Biologist Joey Davis explores how cells build complex structures

Ribosomes, the cellular machines that assemble proteins, are made from dozens of proteins and RNA molecules. Putting all of those pieces together is a complex puzzle — one that MIT Associate Professor Joey Davis PhD ’10 revels in trying to solve.

Understanding how these structures form and later break down could help researchers learn more about how disruptions of these fundamental processes can lead to disease. But, as Davis points out, it’s also an interesting biological question.

“Our long-term goal is to really understand how the natural world assembles these huge complexes rapidly and efficiently. It’s a fundamentally interesting question to think about how these things get put together,” he says.

His work has helped reveal that unlike building a house, which happens in a prescribed sequence of steps — pouring the foundation, building the frame, putting on the roof, then doing electrical and plumbing work — ribosomes can be assembled in a more flexible way. Cells can even skip an assembly step and then come back to it later.

“In these natural systems, it seems like the assembly pathways are much more dynamic and flexible,” he says. “It appears that evolution has selected pathways that aren’t strictly ordered in the way we would think about an assembly line, where you always put in one component, then the next, and then the next. We’re excited to understand the selective advantages of such approaches.”

A love of discovery

Davis’ interest in how things are put together developed early in life, inspired by his father, a carpenter who framed houses. During the mid-1980s, the family moved from Colorado to Southern California, where his father worked in construction during a housing boom there.

“I was always interested in building things, which I think probably came from being around my dad and other builders,” Davis says.

As an undergraduate at the University of California at Berkeley, where he majored in computer science and biological engineering, Davis’ interests turned toward smaller scales, in the realm of cells and molecules. During his junior year, he started working in the lab of chemistry professor Michael Marletta, who studies molecular-level biological interactions.

In the lab, Davis investigated how enzymes that contain heme are able to preferentially bind to either oxygen or nitric oxide, two gases that are very similar in structure. That work kindled a love of studying the natural world and pursuing discoveries in fundamental science.

“Being in the Marletta lab and seeing students and postdocs that were really passionate about these problems had a big impact on me,” Davis says. “The goal was to understand the fundamentals of how molecular discrimination works, and the idea of discovery for the sake of discovery was thrilling.”

After graduating from Berkeley, Davis spent another year working in Marletta’s lab, and then a year working odd jobs, before heading to MIT to pursue a PhD in biology. There, he worked with Professor Bob Sauer, now emeritus, who studied the relationship between protein structure and function, with a particular focus on the molecular machines that degrade or remodel proteins.

Davis’ thesis research centered on enzymes called AAA proteases, which remove damaged proteins from cellular membranes and send them to cell organelles that break them down. In addition to studying the structure and function of the proteases, Davis worked on ways to engineer them to tag specific proteins for destruction.

That work led him into synthetic biology, which he used to develop genetic parts that drive production of proteins of interest. Some of those parts ended up being used by the biotech startup Ginkgo Bioworks, where Davis took a job as a senior scientist after graduating.

Working at Ginkgo Bioworks allowed Davis to stay in Boston while his partner finished her PhD. The couple then moved back to California, where Davis worked as a postdoc at Scripps Research, which was home to one of the first direct electron detection cameras for cryo-electron microscopy (cryo-EM). These detectors allow researchers to generate structures with near atomic resolution. At Scripps, Davis began using them to study ribosomes as they were being assembled.

Peering into the ribosome

After joining the MIT faculty in 2017, Davis continued his work on ribosomes and assembled a lab group that includes students from a variety of backgrounds who work together to develop new ways to explore biological phenomena.

“I have a mix of method developers and biologists in the group, and the work from each of them informs each other,” Davis says. “My lab goes back and forth between building sets of tools to answer biological questions, and then as we’re answering those questions, it motivates the next generation of tool development.”

During ribosome assembly, RNA molecules fold themselves into the correct shapes, creating docking sites for proteins to attach. Then, more RNA molecules come in and fold themselves into the structure.

“It’s a beautifully coupled process by which the cell folds hundreds of RNA helices and binds on the order of 50 proteins, and it does it in two minutes from start to finish. E. coli does this 100,000 times per hour, and it’s amazing how rapid and efficient the process is,” Davis says.

Cryo-EM allows scientists to capture this process in minute detail. It can be used to take hundreds of thousands of two-dimensional images of ribosome samples frozen in a thin layer of ice, from different angles. Computer algorithms then piece together these images into a three-dimensional representation of the ribosome.

To gain insight into how ribosomes are assembled, researchers can stall the process at different points and then analyze the resulting structures. In 2021, Davis’s lab developed a new method called CryoDRGN, which uses neural networks to analyze cryo-EM data and generate the full ensemble of structures that were present in the sample.

This work has shown that when certain steps of ribosome assembly are blocked, many different structures result, suggesting that the assembly can occur in a variety of ways.

In future work, Davis aims to dramatically increase the throughput of cryo-EM to generate datasets of protein structures that could help improve the AI-based models that are now used to predict protein structures.

“There are still huge swaths of sequence space that these models are very poor at predicting, but if we could collect data on those sequences en masse, that could potentially serve as key training data for a next-generation protein structure prediction method that could fill out that space,” he says.

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Rett syndrome study highlights potential for personalized treatments

Although many studies approach the developmental disorder Rett syndrome as a single condition arising from general loss of function in the gene MECP2, a new study by neuroscientists in The Picower Institute for Learning and Memory at MIT shows that two different mutations of the gene caused many distinct abnormalities in lab cultures. Moreover, correcting key differences made by each mutation required different treatments.

“Individual mutations matter,” says Mriganka Sur, senior author of the new open-accdess study in Nature Communications and the Newton Professor in the Picower Institute and the Department of Brain and Cognitive Sciences. “This is an approach to personalizing treatment, even for a single-gene disorder.”

The study employed advanced 3D human brain tissue cultures called “organoids” or “minibrains” derived from skin cells or blood cells donated by Rett syndrome patients with each mutation. Lead author Tatsuya Osaki, a Picower Institute research scientist, says that the organoids’ ability to model the specific consequences of each mutation enabled him to gain mutation-specific insights that haven’t emerged in prior studies, where scientists just knocked out MECP2 overall. The organoids also provided a novel opportunity to understand how each mutation affected different cell types and their interactions.

Distinct effects

More than 800 mutations in MECP2 can cause Rett syndrome, but just eight account for more than 60 percent of cases. Sur and Osaki chose one of these, R306C, which involves a difference of just one DNA base pair (916C>T), because it represents 7-8 percent of Rett syndrome cases. The other mutation they chose, V247X, is much more rare and severe because it cuts off production of the gene’s protein product by a single DNA base deletion (705Gdel), leaving the protein not just errant, but incomplete.

In organoids cultured for three months, each mutation produced some common but also sometimes distinct consequences compared to control organoids with non-mutated MECP2. For many of their experiments, the team used “three-photon” microscopes capable of cellular-level resolution all the way through the organoids’ approximate 1 millimeter thickness, resolving both their structure (via “third-harmonic generation” imaging), and the live activity patterns of their neurons (via calcium fluorescence).

For instance, the scientists observed that the V247X organoids exhibited several structural differences from their controls — they were larger and had different thicknesses of various layers — but the R306C ones were much more like their controls. Organoids harboring either mutation exhibited less-developed axon projections from their neurons, compared to their control comparators.

Looking at properties of neural activity and connectivity in the organoids, the scientists found some similar deficits across both mutations. Both showed reduced spiking activity and synchronicity between neurons compared to in their controls.

But when the scientists looked at other properties, the organoids started to diverge from each other. In particular, an indication of the efficiency of their network structure called “small-world propensity” (SWP) was decreased in R306C organoids, and increased in V247X ones, compared to controls. This means that both mutations altered the development of typical network structures for information processing, but in different directions.

To ensure that their results were meaningful for Rett syndrome patients, the team collaborated with Charles Nelson at Boston Children’s Hospital, whose team measured EEG in several children with different Rett mutations. Although the sample was small, the researchers measured indications that the SWP property in the EEG readings was altered in the volunteers, much like in the organoids.

Finally, by labeling excitatory neurons to flash in one color and inhibitory neurons to flash in a different color, the scientists were able to see that connectivity between the different neural types differed significantly from controls in the V247X organoids.

Treatment tests

All the testing showed that each mutation caused several changes in organoid structure, activity, and connectivity, and that the deviations were often particular to the specific mutation.

To understand how these differences emerged, and how they might be corrected, Sur and Osaki’s team turned to examining how the cells in each kind of organoid might be expressing their genes differently than controls. Differences in gene expression often lead to alterations of key molecular pathways in cells that can disrupt their activity and function. Analysis with a technique called single cell RNA sequencing indeed yielded hundreds of differences in each organoid type, where some genes were expressed more than in controls while others were underexpressed.

For instance, the analyses revealed that in R306C organoids a gene called HDAC2 was overexpressed. That protein is known for repressing expression of other genes. Meanwhile, in the V247X organoids, the scientists found reduced expression of genes for some receptors of the inhibitory neurotransmitter GABA. These organoids also showed defects in the function of astrocyte cells, which support many aspects of neural function.

Organoids with either mutation also exhibited aberrations in molecular pathways that enable the development of circuit connections between neurons, called synapses.

Given the specific defects they observed, the scientists decided to treat the organoids with a drug that can inhibit HDAC2 activity and another that increases GABA’s efficacy. The HDAC2 inhibitor restored neuronal activity and SWP to normal levels in the R306C organoids, and the GABA “agonist” baclofen restored SWP to control levels in the V247X organoids.

Osaki notes each of the treatment drugs has already been studied in other disease contexts, meaning they are well-understood drugs that could be repurposed.

Now that the researchers have developed an organoid platform for dissecting individual mutations’ consequences, identifying both their roots and testing treatments, they plan to apply it to studying four more mutations, Sur says, comparing all of them against a standardized control organoid.

In addition to Sur, Osaki, and Nelson, the paper’s other authors are Chloe Delepine, Yuma Osako, Devorah Kranz, April Levin, and Michela Fagiolini.

The National Institutes of Health, a MURI grant, The Freedom Together Foundation, and the Simons Foundation provided support for the research.

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It took 40 years for technology to catch up to this zipper design

In 1985, the Innovative Design Fund placed an ad in Scientific American offering up to $10,000 to support clever prototypes for clothing, home decor, and textiles. William Freeman PhD ’92, then an electrical engineer at Polaroid and now an MIT professor, saw it and submitted a novel idea: a three-sided zipper. Instead of fastening pants, it’d be like a switch that seamlessly flips chairs, tents, and purses between soft and rigid states, making them easier to pack and put together.

Freeman’s blueprint was much like a regular zipper, except triangular. On each side, he nailed a belt to connect narrow wooden “teeth” together. A slider wrapping around the device could be moved up to fasten the three strips into place, straightening them into a triangular tube. His proposal was rejected, but Freeman patented his prototype and stored it in his garage in the hopes it might come in handy one day.

Nearly 40 years later, MIT Computer Science and Artificial Intelligence Laboratory (CSAIL) researchers wanted to revive the project to create items with “tunable stiffness.” Prior attempts to adjust that weren’t easily reversible or required manual assembly, so CSAIL built an automated design tool and adaptable fastener called the “Y-zipper.” The scientists’ software program helps users customize three-sided zippers, which it then builds on its own in a 3D printer using plastics. These devices can be attached or embedded into camping equipment, medical gear, robots, and art installations for more convenient assembly.

“A regular zipper is great for closing up flat objects, like a jacket, but Freeman ideated something more dynamic. Using current fabrication technology, his mechanism can transform more complex items,” says MIT postdoc and CSAIL researcher Jiaji Li, who is a lead author on an open-access paper presenting the project. “We’ve developed a process that builds objects you can rapidly shift from flexible to rigid, and you can be confident they’ll work in the real world.”

Why zippers?

Users can customize how the fasteners look when they’re zipped up in CSAIL’s software program; they can select the length of each strip, as well as the direction and angle at which they’ll bend. They can also choose from one of four motion “primitives” to select how the zipper will appear when it’s zipped up: straight, bent (similar to an arch), coiled (resembling a spring), or twisted (looks like screws).

The Y-zipper that results will appear to “shape-shift” in the real world. When unzipped, it can look like a squid with three sprawling tentacles, and when you close it up, it becomes a more compact structure (like a rod, for instance). This flexibility could be useful when you’re traveling — take pitching a tent, for example. The process can take up to six minutes to do alone, but with the Y-zipper’s help, it can be done in one minute and 20 seconds. You simply attach each arm to a side of the tent, supporting the structure from the top so that the zipper seemingly pops the canopy into place. 

This seamless transition could also unlock more flexible wearables, often useful in medical scenarios. The team wrapped the Y-zipper around a wrist cast, so that a user could loosen it during the day, and zip it up at night to prevent further injuries. In turn, a seemingly stiff device can be made more comfortable, adjusting to a patient’s needs.

The system can also aid users in crafting technology that moves at the push of a button. One can attach a motor to the Y-zipper after fabrication to automate the zipping process, which helps build things like an adaptive robotic quadruped. The robot could potentially change the size of its legs, tightening up into taller limbs and unzipping when it needs to be lower to the ground. Eventually, such rapid adjustments could help the robot explore the uneven terrain of places like canyons or forests. Actuated Y-zippers can also build dynamic art installations — for example, the team created a long, winding flower that “bloomed” thanks to a static motor zipping up the device.

Mastering the material

While Li and his colleagues saw the creative potential of the Y-zipper, it wasn’t yet clear how durable it would be. Could they sustain daily use?

The team ran a series of stress tests to find out. First, they evaluated the strength and flexibility of polylactic acid (PLA) and thermoplastic polyurethane (TPU), two plastics commonly used in 3D printing. Using a machine that bent the Y-zippers down, they found that PLA could handle heavier loads, while TPU was more pliable.

In another experiment, CSAIL researchers used an actuator to continuously open and close the Y-zipper to see how long it’d take to snap. Some 18,000 cycles of zipping and unzipping later, they finally broke. Y-zipper’s secret to durability, according to 3D simulations: its elastic structure, which helps distribute the stress of heavy loads.

Despite these findings, Li envisions an even more durable three-sided zipper using stronger materials, like metal. They may also make the zippers bigger for larger-scale projects, but that’s not yet possible with their current 3D printing platform.

Jiaji also notes that some applications remain unexplored, like space exploration, wherein Y-zipper’s tentacles could be built into a spacecraft to grab nearby rock samples. Likewise, the zippers could be embedded into structures that can be assembled rapidly, helping relief workers quickly set up shelters or medical tents during natural disasters and rescues.

“Reimagining an everyday zipper to tackle 3D morphological transitions is a brilliant approach to dynamic assembly,” says Zhejiang University assistant professor Guanyun Wang, who wasn’t involved in the paper. “More importantly, it effectively bridges the gap between soft and rigid states, offering a highly scalable and innovative fabrication approach that will greatly benefit the future design of embodied intelligence.”

Li and Freeman wrote the paper with Tianjin University PhD student Xiang Chang and MIT CSAIL colleagues: PhD student Maxine Perroni-Scharf; undergraduate Dingning Cao; recent visiting researchers Mingming Li (Zhejiang University), Jeremy Mrzyglocki (Technical University of Munich), and Takumi Yamamoto (Keio University); and MIT Associate Professor Stefanie Mueller, who is a CSAIL principal investigator and senior author on the work. Their research was supported, in part, by a postdoctoral research fellowship from Zhejiang University and the MIT-GIST Program.

The researchers’ work was presented at the ACM’s ​​Computer-Human Interaction (CHI) conference on Human Factors in Computing Systems in April.

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How chromatin movement helps control gene expression

Gene expression is controlled, in part, by the interactions between genes and regulatory elements located along the genome. Those interactions depend on the ability of chromatin — a mix of DNA and proteins — to move around within a crowded space.

In a new study, MIT researchers have measured chromatin movement at timescales ranging from hundreds of microseconds to hours, allowing them to rigorously quantify those dynamics for the first time.

Their analysis revealed that chromatin can exist in two different categories: In one, chromatin moves in a constrained way that allows it to primarily contact only neighboring regions of the genome; in the other, chromatin moves more freely and contacts regions that are farther away, but only over longer timescales.

The findings offer insight into how gene expression is regulated, as well as how chromatin segments come together for other processes such as DNA repair, the researchers say.

“Because we were able to look at chromatin dynamics for the first time at these very fast timescales, and also for the first time across the full dynamic range, we were able to observe chromatin motion over a range that just wasn’t possible before,” says Anders Sejr Hansen, an associate professor of biological engineering at MIT and the senior author of the new study, which appears today in Nature Structural and Molecular Biology.

The paper’s lead authors are MIT postdoc Matteo Mazzocca, Domenic Narducci PhD ’25, and Simon Grosse-Holz PhD ’23. Jessica Matthias, chief commercial officer of Abberior Instruments, and Tatiana Karpova, manager of the National Cancer Institute Optical Microscopy Core, are also authors of the paper.

Constrained movement

In textbooks, chromatin is often depicted as a static structure within the cell nucleus, but in reality, it is constantly moving. Those movements are necessary for genes to interact with DNA regulatory sequences such as enhancers, which can be as far as 1 million base pairs away. They also ensure that when DNA breaks occur, the two ends of DNA can encounter each other to be repaired.

“Chromatin dynamics are foundational to all processes in the nucleus, and especially processes that involve two things finding each other. That’s important in DNA repair, gene regulation, recombination, or moving a particular gene to the right compartment of the nucleus,” Hansen says.

The movement of any particular location on the genome, or locus, is constrained by the fact that DNA is a polymer. After moving in any direction, a locus will be pulled back by the DNA on either side of it.

“Chromosomes are polymers. They’re held together by many nucleotides of DNA. Being part of DNA is a little bit like running while holding hands with other people. If a hundred people are holding hands and you, in the middle of the chain, try to run in one direction, you’ll get pulled back,” Hansen says.

This type of behavior is known as subdiffusive movement. Previous studies have yielded conflicting reports on how subdiffusive chromatin is, mainly because the studies were not able to track the movement over a long enough period of time to obtain statistically robust measurements. Because the movements are so small, on the order of nanometers, data needs to be obtained over long dynamic ranges — from milliseconds to hours.

In those earlier studies, researchers used imaging techniques that can track the position of a single molecule over time by comparing images frame by frame. These are useful but can only be used over a small dynamic range because of the limitations of conventional microscopy.

To generate more statistically robust data, the MIT team used MINFLUX — a super-resolution light microscopy technique that can track the movement of tiny objects such as proteins over longer periods of time. This technique was recently developed by Stefan Hell of the Max Planck Institute, a Nobel laureate for his work in super resolution microscopy. In this study, the MIT team became the first to apply this technique to chromatin in living cells.

“MINFLUX allowed us to get around the limitations of conventional microscopy, letting us measure chromatin movement faster and for a longer period of time than ever before,” Narducci says. “To our knowledge, it’s the first time this technique has been used this way.”

Using MINFLUX, the researchers were able to study cells over timescales that covered four orders of magnitude — from 200 microseconds to 10 seconds. And by combining MINFLUX with two traditional imaging techniques, they could track chromatin movement over seven orders of magnitude across time, from hundreds of microseconds to several hours.

“Region of influence”

These studies, performed across several different mouse and human cell types, allowed the researchers to identify two distinct classes of chromatin dynamics. In both classes, over short and intermediate timescales (up to 200 seconds), any given locus tends to move only within about 200 nanometers. This suggests that the subdiffusive pull is stronger than had been previously thought.

“One of the main takeaways is that you have this region of influence where a genomic locus has access to other genomic loci, and this is roughly a couple hundred nanometers large,” Grosse-Holz says. “If loci are much closer together than a couple hundred nanometers, they’re effectively in contact all the time. You get a cutoff at a couple hundred nanometers where everything within that region around a given locus can see that locus, and everything outside cannot.”

This constant contact is likely beneficial for DNA repair, as the broken strands remain in close proximity to each other. The findings also suggest that for genes and regulatory elements that are within about 100,000 base pairs, they don’t need any extra help to find each other — they will do so routinely through their normal movement.

“If they are closer than 100,000 bases, and most regulatory elements are, then those elements are going to find their target gene within a few milliseconds or a few minutes,” Mazzocca says. “These are timescales that are completely consistent with transcription.”

In the other class of chromatin dynamics that the researchers identified, chromatin is able to move over a wider range, but only at longer timescales (a few minutes to hours). This class of chromatin appeared in some types of cells but not others, for reasons that are not yet understood.

“It would be reasonable to assume that the behavior would be more or less the same in all cell types, but that’s not at all what we found,” Hansen says. “It’s very different in different cell types, with no obvious way of categorizing things.”

He adds that the strength of the subdiffusive pull that the researchers found in this study can’t be explained with existing models that have been developed to study chromatin dynamics — the Rouse model and the fractal globule model. This suggests that the models may need to incorporate factors that were previously left out, such as the interactions between chromatin and the crowded nucleoplasm it sits within.

“These findings are significant for two key reasons,” says Luca Giorgetti, a group leader at the Friedrich Miescher Institute for Biomedical Research in Switzerland, who was not involved in the study. “First, they rigorously confirm longstanding but anecdotal observations that chromatin motion is strongly subdiffusive. Second, they demonstrate that this behavior is consistent across multiple cell types and persists across all measured timescales.”

The research was funded, in part, by the National Institutes of Health, a National Science Foundation CAREER Award, a Pew-Stewart Scholar for Cancer Research Award, and the Bridge Project, a partnership between the Koch Institute for Integrative Cancer Research at MIT and the Dana-Farber/Harvard Cancer Center.

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Found Industries aims to strengthen America’s industrial supply chains

Found Industries has gone through several distinct phases in the four years since it was originally formed as Found Energy. There was the scrappy startup stage, in which the company was primarily housed in the basement of founder Peter Godart ’15, SM ’19, PhD ’21. Then there was the demonstration phase, in which the company worked to productize its technology for transforming aluminum into high-density fuel for industrial operations.

Now, after confronting supply chain vulnerabilities related to critical metals in its aluminum fuel business, the company is launching a new division, Found Metals, to extract the critical metal gallium from mineral refineries — a move that builds on its original technology while addressing a major national security need.

Gallium is a critical material in the defense, semiconductor, and energy sectors. In 2024, China produced 99 percent of the world’s primary supply — market dominance the country takes advantage of through export controls.

Godart’s company developed an electrochemical gallium extraction technology for internal use after realizing how dependent it would be on China for the catalyst material at the center of its aluminum fuel reactors. Now, with support from the U.S. Department of Energy, Found is hoping to use that technology to create a new domestic supply chain for gallium and a host of other important metals.

Found Industries is still committed to its aluminum fuel operations, now under its Found Energy division. It is already running a 100-kilowatt-class demonstration plant and is preparing for industrial pilot deployments next year. But with its expansion, which was announced April 21, the company is also working to meet the moment for critical metals production.

“Gallium is the world’s most critical metal, as it’s 99 percent controlled by China,” Godart says. “When you produce 99 percent of something, you also produce 99 percent of the tools required to extract it. We couldn’t get our hands on some of those tools, so we were forced to come up with a new technology. Now we believe we can deploy this at scale to become one the first major Western suppliers of these metals.”

From fuel to metals

Godart focused on robotics as an undergraduate in MIT’s Department of Mechanical Engineering and Department of Electrical Engineering and Computer Science. Following graduation, he worked at NASA’s Jet Propulsion Laboratory, where he explored systems for tapping into high-density fuels like aluminum on other planets.

“I had this crazy idea that you could use aluminum, which is already a common construction material for aerospace, as a fuel on other planets,” Godart says. “You don’t need most of the aluminum on a spacecraft once you land on another planet. Aluminum is around 40 times more energy-dense than lithium-ion batteries, and if you have an oxidizer, like water on an icy moon for example, then you can react that aluminum with water and extract energy as heat and hydrogen.”

Luckily for people who might spill water on aluminum while cooking, the metal is normally very stable when exposed to air. In order to tap into aluminum’s stored energy, it needs to undergo a chemical reaction. Godart began exploring catalyst materials to create that reaction at NASA. He continued that work with professor of mechanical engineering Douglas Hart when he returned to MIT in 2017, this time for applications a little closer to home.

“If we want to think about moving humanity to other planets, we have some problems to solve here first,” Godart says. “That was the impetus for me to go back to MIT to study using aluminum as a fuel for energy distribution on Earth.”

Around 70 million tons of aluminum are already transported around the globe every year. Godart says that gives aluminum an easier path to scale. During his PhD, he created a process for coating aluminum with a gallium-containing alloy to help tap into aluminum’s embodied energy.

“We found a catalyst that, when mixed with aluminum scraps, enabled aluminum to react with water very rapidly and at orders of magnitude higher power density than what had been possible before,” Godart says. “That meant you could use aluminum as a fuel and get megawatt-scale power from compact reactor systems.”

By the time he finished his PhD in 2021, Godart and his collaborators had developed a system that mixes aluminum fuel with those catalysts to continuously produce electricity at the kilowatt scale through a hydrogen fuel cell.

Godart launched Found Energy in 2022, licensing part of his research from MIT’s Technology License Office and receiving support from MIT’s Venture Mentoring Service. The company received an Activate fellowship, and after quickly outgrowing Godart’s basement, moved into its current 20,000 square foot facility in Charlestown, Massachusetts.

Today, Found Energy is working with industrial companies that have abundant aluminum scrap.

“When you invent a fuel, you then have to invent the engine,” Godart says. “Our engine is called a catalyzed aluminum water reactor. You feed in aluminum that’s been treated with the catalyst and water, and you get a steam-hydrogen gas mixture. We call that our power stream. We use it to cogenerate industrial heat and electricity. The reaction byproduct is a hydrated aluminum oxide that can be sold into various industries or recycled back into aluminum, which is the long-term vision.”

As Godart worked to build more of the systems, he became concerned about Found’s reliance on Chinese supply chains for its catalyst material. So, in 2024, he developed a new way to extract gallium from Bayer liquor, an industrial process stream used to produce aluminum. Traditional methods for extracting gallium rely on foreign-controlled organic chemicals or resins to bind and concentrate the gallium.

Found uses a continuous electrochemical process to recover the gallium directly from Bayer liquor and other industrial feedstocks, even at low concentrations.

“We thought of it as a way to future-proof what we were doing,” Godart says. “Necessity was the mother of invention.”

Then, toward the end of 2024, China began restricting the export of critical metals including gallium.

“We realized we had already developed a technique for producing these restricted metals that could be very quickly adapted,” Godart recalls.

Scaling for national security

On April 14, the Department of Energy’s Office of Critical Minerals and Energy Innovation selected Found as part of its $5.4 million program to recover gallium from domestic feedstocks. The company plans to start extracting gallium, along with other critical metals like indium and germanium, by the end of 2027.

Meanwhile, Found is already running a 100-kilowatt-class aluminum fuel demonstration system in Charlestown and is working through a orders of several megawatts from large public companies.

“For our fuel technology, the vision is to go as big as possible,” Godart says. “We envision major power plants. Aluminum refineries today, for example, consume hundreds of megawatts of continuous thermal power. That’s what we aim to deliver.”

Godart says he spends most of his time now on gallium extraction, but both branches of the business could make supply chains more secure in the future.

“The big focus now is critical metals, because the government needs this,” Godart says. “We’re also making these metals for ourselves, so we’re vertically integrating our own supply chain, which is table stakes now for companies that deal in physical goods. You need to be able to control your inputs. By focusing on metals, it improves the likelihood of success for our aluminum fuel business.”

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MIT affiliates awarded 2026 Guggenheim Fellowships

MIT Research Scientist Afreen Siddiqi ’99, SM ’01, PhD ’06; MIT professors Kathleen Thelen and Vinod Vaikuntanathan SM ’05, PhD ’09; as well as Kate Manne PhD ’11 are among 223 scientists, artists, and scholars awarded 2026 fellowships from the John Simon Guggenheim Memorial Foundation. Working across 55 disciplines, the fellows were selected from almost 5,000 applicants for “prior career achievement and exceptional promise.”

Each fellow receives a monetary stipend to pursue independent work at the highest level under “the freest possible conditions.” Since its founding in 1925, the Guggenheim Foundation has awarded nearly $450 million in fellowships to more than 19,000 fellows. This year, MIT faculty and staff were recognized in the categories of geography and environmental studies, political science, and computer science.

Afreen Siddiqi is a research scientist in the Engineering Systems Laboratory in the Department of Aeronautics and Astronautics. Her expertise is in the development of systems-theoretic analytical methods and quantitative modeling for technical systems in space and on Earth that need to operate and adapt in changing environments. Her work has focused on space exploration, satellite Earth observation for informing decisions, and critical infrastructure planning. She has served as a contributing author to the sixth assessment report of 2022 of the Intergovernmental Panel on Climate Change (IPCC) on implications of water, energy, and food interconnections for climate change adaptation. Her work has received teaching awards and fellowships including the Amelia Earhart Fellowship, Richard D. DuPont Fellowship, and the Rene H. Miller Prize in Systems Engineering.

Kathleen Thelen is the Ford International Professor of Political Science. Her work focuses on the political economy of the rich democracies, with a current emphasis on the study of American capitalism in comparative perspective. Her most recent book, “Attention Shoppers! American Retail Capitalism and the Origins of the Amazon Economy,” was published by Princeton University Press in 2025. Her awards include the Friedrich Schiedel-Award for Politics and Technology, the Aaron Wildavsky Enduring Contribution Prize, and the Michael Endres Research Prize (2019). She was elected to the American Academy of Arts and Sciences in 2015.

Vinod Vaikuntanathan is the Ford Foundation Professor of Engineering in the Department of Electrical Engineering and Computer Science. A principal investigator at the Computer Science and Artificial Intelligence Laboratory, his research focuses upon the foundations of cryptography and its applications to theoretical computer science at large. He is known for his work on fully homomorphic encryption (a powerful cryptographic primitive that enables complex computations on encrypted data), as well as lattice-based cryptography (which lays down a new mathematical foundation for cryptography in the post-quantum world). His awards include the Harold E. Edgerton Faculty Award, the Godel Prize, the Simons Investigator Award, the Distinguished Alumnus Award from Indian Institute of Technology Madras, a Best Paper Award from CRYPTO 2024, test of time awards from IEEE Symposium on Foundations of Computer Science and CRYPTO conferences, and he was named a MacVicar Faculty Fellow in 2024 and an International Association for Cryptologic Research Fellow in 2026.

Kate Manne, who earned her PhD in philosophy at MIT in 2011, is now a professor at Cornell University.

“Our new class of Guggenheim Fellows is representative of the world’s best thinkers, innovators, and creators in art, science, and scholarship,” says Edward Hirsch, award-winning poet and president of the Guggenheim Foundation. “As the foundation enters its second century and looks to the future, I feel confident that this new class of 223 individuals will do bold and inspiring work, undaunted by the challenges ahead. We are honored to support their visionary contributions.”

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Testing sustainable agriculture in Barcelona

A dozen MIT students recently set out for Barcelona — not just to study climate resilience, but to experience it firsthand. As part of STS.S22 (How to Grow Resilient Futures: Regenerative Agriculture and Economies in Catalunya, Spain), an Independent Activities Period course taught by Kate Brown, the Thomas M. Siebel Distinguished Professor in the History of Science, they stepped beyond the classroom and into living systems of sustainability.

Offered as a Global Classroom through MIT International Science and Technology (MISTI), the course reimagined what learning could look like. Instead of working their way through a syllabus containing texts about sustainable farming and the power of cooperatives, Brown’s students got their hands dirty. 

In fact, quite literally: They visited local farms and slaughterhouses; prepped, cooked, and served a cooperative dinner to migrants; and constructed a working greenhouse. In the process, they built a lasting community and forged their own visions about sustainability and how they are compelled to confront climate change — as MIT students now, and eventually as alumni. 

“I wanted the students to think about alternatives to the notion of capitalist development, where the latest technology is seen as the solution to every social problem that emerges. I wanted them to see ways people are solving problems in a place like Barcelona, where communities and ecologies are centered as part of the solution,” Brown says.

Through Brown’s partnerships at the Barcelona Urban Research Institute and Research and Degrowth (R&D)  — and MISTI Spain’s infrastructure — the group of eight undergraduates and four graduate students had the opportunity to examine the historical roots of cooperative movements in the region while simultaneously experiencing today’s iteration of co-op work. 

Brown intentionally designed the three-week syllabus to push students beyond the classroom walls and get them face-to-face with local MISTI Spain collaborators from across the farming and ecology sectors. For example, the class met with Pino Delàs, a pig farmer who left the industrial system to start his own localized, cyclical operation, called Llavora, which supported community farming and generated significantly less waste. 

Rooted in community 

With more than a century of creating cooperatives — both workers and farms — Barcelona and its Catalan roots provided an ideal environment for the students to consider Brown’s questions through fieldwork rooted in community. 

Within their first week on the ground, they collaborated with volunteers at the Agora Squat. The small “pocket park” was initially slated to be developed into a luxury hotel, but a local group of 200 neighborhood residents came together to protest the plan, instead exercising their legal right to use the land, a caveat in Spanish law that allows neighbors to make a case for possessing land that isn’t being used productively. Now, the lush green square boasts a community kitchen and gardens. One night a week, volunteers provide dinner for upward of 60 recent North African migrants, using ingredients sourced from local fruiterias and shops that would have otherwise gone to waste at the close of business. 

On this particular Thursday, Brown’s students became nonprofit managers and chefs, but they also became community members themselves. In just a few hours from start to finish, the students had to source donated produce from the local vendors, come up with a recipe using what they’d gathered, and then prepare a meal in the rudimentary kitchen. “They received a lot of turnips and had to create a recipe to use them,” Brown says. In the end, a flavorful stew simmered in a massive metal pan over propane burners, brought alive with fresh chilies picked from the garden. 

“This was way outside some students’ comfort zones,” Brown says. Yet, that was exactly the point of the activity. By the end of the evening, the students discovered that sometimes the most profound educational moments take shape only after challenging the limits of learning. 

“Many of us do not consider ourselves chefs, so it was empowering to discover that, together, we had the capacity to create a nourishing meal for 70 people, with produce that would have otherwise gone to waste. This meal that we created on the spot, in combination with many of the other workshops during the program, was a strong reminder of how much agency each of us has to effect change within isolating and constraining systems, especially in community with like-minded individuals,” says Sonia Torres Rodriguez, a first-year PhD student in urban studies and planning.

Torres Rodriguez focuses her doctoral research on affordable and climate-resilient housing. She was drawn to the IAP program's exploration of innovative approaches to more equitably distributing the means of producing housing and food, and was excited to be learning in person in Spain. “Cooking together, admiring healthy regenerative soil, foraging, learning traditional methods to braid grass, installing mini solar panels, and hosting poetry circles, would have been impossible to replicate on Zoom,” she says. 

Calvin Macatantan, a senior in computer science and urban studies and planning, was initially drawn to the program because of his interest in resilient economies and how they support the communities they serve. Other than visiting family in the Philippines, he’d never left the United States before. He was especially moved by the group’s stay at La Bruguera, an eco-resort partnered with R&D that serves as a “living laboratory.” The cohort heard from local experts in regenerative agriculture, soil health, and low-tech agroforestry, alongside hands-on activities such as eco-art sessions, weaving lessons, and the rebuilding of a greenhouse. 

As part of a final project for the course, Macatantan and another student wrote and illustrated a children’s book that explains La Bruguera’s work by making the soil come to life as the main protagonist for young readers. 

Brown’s course pushed Sofia Espindola de La Mora to think more critically about everyday systems and their environmental impact. Originally from Puerto Rico, the first-year student has watched helplessly in recent years as climate change has increased the frequency and magnitude of natural disasters at home.

She came to MIT looking for answers and wanting to make a difference, and signed up for Brown’s course as part of that quest. “It was fascinating to see firsthand that the degrowth movement doesn’t mean slowing down is a bad thing, but instead that the constant striving for more is what has led us to many of the predicaments we now face as a society. It forced me to think about whether it would even be possible for me to sustain the life I have now using renewable energy,” Espindola de La Mora says. The course convinced her to focus her studies on climate system science and engineering. 

A climate context

Broadening students’ perspectives was a priority for Brown, whose research lies at the intersection of history, science, technology, and bio-politics. She’s known on campus for courses like STS.038 (Risky Business: Food Production, Environment, and Health). Her 2026 book, “Tiny Gardens Everywhere: The Past, Present and Future of the Self-Provisioning City,” examines urban systems, including gardens. 

When Brown was designing the Global Classroom — made possible through MISTI, with additional support from the MIT Energy Initiative — she centered a value she considers imperative in any course today: addressing climate and other human-driven environmental challenges.

“I’m focused on training students to approach these problems at the local level, so they see what happens when they’re working through communities, rather than prescribing to them something to scale all over the world,” Brown says.

That localized, individualized approach helped expand on what the students initially believed was possible, and compelled them to become part of the solution through their studies and in their professional lives. 

Since their return to campus, Brown’s students have continued to lean on one another and build community, one meal at a time. Many Tuesday nights, they come together to cook dinner, Barcelona squat style. Each individual brings their ingredients, and together they create a recipe that nourishes and sustains.  

“I was losing a lot of faith in the world before this trip,” Macatantan admits. “We’re constantly surrounded by consumption and the drive to do more. This experience helped me realize that I want to do something that impacts people. For me, that will look like research. I want to become an expert in a subject and become someone who can help communicate that knowledge to people who need it.” 

“MISTI Global Classrooms like this show what happens when learning extends beyond the MIT campus,” says Alicia Goldstein Raun, associate director of MISTI and managing director of the MIT-Spain Program at the Center for International Studies. “I was excited when Professor Brown approached me to help shape this new class, knowing it would resonate with students,” says Raun. “The students tackled global challenges like climate change and explored the degrowth movement while immersing themselves in Spanish communities and culture.”

For faculty interested in designing a MISTI Global Classroom, more information can be found here.

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