amount				$ 105,000,000		$ 38,300,000	$ 15,000,000
Debt Instrument, Interest Rate, Stated Percentage				1.50%
Proceeds from Convertible Debt						15,000,000
Debt Conversion, Converted Instrument, Amount	5,000,000	0	0			23,300,000
Debt Instrument, Convertible, Common Stock, Shares								1,677,852
Future Proceeds from Convertible Debt				21,700,000						10,850,000	10,850,000
Debt Instrument, Convertible, Conversion Price								$ 2.98
Debt Instrument, Interest Rate, Default Rate, Stated Percentage				2.50%
Debt Instrument, Convertible, Period Prior to Maturity to Eligible For Conversion				10 days
Period of Lock-up Upon Conversion of Debt				6 months
Extinguishment of Debt, Amount									5,000,000
Convertible Debt, Amount Outstanding					53,300,000
Debt Instrument, Early Repayment, Percentage of Principal				101.00%
Debt Instrument, Debt Convenant, Outstanding Debt, Maximum				200,000,000.0
Debt Instrument, Debt Convenant, Percentage of Consolidated Total Assets, Maximum				50.00%
Debt Instrument, Debt Convenant, Outstanding Secured Debt, Maximum				$ 125,000,000.0
Debt Instrument, Debt Convenant, Secured Debt, Percentage of Consolidated Total Assets, Maximum				30.00%

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Restructuring (Tables)

12 Months Ended

Dec. 31, 2012

Restructuring and Related Activities [Abstract]

Schedule of Restructuring and Related Costs [Table Text Block]

The following table summarizes the liability and utilization by cost type associated with the restructuring (in thousands):

	Exit Costs			Deferred Rent			Total
Accrued restructuring as of December 31, 2009	$	5,078		$	—		$	5,078
Cash payments	(906		)	—			(906		)
Accretion expense	395			—			395
Reversal of restructuring liability	(2,061		)	(2,506		)	(4,567		)
Accrued restructuring as of December 31, 2010	$	2,506		$	(2,506	)	$	—

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Stock-Based Compensation Plans

12 Months Ended

Dec. 31, 2012

Disclosure of Compensation Related Costs, Share-based Payments [Abstract]

Stock-Based Compensation Plans

Stock-Based Compensation Plans

2010 Equity Incentive Plan

The Company's 2010 Equity Incentive Plan (“2010 Equity Plan”) became effective on September 28, 2010 and will terminate in 2020. Pursuant to the 2010 Equity Plan, any shares of the Company’s common stock (i) issued upon exercise of stock options granted under the Company's 2005 Stock Option/Stock Issuance Plan (the "2005 Plan") that cease to be subject to such option and (ii) issued under the 2005 Plan that are forfeited or repurchased by the Company at the original purchase price will become part of the 2010 Equity Plan. Subsequent to the effective date of the 2010 Equity Plan, an additional 803,944 shares that were forfeited under the 2005 Plan were added to the shares reserved for issuance under the 2010 Equity Plan.

The number of shares reserved for issuance under the 2010 Equity Plan increase automatically on January 1^st of each year starting with January 1, 2011, by a number of shares equal to 5.0% percent of the Company’s total outstanding shares as of the immediately preceding December 31^st. The Company’s Board of Directors or the Leadership Development and Compensation Committee of the Board of Directors is able to reduce the amount of the increase in any particular year. The 2010 Equity Plan provides for the granting of common stock options, restricted stock awards, stock bonuses, stock appreciation rights, restricted stock units and performance awards. It allows for time-based or performance-based vesting for the awards. Options granted under the 2010 Equity Plan may be either incentive stock options ("ISOs") or non-statutory stock options ("NSOs"). ISOs may be granted only to Company employees (including officers and directors who are also employees). NSOs may be granted to Company employees, non-employee directors and consultants. The Company will be able to issue no more than 30,000,000 shares pursuant to the grant of ISOs under the 2010 Equity Plan. Options under the 2010 Equity Plan may be granted for periods of up to ten years. All options issued to date have had a ten year life. Under the plan, the exercise price of any ISOs and NSOs may not be less than 100% of the fair market value of the shares on the date of grant. The exercise price of any ISOs and NSOs granted to a 10% stockholder may not be less than 110% of the fair value of the underlying stock on the date of grant. The options granted to date generally vest over four to five years.

As of December 31, 2012, options to purchase 5,708,475 shares of the Company's common stock granted from the 2010 Equity Plan were outstanding and 1,059,715 shares of the Company’s common stock remained available for future awards that may be granted from the 2010 Equity Plan. The options outstanding as of December 31, 2012 had a weighted-average exercise price of approximately $9.84 per share.

2005 Stock Option/Stock Issuance Plan

In 2005, the Company established its 2005 Plan which provided for the granting of common stock options, restricted stock units, restricted stock and stock purchase rights awards to employees and consultants of the Company. The 2005 Plan allowed for time-based or performance-based vesting for the awards. Options granted under the 2005 Plan were ISOs or NSOs. ISOs were granted only to Company employees (including officers and directors who are also employees). NSOs were granted to Company employees, non-employee directors, and consultants.

All options issued under the 2005 Plan have had a ten year life. The exercise prices of ISOs and NSOs granted under the 2005 Plan were not less than 100% of the estimated fair value of the shares on the date of grant, as determined by the Board of Directors. The exercise price of an ISO and NSO granted to a 10% stockholder could not be less than 110% of the estimated fair value of the underlying stock on the date of grant as determined by the Board of Directors. The options generally vested over 5 years.

As of December 31, 2012, options to purchase 3,178,117 shares of the Company’s common stock granted from the 2005 Stock Option/Stock Issuance Plan remained outstanding and, as a result of the adoption of the 2010 Equity Incentive Plan discussed above, zero shares of the Company’s common stock remained available for issuance under the 2005 Plan. The options outstanding under the 2005 Plan as of December 31, 2012 had a weighted-average exercise price of approximately $7.79 per share.

No income tax benefit has been recognized relating to stock-based compensation expense and no tax benefits have been realized from exercised stock options or release of restricted stock units.

2010 Employee Stock Purchase Plan

The 2010 Employee Stock Purchase Plan (the “2010 ESPP”) became effective on September 28, 2010. The 2010 ESPP is designed to enable eligible employees to purchase shares of the Company’s common stock at a discount. Each offering period is for one year and consists of two six-month purchase periods. Each twelve-month offering period generally commences on May 16^th and November 16^th, each consisting of two six-month purchase periods. The purchase price for shares of common stock under the 2010 ESPP is the lesser of 85% of the fair market value of the Company’s common stock on the first day of the applicable offering period or the last day of each purchase period. A total of 168,627 shares of common stock were initially reserved for future issuance under the 2010 Employee Stock Purchase Plan. During the first eight years of the life of the 2010 ESPP, the number of shares reserved for issuance increases automatically on January 1^st of each year, starting with January 1, 2011, by a number of shares equal to 1% of the Company’s total outstanding shares as of the immediately preceding December 31^st. Pursuant to the automatic increase provision, an additional 459,325 shares were reserved for issuance during the year ended December 31, 2012 for a cumulative total of 897,799 additional shares reserved for issuance under the automatic increase provision. The Company’s Board of Directors or the Leadership Development and Compensation Committee of the Board of Directors is able to reduce the amount of the increase in any particular year. No more than 10,000,000 shares of the Company’s common stock may be issued under the 2010 ESPP and no other shares may be added to this plan without the approval of the Company’s stockholders.

During the year ended December 31, 2012, 579,167 shares of the Company's common stock were purchased under the 2010 ESPP. At December 31, 2012, 186,700 shares of the Company’s common stock remained available for issuance under the 2010 ESPP.

Stock Option Activity

The Company’s stock option activity and related information for the year ended December 31, 2012 was as follows:

		Number Outstanding		Weighted - Average Exercise Price		Weighted - Average Remaining Contractual Life (Years)	Aggregate Intrinsic Value
							(in thousands)
Outstanding - December 31, 2011		8,377,016		$	14.05	7.9	$	29,127
	Options granted	3,592,593		$	3.49
	Options exercised	(866,203	)	$	0.72
	Options cancelled	(2,156,814	)	$	15.78
Outstanding - December 31, 2012		8,946,592		$	9.07	7.5	$	954
Vested and expected to vest after December 31, 2012		8,281,330		$	9.18	7.3	$	893
Exercisable at December 31, 2012		4,134,023		$	9.94	5.8	$	575

The aggregate intrinsic value of options exercised under all option plans was $2.7 million, $28.7 million and $934,000 for the years ended December 31, 2012, 2011 and 2010, respectively, determined as of the date of option exercise.

The Company’s restricted stock units and restricted stock activity and related information for the year ended December 31, 2012 was as follows:

	RSUs		Weighted Average Grant-Date Fair Value		Weighted Average Remaining Contractual Life (Years)
Outstanding - December 31, 2011	375,189		$	29.84	1.4
Awarded	2,966,900		$	3.45	—
Vested	(415,792	)	$	13.47	—
Forfeited	(375,498	)	$	10.28	—
Outstanding - December 31, 2012	2,550,799		$	7.92	1.3
Expected to vest after December 31, 2012	2,237,365		$	7.92	1.2

The following table summarizes information about stock options outstanding as of December 31, 2012:

	Options Outstanding				Options Exercisable
Exercise Price	Number of Options	Weighted - Average Remaining Contractual Life (Years)	Weighted Average Exercise Price		Number of Options	Weighted Average Exercise Price
$0.10—$2.76	1,129,158	8.1	$	2.31	279,345	$	1.06
$3.04—$3.55	768,990	9.7	$	3.12	10,936	$	3.13
$3.86—$3.86	1,424,649	8.9	$	3.86	296,482	$	3.86
$3.93—$3.93	1,198,288	3.9	$	3.93	1,152,673	$	3.93
$4.06—$9.32	1,351,331	6.8	$	6.37	799,576	$	6.38
$10.44—$14.28	326,936	7.2	$	12.61	190,964	$	13.51
$16.00—$16.00	1,174,667	8.0	$	16.00	531,966	$	16.00
$16.50—$20.41	959,303	7.0	$	18.72	552,878	$	18.77
$24.20—$27.13	533,270	7.5	$	26.32	272,539	$	26.15
$30.17—$30.17	80,000	8.2	$	30.17	46,664	$	30.17
$0.10—$30.17	8,946,592	7.5	$	9.07	4,134,023	$	9.94

Common Stock Subject to Repurchase

Historically under the 2005 Plan, the Company allowed employees to exercise options prior to vesting. The Company has the right to repurchase at the original purchase price any unvested (but issued) common shares upon termination of service of an employee. The consideration received for an early exercise of an option is considered to be a deposit of the exercise price and the related dollar amount is recorded as a liability. The shares and liability are reclassified into equity on a ratable basis as the award vests. The Company recorded a liability in accrued expenses of $197 and $30,000, respectively, relating to options for 51 and 7,929 shares of common stock that were exercised and unvested as of December 31, 2012 and 2011, respectively. These shares were subject to a repurchase right held by the Company and are included in issued and outstanding shares as of December 31, 2012 and 2011, respectively.

Stock-Based Compensation Expense

Stock-based compensation expense related to options and restricted stock units granted to employees and nonemployees was allocated to research and development expense and sales, general and administrative expense as follows (in thousands):

	Years Ended December 31,
	2012		2011		2010
Research and development	$	6,451	$	6,345	$	2,161
Sales, general and administrative	21,022		19,147		8,271
Total stock-based compensation expense	$	27,473	$	25,492	$	10,432

Employee Stock–Based Compensation

During the years ended December 31, 2012, 2011 and 2010, the Company granted options to purchase 3,589,593 shares, 2,677,249 shares, and 2,918,440 shares of its common stock, respectively, to employees with weighted average grant date fair values of $2.28, $18.41, and $11.84 per share, respectively. As of December 31, 2012 and 2011, there were unrecognized compensation costs of $51.2 million, and $54.7 million, respectively, related to these stock options. The Company expects to recognize those costs over a weighted average period of 2.9 years as of December 31, 2012. Future option grants will increase the amount of compensation expense to be recorded in these periods.

In August 2012, the Company's CEO exercised outstanding options to purchase 668,730 shares of the Company's common stock and sold the shares to certain members of the Company's Board of Directors or their affiliates through a private sale at a price of $3.70, which was greater than the fair market value of the stock at the date of sale. The Company recorded $388,000 in stock-based compensation expense as an excess of the sale price over the fair market value of shares in this transaction during the year ended December 31, 2012.

During the years ended December 31, 2012 and 2011, 2,956,900 and 352,301 of restricted stock units, respectively, were granted to employees with a weighted average service-inception date fair value of $3.46 and $29.85 per unit, respectively . The Company recognized a total of $6.3 million and $3.6 million, respectively, in December 31, 2012 and 2011 in stock-based compensation expense for restricted stock units granted to employees. No restricted stock units was granted to employees in 2010. As of December 31, 2012 and 2011, there were unrecognized compensation costs of $7.8 million and $6.0 million, respectively, related to these restricted stock units.

During the years ended December 31, 2012, 2011 and 2010, the Company also recognized stock-based compensation expense related to its 2010 ESPP of $0.8 million, $1.9 million, and $0.5 million, respectively.

Compensation expense was recorded for stock-based awards granted to employees based on the grant date estimated fair value (in thousands):

	Years Ended December 31,
	2012		2011		2010
Research and development	$	6,442	$	6,306	$	2,086
Sales, general and administrative	20,887		18,288		5,696
Total stock-based compensation expense	$	27,329	$	24,594	$	7,782

Employee stock-based compensation expense recognized for the year ended December 31, 2012 included $907,000, related to option modifications. As part of separation agreements with certain former senior employees, the Company agreed to accelerate the vesting of options for 825,523 shares of common stock and extend the exercise period for certain grants. The stock-based compensation expense above includes the impact of a repricing of stock options in June 2012 under which certain non-executive employees received a one-time reduction in the exercise price for such options with per share exercise prices per share higher than $24.00 held by U.S. employees of Amyris and the new exercise price for such options was $16.00, our initial public offering price. The total amount of the stock-based compensation associated with repricing was immaterial to the consolidated financial statements.

In the quarter ended June 30, 2011, the Company commenced sales of farnesene-derived products which were produced by contracted third parties. Accordingly, the Company did not have any dedicated production headcount so there is no stock-based compensation expense recorded in cost of products sold.

Stock-based compensation cost for RSUs is measured based on the closing fair market value of the Company's common stock on the date of grant. Stock-based compensation cost for stock options and employee stock purchase plan rights is estimated at the grant date and offering date, respectively, based on the fair-value using the Black-Scholes option pricing model. The fair value of employee stock options is being amortized on a straight-line basis over the requisite service period of the awards. The fair value of employee stock options was estimated using the following weighted-average assumptions:

	Years Ended December 31,
	2012		2011		2010
Expected dividend yield	—	%	—	%	—	%
Risk-free interest rate	1.1	%	2.3	%	2.5	%
Expected term (in years)	6.0		5.8		6.0
Expected volatility	77	%	86	%	96	%

Expected Dividend Yield—The Company has never paid dividends and does not expect to pay dividends.

Risk-Free Interest Rate—The risk-free interest rate was based on the market yield currently available on United States Treasury securities with maturities approximately equal to the option’s expected term.

Expected Term—Expected term represents the period that the Company’s stock-based awards are expected to be outstanding. The Company’s assumptions about the expected term have been based on that of companies that have similar industry, life cycle, revenue, and market capitalization and the historical data on employee exercises.

Expected Volatility—The expected volatility is based on a combination of historical volatility for the Company's stock and the historical stock volatilities of several of the Company’s publicly listed comparable companies over a period equal to the expected terms of the options, as the Company does not have a long trading history.

Fair Value of Common Stock— Prior to the IPO, the fair value of the shares of common stock underlying the stock options was determined by the Board of Directors. Because there was no public market for the Company’s common stock, the Board of Directors determined the fair value of the common stock at the time of grant of the option by considering a number of objective and subjective factors including valuation of comparable companies, sales of convertible preferred stock to unrelated third parties, operating and financial performance, the lack of liquidity of capital stock and general and industry specific economic outlook, amongst other factors. The Company’s common stock started trading in the NASDAQ Global Market under ticker symbol AMRS on September 28, 2010. Consequently, after the IPO, the fair value of the shares of common stock underlying the stock options is the closing price on the option grant date.

Forfeiture Rate—The Company estimates its forfeiture rate based on an analysis of its actual forfeitures and will continue to evaluate the adequacy of the forfeiture rate based on actual forfeiture experience, analysis of employee turnover behavior, and other factors. The impact from a forfeiture rate adjustment will be recognized in full in the period of adjustment, and if the actual number of future forfeitures differs from that estimated by the Company, the Company may be required to record adjustments to stock-based compensation expense in future periods.

Each of the inputs discussed above is subjective and generally requires significant management and director judgment to determine.

Nonemployee Stock–Based Compensation

During the years ended December 31, 2012, 2011 and 2010, the Company granted nonemployee options to purchase 3,000, 15,000 and 101,000 shares of its common stock, respectively, to nonemployees in exchange for services. Compensation expense of $86,000, $797,000 and $834,000 was recorded for the years ended December 31, 2012, 2011 and 2010, respectively, for stock-based awards granted to nonemployees. The nonemployee options were valued using the Black-Scholes option pricing model.

During the years ended December 31, 2012, 2011 and 2010, 10,000, 32,855 and 126,272 restricted stock units, respectively, were granted to nonemployees and a total of $58,000, $101,000 and $1.8 million, respectively, in stock-based compensation expense was recognized by the Company for the years ended December 31, 2012, 2011 and 2010. The 126,272 restricted stock units that were granted in 2010 were awarded to a related party as compensation for advisory services rendered. These restricted stock units vested quarterly and became fully vested as of September 30, 2010.

The fair value of nonemployee stock options was estimated using the following weighted-average assumptions:

	Years Ended December 31,
	2012		2011		2010
Expected dividend yield	—	%	—	%	—	%
Risk-free interest rate	1.4	%	2.1	%	3.2	%
Expected term (in years)	7.0		7.8		8.6
Expected volatility	77	%	86	%	95	%

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Income Taxes - Deferred Tax Assets and Liabilities (Details) (USD $)	12 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Deferred Tax Assets and Liabilities [Line Items]
Net operating loss carry forwards	$ 145,324,000	$ 103,390,000	$ 56,615,000
Fixed assets	0	0	340,000
Research and development credits	7,259,000	5,937,000	3,325,000
Foreign Tax Credit	1,782,000	801,000	0
Accruals and reserves	15,997,000	12,150,000	2,257,000
Stock-based compensation	15,882,000	11,351,000	4,316,000
Capitalized start-up costs	16,070,000	22,974,000	8,993,000
Capitalized research and development costs	26,850,000	0	0
Other	7,649,000	2,904,000	225,000
Total deferred tax assets	236,813,000	159,507,000	76,071,000
Fixed assets	(525,000)	(2,742,000)	0
Other	0	0	0
Total deferred tax liabilities	(525,000)	(2,742,000)	0
Net deferred tax asset prior to valuation allowance	236,288,000	156,765,000	76,071,000
Less: Valuation allowance	(236,288,000)	(156,765,000)	(76,071,000)
Net deferred tax assets (liabilities)	0	0	0
Valuation Allowance, Deferred Tax Asset, Change in Amount	79,500,000	80,700,000	28,300,000
Adjustments to Additional Paid in Capital, Income Tax Benefit from Share-based Compensation, Estimated	9,500,000
Federal R&D tax credit	5,100,000
Internal Revenue Service (IRS) [Member]
Deferred Tax Assets and Liabilities [Line Items]
Net operating loss carry forwards	373,700,000
Deferred Tax Assets, Tax Deferred Expense, Compensation and Benefits, Share-based Compensation Cost, Not Recognized	25,700,000
State and Local Jurisdiction [Member]
Deferred Tax Assets and Liabilities [Line Items]
Net operating loss carry forwards	202,400,000
Deferred Tax Assets, Tax Deferred Expense, Compensation and Benefits, Share-based Compensation Cost, Not Recognized	12,700,000
California [Member]
Deferred Tax Assets and Liabilities [Line Items]
Research and development credits	$ 7,900,000