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      in Energy

      Finding community in high-energy-density physics

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      Skylar Dannhoff knew one thing: She did not want to be working alone.

      As an undergraduate at Case Western Reserve University, she had committed to a senior project that often felt like solitary lab work, a feeling heightened by the pandemic. Though it was an enriching experience, she was determined to find a graduate school environment that would foster community, one “with lots of people, lots of collaboration; where it’s impossible to work until 3 a.m. without anyone noticing.” A unique group at the Plasma Science and Fusion Center (PSFC) looked promising: the High-Energy-Density Physics (HEDP) division, a lead partner in the National Nuclear Security Administration’s Center for Excellence at MIT.

      “It was a shot in the dark, just more of a whim than anything,” she says of her request to join HEDP on her application to MIT’s Department of Physics. “And then, somehow, they reached out to me. I told them I’m willing to learn about plasma. I didn’t know anything about it.”

      What she did know was that the HEDP group collaborates with other U.S. laboratories on an approach to creating fusion energy known as inertial confinement fusion (ICF). One version of the technique, known as direct-drive ICF, aims multiple laser beams symmetrically onto a spherical capsule filled with nuclear fuel. The other, indirect-drive ICF, instead aims multiple lasers beams into a gold cylindrical cavity called a hohlraum, within which the spherical fuel capsule is positioned. The laser beams are configured to hit the inner hohlraum wall, generating a “bath” of X-rays, which in turn compress the fuel capsule.

      Imploding the capsule generates intense fusion energy within a tiny fraction of a second (an order of tens of picoseconds). In August 2021, the National Ignition Facility (NIF) at Lawrence Livermore National Laboratory (LLNL) used this method to produce an historic fusion yield of 1.3 megajoules, putting researchers within reach of “ignition,” the point where the self-sustained fusion burn spreads into the surrounding fuel, leading to a high fusion-energy gain.  

      Joining the group just a month before this long-sought success, Dannhoff was impressed more with the response of her new teammates and the ICF community than with the scientific milestone. “I got a better appreciation for people who had spent their entire careers working on this project, just chugging along doing their best, ignoring the naysayers. I was excited for the people.”

      Dannhoff is now working toward extending the success of NIF and other ICF experiments, like the OMEGA laser at the University of Rochester’s Laboratory for Laser Energetics. Under the supervision of Senior Research Scientist Chikang Li, she is studying what happens to the flow of plasma within the hohlraum cavity during indirect ICF experiments, particularly for hohlraums with inner-wall aerogel foam linings. Experiments, over the last decade, have shown just how excruciatingly precise the symmetry in ICF targets must be. The more symmetric the X-ray drive, the more effective the implosion, and it is possible that these foam linings will improve the X-ray symmetry and drive efficiency.

      Dannhoff is specifically interested in studying the behavior of silicon and tantalum-based foam liners. She is as concerned with the challenges of the people at General Atomics (GA) and LLNL who are creating these targets as she is with the scientific outcome.

      “I just had a meeting with GA yesterday,” she notes. “And it’s a really tricky process. It’s kind of pushing the boundaries of what is doable at the moment. I got a much better sense of how demanding this project is for them, how much we’re asking of them.”

      What excites Dannhoff is the teamwork she observes, both at MIT and between ICF institutions around the United States. With roughly 10 graduate students and postdocs down the hall, each with an assigned lead role in lab management, she knows she can consult an expert on almost any question. And collaborators across the country are just an email away. “Any information that people can give you, they will give you, and usually very freely,” she notes. “Everyone just wants to see this work.”

      That Dannhoff is a natural team player is also evidenced in her hobbies. A hockey goalie, she prioritizes playing with MIT’s intramural teams, “because goalies are a little hard to come by. I just play with whoever needs a goalie on that night, and it’s a lot of fun.”

      She is also a member of the radio community, a fellowship she first embraced at Case Western — a moment she describes as a turning point in her life. “I literally don’t know who I would be today if I hadn’t figured out radio is something I’m interested in,” she admits. The MIT Radio Society provided the perfect landing pad for her arrival in Cambridge, full of the kinds of supportive, interesting, knowledgeable students she had befriended as an undergraduate. She credits radio with helping her realize that she could make her greatest contributions to science by focusing on engineering.

      Danhoff gets philosophical as she marvels at the invisible waves that surround us.

      “Not just radio waves: every wave,” she asserts. “The voice is the everywhere. Music, signal, space phenomena: it’s always around. And all we have to do is make the right little device and have the right circuit elements put in the right order to unmix and mix the signals and amplify them. And bada-bing, bada-boom, we’re talking with the universe.”

      “Maybe that epitomizes physics to me,” she adds. “We’re trying to listen to the universe, and it’s talking to us. We just have to come up with the right tools and hear what it’s trying to say.” More

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      in Environment

      Small eddies play a big role in feeding ocean microbes

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      Subtropical gyres are enormous rotating ocean currents that generate sustained circulations in the Earth’s subtropical regions just to the north and south of the equator. These gyres are slow-moving whirlpools that circulate within massive basins around the world, gathering up nutrients, organisms, and sometimes trash, as the currents rotate from coast to coast.

      For years, oceanographers have puzzled over conflicting observations within subtropical gyres. At the surface, these massive currents appear to host healthy populations of phytoplankton — microbes that feed the rest of the ocean food chain and are responsible for sucking up a significant portion of the atmosphere’s carbon dioxide.

      But judging from what scientists know about the dynamics of gyres, they estimated the currents themselves wouldn’t be able to maintain enough nutrients to sustain the phytoplankton they were seeing. How, then, were the microbes able to thrive?

      Now, MIT researchers have found that phytoplankton may receive deliveries of nutrients from outside the gyres, and that the delivery vehicle is in the form of eddies — much smaller currents that swirl at the edges of a gyre. These eddies pull nutrients in from high-nutrient equatorial regions and push them into the center of a gyre, where the nutrients are then taken up by other currents and pumped to the surface to feed phytoplankton.

      Ocean eddies, the team found, appear to be an important source of nutrients in subtropical gyres. Their replenishing effect, which the researchers call a “nutrient relay,” helps maintain populations of phytoplankton, which play a central role in the ocean’s ability to sequester carbon from the atmosphere. While climate models tend to project a decline in the ocean’s ability to sequester carbon over the coming decades, this “nutrient relay” could help sustain carbon storage over the subtropical oceans.

      “There’s a lot of uncertainty about how the carbon cycle of the ocean will evolve as climate continues to change, ” says Mukund Gupta, a postdoc at Caltech who led the study as a graduate student at MIT. “As our paper shows, getting the carbon distribution right is not straightforward, and depends on understanding the role of eddies and other fine-scale motions in the ocean.”

      Gupta and his colleagues report their findings this week in the Proceedings of the National Academy of Sciences. The study’s co-authors are Jonathan Lauderdale, Oliver Jahn, Christopher Hill, Stephanie Dutkiewicz, and Michael Follows at MIT, and Richard Williams at the University of Liverpool.

      A snowy puzzle

      A cross-section of an ocean gyre resembles a stack of nesting bowls that is stratified by density: Warmer, lighter layers lie at the surface, while colder, denser waters make up deeper layers. Phytoplankton live within the ocean’s top sunlit layers, where the microbes require sunlight, warm temperatures, and nutrients to grow.

      When phytoplankton die, they sink through the ocean’s layers as “marine snow.” Some of this snow releases nutrients back into the current, where they are pumped back up to feed new microbes. The rest of the snow sinks out of the gyre, down to the deepest layers of the ocean. The deeper the snow sinks, the more difficult it is for it to be pumped back to the surface. The snow is then trapped, or sequestered, along with any unreleased carbon and nutrients.

      Oceanographers thought that the main source of nutrients in subtropical gyres came from recirculating marine snow. But as a portion of this snow inevitably sinks to the bottom, there must be another source of nutrients to explain the healthy populations of phytoplankton at the surface. Exactly what that source is “has left the oceanography community a little puzzled for some time,” Gupta says.

      Swirls at the edge

      In their new study, the team sought to simulate a subtropical gyre to see what other dynamics may be at work. They focused on the North Pacific gyre, one of the Earth’s five major gyres, which circulates over most of the North Pacific Ocean, and spans more than 20 million square kilometers. 

      The team started with the MITgcm, a general circulation model that simulates the physical circulation patterns in the atmosphere and oceans. To reproduce the North Pacific gyre’s dynamics as realistically as possible, the team used an MITgcm algorithm, previously developed at NASA and MIT, which tunes the model to match actual observations of the ocean, such as ocean currents recorded by satellites, and temperature and salinity measurements taken by ships and drifters.  

      “We use a simulation of the physical ocean that is as realistic as we can get, given the machinery of the model and the available observations,” Lauderdale says.

      Play video

      An animation of the North Pacific Ocean shows phosphate nutrient concentrations at 500 meters below the ocean surface. The swirls represent small eddies transporting phosphate from the nutrient-rich equator (lighter colors), northward toward the nutrient-depleted subtropics (darker colors). This nutrient relay mechanism helps sustain biological activity and carbon sequestration in the subtropical ocean. Credit: Oliver Jahn

      The realistic model captured finer details, at a resolution of less than 20 kilometers per pixel, compared to other models that have a more limited resolution. The team combined the simulation of the ocean’s physical behavior with the Darwin model — a simulation of microbe communities such as phytoplankton, and how they grow and evolve with ocean conditions.

      The team ran the combined simulation of the North Pacific gyre over a decade, and created animations to visualize the pattern of currents and the nutrients they carried, in and around the gyre. What emerged were small eddies that ran along the edges of the enormous gyre and appeared to be rich in nutrients.

      “We were picking up on little eddy motions, basically like weather systems in the ocean,” Lauderdale says. “These eddies were carrying packets of high-nutrient waters, from the equator, north into the center of the gyre and downwards along the sides of the bowls. We wondered if these eddy transfers made an important delivery mechanism.”

      Surprisingly, the nutrients first move deeper, away from the sunlight, before being returned upwards where the phytoplankton live. The team found that ocean eddies could supply up to 50 percent of the nutrients in subtropical gyres.

      “That is very significant,” Gupta says. “The vertical process that recycles nutrients from marine snow is only half the story. The other half is the replenishing effect of these eddies. As subtropical gyres contribute a significant part of the world’s oceans, we think this nutrient relay is of global importance.”

      This research was supported, in part, by the Simons Foundation and NASA. More

    • 113 Shares149 Views

      in Energy

      MIT students contribute to success of historic fusion experiment

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      For more than half a century, researchers around the world have been engaged in attempts to achieve fusion ignition in a laboratory, a grand challenge of the 21st century. The High-Energy-Density Physics (HEDP) group at MIT’s Plasma Science and Fusion Center has focused on an approach called inertial confinement fusion (ICF), which uses lasers to implode a pellet of fuel in a quest for ignition. This group, including nine former and current MIT students, was crucial to an historic ICF ignition experiment performed in 2021; the results were published on the anniversary of that success.

      On Aug. 8, 2021, researchers at the National Ignition Facility (NIF), Lawrence Livermore National Laboratory (LLNL), used 192 laser beams to illuminate the inside of a tiny gold cylinder encapsulating a spherical capsule filled with deuterium-tritium fuel in their quest to produce significant fusion energy. Although researchers had followed this process many times before, using different parameters, this time the ensuing implosion produced an historic fusion yield of 1.37 megaJoules, as measured by a suite of neutron diagnostics. These included the MIT-developed and analyzed Magnetic Recoil Spectrometer (MRS). This result was published in Physical Review Letters on Aug. 8, the one-year anniversary of the ground-breaking development, unequivocally indicating that the first controlled fusion experiment reached ignition.

      Governed by the Lawson criterion, a plasma ignites when the internal fusion heating power is high enough to overcome the physical processes that cool the fusion plasma, creating a positive thermodynamic feedback loop that very rapidly increases the plasma temperature. In the case of ICF, ignition is a state where the fusion plasma can initiate a “fuel burn propagation” into the surrounding dense and cold fuel, enabling the possibility of high fusion-energy gain.

      “This historic result certainly demonstrates that the ignition threshold is a real concept, with well-predicted theoretical calculations, and that a fusion plasma can be ignited in a laboratory” says HEDP Division Head Johan Frenje.

      The HEDP division has contributed to the success of the ignition program at the NIF for more than a decade by providing and using a dozen diagnostics, implemented by MIT PhD students and staff, which have been critical for assessing the performance of an implosion. The hundreds of co-authors on the paper attest to the collaborative effort that went into this milestone. MIT’s contributors included the only student co-authors.

      “The students are responsible for implementing and using a diagnostic to obtain data important to the ICF program at the NIF, says Frenje. “Being responsible for running a diagnostic at the NIF has allowed them to actively participate in the scientific dialog and thus get directly exposed to cutting-edge science.”

      Students involved from the MIT Department of Physics were Neel Kabadi, Graeme Sutcliffe, Tim Johnson, Jacob Pearcy, and Ben Reichelt; students from the Department of Nuclear Science and Engineering included Brandon Lahmann, Patrick Adrian, and Justin Kunimune.

      In addition, former student Alex Zylstra PhD ’15, now a physicist at LLNL, was the experimental lead of this record implosion experiment. More

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      in Energy

      How the universe got its magnetic field

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      When we look out into space, all of the astrophysical objects that we see are embedded in magnetic fields. This is true not only in the neighborhood of stars and planets, but also in the deep space between galaxies and galactic clusters. These fields are weak — typically much weaker than those of a refrigerator magnet — but they are dynamically significant in the sense that they have profound effects on the dynamics of the universe. Despite decades of intense interest and research, the origin of these cosmic magnetic fields remains one of the most profound mysteries in cosmology.

      In previous research, scientists came to understand how turbulence, the churning motion common to fluids of all types, could amplify preexisting magnetic fields through the so-called dynamo process. But this remarkable discovery just pushed the mystery one step deeper. If a turbulent dynamo could only amplify an existing field, where did the “seed” magnetic field come from in the first place?

      We wouldn’t have a complete and self-consistent answer to the origin of astrophysical magnetic fields until we understood how the seed fields arose. New work carried out by MIT graduate student Muni Zhou, her advisor Nuno Loureiro, a professor of nuclear science and engineering at MIT, and colleagues at Princeton University and the University of Colorado at Boulder provides an answer that shows the basic processes that generate a field from a completely unmagnetized state to the point where it is strong enough for the dynamo mechanism to take over and amplify the field to the magnitudes that we observe.

      Magnetic fields are everywhere

      Naturally occurring magnetic fields are seen everywhere in the universe. They were first observed on Earth thousands of years ago, through their interaction with magnetized minerals like lodestone, and used for navigation long before people had any understanding of their nature or origin. Magnetism on the sun was discovered at the beginning of the 20th century by its effects on the spectrum of light that the sun emitted. Since then, more powerful telescopes looking deep into space found that the fields were ubiquitous.

      And while scientists had long learned how to make and use permanent magnets and electromagnets, which had all sorts of practical applications, the natural origins of magnetic fields in the universe remained a mystery. Recent work has provided part of the answer, but many aspects of this question are still under debate.

      Amplifying magnetic fields — the dynamo effect

      Scientists started thinking about this problem by considering the way that electric and magnetic fields were produced in the laboratory. When conductors, like copper wire, move in magnetic fields, electric fields are created. These fields, or voltages, can then drive electrical currents. This is how the electricity that we use every day is produced. Through this process of induction, large generators or “dynamos” convert mechanical energy into the electromagnetic energy that powers our homes and offices. A key feature of dynamos is that they need magnetic fields in order to work.

      But out in the universe, there are no obvious wires or big steel structures, so how do the fields arise? Progress on this problem began about a century ago as scientists pondered the source of the Earth’s magnetic field. By then, studies of the propagation of seismic waves showed that much of the Earth, below the cooler surface layers of the mantle, was liquid, and that there was a core composed of molten nickel and iron. Researchers theorized that the convective motion of this hot, electrically conductive liquid and the rotation of the Earth combined in some way to generate the Earth’s field.

      Eventually, models emerged that showed how the convective motion could amplify an existing field. This is an example of “self-organization” — a feature often seen in complex dynamical systems — where large-scale structures grow spontaneously from small-scale dynamics. But just like in a power station, you needed a magnetic field to make a magnetic field.

      A similar process is at work all over the universe. However, in stars and galaxies and in the space between them, the electrically conducting fluid is not molten metal, but plasma — a state of matter that exists at extremely high temperatures where the electrons are ripped away from their atoms. On Earth, plasmas can be seen in lightning or neon lights. In such a medium, the dynamo effect can amplify an existing magnetic field, provided it starts at some minimal level.

      Making the first magnetic fields

      Where does this seed field come from? That’s where the recent work of Zhou and her colleagues, published May 5 in PNAS, comes in. Zhou developed the underlying theory and performed numerical simulations on powerful supercomputers that show how the seed field can be produced and what fundamental processes are at work. An important aspect of the plasma that exists between stars and galaxies is that it is extraordinarily diffuse — typically about one particle per cubic meter. That is a very different situation from the interior of stars, where the particle density is about 30 orders of magnitude higher. The low densities mean that the particles in cosmological plasmas never collide, which has important effects on their behavior that had to be included in the model that these researchers were developing.   

      Calculations performed by the MIT researchers followed the dynamics in these plasmas, which developed from well-ordered waves but became turbulent as the amplitude grew and the interactions became strongly nonlinear. By including detailed effects of the plasma dynamics at small scales on macroscopic astrophysical processes, they demonstrated that the first magnetic fields can be spontaneously produced through generic large-scale motions as simple as sheared flows. Just like the terrestrial examples, mechanical energy was converted into magnetic energy.

      An important output of their computation was the amplitude of the expected spontaneously generated magnetic field. What this showed was that the field amplitude could rise from zero to a level where the plasma is “magnetized” — that is, where the plasma dynamics are strongly affected by the presence of the field. At this point, the traditional dynamo mechanism can take over and raise the fields to the levels that are observed. Thus, their work represents a self-consistent model for the generation of magnetic fields at cosmological scale.

      Professor Ellen Zweibel of the University of Wisconsin at Madison notes that “despite decades of remarkable progress in cosmology, the origin of magnetic fields in the universe remains unknown. It is wonderful to see state-of-the-art plasma physics theory and numerical simulation brought to bear on this fundamental problem.”

      Zhou and co-workers will continue to refine their model and study the handoff from the generation of the seed field to the amplification phase of the dynamo. An important part of their future research will be to determine if the process can work on a time scale consistent with astronomical observations. To quote the researchers, “This work provides the first step in the building of a new paradigm for understanding magnetogenesis in the universe.”

      This work was funded by the National Science Foundation CAREER Award and the Future Investigators of NASA Earth and Space Science Technology (FINESST) grant. More

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      in Energy

      MIT expands research collaboration with Commonwealth Fusion Systems to build net energy fusion machine, SPARC

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      MIT’s Plasma Science and Fusion Center (PSFC) will substantially expand its fusion energy research and education activities under a new five-year agreement with Institute spinout Commonwealth Fusion Systems (CFS).

      “This expanded relationship puts MIT and PSFC in a prime position to be an even stronger academic leader that can help deliver the research and education needs of the burgeoning fusion energy industry, in part by utilizing the world’s first burning plasma and net energy fusion machine, SPARC,” says PSFC director Dennis Whyte. “CFS will build SPARC and develop a commercial fusion product, while MIT PSFC will focus on its core mission of cutting-edge research and education.”

      Commercial fusion energy has the potential to play a significant role in combating climate change, and there is a concurrent increase in interest from the energy sector, governments, and foundations. The new agreement, administered by the MIT Energy Initiative (MITEI), where CFS is a startup member, will help PSFC expand its fusion technology efforts with a wider variety of sponsors. The collaboration enables rapid execution at scale and technology transfer into the commercial sector as soon as possible.

      This new agreement doubles CFS’ financial commitment to PSFC, enabling greater recruitment and support of students, staff, and faculty. “We’ll significantly increase the number of graduate students and postdocs, and just as important they will be working on a more diverse set of fusion science and technology topics,” notes Whyte. It extends the collaboration between PSFC and CFS that resulted in numerous advances toward fusion power plants, including last fall’s demonstration of a high-temperature superconducting (HTS) fusion electromagnet with record-setting field strength of 20 tesla.

      The combined magnetic fusion efforts at PSFC will surpass those in place during the operations of the pioneering Alcator C-Mod tokamak device that operated from 1993 to 2016. This increase in activity reflects a moment when multiple fusion energy technologies are seeing rapidly accelerating development worldwide, and the emergence of a new fusion energy industry that would require thousands of trained people.

      MITEI director Robert Armstrong adds, “Our goal from the beginning was to create a membership model that would allow startups who have specific research challenges to leverage the MITEI ecosystem, including MIT faculty, students, and other MITEI members. The team at the PSFC and MITEI have worked seamlessly to support CFS, and we are excited for this next phase of the relationship.”

      PSFC is supporting CFS’ efforts toward realizing the SPARC fusion platform, which facilitates rapid development and refinement of elements (including HTS magnets) needed to build ARC, a compact, modular, high-field fusion power plant that would set the stage for commercial fusion energy production. The concepts originated in Whyte’s nuclear science and engineering class 22.63 (Principles of Fusion Engineering) and have been carried forward by students and PSFC staff, many of whom helped found CFS; the new activity will expand research into advanced technologies for the envisioned pilot plant.

      “This has been an incredibly effective collaboration that has resulted in a major breakthrough for commercial fusion with the successful demonstration of revolutionary fusion magnet technology that will enable the world’s first commercially relevant net energy fusion device, SPARC, currently under construction,” says Bob Mumgaard SM ’15, PhD ’15, CEO of Commonwealth Fusion Systems. “We look forward to this next phase in the collaboration with MIT as we tackle the critical research challenges ahead for the next steps toward fusion power plant development.”

      In the push for commercial fusion energy, the next five years are critical, requiring intensive work on materials longevity, heat transfer, fuel recycling, maintenance, and other crucial aspects of power plant development. It will need innovation from almost every engineering discipline. “Having great teams working now, it will cut the time needed to move from SPARC to ARC, and really unleash the creativity. And the thing MIT does so well is cut across disciplines,” says Whyte.

      “To address the climate crisis, the world needs to deploy existing clean energy solutions as widely and as quickly as possible, while at the same time developing new technologies — and our goal is that those new technologies will include fusion power,” says Maria T. Zuber, MIT’s vice president for research. “To make new climate solutions a reality, we need focused, sustained collaborations like the one between MIT and Commonwealth Fusion Systems. Delivering fusion power onto the grid is a monumental challenge, and the combined capabilities of these two organizations are what the challenge demands.”

      On a strategic level, climate change and the imperative need for widely implementable carbon-free energy have helped orient the PSFC team toward scalability. “Building one or 10 fusion plants doesn’t make a difference — we have to build thousands,” says Whyte. “The design decisions we make will impact the ability to do that down the road. The real enemy here is time, and we want to remove as many impediments as possible and commit to funding a new generation of scientific leaders. Those are critically important in a field with as much interdisciplinary integration as fusion.” More

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      in Security

      Structures considered key to gene expression are surprisingly fleeting

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      In human chromosomes, DNA is coated by proteins to form an exceedingly long beaded string. This “string” is folded into numerous loops, which are believed to help cells control gene expression and facilitate DNA repair, among other functions. A new study from MIT suggests that these loops are very dynamic and shorter-lived than previously thought.

      In the new study, the researchers were able to monitor the movement of one stretch of the genome in a living cell for about two hours. They saw that this stretch was fully looped for only 3 to 6 percent of the time, with the loop lasting for only about 10 to 30 minutes. The findings suggest that scientists’ current understanding of how loops influence gene expression may need to be revised, the researchers say.

      “Many models in the field have been these pictures of static loops regulating these processes. What our new paper shows is that this picture is not really correct,” says Anders Sejr Hansen, the Underwood-Prescott Career Development Assistant Professor of Biological Engineering at MIT. “We suggest that the functional state of these domains is much more dynamic.”

      Hansen is one of the senior authors of the new study, along with Leonid Mirny, a professor in MIT’s Institute for Medical Engineering and Science and the Department of Physics, and Christoph Zechner, a group leader at the Max Planck Institute of Molecular Cell Biology and Genetics in Dresden, Germany, and the Center for Systems Biology Dresden. MIT postdoc Michele Gabriele, recent Harvard University PhD recipient Hugo Brandão, and MIT graduate student Simon Grosse-Holz are the lead authors of the paper, which appears today in Science.

      Out of the loop

      Using computer simulations and experimental data, scientists including Mirny’s group at MIT have shown that loops in the genome are formed by a process called extrusion, in which a molecular motor promotes the growth of progressively larger loops. The motor stops each time it encounters a “stop sign” on DNA. The motor that extrudes such loops is a protein complex called cohesin, while the DNA-bound protein CTCF serves as the stop sign. These cohesin-mediated loops between CTCF sites were seen in previous experiments.

      However, those experiments only offered a snapshot of a moment in time, with no information on how the loops change over time. In their new study, the researchers developed techniques that allowed them to fluorescently label CTCF DNA sites so they could image the DNA loops over several hours. They also created a new computational method that can infer the looping events from the imaging data.

      “This method was crucial for us to distinguish signal from noise in our experimental data and quantify looping,” Zechner says. “We believe that such approaches will become increasingly important for biology as we continue to push the limits of detection with experiments.”

      The researchers used their method to image a stretch of the genome in mouse embryonic stem cells. “If we put our data in the context of one cell division cycle, which lasts about 12 hours, the fully formed loop only actually exists for about 20 to 45 minutes, or about 3 to 6 percent of the time,” Grosse-Holz says.

      “If the loop is only present for such a tiny period of the cell cycle and very short-lived, we shouldn’t think of this fully looped state as being the primary regulator of gene expression,” Hansen says. “We think we need new models for how the 3D structure of the genome regulates gene expression, DNA repair, and other functional downstream processes.”

      While fully formed loops were rare, the researchers found that partially extruded loops were present about 92 percent of the time. These smaller loops have been difficult to observe with the previous methods of detecting loops in the genome.

      “In this study, by integrating our experimental data with polymer simulations, we have now been able to quantify the relative extents of the unlooped, partially extruded, and fully looped states,” Brandão says.

      “Since these interactions are very short, but very frequent, the previous methodologies were not able to fully capture their dynamics,” Gabriele adds. “With our new technique, we can start to resolve transitions between fully looped and unlooped states.”

      Play video

      The researchers hypothesize that these partial loops may play more important roles in gene regulation than fully formed loops. Strands of DNA run along each other as loops begin to form and then fall apart, and these interactions may help regulatory elements such as enhancers and gene promoters find each other.

      “More than 90 percent of the time, there are some transient loops, and presumably what’s important is having those loops that are being perpetually extruded,” Mirny says. “The process of extrusion itself may be more important than the fully looped state that only occurs for a short period of time.”

      More loops to study

      Since most of the other loops in the genome are weaker than the one the researchers studied in this paper, they suspect that many other loops will also prove to be highly transient. They now plan to use their new technique study some of those other loops, in a variety of cell types.

      “There are about 10,000 of these loops, and we’ve looked at one,” Hansen says. “We have a lot of indirect evidence to suggest that the results would be generalizable, but we haven’t demonstrated that. Using the technology platform we’ve set up, which combines new experimental and computational methods, we can begin to approach other loops in the genome.”

      The researchers also plan to investigate the role of specific loops in disease. Many diseases, including a neurodevelopmental disorder called FOXG1 syndrome, could be linked to faulty loop dynamics. The researchers are now studying how both the normal and mutated form of the FOXG1 gene, as well as the cancer-causing gene MYC, are affected by genome loop formation.

      The research was funded by the National Institutes of Health, the National Science Foundation, the Mathers Foundation, a Pew-Stewart Cancer Research Scholar grant, the Chaires d’excellence Internationale Blaise Pascal, an American-Italian Cancer Foundation research scholarship, and the Max Planck Institute for Molecular Cell Biology and Genetics. More

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      in Energy

      Finding the questions that guide MIT fusion research

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      “One of the things I learned was, doing good science isn’t so much about finding the answers as figuring out what the important questions are.”

      As Martin Greenwald retires from the responsibilities of senior scientist and deputy director of the MIT Plasma Science and Fusion Center (PSFC), he reflects on his almost 50 years of science study, 43 of them as a researcher at MIT, pursuing the question of how to make the carbon-free energy of fusion a reality.

      Most of Greenwald’s important questions about fusion began after graduating from MIT with a BS in both physics and chemistry. Beginning graduate work at the University of California at Berkeley, he felt compelled to learn more about fusion as an energy source that could have “a real societal impact.” At the time, researchers were exploring new ideas for devices that could create and confine fusion plasmas. Greenwald worked on Berkeley’s “alternate concept” TORMAC, a Toroidal Magnetic Cusp. “It didn’t work out very well,” he laughs. “The first thing I was known for was making the measurements that shut down the program.”

      Believing the temperature of the plasma generated by the device would not be as high as his group leader expected, Greenwald developed hardware that could measure the low temperatures predicted by his own “back of the envelope calculations.” As he anticipated, his measurements showed that “this was not a fusion plasma; this was hardly a confined plasma at all.”

      With a PhD from Berkeley, Greenwald returned to MIT for a research position at the PSFC, attracted by the center’s “esprit de corps.”

      He arrived in time to participate in the final experiments on Alcator A, the first in a series of tokamaks built at MIT, all characterized by compact size and featuring high-field magnets. The tokamak design was then becoming favored as the most effective route to fusion: its doughnut-shaped vacuum chamber, surrounded by electromagnets, could confine the turbulent plasma long enough, while increasing its heat and density, to make fusion occur.

      Alcator A showed that the energy confinement time improves in relation to increasing plasma density. MIT’s succeeding device, Alcator C, was designed to use higher magnetic fields, boosting expectations that it would reach higher densities and better confinement. To attain these goals, however, Greenwald had to pursue a new technique that increased density by injecting pellets of frozen fuel into the plasma, a method he likens to throwing “snowballs in hell.” This work was notable for the creation of a new regime of enhanced plasma confinement on Alcator C. In those experiments, a confined plasma surpassed for the first time one of the two Lawson criteria — the minimum required value for the product of the plasma density and confinement time — for making net power from fusion. This had been a milestone for fusion research since their publication by John Lawson in 1957.

      Greenwald continued to make a name for himself as part of a larger study into the physics of the Compact Ignition Tokamak — a high-field burning plasma experiment that the U.S. program was proposing to build in the late 1980s. The result, unexpectedly, was a new scaling law, later known as the “Greenwald Density Limit,” and a new theory for the mechanism of the limit. It has been used to accurately predict performance on much larger machines built since.

      The center’s next tokamak, Alcator C-Mod, started operation in 1993 and ran for more than 20 years, with Greenwald as the chair of its Experimental Program Committee. Larger than Alcator C, the new device supported a highly shaped plasma, strong radiofrequency heating, and an all-metal plasma-facing first wall. All of these would eventually be required in a fusion power system.

      C-Mod proved to be MIT’s most enduring fusion experiment to date, producing important results for 20 years. During that time Greenwald contributed not only to the experiments, but to mentoring the next generation. Research scientist Ryan Sweeney notes that “Martin quickly gained my trust as a mentor, in part due to his often casual dress and slightly untamed hair, which are embodiments of his transparency and his focus on what matters. He can quiet a room of PhDs and demand attention not by intimidation, but rather by his calmness and his ability to bring clarity to complicated problems, be they scientific or human in nature.”

      Greenwald worked closely with the group of students who, in PSFC Director Dennis Whyte’s class, came up with the tokamak concept that evolved into SPARC. MIT is now pursuing this compact, high-field tokamak with Commonwealth Fusion Systems, a startup that grew out of the collective enthusiasm for this concept, and the growing realization it could work. Greenwald now heads the Physics Group for the SPARC project at MIT. He has helped confirm the device’s physics basis in order to predict performance and guide engineering decisions.

      “Martin’s multifaceted talents are thoroughly embodied by, and imprinted on, SPARC” says Whyte. “First, his leadership in its plasma confinement physics validation and publication place SPARC on a firm scientific footing. Secondly, the impact of the density limit he discovered, which shows that fuel density increases with magnetic field and decreasing the size of the tokamak, is critical in obtaining high fusion power density not just in SPARC, but in future power plants. Third, and perhaps most impressive, is Martin’s mentorship of the SPARC generation of leadership.”

      Greenwald’s expertise and easygoing personality have made him an asset as head of the PSFC Office for Computer Services and group leader for data acquisition and computing, and sought for many professional committees. He has been an APS Fellow since 2000, and was an APS Distinguished Lecturer in Plasma Physics (2001-02). He was also presented in 2014 with a Leadership Award from Fusion Power Associates. He is currently an associate editor for Physics of Plasmas and a member of the Lawrence Livermore National Laboratory Physical Sciences Directorate External Review Committee.

      Although leaving his full-time responsibilities, Greenwald will remain at MIT as a visiting scientist, a role he says will allow him to “stick my nose into everything without being responsible for anything.”

      “At some point in the race you have to hand off the baton,“ he says. “And it doesn’t mean you’re not interested in the outcome; and it doesn’t mean you’re just going to walk away into the stands. I want to be there at the end when we succeed.” More

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      in Energy

      Tuning in to invisible waves on the JET tokamak

      by

      Research scientist Alex Tinguely is readjusting to Cambridge and Boston.

      As a postdoc with the Plasma Science and Fusion Center (PSFC), the MIT graduate spent the last two years in Oxford, England, a city he recalls can be traversed entirely “in the time it takes to walk from MIT to Harvard.” With its ancient stone walls, cathedrals, cobblestone streets, and winding paths, that small city was his home base for a big project: JET, a tokamak that is currently the largest operating magnetic fusion energy experiment in the world.

      Located at the Culham Center for Fusion Energy (CCFE), part of the U.K. Atomic Energy Authority, this key research center of the European Fusion Program has recently announced historic success. Using a 50-50 deuterium-tritium fuel mixture for the first time since 1997, JET established a fusion power record of 10 megawatts output over five seconds. It produced 59 megajoules of fusion energy, more than doubling the 22 megajoule record it set in 1997. As a member of the JET Team, Tinguely has overseen the measurement and instrumentation systems (diagnostics) contributed by the MIT group.

      A lucky chance

      The postdoctoral opportunity arose just as Tinguely was graduating with a PhD in physics from MIT. Managed by Professor Miklos Porkolab as the principal investigator for over 20 years, this postdoctoral program has prepared multiple young researchers for careers in fusion facilities around the world. The collaborative research provided Tinguely the chance to work on a fusion device that would be adding tritium to the usual deuterium fuel.

      Fusion, the process that fuels the sun and other stars, could provide a long-term source of carbon-free power on Earth, if it can be harnessed. For decades researchers have tried to create an artificial star in a doughnut-shaped bottle, or “tokamak,” using magnetic fields to keep the turbulent plasma fuel confined and away from the walls of its container long enough for fusion to occur.

      In his graduate student days at MIT, Tinguely worked on the PSFC’s Alcator C-Mod tokamak, now decommissioned, which, like most magnetic fusion devices, used deuterium to create the plasmas for experiments. JET, since beginning operation in 1983, has done the same, later joining a small number of facilities that added tritium, a radioactive isotope of hydrogen. While this addition increases the amount of fusion, it also creates much more radiation and activation.

      Tinguely considers himself fortunate to have been placed at JET.

      “There aren’t that many operating tokamaks in the U.S. right now,” says Tinguely, “not to mention one that would be running deuterium-tritium (DT), which hasn’t been run for over 20 years, and which would be making some really important measurements. I got a very lucky spot where I was an MIT postdoc, but I lived in Oxford, working on a very international project.”

      Strumming magnetic field lines

      The measurements that interest Tinguely are of low-frequency electromagnetic waves in tokamak plasmas. Tinguely uses an antenna diagnostic developed by MIT, EPFL Swiss Plasma Center, and CCFE to probe the so-called Alfvén eigenmodes when they are stable, before the energetic alpha particles produced by DT fusion plasmas can drive them toward instability.

      What makes MIT’s “Alfvén Eigenmode Active Diagnostic” essential is that without it researchers cannot see, or measure, stable eigenmodes. Unstable modes show up clearly as magnetic fluctuations in the data, but stable waves are invisible without prompting from the antenna. These measurements help researchers understand the physics of Alfvén waves and their potential for degrading fusion performance, providing insights that will be increasingly important for future DT fusion devices.

      Tinguely likens the diagnostic to fingers on guitar strings.

      “The magnetic field lines in the tokamak are like guitar strings. If you have nothing to give energy to the strings — or give energy to the waves of the magnetic field lines — they just sit there, they don’t do anything. The energetic plasma particles can essentially ‘play the guitar strings,’ strum the magnetic field lines of the plasma, and that’s when you can see the waves in your plasma. But if the energetic particle drive of the waves is not strong enough you won’t see them, so you need to come along and ‘pluck the strings’ with our antenna. And that’s how you learn some information about the waves.”

      Much of Tinguely’s experience on JET took place during the Covid-19 pandemic, when off-site operation and analysis were the norm. However, because the MIT diagnostic needed to be physically turned on and off, someone from Tinguely’s team needed to be on site twice a day, a routine that became even less convenient when tritium was introduced.

      “When you have deuterium and tritium, you produce a lot of neutrons. So, some of the buildings became off-limits during operation, which meant they had to be turned on really early in the morning, like 6:30 a.m., and then turned off very late at night, around 10:30 p.m.”

      Looking to the future

      Now a research scientist at the PSFC, Tinguely continues to work at JET remotely. He sometimes wishes he could again ride that train from Oxford to Culham — which he fondly remembers for its clean, comfortable efficiency — to see work colleagues and to visit local friends. The life he created for himself in England included practice and performance with the 125-year-old Oxford Bach Choir, as well as weekly dinner service at The Gatehouse, a facility that offers free support for the local homeless and low-income communities.

      “Being back is exciting too,” he says. “It’s fun to see how things have changed, how people and projects have grown, what new opportunities have arrived.”

      He refers specifically to a project that is beginning to take up more of his time: SPARC, the tokamak the PSFC supports in collaboration with Commonwealth Fusion Systems. Designed to use deuterium-tritium to make net fusion gains, SPARC will be able to use the latest research on JET to advantage. Tinguely is already exploring how his expertise with Alfvén eigenmodes can support the experiment.

      “I actually had an opportunity to do my PhD — or DPhil as they would call it — at Oxford University, but I went to MIT for grad school instead,” Tinguely reveals. “So, this is almost like closure, in a sense. I got to have my Oxford experience in the end, just in a different way, and have the MIT experience too.”

      He adds, “And I see myself being here at MIT for some time.” More