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    Helping cassava farmers by extending crop life

    The root vegetable cassava is a major food staple in dozens of countries across the world. Drought-resistant, nutritious, and tasty, it has also become a major source of income for small-scale, rural farmers in places like West Africa and Southeast Asia.

    But the utility of cassava has always been limited by its short postharvest shelf life of two to three days. That puts millions of farmers who rely on the crop in a difficult position. The farmers can’t plant more than they can sell quickly in local markets, and they’re often forced to sell below market prices because buyers know the harvest will spoil rapidly. As a result, cassava farmers are among the world’s poorest people.

    Now the startup CassVita is buying cassava directly from farmers and applying a patent-pending biotechnology to extend its shelf life to 18 months. The approach has the potential to transform economies in rural, impoverished regions where millions of families rely on the crop for income.

    CassVita tells farmers how much cassava the company will buy each month, and processes the cassava at a manufacturing facility in Cameroon. It currently sells the first version of its product as a powdered food to people in Cameroon and to West African immigrants in the U.S.

    But CassVita founder and CEO Pelkins Ajanoh ’18 says the future of the company will revolve around its next product: a cassava-based flour that can act as a direct substitute for wheat. The wheat substitute would dramatically broaden CassVita’s target market to include the fast-growing, trillion-dollar healthy food market.

    Ajanoh says CassVita is currently able to increase farmers’ incomes by about 400 percent through its purchases.

    “Our objective is to leverage proprietary technology to offer a healthier and better-tasting alternative to wheat while creating prosperity for local farmers,” Ajanoh says. “We’re hoping to tap into this huge market while empowering farmers, all by minimizing spoilage and incentivizing farmers to plant more.”

    Gaining confidence to help a community

    While growing up in Cameroon, Ajanoh’s parents always emphasized the importance of education for him and his three siblings. But Ajanoh lost his father when he was 13, and his mother moved to the U.S. a year later to help provide for the family. During that time, Ajanoh lived with his grandmother, a cassava farmer. For many years, Ajanoh watched his grandmother harvest cassava without making any lasting financial gains. He remembers feeling powerless as his grandmother struggled to pay for things like diabetes medication.

    Then Ajanoh earned the top marks on the national exams that Cameroonian students take before college. After high school, he joined his mother in the U.S. and came to MIT to study mechanical engineering. Once on campus, Ajanoh says he had lunch with new people all the time to learn from them.

    “I’d never had this community of intellectuals — and they were from all over the world — so I soaked up as much as I could,” Ajanoh says. “That sparked an interest in entrepreneurship, because MIT is super entrepreneurial. Everyone’s thinking of starting something cool.”

    Ajanoh also got a confidence boost during an internship in the summer after his junior year, when he created self-driving technology for General Motors that was eventually patented.

    “It made me realize I could do something really valuable for the world, and by the end of that internship I was thinking, ‘Now I want to solve a problem in my community,’” he says.

    Returning to the crop he knew well, Ajanoh received a series of grants from the MIT Sandbox Innovation Fund to experiment with ways to extend the shelf life of cassava. In the summer of 2018, the MIT-Africa program sponsored three MIT students to fly to Cameroon with him to participate in internships with the company.

    Today CassVita partners with development banks to help farmers get loans to buy the cassava sticks used for planting. Ajanoh says CassVita decided on a powdered food for its first product because it requires less marketing to sell to West Africans, who are familiar with the dish. Now the company is working on a cassava flour that it will market to all consumers looking for healthy alternatives to wheat that can be used in pastries and other baked goods.

    “Cassava makes sense as a global substitute to wheat because it’s gluten free, grain free, nut free, and it also helps with glucose regulation, to normalize blood sugar levels, to lower triglycerides, so the health benefits are exciting,” Ajanoh says. “But the farmers were still living in poverty, so if we could solve the shelf-life problem then we could empower these farmers to offer healthier wheat alternatives to the global market.”

    The project has taken on additional urgency now that the war in Ukraine is limiting that country’s wheat and grain exports, raising prices, and heightening food insecurity in regions around the globe.

    Showing the value of helping farmers

    Ajanoh says the majority of people farming cassava are women, and he says the challenges related to cassava’s shelf life have contributed to gender inequities in many communities. In fact, of the roughly 500 farmers CassVita works with in Cameroon, 95 percent are women.

    “That has always excited me because I was raised by women, so working on something that could empower women in their communities and give them authority is fulfilling,” Ajanoh says.

    Ajanoh has already heard from farmers who have been able to send their children to school for the first time because of improved financial situations. Now, as CassVita continues to scale, Ajanoh wants to stay focused on the technology that enables these new business models.

    “We’re evolving into a food technology company,” Ajanoh says. “We prefer to focus on leveraging technology to impact lives and improve outcomes in these communities. Right now, we’re going all the way to consumers because this is an opportunity the Nestles and the Unilevers of the world won’t pick up because the market doesn’t make sense to them yet. So, we have to build this company and show them the value.” More

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    Could used beer yeast be the solution to heavy metal contamination in water?

    A new analysis by researchers at MIT’s Center for Bits and Atoms (CBA) has found that inactive yeast could be effective as an inexpensive, abundant, and simple material for removing lead contamination from drinking water supplies. The study shows that this approach can be efficient and economic, even down to part-per-billion levels of contamination. Serious damage to human health is known to occur even at these low levels.

    The method is so efficient that the team has calculated that waste yeast discarded from a single brewery in Boston would enough to treat the city’s entire water supply. Such a fully sustainable system would not only purify the water but also divert what would otherwise be a waste stream needing disposal.

    The findings are detailed today in the journal Nature Communications Earth and Environment, in a paper by MIT Research Scientist Patritsia Statathou; Brown University postdoc and MIT Visiting Scholar Christos Athanasiou; MIT Professor Neil Gershenfeld, the director of CBA; and nine others at MIT, Brown, Wellesley College, Nanyang Technological University, and National Technical University of Athens.

    Lead and other heavy metals in water are a significant global problem that continues to grow because of electronic waste and discharges from mining operations. In the U.S. alone, more than 12,000 miles of waterways are impacted by acidic mine-drainage-water rich in heavy metals, the country’s leading source of water pollution. And unlike organic pollutants, most of which can be eventually broken down, heavy metals don’t biodegrade, but persist indefinitely and bioaccumulate. They are either impossible or very expensive to completely remove by conventional methods such as chemical precipitation or membrane filtration.

    Lead is highly toxic, even at tiny concentrations, especially affecting children as they grow. The European Union has reduced its standard for allowable lead in drinking water from 10 parts per billion to 5 parts per billion. In the U.S., the Environmental Protection Agency has declared that no level at all in water supplies is safe. And average levels in bodies of surface water globally are 10 times higher than they were 50 years ago, ranging from 10 parts per billion in Europe to hundreds of parts per billion in South America.

    “We don’t just need to minimize the existence of lead; we need to eliminate it in drinking water,” says Stathatou. “And the fact is that the conventional treatment processes are not doing this effectively when the initial concentrations they have to remove are low, in the parts-per-billion scale and below. They either fail to completely remove these trace amounts, or in order to do so they consume a lot of energy and they produce toxic byproducts.”

    The solution studied by the MIT team is not a new one — a process called biosorption, in which inactive biological material is used to remove heavy metals from water, has been known for a few decades. But the process has been studied and characterized only at much higher concentrations, at more than one part-per-million levels. “Our study demonstrates that the process can indeed work efficiently at the much lower concentrations of typical real-world water supplies, and investigates in detail the mechanisms involved in the process,” Athanasiou says.

    The team studied the use of a type of yeast widely used in brewing and in industrial processes, called S. cerevisiae, on pure water spiked with trace amounts of lead. They demonstrated that a single gram of the inactive, dried yeast cells can remove up to 12 milligrams of lead in aqueous solutions with initial lead concentrations below 1 part per million. They also showed that the process is very rapid, taking less than five minutes to complete.

    Because the yeast cells used in the process are inactive and desiccated, they require no particular care, unlike other processes that rely on living biomass to perform such functions which require nutrients and sunlight to keep the materials active. What’s more, yeast is abundantly available already, as a waste product from beer brewing and from various other fermentation-based industrial processes.

    Stathatou has estimated that to clean a water supply for a city the size of Boston, which uses about 200 million gallons a day, would require about 20 tons of yeast per day, or about 7,000 tons per year. By comparison, one single brewery, the Boston Beer Company, generates 20,000 tons a year of surplus yeast that is no longer useful for fermentation.

    The researchers also performed a series of tests to determine that the yeast cells are responsible for biosorption. Athanasiou says that “exploring biosorption mechanisms at such challenging concentrations is a tough problem. We were the first to use a mechanics perspective to unravel biosorption mechanisms, and we discovered that the mechanical properties of the yeast cells change significantly after lead uptake. This provides fundamentally new insights for the process.”

    Devising a practical system for processing the water and retrieving the yeast, which could then be separated from the lead for reuse, is the next stage of the team’s research, they say.

    “To scale up the process and actually put it in place, you need to embed these cells in a kind of filter, and this is the work that’s currently ongoing,” Stathatou says. They are also looking at ways of recovering both the cells and the lead. “We need to conduct further experiments, but there is the option to get both back,” she says.

    The same material can potentially be used to remove other heavy metals, such as cadmium and copper, but that will require further research to quantify the effective rates for those processes, the researchers say.

    “This research revealed a very promising, inexpensive, and environmentally friendly solution for lead removal,” says Sivan Zamir, vice president of Xylem Innovation Labs, a water technology research firm, who was not associated with this research. “It also deepened our understanding of the biosorption process, paving the way for the development of materials tailored to removal of other heavy metals.”

    The team also included Marios Tsezos at the National Technical University of Athens, in Greece; John Gross at Wellesley College; Camron Blackburn, Filippos Tourlomousis, and Andreas Mershin at MIT’s CBA; Brian Sheldon, Nitin Padture, Eric Darling at Brown University; and Huajian Gao at Brown University and Nanyang Technological University, in Singapore. More

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    Engineers use artificial intelligence to capture the complexity of breaking waves

    Waves break once they swell to a critical height, before cresting and crashing into a spray of droplets and bubbles. These waves can be as large as a surfer’s point break and as small as a gentle ripple rolling to shore. For decades, the dynamics of how and when a wave breaks have been too complex to predict.

    Now, MIT engineers have found a new way to model how waves break. The team used machine learning along with data from wave-tank experiments to tweak equations that have traditionally been used to predict wave behavior. Engineers typically rely on such equations to help them design resilient offshore platforms and structures. But until now, the equations have not been able to capture the complexity of breaking waves.

    The updated model made more accurate predictions of how and when waves break, the researchers found. For instance, the model estimated a wave’s steepness just before breaking, and its energy and frequency after breaking, more accurately than the conventional wave equations.

    Their results, published today in the journal Nature Communications, will help scientists understand how a breaking wave affects the water around it. Knowing precisely how these waves interact can help hone the design of offshore structures. It can also improve predictions for how the ocean interacts with the atmosphere. Having better estimates of how waves break can help scientists predict, for instance, how much carbon dioxide and other atmospheric gases the ocean can absorb.

    “Wave breaking is what puts air into the ocean,” says study author Themis Sapsis, an associate professor of mechanical and ocean engineering and an affiliate of the Institute for Data, Systems, and Society at MIT. “It may sound like a detail, but if you multiply its effect over the area of the entire ocean, wave breaking starts becoming fundamentally important to climate prediction.”

    The study’s co-authors include lead author and MIT postdoc Debbie Eeltink, Hubert Branger and Christopher Luneau of Aix-Marseille University, Amin Chabchoub of Kyoto University, Jerome Kasparian of the University of Geneva, and T.S. van den Bremer of Delft University of Technology.

    Learning tank

    To predict the dynamics of a breaking wave, scientists typically take one of two approaches: They either attempt to precisely simulate the wave at the scale of individual molecules of water and air, or they run experiments to try and characterize waves with actual measurements. The first approach is computationally expensive and difficult to simulate even over a small area; the second requires a huge amount of time to run enough experiments to yield statistically significant results.

    The MIT team instead borrowed pieces from both approaches to develop a more efficient and accurate model using machine learning. The researchers started with a set of equations that is considered the standard description of wave behavior. They aimed to improve the model by “training” the model on data of breaking waves from actual experiments.

    “We had a simple model that doesn’t capture wave breaking, and then we had the truth, meaning experiments that involve wave breaking,” Eeltink explains. “Then we wanted to use machine learning to learn the difference between the two.”

    The researchers obtained wave breaking data by running experiments in a 40-meter-long tank. The tank was fitted at one end with a paddle which the team used to initiate each wave. The team set the paddle to produce a breaking wave in the middle of the tank. Gauges along the length of the tank measured the water’s height as waves propagated down the tank.

    “It takes a lot of time to run these experiments,” Eeltink says. “Between each experiment you have to wait for the water to completely calm down before you launch the next experiment, otherwise they influence each other.”

    Safe harbor

    In all, the team ran about 250 experiments, the data from which they used to train a type of machine-learning algorithm known as a neural network. Specifically, the algorithm is trained to compare the real waves in experiments with the predicted waves in the simple model, and based on any differences between the two, the algorithm tunes the model to fit reality.

    After training the algorithm on their experimental data, the team introduced the model to entirely new data — in this case, measurements from two independent experiments, each run at separate wave tanks with different dimensions. In these tests, they found the updated model made more accurate predictions than the simple, untrained model, for instance making better estimates of a breaking wave’s steepness.

    The new model also captured an essential property of breaking waves known as the “downshift,” in which the frequency of a wave is shifted to a lower value. The speed of a wave depends on its frequency. For ocean waves, lower frequencies move faster than higher frequencies. Therefore, after the downshift, the wave will move faster. The new model predicts the change in frequency, before and after each breaking wave, which could be especially relevant in preparing for coastal storms.

    “When you want to forecast when high waves of a swell would reach a harbor, and you want to leave the harbor before those waves arrive, then if you get the wave frequency wrong, then the speed at which the waves are approaching is wrong,” Eeltink says.

    The team’s updated wave model is in the form of an open-source code that others could potentially use, for instance in climate simulations of the ocean’s potential to absorb carbon dioxide and other atmospheric gases. The code can also be worked into simulated tests of offshore platforms and coastal structures.

    “The number one purpose of this model is to predict what a wave will do,” Sapsis says. “If you don’t model wave breaking right, it would have tremendous implications for how structures behave. With this, you could simulate waves to help design structures better, more efficiently, and without huge safety factors.”

    This research is supported, in part, by the Swiss National Science Foundation, and by the U.S. Office of Naval Research. More

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    From seawater to drinking water, with the push of a button

    MIT researchers have developed a portable desalination unit, weighing less than 10 kilograms, that can remove particles and salts to generate drinking water.

    The suitcase-sized device, which requires less power to operate than a cell phone charger, can also be driven by a small, portable solar panel, which can be purchased online for around $50. It automatically generates drinking water that exceeds World Health Organization quality standards. The technology is packaged into a user-friendly device that runs with the push of one button.

    Unlike other portable desalination units that require water to pass through filters, this device utilizes electrical power to remove particles from drinking water. Eliminating the need for replacement filters greatly reduces the long-term maintenance requirements.

    This could enable the unit to be deployed in remote and severely resource-limited areas, such as communities on small islands or aboard seafaring cargo ships. It could also be used to aid refugees fleeing natural disasters or by soldiers carrying out long-term military operations.

    “This is really the culmination of a 10-year journey that I and my group have been on. We worked for years on the physics behind individual desalination processes, but pushing all those advances into a box, building a system, and demonstrating it in the ocean, that was a really meaningful and rewarding experience for me,” says senior author Jongyoon Han, a professor of electrical engineering and computer science and of biological engineering, and a member of the Research Laboratory of Electronics (RLE).

    Joining Han on the paper are first author Junghyo Yoon, a research scientist in RLE; Hyukjin J. Kwon, a former postdoc; SungKu Kang, a postdoc at Northeastern University; and Eric Brack of the U.S. Army Combat Capabilities Development Command (DEVCOM). The research has been published online in Environmental Science and Technology.

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    Filter-free technology

    Commercially available portable desalination units typically require high-pressure pumps to push water through filters, which are very difficult to miniaturize without compromising the energy-efficiency of the device, explains Yoon.

    Instead, their unit relies on a technique called ion concentration polarization (ICP), which was pioneered by Han’s group more than 10 years ago. Rather than filtering water, the ICP process applies an electrical field to membranes placed above and below a channel of water. The membranes repel positively or negatively charged particles — including salt molecules, bacteria, and viruses — as they flow past. The charged particles are funneled into a second stream of water that is eventually discharged.

    The process removes both dissolved and suspended solids, allowing clean water to pass through the channel. Since it only requires a low-pressure pump, ICP uses less energy than other techniques.

    But ICP does not always remove all the salts floating in the middle of the channel. So the researchers incorporated a second process, known as electrodialysis, to remove remaining salt ions.

    Yoon and Kang used machine learning to find the ideal combination of ICP and electrodialysis modules. The optimal setup includes a two-stage ICP process, with water flowing through six modules in the first stage then through three in the second stage, followed by a single electrodialysis process. This minimized energy usage while ensuring the process remains self-cleaning.

    “While it is true that some charged particles could be captured on the ion exchange membrane, if they get trapped, we just reverse the polarity of the electric field and the charged particles can be easily removed,” Yoon explains.

    They shrunk and stacked the ICP and electrodialysis modules to improve their energy efficiency and enable them to fit inside a portable device. The researchers designed the device for nonexperts, with just one button to launch the automatic desalination and purification process. Once the salinity level and the number of particles decrease to specific thresholds, the device notifies the user that the water is drinkable.

    The researchers also created a smartphone app that can control the unit wirelessly and report real-time data on power consumption and water salinity.

    Beach tests

    After running lab experiments using water with different salinity and turbidity (cloudiness) levels, they field-tested the device at Boston’s Carson Beach.

    Yoon and Kwon set the box near the shore and tossed the feed tube into the water. In about half an hour, the device had filled a plastic drinking cup with clear, drinkable water.

    “It was successful even in its first run, which was quite exciting and surprising. But I think the main reason we were successful is the accumulation of all these little advances that we made along the way,” Han says.

    The resulting water exceeded World Health Organization quality guidelines, and the unit reduced the amount of suspended solids by at least a factor of 10. Their prototype generates drinking water at a rate of 0.3 liters per hour, and requires only 20 watts of power per liter.

    “Right now, we are pushing our research to scale up that production rate,” Yoon says.

    One of the biggest challenges of designing the portable system was engineering an intuitive device that could be used by anyone, Han says.

    Yoon hopes to make the device more user-friendly and improve its energy efficiency and production rate through a startup he plans to launch to commercialize the technology.

    In the lab, Han wants to apply the lessons he’s learned over the past decade to water-quality issues that go beyond desalination, such as rapidly detecting contaminants in drinking water.

    “This is definitely an exciting project, and I am proud of the progress we have made so far, but there is still a lot of work to do,” he says.

    For example, while “development of portable systems using electro-membrane processes is an original and exciting direction in off-grid, small-scale desalination,” the effects of fouling, especially if the water has high turbidity, could significantly increase maintenance requirements and energy costs, notes Nidal Hilal, professor of engineering and director of the New York University Abu Dhabi Water research center, who was not involved with this research.

    “Another limitation is the use of expensive materials,” he adds. “It would be interesting to see similar systems with low-cost materials in place.”

    The research was funded, in part, by the DEVCOM Soldier Center, the Abdul Latif Jameel Water and Food Systems Lab (J-WAFS), the Experimental AI Postdoc Fellowship Program of Northeastern University, and the Roux AI Institute. More

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    MIT engineers introduce the Oreometer

    When you twist open an Oreo cookie to get to the creamy center, you’re mimicking a standard test in rheology — the study of how a non-Newtonian material flows when twisted, pressed, or otherwise stressed. MIT engineers have now subjected the sandwich cookie to rigorous materials tests to get to the center of a tantalizing question: Why does the cookie’s cream stick to just one wafer when twisted apart?

    “There’s the fascinating problem of trying to get the cream to distribute evenly between the two wafers, which turns out to be really hard,” says Max Fan, an undergraduate in MIT’s Department of Mechanical Engineering.

    In pursuit of an answer, the team subjected cookies to standard rheology tests in the lab and found that no matter the flavor or amount of stuffing, the cream at the center of an Oreo almost always sticks to one wafer when twisted open. Only for older boxes of cookies does the cream sometimes separate more evenly between both wafers.

    The researchers also measured the torque required to twist open an Oreo, and found it to be similar to the torque required to turn a doorknob and about 1/10th what’s needed to twist open a bottlecap. The cream’s failure stress — i.e. the force per area required to get the cream to flow, or deform — is twice that of cream cheese and peanut butter, and about the same magnitude as mozzarella cheese. Judging from the cream’s response to stress, the team classifies its texture as “mushy,” rather than brittle, tough, or rubbery.

    So, why does the cookie’s cream glom to one side rather than splitting evenly between both? The manufacturing process may be to blame.

    “Videos of the manufacturing process show that they put the first wafer down, then dispense a ball of cream onto that wafer before putting the second wafer on top,” says Crystal Owens, an MIT mechanical engineering PhD candidate who studies the properties of complex fluids. “Apparently that little time delay may make the cream stick better to the first wafer.”

    The team’s study isn’t simply a sweet diversion from bread-and-butter research; it’s also an opportunity to make the science of rheology accessible to others. To that end, the researchers have designed a 3D-printable “Oreometer” — a simple device that firmly grasps an Oreo cookie and uses pennies and rubber bands to control the twisting force that progressively twists the cookie open. Instructions for the tabletop device can be found here.

    The new study, “On Oreology, the fracture and flow of ‘milk’s favorite cookie,’” appears today in Kitchen Flows, a special issue of the journal Physics of Fluids. It was conceived of early in the Covid-19 pandemic, when many scientists’ labs were closed or difficult to access. In addition to Owens and Fan, co-authors are mechanical engineering professors Gareth McKinley and A. John Hart.

    Confection connection

    A standard test in rheology places a fluid, slurry, or other flowable material onto the base of an instrument known as a rheometer. A parallel plate above the base can be lowered onto the test material. The plate is then twisted as sensors track the applied rotation and torque.

    Owens, who regularly uses a laboratory rheometer to test fluid materials such as 3D-printable inks, couldn’t help noting a similarity with sandwich cookies. As she writes in the new study:

    “Scientifically, sandwich cookies present a paradigmatic model of parallel plate rheometry in which a fluid sample, the cream, is held between two parallel plates, the wafers. When the wafers are counter-rotated, the cream deforms, flows, and ultimately fractures, leading to separation of the cookie into two pieces.”

    While Oreo cream may not appear to possess fluid-like properties, it is considered a “yield stress fluid” — a soft solid when unperturbed that can start to flow under enough stress, the way toothpaste, frosting, certain cosmetics, and concrete do.

    Curious as to whether others had explored the connection between Oreos and rheology, Owens found mention of a 2016 Princeton University study in which physicists first reported that indeed, when twisting Oreos by hand, the cream almost always came off on one wafer.

    “We wanted to build on this to see what actually causes this effect and if we could control it if we mounted the Oreos carefully onto our rheometer,” she says.

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    Cookie twist

    In an experiment that they would repeat for multiple cookies of various fillings and flavors, the researchers glued an Oreo to both the top and bottom plates of a rheometer and applied varying degrees of torque and angular rotation, noting the values  that successfully twisted each cookie apart. They plugged the measurements into equations to calculate the cream’s viscoelasticity, or flowability. For each experiment, they also noted the cream’s “post-mortem distribution,” or where the cream ended up after twisting open.

    In all, the team went through about 20 boxes of Oreos, including regular, Double Stuf, and Mega Stuf levels of filling, and regular, dark chocolate, and “golden” wafer flavors. Surprisingly, they found that no matter the amount of cream filling or flavor, the cream almost always separated onto one wafer.

    “We had expected an effect based on size,” Owens says. “If there was more cream between layers, it should be easier to deform. But that’s not actually the case.”

    Curiously, when they mapped each cookie’s result to its original position in the box, they noticed the cream tended to stick to the inward-facing wafer: Cookies on the left side of the box twisted such that the cream ended up on the right wafer, whereas cookies on the right side separated with cream mostly on the left wafer. They suspect this box distribution may be a result of post-manufacturing environmental effects, such as heating or jostling that may cause cream to peel slightly away from the outer wafers, even before twisting.

    The understanding gained from the properties of Oreo cream could potentially be applied to the design of other complex fluid materials.

    “My 3D printing fluids are in the same class of materials as Oreo cream,” she says. “So, this new understanding can help me better design ink when I’m trying to print flexible electronics from a slurry of carbon nanotubes, because they deform in almost exactly the same way.”

    As for the cookie itself, she suggests that if the inside of Oreo wafers were more textured, the cream might grip better onto both sides and split more evenly when twisted.

    “As they are now, we found there’s no trick to twisting that would split the cream evenly,” Owens concludes.

    This research was supported, in part, by the MIT UROP program and by the National Defense Science and Engineering Graduate Fellowship Program. More

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    Structures considered key to gene expression are surprisingly fleeting

    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.”

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    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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    Q&A: Latifah Hamzah ’12 on creating sustainable solutions in Malaysia and beyond

    Latifah Hamzah ’12 graduated from MIT with a BS in mechanical engineering and minors in energy studies and music. During their time at MIT, Latifah participated in various student organizations, including the MIT Symphony Orchestra, Alpha Phi Omega, and the MIT Design/Build/Fly team. They also participated in the MIT Energy Initiative’s Undergraduate Research Opportunities Program (UROP) in the lab of former professor of mechanical engineering Alexander Mitsos, examining solar-powered thermal and electrical co-generation systems.

    After graduating from MIT, Latifah worked as a subsea engineer at Shell Global Solutions and co-founded Engineers Without Borders – Malaysia, a nonprofit organization dedicated to finding sustainable and empowering solutions that impact disadvantaged populations in Malaysia. More recently, Latifah received a master of science in mechanical engineering from Stanford University, where they are currently pursuing a PhD in environmental engineering with a focus on water and sanitation in developing contexts.

    Q: What inspired you to pursue energy studies as an undergraduate student at MIT?

    A: I grew up in Malaysia, where I was at once aware of both the extent to which the oil and gas industry is a cornerstone of the economy and the need to transition to a lower-carbon future. The Energy Studies minor was therefore enticing because it gave me a broader view of the energy space, including technical, policy, economic, and other viewpoints. This was my first exposure to how things worked in the real world — in that many different fields and perspectives had to be considered cohesively in order to have a successful, positive, and sustained impact. Although the minor was predominantly grounded in classroom learning, what I learned drove me to want to discover for myself how the forces of technology, society, and policy interacted in the field in my subsequent endeavors.

    In addition to the breadth that the minor added to my education, it also provided a structure and focus for me to build on my technical fundamentals. This included taking graduate-level classes and participating in UROPs that had specific energy foci. These were my first forays into questions that, while still predominantly technical, were more open-ended and with as-yet-unknown answers that would be substantially shaped by the framing of the question. This shift in mindset required from typical undergraduate classes and problem sets took a bit of adjusting to, but ultimately gave me the confidence and belief that I could succeed in a more challenging environment.

    Q: How did these experiences with energy help shape your path forward, particularly in regard to your work with Engineers Without Borders – Malaysia and now at Stanford?

    A: When I returned home after graduation, I was keen to harness my engineering education and explore in practice what the Energy Studies minor curriculum had taught by theory and case studies: to consider context, nuance, and interdisciplinary and myriad perspectives to craft successful, sustainable solutions. Recognizing that there were many underserved communities in Malaysia, I co-founded Engineers Without Borders – Malaysia with some friends with the aim of working with these communities to bring simple and sustainable engineering solutions. Many of these projects did have an energy focus. For example, we designed, sized, and installed micro-hydro or solar-power systems for various indigenous communities, allowing them to continue living on their ancestral lands while reducing energy poverty. Many other projects incorporated other aspects of engineering, such as hydrotherapy pools for folks with special needs, and water and sanitation systems for stateless maritime communities.

    Through my work with Engineers Without Borders – Malaysia, I found a passion for the broader aspects of sustainability, development, and equity. By spending time with communities in the field and sharing in their experiences, I recognized gaps in my skill set that I could work on to be more effective in advocating for social and environmental justice. In particular, I wanted to better understand communities and their perspectives while being mindful of my positionality. In addition, I wanted to address the more systemic aspects of the problems they faced, which I felt in many cases would only be possible through a combination of research, evidence, and policy. To this end, I embarked on a PhD in environmental engineering with a minor in anthropology and pursued a Community-Based Research Fellowship with Stanford’s Haas Center for Public Service. I have also participated in the Rising Environmental Leaders Program (RELP), which helps graduate students “hone their leadership and communications skills to maximize the impact of their research.” RELP afforded me the opportunity to interact with representatives from government, NGOs [nongovernmental organizations], think tanks, and industry, from which I gained a better understanding of the policy and adjacent ecosystems at both the federal and state levels.

    Q: What are you currently studying, and how does it relate to your past work and educational experiences?

    A: My dissertation investigates waste management and monitoring for improved planetary health in three distinct projects. Suboptimal waste management can lead to poor outcomes, including environmental contamination, overuse of resources, and lost economic and environmental opportunities in resource recovery. My first project showed that three combinations of factors resulted in ruminant feces contaminating the stored drinking water supplies of households in rural Kenya, and the results were published in the International Journal of Environmental Research and Public Health. Consequently, water and sanitation interventions must also consider animal waste for communities to have safe drinking water.

    My second project seeks to establish a circular economy in the chocolate industry with indigenous Malaysian farmers and the Chocolate Concierge, a tree-to-bar social enterprise. Having designed and optimized apparatuses and processes to create biochar from cacao husk waste, we are now examining its impact on the growth of cacao saplings and their root systems. The hope is that biochar will increase the resilience of saplings for when they are transplanted from the nursery to the farm. As biochar can improve soil health and yield while reducing fertilizer inputs and sequestering carbon, farmers can accrue substantial economic and environmental benefits, especially if they produce, use, and sell it themselves.

    My third project investigates the gap in sanitation coverage worldwide and potential ways of reducing it. Globally, 46 percent of the population lacks access to safely managed sanitation, while the majority of the 54 percent who do have access use on-site sanitation facilities such as septic tanks and latrines. Given that on-site, decentralized systems typically have a lower space and resource footprint, are cheaper to build and maintain, and can be designed to suit various contexts, they could represent the best chance of reaching the sanitation Sustainable Development Goal. To this end, I am part of a team of researchers at the Criddle Group at Stanford working to develop a household-scale system as part of the Gates Reinvent the Toilet Challenge, an initiative aimed at developing new sanitation and toilet technologies for developing contexts.

    The thread connecting these projects is a commitment to investigating both the technical and socio-anthropological dimensions of an issue to develop sustainable, reliable, and environmentally sensitive solutions, especially in low- and middle-income countries (LMICs). I believe that an interdisciplinary approach can provide a better understanding of the problem space, which will hopefully lead to effective potential solutions that can have a greater community impact.

    Q: What do you plan to do once you obtain your PhD?

    A: I hope to continue working in the spheres of water and sanitation and/or sustainability post-PhD. It is a fascinating moment to be in this space as a person of color from an LMIC, especially as ideas such as community-based research and decolonizing fields and institutions are becoming more widespread and acknowledged. Even during my time at Stanford, I have noticed some shifts in the discourse, although we still have a long way to go to achieve substantive and lasting change. Folks like me are underrepresented in forums where the priorities, policies, and financing of aid and development are discussed at the international or global scale. I hope I’ll be able to use my qualifications, experience, and background to advocate for more just outcomes.

    This article appears in the Autumn 2021 issue of Energy Futures, the magazine of the MIT Energy Initiative More

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    Using soap to remove micropollutants from water

    Imagine millions of soapy sponges the size of human cells that can clean water by soaking up contaminants. This simplistic model is used to describe technology that MIT chemical engineers have recently developed to remove micropollutants from water — a concerning, worldwide problem.

    Patrick S. Doyle, the Robert T. Haslam Professor of Chemical Engineering, PhD student Devashish Pratap Gokhale, and undergraduate Ian Chen recently published their research on micropollutant removal in the journal ACS Applied Polymer Materials. The work is funded by MIT’s Abdul Latif Jameel Water and Food Systems Lab (J-WAFS).

    In spite of their low concentrations (about 0.01–100 micrograms per liter), micropollutants can be hazardous to the ecosystem and to human health. They come from a variety of sources and have been detected in almost all bodies of water, says Gokhale. Pharmaceuticals passing through people and animals, for example, can end up as micropollutants in the water supply. Others, like endocrine disruptor bisphenol A (BPA), can leach from plastics during industrial manufacturing. Pesticides, dyes, petrochemicals, and per-and polyfluoroalkyl substances, more commonly known as PFAS, are also examples of micropollutants, as are some heavy metals like lead and arsenic. These are just some of the kinds of micropollutants, all of which can be toxic to humans and animals over time, potentially causing cancer, organ damage, developmental defects, or other adverse effects.

    Micropollutants are numerous but since their collective mass is small, they are difficult to remove from water. Currently, the most common practice for removing micropollutants from water is activated carbon adsorption. In this process, water passes through a carbon filter, removing only 30 percent of micropollutants. Activated carbon requires high temperatures to produce and regenerate, requiring specialized equipment and consuming large amounts of energy. Reverse osmosis can also be used to remove micropollutants from water; however, “it doesn’t lead to good elimination of this class of molecules, because of both their concentration and their molecular structure,” explains Doyle.

    Inspired by soap

    When devising their solution for how to remove micropollutants from water, the MIT researchers were inspired by a common household cleaning supply — soap. Soap cleans everything from our hands and bodies to dirty dishes to clothes, so perhaps the chemistry of soap could also be applied to sanitizing water. Soap has molecules called surfactants which have both hydrophobic (water-hating) and hydrophilic (water-loving) components. When water comes in contact with soap, the hydrophobic parts of the surfactant stick together, assembling into spherical structures called micelles with the hydrophobic portions of the molecules in the interior. The hydrophobic micelle cores trap and help carry away oily substances like dirt. 

    Doyle’s lab synthesized micelle-laden hydrogel particles to essentially cleanse water. Gokhale explains that they used microfluidics which “involve processing fluids on very small, micron-like scales” to generate uniform polymeric hydrogel particles continuously and reproducibly. These hydrogels, which are porous and absorbent, incorporate a surfactant, a photoinitiator (a molecule that creates reactive species), and a cross-linking agent known as PEGDA. The surfactant assembles into micelles that are chemically bonded to the hydrogel using ultraviolet light. When water flows through this micro-particle system, micropollutants latch onto the micelles and separate from the water. The physical interaction used in the system is strong enough to pull micropollutants from water, but weak enough that the hydrogel particles can be separated from the micropollutants, restabilized, and reused. Lab testing shows that both the speed and extent of pollutant removal increase when the amount of surfactant incorporated into the hydrogels is increased.

    “We’ve shown that in terms of rate of pullout, which is what really matters when you scale this up for industrial use, that with our initial format, we can already outperform the activated carbon,” says Doyle. “We can actually regenerate these particles very easily at room temperature. Nearly 10 regeneration cycles with minimal change in performance,” he adds.

    Regeneration of the particles occurs by soaking the micelles in 90 percent ethanol, whereby “all the pollutants just come out of the particles and back into the ethanol” says Gokhale. Ethanol is biosafe at low concentrations, inexpensive, and combustible, allowing for safe and economically feasible disposal. The recycling of the hydrogel particles makes this technology sustainable, which is a large advantage over activated carbon. The hydrogels can also be tuned to any hydrophobic micropollutant, making this system a novel, flexible approach to water purification.

    Scaling up

    The team experimented in the lab using 2-naphthol, a micropollutant that is an organic pollutant of concern and known to be difficult to remove by using conventional water filtration methods. They hope to continue testing with real water samples. 

    “Right now, we spike one micropollutant into pure lab water. We’d like to get water samples from the natural environment, that we can study and look at experimentally,” says Doyle. 

    By using microfluidics to increase particle production, Doyle and his lab hope to make household-scale filters to be tested with real wastewater. They then anticipate scaling up to municipal water treatment or even industrial wastewater treatment. 

    The lab recently filed an international patent application for their hydrogel technology that uses immobilized micelles. They plan to continue this work by experimenting with different kinds of hydrogels for the removal of heavy metal contaminants like lead from water. 

    Societal impacts

    Funded by a 2019 J-WAFS seed grant that is currently ongoing, this research has the potential to improve the speed, precision, efficiency, and environmental sustainability of water purification systems across the world. 

    “I always wanted to do work which had a social impact, and I was also always interested in water, because I think it’s really cool,” says Gokhale. He notes, “it’s really interesting how water sort of fits into different kinds of fields … we have to consider the cultures of peoples, how we’re going to use this, and then just the equity of these water processes.” Originally from India, Gokhale says he’s seen places that have barely any water at all and others that have floods year after year. “There’s a lot of interesting work to be done, and I think it’s work in this area that’s really going to impact a lot of people’s lives in years to come,” Gokhale says.

    Doyle adds, “water is the most important thing, perhaps for the next decades to come, so it’s very fulfilling to work on something that is so important to the whole world.” More