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    Exploring the cellular neighborhood

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    Cells rely on complex molecular machines composed of protein assemblies to perform essential functions such as energy production, gene expression, and protein synthesis. To better understand how these machines work, scientists capture snapshots of them by isolating proteins from cells and using various methods to determine their structures. However, isolating proteins from cells also removes them from the context of their native environment, including protein interaction partners and cellular location.

    Recently, cryogenic electron tomography (cryo-ET) has emerged as a way to observe proteins in their native environment by imaging frozen cells at different angles to obtain three-dimensional structural information. This approach is exciting because it allows researchers to directly observe how and where proteins associate with each other, revealing the cellular neighborhood of those interactions within the cell.

    With the technology available to image proteins in their native environment, MIT graduate student Barrett Powell wondered if he could take it one step further: What if molecular machines could be observed in action? In a paper published March 8 in Nature Methods, Powell describes the method he developed, called tomoDRGN, for modeling structural differences of proteins in cryo-ET data that arise from protein motions or proteins binding to different interaction partners. These variations are known as structural heterogeneity. 

    Although Powell had joined the lab of MIT associate professor of biology Joey Davis as an experimental scientist, he recognized the potential impact of computational approaches in understanding structural heterogeneity within a cell. Previously, the Davis Lab developed a related methodology named cryoDRGN to understand structural heterogeneity in purified samples. As Powell and Davis saw cryo-ET rising in prominence in the field, Powell took on the challenge of re-imagining this framework to work in cells.

    When solving structures with purified samples, each particle is imaged only once. By contrast, cryo-ET data is collected by imaging each particle more than 40 times from different angles. That meant tomoDRGN needed to be able to merge the information from more than 40 images, which was where the project hit a roadblock: the amount of data led to an information overload.

    To address this, Powell successfully rebuilt the cryoDRGN model to prioritize only the highest-quality data. When imaging the same particle multiple times, radiation damage occurs. The images acquired earlier, therefore, tend to be of higher quality because the particles are less damaged.

    “By excluding some of the lower-quality data, the results were actually better than using all of the data — and the computational performance was substantially faster,” Powell says.

    Just as Powell was beginning work on testing his model, he had a stroke of luck: The authors of a groundbreaking new study that visualized, for the first time, ribosomes inside cells at near-atomic resolution, shared their raw data on the Electric Microscopy Public Image Archive (EMPIAR). This dataset was an exemplary test case for Powell, through which he demonstrated that tomoDRGN could uncover structural heterogeneity within cryo-ET data. 

    According to Powell, one exciting result is what tomoDRGN found surrounding a subset of ribosomes in the EMPIAR dataset. Some of the ribosomal particles were associated with a bacterial cell membrane and engaged in a process called cotranslational translocation. This occurs when a protein is being simultaneously synthesized and transported across a membrane. Researchers can use this result to make new hypotheses about how the ribosome functions with other protein machinery integral to transporting proteins outside of the cell, now guided by a structure of the complex in its native environment. 

    After seeing that tomoDRGN could resolve structural heterogeneity from a structurally diverse dataset, Powell was curious: How small of a population could tomoDRGN identify? For that test, he chose a protein named apoferritin, which is a commonly used benchmark for cryo-ET and is often treated as structurally homogeneous. Ferritin is a protein used for iron storage and is referred to as apoferritin when it lacks iron.

    Surprisingly, in addition to the expected particles, tomoDRGN revealed a minor population of ferritin particles — with iron bound — making up just 2 percent of the dataset, that was not previously reported. This result further demonstrated tomoDRGN’s ability to identify structural states that occur so infrequently that they would be averaged out of a 3D reconstruction. 

    Powell and other members of the Davis Lab are excited to see how tomoDRGN can be applied to further ribosomal studies and to other systems. Davis works on understanding how cells assemble, regulate, and degrade molecular machines, so the next steps include exploring ribosome biogenesis within cells in greater detail using this new tool.

    “What are the possible states that we may be losing during purification?” Davis asks. “Perhaps more excitingly, we can look at how they localize within the cell and what partners and protein complexes they may be interacting with.” More

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      in Data Management & Statistics

      Study: Global deforestation leads to more mercury pollution

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      About 10 percent of human-made mercury emissions into the atmosphere each year are the result of global deforestation, according to a new MIT study.

      The world’s vegetation, from the Amazon rainforest to the savannahs of sub-Saharan Africa, acts as a sink that removes the toxic pollutant from the air. However, if the current rate of deforestation remains unchanged or accelerates, the researchers estimate that net mercury emissions will keep increasing.

      “We’ve been overlooking a significant source of mercury, especially in tropical regions,” says Ari Feinberg, a former postdoc in the Institute for Data, Systems, and Society (IDSS) and lead author of the study.

      The researchers’ model shows that the Amazon rainforest plays a particularly important role as a mercury sink, contributing about 30 percent of the global land sink. Curbing Amazon deforestation could thus have a substantial impact on reducing mercury pollution.

      The team also estimates that global reforestation efforts could increase annual mercury uptake by about 5 percent. While this is significant, the researchers emphasize that reforestation alone should not be a substitute for worldwide pollution control efforts.

      “Countries have put a lot of effort into reducing mercury emissions, especially northern industrialized countries, and for very good reason. But 10 percent of the global anthropogenic source is substantial, and there is a potential for that to be even greater in the future. [Addressing these deforestation-related emissions] needs to be part of the solution,” says senior author Noelle Selin, a professor in IDSS and MIT’s Department of Earth, Atmospheric and Planetary Sciences.

      Feinberg and Selin are joined on the paper by co-authors Martin Jiskra, a former Swiss National Science Foundation Ambizione Fellow at the University of Basel; Pasquale Borrelli, a professor at Roma Tre University in Italy; and Jagannath Biswakarma, a postdoc at the Swiss Federal Institute of Aquatic Science and Technology. The paper appears today in Environmental Science and Technology.

      Modeling mercury

      Over the past few decades, scientists have generally focused on studying deforestation as a source of global carbon dioxide emissions. Mercury, a trace element, hasn’t received the same attention, partly because the terrestrial biosphere’s role in the global mercury cycle has only recently been better quantified.

      Plant leaves take up mercury from the atmosphere, in a similar way as they take up carbon dioxide. But unlike carbon dioxide, mercury doesn’t play an essential biological function for plants. Mercury largely stays within a leaf until it falls to the forest floor, where the mercury is absorbed by the soil.

      Mercury becomes a serious concern for humans if it ends up in water bodies, where it can become methylated by microorganisms. Methylmercury, a potent neurotoxin, can be taken up by fish and bioaccumulated through the food chain. This can lead to risky levels of methylmercury in the fish humans eat.

      “In soils, mercury is much more tightly bound than it would be if it were deposited in the ocean. The forests are doing a sort of ecosystem service, in that they are sequestering mercury for longer timescales,” says Feinberg, who is now a postdoc in the Blas Cabrera Institute of Physical Chemistry in Spain.

      In this way, forests reduce the amount of toxic methylmercury in oceans.

      Many studies of mercury focus on industrial sources, like burning fossil fuels, small-scale gold mining, and metal smelting. A global treaty, the 2013 Minamata Convention, calls on nations to reduce human-made emissions. However, it doesn’t directly consider impacts of deforestation.

      The researchers launched their study to fill in that missing piece.

      In past work, they had built a model to probe the role vegetation plays in mercury uptake. Using a series of land use change scenarios, they adjusted the model to quantify the role of deforestation.

      Evaluating emissions

      This chemical transport model tracks mercury from its emissions sources to where it is chemically transformed in the atmosphere and then ultimately to where it is deposited, mainly through rainfall or uptake into forest ecosystems.

      They divided the Earth into eight regions and performed simulations to calculate deforestation emissions factors for each, considering elements like type and density of vegetation, mercury content in soils, and historical land use.

      However, good data for some regions were hard to come by.

      They lacked measurements from tropical Africa or Southeast Asia — two areas that experience heavy deforestation. To get around this gap, they used simpler, offline models to simulate hundreds of scenarios, which helped them improve their estimations of potential uncertainties.

      They also developed a new formulation for mercury emissions from soil. This formulation captures the fact that deforestation reduces leaf area, which increases the amount of sunlight that hits the ground and accelerates the outgassing of mercury from soils.

      The model divides the world into grid squares, each of which is a few hundred square kilometers. By changing land surface and vegetation parameters in certain squares to represent deforestation and reforestation scenarios, the researchers can capture impacts on the mercury cycle.

      Overall, they found that about 200 tons of mercury are emitted to the atmosphere as the result of deforestation, or about 10 percent of total human-made emissions. But in tropical and sub-tropical countries, deforestation emissions represent a higher percentage of total emissions. For example, in Brazil deforestation emissions are 40 percent of total human-made emissions.

      In addition, people often light fires to prepare tropical forested areas for agricultural activities, which causes more emissions by releasing mercury stored by vegetation.

      “If deforestation was a country, it would be the second highest emitting country, after China, which emits around 500 tons of mercury a year,” Feinberg adds.

      And since the Minamata Convention is now addressing primary mercury emissions, scientists can expect deforestation to become a larger fraction of human-made emissions in the future.

      “Policies to protect forests or cut them down have unintended effects beyond their target. It is important to consider the fact that these are systems, and they involve human activities, and we need to understand them better in order to actually solve the problems that we know are out there,” Selin says.

      By providing this first estimate, the team hopes to inspire more research in this area.

      In the future, they want to incorporate more dynamic Earth system models into their analysis, which would enable them to interactively track mercury uptake and better model the timescale of vegetation regrowth.

      “This paper represents an important advance in our understanding of global mercury cycling by quantifying a pathway that has long been suggested but not yet quantified. Much of our research to date has focused on primary anthropogenic emissions — those directly resulting from human activity via coal combustion or mercury-gold amalgam burning in artisanal and small-scale gold mining,” says Jackie Gerson, an assistant professor in the Department of Earth and Environmental Sciences at Michigan State University, who was not involved with this research. “This research shows that deforestation can also result in substantial mercury emissions and needs to be considered both in terms of global mercury models and land management policies. It therefore has the potential to advance our field scientifically as well as to promote policies that reduce mercury emissions via deforestation.

      This work was funded, in part, by the U.S. National Science Foundation, the Swiss National Science Foundation, and Swiss Federal Institute of Aquatic Science and Technology. More

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      in Data Management & Statistics

      Creating new skills and new connections with MIT’s Quantitative Methods Workshop

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      Starting on New Year’s Day, when many people were still clinging to holiday revelry, scores of students and faculty members from about a dozen partner universities instead flipped open their laptops for MIT’s Quantitative Methods Workshop, a jam-packed, weeklong introduction to how computational and mathematical techniques can be applied to neuroscience and biology research. But don’t think of QMW as a “crash course.” Instead the program’s purpose is to help elevate each participant’s scientific outlook, both through the skills and concepts it imparts and the community it creates.

      “It broadens their horizons, it shows them significant applications they’ve never thought of, and introduces them to people whom as researchers they will come to know and perhaps collaborate with one day,” says Susan L. Epstein, a Hunter College computer science professor and education coordinator of MIT’s Center for Brains, Minds, and Machines, which hosts the program with the departments of Biology and Brain and Cognitive Sciences and The Picower Institute for Learning and Memory. “It is a model of interdisciplinary scholarship.”

      This year 83 undergraduates and faculty members from institutions that primarily serve groups underrepresented in STEM fields took part in the QMW, says organizer Mandana Sassanfar, senior lecturer and director of diversity and science outreach across the four hosting MIT entities. Since the workshop launched in 2010, it has engaged more than 1,000 participants, of whom more than 170 have gone on to participate in MIT Summer Research Programs (such as MSRP-BIO), and 39 have come to MIT for graduate school.

      Individual goals, shared experience

      Undergraduates and faculty in various STEM disciplines often come to QMW to gain an understanding of, or expand their expertise in, computational and mathematical data analysis. Computer science- and statistics-minded participants come to learn more about how such techniques can be applied in life sciences fields. In lectures; in hands-on labs where they used the computer programming language Python to process, analyze, and visualize data; and in less formal settings such as tours and lunches with MIT faculty, participants worked and learned together, and informed each other’s perspectives.

      Brain and Cognitive Sciences Professor Nancy Kanwisher delivers a lecture in MIT’s Building 46 on functional brain imaging to QMW participants.

      Photo: Mandana Sassanfar

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      And regardless of their field of study, participants made connections with each other and with the MIT students and faculty who taught and spoke over the course of the week.

      Hunter College computer science sophomore Vlad Vostrikov says that while he has already worked with machine learning and other programming concepts, he was interested to “branch out” by seeing how they are used to analyze scientific datasets. He also valued the chance to learn the experiences of the graduate students who teach QMW’s hands-on labs.

      “This was a good way to explore computational biology and neuroscience,” Vostrikov says. “I also really enjoy hearing from the people who teach us. It’s interesting to hear where they come from and what they are doing.”

      Jariatu Kargbo, a biology and chemistry sophomore at University of Maryland Baltimore County, says when she first learned of the QMW she wasn’t sure it was for her. It seemed very computation-focused. But her advisor Holly Willoughby encouraged Kargbo to attend to learn about how programming could be useful in future research — currently she is taking part in research on the retina at UMBC. More than that, Kargbo also realized it would be a good opportunity to make connections at MIT in advance of perhaps applying for MSRP this summer.

      “I thought this would be a great way to meet up with faculty and see what the environment is like here because I’ve never been to MIT before,” Kargbo says. “It’s always good to meet other people in your field and grow your network.”

      QMW is not just for students. It’s also for their professors, who said they can gain valuable professional education for their research and teaching.

      Fayuan Wen, an assistant professor of biology at Howard University, is no stranger to computational biology, having performed big data genetic analyses of sickle cell disease (SCD). But she’s mostly worked with the R programming language and QMW’s focus is on Python. As she looks ahead to projects in which she wants analyze genomic data to help predict disease outcomes in SCD and HIV, she says a QMW session delivered by biology graduate student Hannah Jacobs was perfectly on point.

      “This workshop has the skills I want to have,” Wen says.

      Moreover, Wen says she is looking to start a machine-learning class in the Howard biology department and was inspired by some of the teaching materials she encountered at QMW — for example, online curriculum modules developed by Taylor Baum, an MIT graduate student in electrical engineering and computer science and Picower Institute labs, and Paloma Sánchez-Jáuregui, a coordinator who works with Sassanfar.

      Tiziana Ligorio, a Hunter College computer science doctoral lecturer who together with Epstein teaches a deep machine-learning class at the City University of New York campus, felt similarly. Rather than require a bunch of prerequisites that might drive students away from the class, Ligorio was looking to QMW’s intense but introductory curriculum as a resource for designing a more inclusive way of getting students ready for the class.

      Instructive interactions

      Each day runs from 9 a.m. to 5 p.m., including morning and afternoon lectures and hands-on sessions. Class topics ranged from statistical data analysis and machine learning to brain-computer interfaces, brain imaging, signal processing of neural activity data, and cryogenic electron microscopy.

      “This workshop could not happen without dedicated instructors — grad students, postdocs, and faculty — who volunteer to give lectures, design and teach hands-on computer labs, and meet with students during the very first week of January,” Saassanfar says.

      MIT assistant professor of biology Brady Weissbourd (center) converses with QMW student participants during a lunch break.

      Photo: Mandana Sassanfar

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      The sessions surround student lunches with MIT faculty members. For example, at midday Jan. 2, assistant professor of biology Brady Weissbourd, an investigator in the Picower Institute, sat down with seven students in one of Building 46’s curved sofas to field questions about his neuroscience research in jellyfish and how he uses quantitative techniques as part of that work. He also described what it’s like to be a professor, and other topics that came to the students’ minds.

      Then the participants all crossed Vassar Street to Building 26’s Room 152, where they formed different but similarly sized groups for the hands-on lab “Machine learning applications to studying the brain,” taught by Baum. She guided the class through Python exercises she developed illustrating “supervised” and “unsupervised” forms of machine learning, including how the latter method can be used to discern what a person is seeing based on magnetic readings of brain activity.

      As students worked through the exercises, tablemates helped each other by supplementing Baum’s instruction. Ligorio, Vostrikov, and Kayla Blincow, assistant professor of biology at the University of the Virgin Islands, for instance, all leapt to their feet to help at their tables.

      Hunter College lecturer of computer science Tiziana Ligorio (standing) explains a Python programming concept to students at her table during a workshop session.

      Photo: David Orenstein

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      At the end of the class, when Baum asked students what they had learned, they offered a litany of new knowledge. Survey data that Sassanfar and Sánchez-Jáuregui use to anonymously track QMW outcomes, revealed many more such attestations of the value of the sessions. With a prompt asking how one might apply what they’ve learned, one respondent wrote: “Pursue a research career or endeavor in which I apply the concepts of computer science and neuroscience together.”

      Enduring connections

      While some new QMW attendees might only be able to speculate about how they’ll apply their new skills and relationships, Luis Miguel de Jesús Astacio could testify to how attending QMW as an undergraduate back in 2014 figured into a career where he is now a faculty member in physics at the University of Puerto Rico Rio Piedras Campus. After QMW, he returned to MIT that summer as a student in the lab of neuroscientist and Picower Professor Susumu Tonegawa. He came back again in 2016 to the lab of physicist and Francis Friedman Professor Mehran Kardar. What’s endured for the decade has been his connection to Sassanfar. So while he was once a student at QMW, this year he was back with a cohort of undergraduates as a faculty member.

      Michael Aldarondo-Jeffries, director of academic advancement programs at the University of Central Florida, seconded the value of the networking that takes place at QMW. He has brought students for a decade, including four this year. What he’s observed is that as students come together in settings like QMW or UCF’s McNair program, which helps to prepare students for graduate school, they become inspired about a potential future as researchers.

      “The thing that stands out is just the community that’s formed,” he says. “For many of the students, it’s the first time that they’re in a group that understands what they’re moving toward. They don’t have to explain why they’re excited to read papers on a Friday night.”

      Or why they are excited to spend a week including New Year’s Day at MIT learning how to apply quantitative methods to life sciences data. More

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      Co-creating climate futures with real-time data and spatial storytelling

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      Virtual story worlds and game engines aren’t just for video games anymore. They are now tools for scientists and storytellers to digitally twin existing physical spaces and then turn them into vessels to dream up speculative climate stories and build collective designs of the future. That’s the theory and practice behind the MIT WORLDING initiative.

      Twice this year, WORLDING matched world-class climate story teams working in XR (extended reality) with relevant labs and researchers across MIT. One global group returned for a virtual gathering online in partnership with Unity for Humanity, while another met for one weekend in person, hosted at the MIT Media Lab.

      “We are witnessing the birth of an emergent field that fuses climate science, urban planning, real-time 3D engines, nonfiction storytelling, and speculative fiction, and it is all fueled by the urgency of the climate crises,” says Katerina Cizek, lead designer of the WORLDING initiative at the Co-Creation Studio of MIT Open Documentary Lab. “Interdisciplinary teams are forming and blossoming around the planet to collectively imagine and tell stories of healthy, livable worlds in virtual 3D spaces and then finding direct ways to translate that back to earth, literally.”

      At this year’s virtual version of WORLDING, five multidisciplinary teams were selected from an open call. In a week-long series of research and development gatherings, the teams met with MIT scientists, staff, fellows, students, and graduates, as well as other leading figures in the field. Guests ranged from curators at film festivals such as Sundance and Venice, climate policy specialists, and award-winning media creators to software engineers and renowned Earth and atmosphere scientists. The teams heard from MIT scholars in diverse domains, including geomorphology, urban planning as acts of democracy, and climate researchers at MIT Media Lab.

      Mapping climate data

      “We are measuring the Earth’s environment in increasingly data-driven ways. Hundreds of terabytes of data are taken every day about our planet in order to study the Earth as a holistic system, so we can address key questions about global climate change,” explains Rachel Connolly, an MIT Media Lab research scientist focused in the “Future Worlds” research theme, in a talk to the group. “Why is this important for your work and storytelling in general? Having the capacity to understand and leverage this data is critical for those who wish to design for and successfully operate in the dynamic Earth environment.”

      Making sense of billions of data points was a key theme during this year’s sessions. In another talk, Taylor Perron, an MIT professor of Earth, atmospheric and planetary sciences, shared how his team uses computational modeling combined with many other scientific processes to better understand how geology, climate, and life intertwine to shape the surfaces of Earth and other planets. His work resonated with one WORLDING team in particular, one aiming to digitally reconstruct the pre-Hispanic Lake Texcoco — where current day Mexico City is now situated — as a way to contrast and examine the region’s current water crisis.

      Democratizing the future

      While WORLDING approaches rely on rigorous science and the interrogation of large datasets, they are also founded on democratizing community-led approaches.

      MIT Department of Urban Studies and Planning graduate Lafayette Cruise MCP ’19 met with the teams to discuss how he moved his own practice as a trained urban planner to include a futurist component involving participatory methods. “I felt we were asking the same limited questions in regards to the future we were wanting to produce. We’re very limited, very constrained, as to whose values and comforts are being centered. There are so many possibilities for how the future could be.”

      Scaling to reach billions

      This work scales from the very local to massive global populations. Climate policymakers are concerned with reaching billions of people in the line of fire. “We have a goal to reach 1 billion people with climate resilience solutions,” says Nidhi Upadhyaya, deputy director at Atlantic Council’s Adrienne Arsht-Rockefeller Foundation Resilience Center. To get that reach, Upadhyaya is turning to games. “There are 3.3 billion-plus people playing video games across the world. Half of these players are women. This industry is worth $300 billion. Africa is currently among the fastest-growing gaming markets in the world, and 55 percent of the global players are in the Asia Pacific region.” She reminded the group that this conversation is about policy and how formats of mass communication can be used for policymaking, bringing about change, changing behavior, and creating empathy within audiences.

      Socially engaged game development is also connected to education at Unity Technologies, a game engine company. “We brought together our education and social impact work because we really see it as a critical flywheel for our business,” said Jessica Lindl, vice president and global head of social impact/education at Unity Technologies, in the opening talk of WORLDING. “We upscale about 900,000 students, in university and high school programs around the world, and about 800,000 adults who are actively learning and reskilling and upskilling in Unity. Ultimately resulting in our mission of the ‘world is a better place with more creators in it,’ millions of creators who reach billions of consumers — telling the world stories, and fostering a more inclusive, sustainable, and equitable world.”

      Access to these technologies is key, especially the hardware. “Accessibility has been missing in XR,” explains Reginé Gilbert, who studies and teaches accessibility and disability in user experience design at New York University. “XR is being used in artificial intelligence, assistive technology, business, retail, communications, education, empathy, entertainment, recreation, events, gaming, health, rehabilitation meetings, navigation, therapy, training, video programming, virtual assistance wayfinding, and so many other uses. This is a fun fact for folks: 97.8 percent of the world hasn’t tried VR [virtual reality] yet, actually.”

      Meanwhile, new hardware is on its way. The WORLDING group got early insights into the highly anticipated Apple Vision Pro headset, which promises to integrate many forms of XR and personal computing in one device. “They’re really pushing this kind of pass-through or mixed reality,” said Dan Miller, a Unity engineer on the poly spatial team, collaborating with Apple, who described the experience of the device as “You are viewing the real world. You’re pulling up windows, you’re interacting with content. It’s a kind of spatial computing device where you have multiple apps open, whether it’s your email client next to your messaging client with a 3D game in the middle. You’re interacting with all these things in the same space and at different times.”

      “WORLDING combines our passion for social-impact storytelling and incredible innovative storytelling,” said Paisley Smith of the Unity for Humanity Program at Unity Technologies. She added, “This is an opportunity for creators to incubate their game-changing projects and connect with experts across climate, story, and technology.”

      Meeting at MIT

      In a new in-person iteration of WORLDING this year, organizers collaborated closely with Connolly at the MIT Media Lab to co-design an in-person weekend conference Oct. 25 – Nov. 7 with 45 scholars and professionals who visualize climate data at NASA, the National Oceanic and Atmospheric Administration, planetariums, and museums across the United States.

      A participant said of the event, “An incredible workshop that had had a profound effect on my understanding of climate data storytelling and how to combine different components together for a more [holistic] solution.”

      “With this gathering under our new Future Worlds banner,” says Dava Newman, director of the MIT Media Lab and Apollo Program Professor of Astronautics chair, “the Media Lab seeks to affect human behavior and help societies everywhere to improve life here on Earth and in worlds beyond, so that all — the sentient, natural, and cosmic — worlds may flourish.” 

      “WORLDING’s virtual-only component has been our biggest strength because it has enabled a true, international cohort to gather, build, and create together. But this year, an in-person version showed broader opportunities that spatial interactivity generates — informal Q&As, physical worksheets, and larger-scale ideation, all leading to deeper trust-building,” says WORLDING producer Srushti Kamat SM ’23.

      The future and potential of WORLDING lies in the ongoing dialogue between the virtual and physical, both in the work itself and in the format of the workshops. More

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      Technique could efficiently solve partial differential equations for numerous applications

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      In fields such as physics and engineering, partial differential equations (PDEs) are used to model complex physical processes to generate insight into how some of the most complicated physical and natural systems in the world function.

      To solve these difficult equations, researchers use high-fidelity numerical solvers, which can be very time-consuming and computationally expensive to run. The current simplified alternative, data-driven surrogate models, compute the goal property of a solution to PDEs rather than the whole solution. Those are trained on a set of data that has been generated by the high-fidelity solver, to predict the output of the PDEs for new inputs. This is data-intensive and expensive because complex physical systems require a large number of simulations to generate enough data. 

      In a new paper, “Physics-enhanced deep surrogates for partial differential equations,” published in December in Nature Machine Intelligence, a new method is proposed for developing data-driven surrogate models for complex physical systems in such fields as mechanics, optics, thermal transport, fluid dynamics, physical chemistry, and climate models.

      The paper was authored by MIT’s professor of applied mathematics Steven G. Johnson along with Payel Das and Youssef Mroueh of the MIT-IBM Watson AI Lab and IBM Research; Chris Rackauckas of Julia Lab; and Raphaël Pestourie, a former MIT postdoc who is now at Georgia Tech. The authors call their method “physics-enhanced deep surrogate” (PEDS), which combines a low-fidelity, explainable physics simulator with a neural network generator. The neural network generator is trained end-to-end to match the output of the high-fidelity numerical solver.

      “My aspiration is to replace the inefficient process of trial and error with systematic, computer-aided simulation and optimization,” says Pestourie. “Recent breakthroughs in AI like the large language model of ChatGPT rely on hundreds of billions of parameters and require vast amounts of resources to train and evaluate. In contrast, PEDS is affordable to all because it is incredibly efficient in computing resources and has a very low barrier in terms of infrastructure needed to use it.”

      In the article, they show that PEDS surrogates can be up to three times more accurate than an ensemble of feedforward neural networks with limited data (approximately 1,000 training points), and reduce the training data needed by at least a factor of 100 to achieve a target error of 5 percent. Developed using the MIT-designed Julia programming language, this scientific machine-learning method is thus efficient in both computing and data.

      The authors also report that PEDS provides a general, data-driven strategy to bridge the gap between a vast array of simplified physical models with corresponding brute-force numerical solvers modeling complex systems. This technique offers accuracy, speed, data efficiency, and physical insights into the process.

      Says Pestourie, “Since the 2000s, as computing capabilities improved, the trend of scientific models has been to increase the number of parameters to fit the data better, sometimes at the cost of a lower predictive accuracy. PEDS does the opposite by choosing its parameters smartly. It leverages the technology of automatic differentiation to train a neural network that makes a model with few parameters accurate.”

      “The main challenge that prevents surrogate models from being used more widely in engineering is the curse of dimensionality — the fact that the needed data to train a model increases exponentially with the number of model variables,” says Pestourie. “PEDS reduces this curse by incorporating information from the data and from the field knowledge in the form of a low-fidelity model solver.”

      The researchers say that PEDS has the potential to revive a whole body of the pre-2000 literature dedicated to minimal models — intuitive models that PEDS could make more accurate while also being predictive for surrogate model applications.

      “The application of the PEDS framework is beyond what we showed in this study,” says Das. “Complex physical systems governed by PDEs are ubiquitous, from climate modeling to seismic modeling and beyond. Our physics-inspired fast and explainable surrogate models will be of great use in those applications, and play a complementary role to other emerging techniques, like foundation models.”

      The research was supported by the MIT-IBM Watson AI Lab and the U.S. Army Research Office through the Institute for Soldier Nanotechnologies.  More

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      Search algorithm reveals nearly 200 new kinds of CRISPR systems

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      Microbial sequence databases contain a wealth of information about enzymes and other molecules that could be adapted for biotechnology. But these databases have grown so large in recent years that they’ve become difficult to search efficiently for enzymes of interest.

      Now, scientists at the McGovern Institute for Brain Research at MIT, the Broad Institute of MIT and Harvard, and the National Center for Biotechnology Information (NCBI) at the National Institutes of Health have developed a new search algorithm that has identified 188 kinds of new rare CRISPR systems in bacterial genomes, encompassing thousands of individual systems. The work appears today in Science.

      The algorithm, which comes from the lab of pioneering CRISPR researcher Professor Feng Zhang, uses big-data clustering approaches to rapidly search massive amounts of genomic data. The team used their algorithm, called Fast Locality-Sensitive Hashing-based clustering (FLSHclust) to mine three major public databases that contain data from a wide range of unusual bacteria, including ones found in coal mines, breweries, Antarctic lakes, and dog saliva. The scientists found a surprising number and diversity of CRISPR systems, including ones that could make edits to DNA in human cells, others that can target RNA, and many with a variety of other functions.

      The new systems could potentially be harnessed to edit mammalian cells with fewer off-target effects than current Cas9 systems. They could also one day be used as diagnostics or serve as molecular records of activity inside cells.

      The researchers say their search highlights an unprecedented level of diversity and flexibility of CRISPR and that there are likely many more rare systems yet to be discovered as databases continue to grow.

      “Biodiversity is such a treasure trove, and as we continue to sequence more genomes and metagenomic samples, there is a growing need for better tools, like FLSHclust, to search that sequence space to find the molecular gems,” says Zhang, a co-senior author on the study and the James and Patricia Poitras Professor of Neuroscience at MIT with joint appointments in the departments of Brain and Cognitive Sciences and Biological Engineering. Zhang is also an investigator at the McGovern Institute for Brain Research at MIT, a core institute member at the Broad, and an investigator at the Howard Hughes Medical Institute. Eugene Koonin, a distinguished investigator at the NCBI, is co-senior author on the study as well.

      Searching for CRISPR

      CRISPR, which stands for clustered regularly interspaced short palindromic repeats, is a bacterial defense system that has been engineered into many tools for genome editing and diagnostics.

      To mine databases of protein and nucleic acid sequences for novel CRISPR systems, the researchers developed an algorithm based on an approach borrowed from the big data community. This technique, called locality-sensitive hashing, clusters together objects that are similar but not exactly identical. Using this approach allowed the team to probe billions of protein and DNA sequences — from the NCBI, its Whole Genome Shotgun database, and the Joint Genome Institute — in weeks, whereas previous methods that look for identical objects would have taken months. They designed their algorithm to look for genes associated with CRISPR.

      “This new algorithm allows us to parse through data in a time frame that’s short enough that we can actually recover results and make biological hypotheses,” says Soumya Kannan PhD ’23, who is a co-first author on the study. Kannan was a graduate student in Zhang’s lab when the study began and is currently a postdoc and Junior Fellow at Harvard University. Han Altae-Tran PhD ’23, a graduate student in Zhang’s lab during the study and currently a postdoc at the University of Washington, was the study’s other co-first author.

      “This is a testament to what you can do when you improve on the methods for exploration and use as much data as possible,” says Altae-Tran. “It’s really exciting to be able to improve the scale at which we search.”

      New systems

      In their analysis, Altae-Tran, Kannan, and their colleagues noticed that the thousands of CRISPR systems they found fell into a few existing and many new categories. They studied several of the new systems in greater detail in the lab.

      They found several new variants of known Type I CRISPR systems, which use a guide RNA that is 32 base pairs long rather than the 20-nucleotide guide of Cas9. Because of their longer guide RNAs, these Type I systems could potentially be used to develop more precise gene-editing technology that is less prone to off-target editing. Zhang’s team showed that two of these systems could make short edits in the DNA of human cells. And because these Type I systems are similar in size to CRISPR-Cas9, they could likely be delivered to cells in animals or humans using the same gene-delivery technologies being used today for CRISPR.

      One of the Type I systems also showed “collateral activity” — broad degradation of nucleic acids after the CRISPR protein binds its target. Scientists have used similar systems to make infectious disease diagnostics such as SHERLOCK, a tool capable of rapidly sensing a single molecule of DNA or RNA. Zhang’s team thinks the new systems could be adapted for diagnostic technologies as well.

      The researchers also uncovered new mechanisms of action for some Type IV CRISPR systems, and a Type VII system that precisely targets RNA, which could potentially be used in RNA editing. Other systems could potentially be used as recording tools — a molecular document of when a gene was expressed — or as sensors of specific activity in a living cell.

      Mining data

      The scientists say their algorithm could aid in the search for other biochemical systems. “This search algorithm could be used by anyone who wants to work with these large databases for studying how proteins evolve or discovering new genes,” Altae-Tran says.

      The researchers add that their findings illustrate not only how diverse CRISPR systems are, but also that most are rare and only found in unusual bacteria. “Some of these microbial systems were exclusively found in water from coal mines,” Kannan says. “If someone hadn’t been interested in that, we may never have seen those systems. Broadening our sampling diversity is really important to continue expanding the diversity of what we can discover.”

      This work was supported by the Howard Hughes Medical Institute; the K. Lisa Yang and Hock E. Tan Molecular Therapeutics Center at MIT; Broad Institute Programmable Therapeutics Gift Donors; The Pershing Square Foundation, William Ackman and Neri Oxman; James and Patricia Poitras; BT Charitable Foundation; Asness Family Foundation; Kenneth C. Griffin; the Phillips family; David Cheng; and Robert Metcalfe. More

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      Rewarding excellence in open data

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      The second annual MIT Prize for Open Data, which included a $2,500 cash prize, was recently awarded to 10 individual and group research projects. Presented jointly by the School of Science and the MIT Libraries, the prize highlights the value of open data — research data that is openly accessible and reusable — at the Institute. The prize winners and 12 honorable mention recipients were honored at the Open Data @ MIT event held Oct. 24 at Hayden Library. 

      Conceived by Chris Bourg, director of MIT Libraries, and Rebecca Saxe, associate dean of the School of Science and the John W. Jarve (1978) Professor of Brain and Cognitive Sciences, the prize program was launched in 2022. It recognizes MIT-affiliated researchers who use or share open data, create infrastructure for open data sharing, or theorize about open data. Nominations were solicited from across the Institute, with a focus on trainees: undergraduate and graduate students, postdocs, and research staff. 

      “The prize is explicitly aimed at early-career researchers,” says Bourg. “Supporting and encouraging the next generation of researchers will help ensure that the future of scholarship is characterized by a norm of open sharing.”

      The 2023 awards were presented at a celebratory event held during International Open Access Week. Winners gave five-minute presentations on their projects and the role that open data plays in their research. The program also included remarks from Bourg and Anne White, School of Engineering Distinguished Professor of Engineering, vice provost, and associate vice president for research administration. White reflected on the ways in which MIT has demonstrated its values with the open sharing of research and scholarship and acknowledged the efforts of the honorees and advocates gathered at the event: “Thank you for the active role you’re all playing in building a culture of openness in research,” she said. “It benefits us all.” 

      Winners were chosen from more than 80 nominees, representing all five MIT schools, the MIT Schwarzman College of Computing, and several research centers across the Institute. A committee composed of faculty, staff, and graduate students made the selections:

      Hammaad Adam, graduate student in the Institute for Data, Systems, and Society, accepted on behalf of the team behind Organ Retrieval and Collection of Health Information for Donation (ORCHID), the first ever multi-center dataset dedicated to the organ procurement process. ORCHID provides the first opportunity to quantitatively analyze organ procurement organization decisions and identify operational inefficiencies.
      Adam Atanas, postdoc in the Department of Brain and Cognitive Sciences (BCS), and Jungsoo Kim, graduate student in BCS, created WormWideWeb.org. The site, allowing researchers to easily browse and download C. elegans whole-brain datasets, will be useful to C. elegans neuroscientists and theoretical/computational neuroscientists. 
      Paul Berube, research scientist in the Department of Civil and Environmental Engineering, and Steven Biller, assistant professor of biological sciences at Wellesley College, won for “Unlocking Marine Microbiomes with Open Data.” Open data of genomes and metagenomes for marine ecosystems, with a focus on cyanobacteria, leverage the power of contemporaneous data from GEOTRACES and other long-standing ocean time-series programs to provide underlying information to answer questions about marine ecosystem function. 
      Jack Cavanagh, Sarah Kopper, and Diana Horvath of the Abdul Latif Jameel Poverty Action Lab (J-PAL) were recognized for J-PAL’s Data Publication Infrastructure, which includes a trusted repository of open-access datasets, a dedicated team of data curators, and coding tools and training materials to help other teams publish data in an efficient and ethical manner. 
      Jerome Patrick Cruz, graduate student in the Department of Political Science, won for OpenAudit, leveraging advances in natural language processing and machine learning to make data in public audit reports more usable for academics and policy researchers, as well as governance practitioners, watchdogs, and reformers. This work was done in collaboration with colleagues at Ateneo de Manila University in the Philippines. 
      Undergraduate student Daniel Kurlander created a tool for planetary scientists to rapidly access and filter images of the comet 67P/Churyumov-Gerasimenko. The web-based tool enables searches by location and other properties, does not require a time-intensive download of a massive dataset, allows analysis of the data independent of the speed of one’s computer, and does not require installation of a complex set of programs. 
      Halie Olson, postdoc in BCS, was recognized for sharing data from a functional magnetic resonance imaging (fMRI) study on language processing. The study used video clips from “Sesame Street” in which researchers manipulated the comprehensibility of the speech stream, allowing them to isolate a “language response” in the brain.
      Thomas González Roberts, graduate student in the Department of Aeronautics and Astronautics, won for the International Telecommunication Union Compliance Assessment Monitor. This tool combats the heritage of secrecy in outer space operations by creating human- and machine-readable datasets that succinctly describe the international agreements that govern satellite operations. 
      Melissa Kline Struhl, research scientist in BCS, was recognized for Children Helping Science, a free, open-source platform for remote studies with babies and children that makes it possible for researchers at more than 100 institutions to conduct reproducible studies. 
      JS Tan, graduate student in the Department of Urban Studies and Planning, developed the Collective Action in Tech Archive in collaboration with Nataliya Nedzhvetskaya of the University of California at Berkeley. It is an open database of all publicly recorded collective actions taken by workers in the global tech industry. 
      A complete list of winning projects and honorable mentions, including links to the research data, is available on the MIT Libraries website. More

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      Forging climate connections across the Institute

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      Climate change is the ultimate cross-cutting issue: Not limited to any one discipline, it ranges across science, technology, policy, culture, human behavior, and well beyond. The response to it likewise requires an all-of-MIT effort.

      Now, to strengthen such an effort, a new grant program spearheaded by the Climate Nucleus, the faculty committee charged with the oversight and implementation of Fast Forward: MIT’s Climate Action Plan for the Decade, aims to build up MIT’s climate leadership capacity while also supporting innovative scholarship on diverse climate-related topics and forging new connections across the Institute.

      Called the Fast Forward Faculty Fund (F^4 for short), the program has named its first cohort of six faculty members after issuing its inaugural call for proposals in April 2023. The cohort will come together throughout the year for climate leadership development programming and networking. The program provides financial support for graduate students who will work with the faculty members on the projects — the students will also participate in leadership-building activities — as well as $50,000 in flexible, discretionary funding to be used to support related activities. 

      “Climate change is a crisis that truly touches every single person on the planet,” says Noelle Selin, co-chair of the nucleus and interim director of the Institute for Data, Systems, and Society. “It’s therefore essential that we build capacity for every member of the MIT community to make sense of the problem and help address it. Through the Fast Forward Faculty Fund, our aim is to have a cohort of climate ambassadors who can embed climate everywhere at the Institute.”

      F^4 supports both faculty who would like to begin doing climate-related work, as well as faculty members who are interested in deepening their work on climate. The program has the core goal of developing cohorts of F^4 faculty and graduate students who, in addition to conducting their own research, will become climate leaders at MIT, proactively looking for ways to forge new climate connections across schools, departments, and disciplines.

      One of the projects, “Climate Crisis and Real Estate: Science-based Mitigation and Adaptation Strategies,” led by Professor Siqi Zheng of the MIT Center for Real Estate in collaboration with colleagues from the MIT Sloan School of Management, focuses on the roughly 40 percent of carbon dioxide emissions that come from the buildings and real estate sector. Zheng notes that this sector has been slow to respond to climate change, but says that is starting to change, thanks in part to the rising awareness of climate risks and new local regulations aimed at reducing emissions from buildings.

      Using a data-driven approach, the project seeks to understand the efficient and equitable market incentives, technology solutions, and public policies that are most effective at transforming the real estate industry. Johnattan Ontiveros, a graduate student in the Technology and Policy Program, is working with Zheng on the project.

      “We were thrilled at the incredible response we received from the MIT faculty to our call for proposals, which speaks volumes about the depth and breadth of interest in climate at MIT,” says Anne White, nucleus co-chair and vice provost and associate vice president for research. “This program makes good on key commitments of the Fast Forward plan, supporting cutting-edge new work by faculty and graduate students while helping to deepen the bench of climate leaders at MIT.”

      During the 2023-24 academic year, the F^4 faculty and graduate student cohorts will come together to discuss their projects, explore opportunities for collaboration, participate in climate leadership development, and think proactively about how to deepen interdisciplinary connections among MIT community members interested in climate change.

      The six inaugural F^4 awardees are:

      Professor Tristan Brown, History Section: Humanistic Approaches to the Climate Crisis  

      With this project, Brown aims to create a new community of practice around narrative-centric approaches to environmental and climate issues. Part of a broader humanities initiative at MIT, it brings together a global working group of interdisciplinary scholars, including Serguei Saavedra (Department of Civil and Environmental Engineering) and Or Porath (Tel Aviv University; Religion), collectively focused on examining the historical and present links between sacred places and biodiversity for the purposes of helping governments and nongovernmental organizations formulate better sustainability goals. Boyd Ruamcharoen, a PhD student in the History, Anthropology, and Science, Technology, and Society (HASTS) program, will work with Brown on this project.

      Professor Kerri Cahoy, departments of Aeronautics and Astronautics and Earth, Atmospheric, and Planetary Sciences (AeroAstro): Onboard Autonomous AI-driven Satellite Sensor Fusion for Coastal Region Monitoring

      The motivation for this project is the need for much better data collection from satellites, where technology can be “20 years behind,” says Cahoy. As part of this project, Cahoy will pursue research in the area of autonomous artificial intelligence-enabled rapid sensor fusion (which combines data from different sensors, such as radar and cameras) onboard satellites to improve understanding of the impacts of climate change, specifically sea-level rise and hurricanes and flooding in coastal regions. Graduate students Madeline Anderson, a PhD student in electrical engineering and computer science (EECS), and Mary Dahl, a PhD student in AeroAstro, will work with Cahoy on this project.

      Professor Priya Donti, Department of Electrical Engineering and Computer Science: Robust Reinforcement Learning for High-Renewables Power Grids 

      With renewables like wind and solar making up a growing share of electricity generation on power grids, Donti’s project focuses on improving control methods for these distributed sources of electricity. The research will aim to create a realistic representation of the characteristics of power grid operations, and eventually inform scalable operational improvements in power systems. It will “give power systems operators faith that, OK, this conceptually is good, but it also actually works on this grid,” says Donti. PhD candidate Ana Rivera from EECS is the F^4 graduate student on the project.

      Professor Jason Jackson, Department of Urban Studies and Planning (DUSP): Political Economy of the Climate Crisis: Institutions, Power and Global Governance

      This project takes a political economy approach to the climate crisis, offering a distinct lens to examine, first, the political governance challenge of mobilizing climate action and designing new institutional mechanisms to address the global and intergenerational distributional aspects of climate change; second, the economic challenge of devising new institutional approaches to equitably finance climate action; and third, the cultural challenge — and opportunity — of empowering an adaptive socio-cultural ecology through traditional knowledge and local-level social networks to achieve environmental resilience. Graduate students Chen Chu and Mrinalini Penumaka, both PhD students in DUSP, are working with Jackson on the project.

      Professor Haruko Wainwright, departments of Nuclear Science and Engineering (NSE) and Civil and Environmental Engineering: Low-cost Environmental Monitoring Network Technologies in Rural Communities for Addressing Climate Justice 

      This project will establish a community-based climate and environmental monitoring network in addition to a data visualization and analysis infrastructure in rural marginalized communities to better understand and address climate justice issues. The project team plans to work with rural communities in Alaska to install low-cost air and water quality, weather, and soil sensors. Graduate students Kay Whiteaker, an MS candidate in NSE, and Amandeep Singh, and MS candidate in System Design and Management at Sloan, are working with Wainwright on the project, as is David McGee, professor in earth, atmospheric, and planetary sciences.

      Professor Siqi Zheng, MIT Center for Real Estate and DUSP: Climate Crisis and Real Estate: Science-based Mitigation and Adaptation Strategies 

      See the text above for the details on this project. More

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      Improving US air quality, equitably

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      Decarbonization of national economies will be key to achieving global net-zero emissions by 2050, a major stepping stone to the Paris Agreement’s long-term goal of keeping global warming well below 2 degrees Celsius (and ideally 1.5 C), and thereby averting the worst consequences of climate change. Toward that end, the United States has pledged to reduce its greenhouse gas emissions by 50-52 percent from 2005 levels by 2030, backed by its implementation of the 2022 Inflation Reduction Act. This strategy is consistent with a 50-percent reduction in carbon dioxide (CO2) by the end of the decade.

      If U.S. federal carbon policy is successful, the nation’s overall air quality will also improve. Cutting CO2 emissions reduces atmospheric concentrations of air pollutants that lead to the formation of fine particulate matter (PM2.5), which causes more than 200,000 premature deaths in the United States each year. But an average nationwide improvement in air quality will not be felt equally; air pollution exposure disproportionately harms people of color and lower-income populations.

      How effective are current federal decarbonization policies in reducing U.S. racial and economic disparities in PM2.5 exposure, and what changes will be needed to improve their performance? To answer that question, researchers at MIT and Stanford University recently evaluated a range of policies which, like current U.S. federal carbon policies, reduce economy-wide CO2 emissions by 40-60 percent from 2005 levels by 2030. Their findings appear in an open-access article in the journal Nature Communications.

      First, they show that a carbon-pricing policy, while effective in reducing PM2.5 exposure for all racial/ethnic groups, does not significantly mitigate relative disparities in exposure. On average, the white population undergoes far less exposure than Black, Hispanic, and Asian populations. This policy does little to reduce exposure disparities because the CO2 emissions reductions that it achieves primarily occur in the coal-fired electricity sector. Other sectors, such as industry and heavy-duty diesel transportation, contribute far more PM2.5-related emissions.

      The researchers then examine thousands of different reduction options through an optimization approach to identify whether any possible combination of carbon dioxide reductions in the range of 40-60 percent can mitigate disparities. They find that that no policy scenario aligned with current U.S. carbon dioxide emissions targets is likely to significantly reduce current PM2.5 exposure disparities.

      “Policies that address only about 50 percent of CO2 emissions leave many polluting sources in place, and those that prioritize reductions for minorities tend to benefit the entire population,” says Noelle Selin, supervising author of the study and a professor at MIT’s Institute for Data, Systems and Society and Department of Earth, Atmospheric and Planetary Sciences. “This means that a large range of policies that reduce CO2 can improve air quality overall, but can’t address long-standing inequities in air pollution exposure.”

      So if climate policy alone cannot adequately achieve equitable air quality results, what viable options remain? The researchers suggest that more ambitious carbon policies could narrow racial and economic PM2.5 exposure disparities in the long term, but not within the next decade. To make a near-term difference, they recommend interventions designed to reduce PM2.5 emissions resulting from non-CO2 sources, ideally at the economic sector or community level.

      “Achieving improved PM2.5 exposure for populations that are disproportionately exposed across the United States will require thinking that goes beyond current CO2 policy strategies, most likely involving large-scale structural changes,” says Selin. “This could involve changes in local and regional transportation and housing planning, together with accelerated efforts towards decarbonization.” More