
From The DOE’s Lawrence Berkeley National Laboratory
June 30, 2022
Aliyah Kovner
akovner@lbl.gov

Scientists turned to an oddball bacterial molecule that looks like a jaw full of sharp teeth to create a new type of fuel that could be used for all types of vehicles including rockets. (Credit: Jenny Nuss/Berkeley Lab)
Converting petroleum into fuels involves crude chemistry first invented by humans in the 1800s. Meanwhile, bacteria have been producing carbon-based energy molecules for billions of years. Which do you think is better at the job?
Well aware of the advantages biology has to offer, a group of biofuel experts led by Lawrence Berkeley National Laboratory took inspiration from an extraordinary antifungal molecule made by Streptomyces bacteria to develop a totally new type of fuel that has projected energy density greater than the most advanced heavy-duty fuels used today, including the rocket fuels used by NASA.
“This biosynthetic pathway provides a clean route to highly energy-dense fuels that, prior to this work, could only be produced from petroleum using a highly toxic synthesis process,” said project leader Jay Keasling, a synthetic biology pioneer and CEO of the Department of Energy’s Joint BioEnergy Institute (JBEI). “As these fuels would be produced from bacteria fed with plant matter – which is made from carbon dioxide pulled from the atmosphere – burning them in engines will significantly reduce the amount of added greenhouse gas relative to any fuel generated from petroleum.”
The incredible energy potential of these fuel candidate molecules, called POP-FAMEs (for polycylcopropanated fatty acid methyl esters), comes from the fundamental chemistry of their structures. Polycylcopropanated molecules contain multiple triangle-shaped three-carbon rings that force each carbon-carbon bond into a sharp 60-degree angle. The potential energy in this strained bond translates into more energy for combustion than can be achieved with the larger ring structures or carbon-carbon chains typically found in fuels. In addition, these structures enable fuel molecules to pack tightly together in a small volume increasing the mass – and therefore the total energy – of fuel that fits in any given tank.
With petrochemical fuels, you get kind of a soup of different molecules and you don’t have a lot of fine control over those chemical structures. But that’s what we used for a long time and we designed all of our engines to run on petroleum derivatives,” said Eric Sundstrom, an author on the paper describing POP fuel candidates published in the journal Joule and a research scientist at Berkeley Lab’s Advanced Biofuels and Bioproducts Process Development Unit (ABPDU).
“The larger consortium behind this work, Co-Optima, was funded to think about not just recreating the same fuels from biobased feedstocks, but how we can make new fuels with better properties,” said Sundstrom. “The question that led to this is: ‘What kinds of interesting structures can biology make that petrochemistry can’t make?’”
A quest for the ring(s)
Keasling, who is also a professor at UC Berkeley, had his eye on cyclopropane molecules for a long time. He had scoured the scientific literature for organic compounds with three-carbon rings and found just two known examples, both made by Streptomyces bacteria that are nearly impossible to grow in a lab environment. Fortunately, one of the molecules had been studied and genetically analyzed due to interest in its antifungal properties. Discovered in 1990, the natural product is named jawsamycin, because its unprecedented five cyclopropane rings make it look like a jaw filled with pointy teeth.

A culture of the Streptomyces bacteria that makes the jawsamycin. (Credit: Pablo Morales-Cruz)
Keasling’s team, comprised of JBEI and ABPDU scientists, studied the genes from the original strain (S. roseoverticillatus) that encode the jawsamycin-building enzymes and took a deep dive into the genomes of related Streptomyces, looking for a combination of enzymes that could make a molecule with jawsamycin’s toothy rings while skipping the other parts of the structure. Like a baker rewriting recipes to invent the perfect dessert, the team hoped to remix existing bacterial machinery to create a new molecule with ready-to-burn fuel properties.
First author Pablo Cruz-Morales was able to assemble all the necessary ingredients to make POP-FAMEs after discovering new cyclopropane-making enzymes in a strain called S. albireticuli. “We searched in thousands of genomes for pathways that naturally make what we needed. That way we avoided the engineering that may or may not work and used nature’s best solution,” said Cruz-Morales, a senior researcher at the Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark and the co-principal investigator of the yeast natural products lab with Keasling.
Unfortunately, the bacteria weren’t as cooperative when it came to productivity. Ubiquitous in soils on every continent, Streptomyces are famous for their ability to make unusual chemicals. “A lot of the drugs used today, such as immunosuppressants, antibiotics, and anti-cancer drugs, are made by engineered Streptomyces,” said Cruz-Morales. “But they are very capricious and they’re not nice to work with in the lab. They’re talented, but they’re divas.” When two different engineered Streptomyces failed to make POP-FAMEs in sufficient quantities, he and his colleagues had to copy their newly arranged gene cluster into a more “tame” relative.
The resulting fatty acids contain up to seven cyclopropane rings chained on a carbon backbone, earning them the name fuelimycins. In a process similar to biodiesel production, these molecules require only one additional chemical processing step before they can serve as a fuel.
Now we’re cooking with cyclopropane
Though they still haven’t produced enough fuel candidate molecules for field tests – “you need 10 kilograms of fuel to do a test in a real rocket engine, and we’re not there yet,” Cruz-Morales explained with a laugh – they were able to evaluate Keasling’s predictions about energy density.
Colleagues at The DOE’s Pacific Northwest National Laboratory analyzed the POP-FAMEs with nuclear magnetic resonance spectroscopy to prove the presence of the elusive cyclopropane rings. And collaborators at The DOE’s Sandia National Laboratories used computer simulations to estimate how the compounds would perform compared to conventional fuels.
The simulation data suggest that POP fuel candidates are safe and stable at room temperature and will have energy density values of more than 50 megajoules per liter after chemical processing. Regular gasoline has a value of 32 megajoules per liter, JetA, the most common jet fuel, and RP-1, a popular kerosene-based rocket fuel, have around 35.
During the course of their research, the team discovered that their POP-FAMEs are very close in structure to an experimental petroleum-based rocket fuel called Syntin developed in the 1960s by the Soviet Union space agency and used for several successful Soyuz rocket launches in the 70s and 80s. Despite its powerful performance, Syntin manufacturing was halted due to high costs and the unpleasant process involved: a series of synthetic reactions with toxic byproducts and an unstable, explosive intermediate.
“Although POP-FAMEs share similar structures to Syntin, many have superior energy densities. Higher energy densities allow for lower fuel volumes which in a rocket can allow for increased payloads and decreased overall emissions,” said author Alexander Landera, a staff scientist at Sandia. One of the team’s next goals to create a process to remove the two oxygen atoms on each molecule, which add weight but no combustion benefit. “When blended into a jet fuel, properly deoxygenated versions of POP-FAMEs may provide a similar benefit,” Landera added.
Since publishing their proof-of-concept paper, the scientists have begun work to increase the bacteria’s production efficiency even further to generate enough for combustion testing. They are also investigating how the multi-enzyme production pathway could be modified to create polycyclopropanated molecules of different lengths. “We’re working on tuning the chain length to target specific applications,” said Sundstrom. “Longer chain fuels would be solids, well-suited to certain rocket fuel applications, shorter chains might be better for jet fuel, and in the middle might be a diesel-alternative molecule.”
Author Corinne Scown, JBEI’s Director of Technoeconomic Analysis, added: “Energy density is everything when it comes to aviation and rocketry and this is where biology can really shine. The team can make fuel molecules tailored to the applications we need in those rapidly evolving sectors.”
Eventually, the scientists hope to engineer the process into a workhorse bacteria strain that could produce large quantities of POP molecules from plant waste food sources (like inedible agricultural residue and brush cleared for wildfire prevention), potentially making the ultimate carbon-neutral fuel.
See the full article here .

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Bringing Science Solutions to the World
In the world of science, The Lawrence Berkeley National Laboratory (Berkeley Lab) is synonymous with “excellence.” Thirteen Nobel prizes are associated with Berkeley Lab. Seventy Lab scientists are members of the The National Academy of Sciences, one of the highest honors for a scientist in the United States. Thirteen of our scientists have won the National Medal of Science, our nation’s highest award for lifetime achievement in fields of scientific research. Eighteen of our engineers have been elected to the The National Academy of Engineering, and three of our scientists have been elected into the Institute of Medicine. In addition, Berkeley Lab has trained thousands of university science and engineering students who are advancing technological innovations across the nation and around the world.
Berkeley Lab is a member of the national laboratory system supported by the U.S. Department of Energy through its Office of Science. It is managed by the University of California and is charged with conducting unclassified research across a wide range of scientific disciplines. Located on a 202-acre site in the hills above the University of California- Berkeley campus that offers spectacular views of the San Francisco Bay, Berkeley Lab employs approximately 3,232 scientists, engineers and support staff. The Lab’s total costs for FY 2014 were $785 million. A recent study estimates the Laboratory’s overall economic impact through direct, indirect and induced spending on the nine counties that make up the San Francisco Bay Area to be nearly $700 million annually. The Lab was also responsible for creating 5,600 jobs locally and 12,000 nationally. The overall economic impact on the national economy is estimated at $1.6 billion a year. Technologies developed at Berkeley Lab have generated billions of dollars in revenues, and thousands of jobs. Savings as a result of Berkeley Lab developments in lighting and windows, and other energy-efficient technologies, have also been in the billions of dollars.
Berkeley Lab was founded in 1931 by Ernest Orlando Lawrence, a University of California-Berkeley physicist who won the 1939 Nobel Prize in physics for his invention of the cyclotron, a circular particle accelerator that opened the door to high-energy physics. It was Lawrence’s belief that scientific research is best done through teams of individuals with different fields of expertise, working together. His teamwork concept is a Berkeley Lab legacy that continues today.
History
1931–1941
The laboratory was founded on August 26, 1931, by Ernest Lawrence, as the Radiation Laboratory of the University of California, Berkeley, associated with the Physics Department. It centered physics research around his new instrument, the cyclotron, a type of particle accelerator for which he was awarded the Nobel Prize in Physics in 1939.
LBNL 88 inch cyclotron.
LBNL 88 inch cyclotron.
Throughout the 1930s, Lawrence pushed to create larger and larger machines for physics research, courting private philanthropists for funding. He was the first to develop a large team to build big projects to make discoveries in basic research. Eventually these machines grew too large to be held on the university grounds, and in 1940 the lab moved to its current site atop the hill above campus. Part of the team put together during this period includes two other young scientists who went on to establish large laboratories; J. Robert Oppenheimer founded DOE’s Los Alamos Laboratory, and Robert Wilson founded Fermi National Accelerator Laborator.
1942–1950
Leslie Groves visited Lawrence’s Radiation Laboratory in late 1942 as he was organizing the Manhattan Project, meeting J. Robert Oppenheimer for the first time. Oppenheimer was tasked with organizing the nuclear bomb development effort and founded today’s Los Alamos National Laboratory to help keep the work secret. At the RadLab, Lawrence and his colleagues developed the technique of electromagnetic enrichment of uranium using their experience with cyclotrons. The “calutrons” (named after the University) became the basic unit of the massive Y-12 facility in Oak Ridge, Tennessee. Lawrence’s lab helped contribute to what have been judged to be the three most valuable technology developments of the war (the atomic bomb, proximity fuse, and radar). The cyclotron, whose construction was stalled during the war, was finished in November 1946. The Manhattan Project shut down two months later.
1951–2018
After the war, the Radiation Laboratory became one of the first laboratories to be incorporated into the Atomic Energy Commission (AEC) (now Department of Energy . The most highly classified work remained at Los Alamos, but the RadLab remained involved. Edward Teller suggested setting up a second lab similar to Los Alamos to compete with their designs. This led to the creation of an offshoot of the RadLab (now the Lawrence Livermore National Laboratory) in 1952. Some of the RadLab’s work was transferred to the new lab, but some classified research continued at Berkeley Lab until the 1970s, when it became a laboratory dedicated only to unclassified scientific research.
Shortly after the death of Lawrence in August 1958, the UC Radiation Laboratory (both branches) was renamed the Lawrence Radiation Laboratory. The Berkeley location became the Lawrence Berkeley Laboratory in 1971, although many continued to call it the RadLab. Gradually, another shortened form came into common usage, LBNL. Its formal name was amended to Ernest Orlando Lawrence Berkeley National Laboratory in 1995, when “National” was added to the names of all DOE labs. “Ernest Orlando” was later dropped to shorten the name. Today, the lab is commonly referred to as “Berkeley Lab”.
The Alvarez Physics Memos are a set of informal working papers of the large group of physicists, engineers, computer programmers, and technicians led by Luis W. Alvarez from the early 1950s until his death in 1988. Over 1700 memos are available on-line, hosted by the Laboratory.
The lab remains owned by the Department of Energy , with management from the University of California. Companies such as Intel were funding the lab’s research into computing chips.
Science mission
From the 1950s through the present, Berkeley Lab has maintained its status as a major international center for physics research, and has also diversified its research program into almost every realm of scientific investigation. Its mission is to solve the most pressing and profound scientific problems facing humanity, conduct basic research for a secure energy future, understand living systems to improve the environment, health, and energy supply, understand matter and energy in the universe, build and safely operate leading scientific facilities for the nation, and train the next generation of scientists and engineers.
The Laboratory’s 20 scientific divisions are organized within six areas of research: Computing Sciences; Physical Sciences; Earth and Environmental Sciences; Biosciences; Energy Sciences; and Energy Technologies. Berkeley Lab has six main science thrusts: advancing integrated fundamental energy science; integrative biological and environmental system science; advanced computing for science impact; discovering the fundamental properties of matter and energy; accelerators for the future; and developing energy technology innovations for a sustainable future. It was Lawrence’s belief that scientific research is best done through teams of individuals with different fields of expertise, working together. His teamwork concept is a Berkeley Lab tradition that continues today.
Berkeley Lab operates five major National User Facilities for the DOE Office of Science:
The Advanced Light Source (ALS) is a synchrotron light source with 41 beam lines providing ultraviolet, soft x-ray, and hard x-ray light to scientific experiments.
LBNL/ALS
DOE’s Lawrence Berkeley National Laboratory Advanced Light Source .
The ALS is one of the world’s brightest sources of soft x-rays, which are used to characterize the electronic structure of matter and to reveal microscopic structures with elemental and chemical specificity. About 2,500 scientist-users carry out research at ALS every year. Berkeley Lab is proposing an upgrade of ALS which would increase the coherent flux of soft x-rays by two-three orders of magnitude.
The DOE Joint Genome Institute supports genomic research in support of the DOE missions in alternative energy, global carbon cycling, and environmental management. The JGI’s partner laboratories are Berkeley Lab, DOE’s Lawrence Livermore National Laboratory, DOE’s Oak Ridge National Laboratory (ORNL), DOE’s Pacific Northwest National Laboratory (PNNL), and the HudsonAlpha Institute for Biotechnology . The JGI’s central role is the development of a diversity of large-scale experimental and computational capabilities to link sequence to biological insights relevant to energy and environmental research. Approximately 1,200 scientist-users take advantage of JGI’s capabilities for their research every year.
The LBNL Molecular Foundry [above] is a multidisciplinary nanoscience research facility. Its seven research facilities focus on Imaging and Manipulation of Nanostructures; Nanofabrication; Theory of Nanostructured Materials; Inorganic Nanostructures; Biological Nanostructures; Organic and Macromolecular Synthesis; and Electron Microscopy. Approximately 700 scientist-users make use of these facilities in their research every year.
The DOE’s NERSC National Energy Research Scientific Computing Center is the scientific computing facility that provides large-scale computing for the DOE’s unclassified research programs. Its current systems provide over 3 billion computational hours annually. NERSC supports 6,000 scientific users from universities, national laboratories, and industry.
DOE’s NERSC National Energy Research Scientific Computing Center at Lawrence Berkeley National Laboratory.

Cray Cori II supercomputer at National Energy Research Scientific Computing Center at DOE’s Lawrence Berkeley National Laboratory, named after Gerty Cori, the first American woman to win a Nobel Prize in science.
NERSC Hopper Cray XE6 supercomputer.
NERSC Cray XC30 Edison supercomputer.
NERSC GPFS for Life Sciences.
The Genepool system is a cluster dedicated to the DOE Joint Genome Institute’s computing needs. Denovo is a smaller test system for Genepool that is primarily used by NERSC staff to test new system configurations and software.
NERSC PDSF computer cluster in 2003.
PDSF is a networked distributed computing cluster designed primarily to meet the detector simulation and data analysis requirements of physics, astrophysics and nuclear science collaborations.
Cray Shasta Perlmutter SC18 AMD Epyc Nvidia pre-exascale supercomputer.
NERSC is a DOE Office of Science User Facility.



The DOE’s Energy Science Network is a high-speed network infrastructure optimized for very large scientific data flows. ESNet provides connectivity for all major DOE sites and facilities, and the network transports roughly 35 petabytes of traffic each month.
Berkeley Lab is the lead partner in the DOE’s Joint Bioenergy Institute (JBEI), located in Emeryville, California. Other partners are the DOE’s Sandia National Laboratory, the University of California (UC) campuses of Berkeley and Davis, the Carnegie Institution for Science , and DOE’s Lawrence Livermore National Laboratory (LLNL). JBEI’s primary scientific mission is to advance the development of the next generation of biofuels – liquid fuels derived from the solar energy stored in plant biomass. JBEI is one of three new U.S. Department of Energy (DOE) Bioenergy Research Centers (BRCs).
Berkeley Lab has a major role in two DOE Energy Innovation Hubs. The mission of the Joint Center for Artificial Photosynthesis (JCAP) is to find a cost-effective method to produce fuels using only sunlight, water, and carbon dioxide. The lead institution for JCAP is the California Institute of Technology and Berkeley Lab is the second institutional center. The mission of the Joint Center for Energy Storage Research (JCESR) is to create next-generation battery technologies that will transform transportation and the electricity grid. DOE’s Argonne National Laboratory leads JCESR and Berkeley Lab is a major partner.
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