The Navy, Amyris, Emvolon, Haffner Energy and the Incredible Shrinking Refinery

August 28, 2026

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by Jim Lane (Biofuels Digest) ... (R)emember the U.S. Navy’s audacious Great Green Fleet initiative a decade ago, which sought to demonstrate alternative drop-in fuels not as delicate laboratory curiosities, but in everyday operational fleet environments, culminating in the 2016 deployment of the John C. Stennis Carrier Strike Group running on advanced bio-blendstocks alongside a broader suite of energy-efficiency measures. As then-Secretary of the Navy Ray Mabus succinctly framed it, the objective was fundamentally about warfighting capability—allowing ships to go farther, stay longer, and deliver more firepower—and for the emerging advanced-biofuels sector, it provided a galvanizing validation that renewables were not merely an exercise in carbon accounting, but a structural lever of strategic agility.

Yet for all its ambition, the Great Green Fleet era was built squarely around the prevailing fuel philosophy of its time: the drop-in paradigm. The mandate was to engineer a molecule so identical to petroleum that the vast, entrenched infrastructure of the modern oil age—the engines, pipelines, bunkering facilities, and operational doctrine—would not notice the difference. It was an essential step for its era, but three distinct technological developments arriving simultaneously suggest that we are now approaching a far more radical question. We are no longer merely asking whether biology can synthesize a drop-in replacement for crude oil; we are beginning to ask whether emerging conversion platforms can replace the very architecture of the centralized refinery itself.

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Yet almost unnoticed, this long-standing industrial paradigm is coming under coordinated attack from three completely different technological directions.

The first front is being opened by synthetic biology, highlighted by recent work from Amyris in collaboration with the U.S. Department of Defense. Detailed in Green Chemistry, their bio-engineering platform combines an adaptable yeast chassis with automated strain screening and high-throughput fermentation to produce multi-gram quantities of complex, targeted sesquiterpenes in as little as ninety days. Investigating six distinct fermentation-derived molecules for applications ranging from optical materials to aviation, the standout result was a high-performance jet blendstock synthesized from biosynthetic patchouli oil that demonstrated a volumetric heat of combustion 18.7 percent higher than the lower specification limit for Jet-A. This represents a profound conceptual pivot: rather than tasking biology with laboriously replicating the exact hydrocarbon profile of fossil crude, synthetic biology enables us to design mission-specific molecules optimized for higher performance and energy density, effectively miniaturizing part of the traditional refinery’s chemical synthesis capability down into the genetic code of a single living cell.

The second attack approaches the problem from the opposite direction, focusing not on customizing the end molecule, but on standardizing the heterogeneous input. In France, Haffner Energy has advanced its thermolysis technology—recently passing key qualification milestones for its H6 generation—to act as a chemical demolition crew that breaks complex, messy biomass feedstocks down into syngas, a clean mixture of hydrogen and carbon monoxide. Syngas functions as the ultimate set of “Molecular Legos,” providing a standardized baseline of elemental building blocks that established catalytic chemistry can readily snap back together into sustainable aviation fuel, biomethanol, or renewable diesel. Instead of hauling low-density organic waste across vast distances to feed a massive central facility, this architectural shift allows modular systems to move toward the regional landscape, reducing localized agricultural or forestry residues into versatile chemical intermediates right where they originate.

The third and perhaps most provocative leap comes from MIT spin-out Emvolon, which has taken internal combustion engines—the iconic, mass-produced endpoint of the petroleum supply chain—and inverted their purpose under the direct mandate of “turning automotive engines into chemical reactors.” By deploying modified engine assemblies to remote or stranded gas sources like landfills and wastewater facilities, their self-powered modular systems convert localized methane directly into liquid methanol on site, which can then be easily transported in standard isotankers. Rather than dragging a dispersed resource across a complex logistics tail to a giant refinery, Emvolon places the refinery directly at the resource, demonstrating that one of the most ubiquitous mechanical assets of the industrial age can be turned around and told: you are the processing plant now.

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Yet while centralization undeniably wins the peacetime economic argument on pure cost per barrel, a military operational framework introduces a very different variable: systemic vulnerability under active disruption. A giant, highly centralized refinery is a masterpiece of economic efficiency, but it is also an immobile, easily targeted single point of failure; similarly, a long, consolidated fuel-supply tail crossing predictable maritime choke points represents a critical vulnerability in contested environments. Distributed conversion does not make infrastructure immune to attack, but it fundamentally alters the mathematics of loss—replacing catastrophic failure with graceful degradation, where the elimination of a single modular unit removes a fraction of localized capacity rather than crippling an entire theater of operations. READ MORE

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Excerpt from Amyris: Amyris' precision fermentation platform enables partners access to materials that are uniquely available through biomanufacturing

Key Takeaways

Amyris researchers built a modular precision fermentation platform which enables rapid production of sesquiterpenes, delivering high-purity materials not available through conventional production methods.
Collaborators at the Naval Air Warefare Center, Weapons Division (NAWCWD) and the Air Force Research Laboratory (AFRL) tested these molecules across a variety of performance applications, including advanced optical materials, aviation fuels, and elastomers.
Applications testing showed these biomanufactured building blocks can match, or in some cases exceed, the performance of conventionally produced counterparts.
The results show the potential of biological chemistry in expanding the viable chemical space for sustainable materials discovery and design.

Today (August 17, 2026), Amyris and scientists from NAWCWD and AFRL published a new peer-reviewed study in the Royal Society of Chemistry journal Green Chemistry, evaluating sesquiterpenes across defense-related material applications.

With their structural diversity and unique chemical properties, materials scientists have long theorized about the potential of sesquiterpenes across applications. However, sourcing them at the purity and scale needed for testing has been a persistent barrier. Moreover, there was little impetus to seriously investigate these applications before a technology existed that could deliver reliable, industrial-scale sourcing.

Biotechnology as a tool for materials innovation

This changed in the last 15 years, when Amyris demonstrated robust, high-purity, commercial-scale production of numerous sesquiterpenes, reviving interest in the potential of sesquiterpenes in materials applications.

"Synthetic biology is a powerful technique to produce novel molecules that can be challenging to synthesize via conventional synthetic chemistry," said Ben Harvey, Chief Scientist for High-Performance Fuels and Composites at the Naval Air Warfare Center, Weapons Division (NAWCWD), and co-author of the research article. "The unique functionality of bio-based molecules can be used to generate new fuels and polymers that outperform conventional materials."

"Synthetic biology is a powerful technique to produce novel molecules that can be challenging to synthesize via conventional synthetic chemistry."- Ben Harvey, SSTM Distinguished Scientist at the Naval Air Warfare Center, Weapons Division (NAWCWD)

In the new Green Chemistry publication, titled "Use of a Synthetic Biology Pipeline to Rapidly Generate Sesquiterpenes for Chemical Applications Testing," Amyris scientists describe a modular production platform for high-titer sesquiterpene production, enabling rapid generation of high-purity samples for further applications testing. "The pipeline we built on Amyris' core infrastructure enabled us to go from synthase selection to purified, decagram quantities for applications testing in as little as 90 days," said Simone Mantovani, senior scientist and lead author of the article. "Several of the compounds are not previously available through conventional production methods at any relevant quantity, demonstrating how biotechnology is increasingly relevant as a tool for materials innovation."

Enabling differentiated performance through bio-based building blocks

NAWCWD and AFRL then tested six sesquiterpenes across fuel, polymer, and liquid crystal applications. Patchoulane was evaluated as an aviation fuel; caryophyllene, humulene, and germacrene A were explored for their polymerization potential via ring-opening metathesis polymerization (ROMP) and cationic mechanisms; and delta guaiene, delta cadinene, germacrene A and caryophyllene were tested as chiral dopants for cholesteric liquid crystal (CLC) systems. The renewable molecules matched, and in some cases exceeded, the properties of their conventional petrochemical counterparts.

Harvey notes that materials such as these could eventually improve both the performance and sustainability of defense-related applications. For example, said Harvey, "Biosynthetic fuels have the potential to increase the range and performance of both commercial and military jet aircraft while reducing emissions. Elastomers have applications for a myriad of products from solid rocket motors to more mundane components such as tires, seals, gaskets, hoses, and footwear."

Expanding the viable chemical space for sustainable materials design

By linking scalable biosynthesis directly to materials performance, the study expands the viable chemical space for sustainable materials design. "It's exciting to us to leverage our world-leading sesquiterpene platform to enable rapid sample generation for our applications partners at the Navy and Air Force," said Adam Meadows, Director of Data Science at Amyris, and senior author on the study. "Their exploration of new applications and downstream chemistry for this class of biomolecules, combined with Amyris's proven biomanufacturing platform, means that application breakthroughs have a viable manufacturing path to real impact on the world."

The paper's authors see high potential in combining biomanufacturing with synthetic chemistry. As Harvey explains, "We are particularly interested in hybrid approaches that combine synthetic biology with chemical catalysis to develop new materials. This strategy, in combination with AI prediction of fuel/material properties and the use of retrosynthetic algorithms to trace those materials back to readily available biosynthetic precursors, holds the promise of rapidly accelerating material development while reducing costs."

Amyris, NAWCWD and AFRL have collaborated since 2018 on projects funded by DARPA, the Office of the Undersecretary of War for Research and Engineering (OUSW(R&E)) and the Office of Naval Research (ONR), through a cooperative research and development agreement and government contracts. Harvey notes that "Amyris was selected as a partner because of their proven ability to produce high-purity biosynthetic materials at a relevant scale for advanced research and development."

‍About Amyris, Inc.
Amyris is a vertically integrated biomanufacturing company that creates specialty molecules for a range of industries, including flavors and fragrances, advanced materials, beauty and personal care, food, and more. Using advanced fermentation technology, Amyris customizes, creates, and manufactures ingredients that enhance lives, protect ecosystems, and take products to the next level of performance.

Amyris was founded in 2003 with a bold humanitarian vision to transform access to a life-saving antimalarial compound using biotechnology. Now, with over two decades of proven commercial success, Amyris's proprietary platform is redefining the precision, consistency, and sustainability that is possible with renewable biological chemistry. For more information, please visit http://www.amyris.com. READ MORE

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