New fellowship to help advance science journalism in Africa and the Middle East

The Knight Science Journalism Program at MIT has announced a new one-semester fellowship — the Fellowship for Advancing Science Journalism in Africa and the Middle East — that will start this year.

The fellowship, developed through a generous gift from the global publishing company Springer Nature, was created in honor of the influential Egyptian science journalist Mohammed Yahia, who died last year at the age of 41.

Yahia worked for Springer Nature for over 13 years, primarily as managing editor of the Nature Portfolio in the Middle East, where he built an award-winning team. He was widely admired for his work advancing the status of science journalism both in that region and throughout Africa. He was president of the World Federation of Science Journalists from 2017 to 2019, working also to help build a network of science journalists around the globe.

Springer Nature, the founding sponsor of the fellowship, is well-known for its standing as a publisher of some the most high-profile and respected research journals and magazines in the world. “Mohammed was known for his unwavering commitment to science and his talent for simplifying complex research,” says Stephen Pincock, vice president in Springer Nature’s Solutions Group. “With this fellowship we want to inspire more to follow in his footsteps, as trusted communicators of evidence-based research.”

The first Fellowship for Advancing Science Journalism in Africa and the Middle East will be hosted by the Knight Science Journalism Program this fall and will continue in subsequent fall semesters. Thanks to a generous grant from Springer Nature, the program will offer a $40,000 stipend for the fellowship period from Aug. 16 to Dec. 31. KSJ will also cover the fellow’s health insurance and a $5,000 housing stipend to help with relocation costs.

The Knight Science Journalism Program, established at MIT in 1983, is the world’s leading science journalism fellowship program. More than 400 leading science journalists from six continents have graduated from the full-year academic program, which offers a course of study at MIT, Harvard University, and other leading institutions in the Boston area, as well as specialized training workshops, seminars, and science-focused field trips for all attendees.

“The Knight Science Journalism Program is honored to partner with Springer Nature in honoring Mohammed Yahia and in creating this new fellowship to help support science journalism in this important part of the world,” says KSJ Director Deborah Blum. “We believe strongly in the global nature of both science and the importance of telling its story in the most helpful and insightful way. We believe this new fellowship is an excellent way to advance that mission.”

Fellows supported by this new program will join the regular KSJ class of journalists for the fall semester in a program of study at MIT and other Cambridge/Boston area universities and in the program’s seminars, training workshops, and field trips throughout the semester. They will also have access to such benefits as MIT’s program of subsidized public transportation and access to libraries, museums, and other Boston-area programs, as well as connections to a thriving community of science journalists.

The program will open an applications process for journalists from Africa and the Middle East on Feb. 1 and submissions will be accepted until March 1. All journalists from the region with at least three years of experience in covering science, health, and the environment are encouraged to apply. The selected fellow will be announced by the end of March.

For further questions about the fellowship or the application process, please write to info@ksj.mit.edu.

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Blood cell family trees trace how production changes with aging

Blood cells make up the majority of cells in the human body. They perform critical functions and their dysfunction is implicated in many important human diseases, from anemias to blood cancers like leukemia. The many types of blood cells include red blood cells that carry oxygen, platelets that promote clotting, as well as the myriad types of immune cells that protect our bodies from threats such as viruses and bacteria.

What these diverse types of blood cells have in common is that they are all produced by hematopoietic stem cells (HSCs). HSCs must keep producing blood cells in large quantities throughout our entire lives in order to continually replenish our bodies’ supply. Researchers want to better understand HSCs and the dynamics of how they produce the many blood cell types, both in order to understand the fundamentals of human blood production and to understand how blood production changes during aging or in cases of disease.

Jonathan Weissman, an MIT professor of biology, member of the Whitehead Institute for Biomedical Research, and a Howard Hughes Medical Investigator; Vijay Sankaran, a Boston Children’s Hospital and Harvard Medical School associate professor who is also a Broad Institute of MIT and Harvard associate member and attending physician at the Dana Farber Cancer Institute; and Chen Weng, a postdoc in both of their labs, have developed a new method that provides a detailed look at the family trees of human blood cells and the characteristics of the individual cells, providing new insights into the differences between lineages of HSCs. The research, published in the journal Nature on Jan. 22, answers some long-standing questions about blood cell production and how it changes as we age. The work also demonstrates how this new technology can give researchers unprecedented access to any human cells’ histories and insight into how those histories have shaped their current states. This will render open to discovery many questions about our own biology that were previously unanswerable.

“We wanted to ask questions that the existing tools could not allow us to,” Weng says. “This is why we brought together Jonathan and Vijay’s different expertise to develop a new technology that allows us to ask those questions and more, so we can solve some of the important unknowns in blood production.”

How to trace the lineages of human cells

Weissman and others have previously developed methods to map the family trees of cells, a process called lineage tracing, but typically this has been done in animals or engineered cell lines. Weissman has used this approach to shed light on how cancers spread and on when and how they develop mutations that make them more aggressive and deadly. However, while these models can illuminate the general principles of processes such as blood production, they do not give researchers a full picture of what happens inside of a living human. They cannot capture the full diversity of human cells or the implications of that diversity on health and disease.

The only way to get a detailed picture of how blood cell lineages change through the generations and what the consequences of those changes are is to perform lineage tracing on cells from human samples. The challenge is that in the research models used in the previous lineage tracing studies, Weissman and colleagues edited the cells to add a trackable barcode, a string of DNA that changes a little with each cell division, so that researchers can map the changes to match cells to their closest relatives and reconstruct the family tree. Researchers cannot add a barcode to the cells in living humans, so they need to find a natural one: some string of DNA that already exists and changes frequently enough to allow this family tree reconstruction.

Looking for mutations across the whole genome is cost-prohibitive and destroys the material that researchers need to collect to learn about the cells’ states. A few years ago, Sankaran and colleagues realized that mitochondrial DNA could be a good candidate for the natural barcode. Mitochondria are in all of our cells, and they have their own genome, which is relatively small and prone to mutation. In that earlier research, Sankaran and colleagues identified mutations in mitochondrial DNA, but they could not find enough mutations to build a complete family tree: in each cell, they only detected an average of zero to one mutations.

Now, in work led by Weng, the researchers have improved their detection of mitochondrial DNA mutations 10-fold, meaning that in each cell they find around 10 mutations — enough to serve as an identifying barcode. They achieved this through improvements in how they detect mitochondrial DNA mutations experimentally and how they verify that those mutations are genuine computationally. Their new and improved lineage tracing method is called ReDeeM, an acronym drawing from single-cell "regulatory multi-omics with deep mitochondrial mutation profiling." Using the method, they can recreate the family tree of thousands of blood cells from a human blood sample, as well as gather information about each individual cell’s state: its gene expression levels and differences in its epigenome, or the availability of regions of DNA to be expressed.

Combining cells’ family trees with each individual cell’s state is key for making sense of how cell lineages change over time and what the effects of those changes are. If a researcher pinpoints the place in the family tree where a blood cell lineage, for example, becomes biased toward producing a certain type of blood cell, they can then look at what changed in the cells’ state preceding that shift in order to figure out what genes and pathways drove that change in behavior. In other words, they can use the combination of data to understand not just that a change occurred, but what mechanisms contributed to that change.

“The goal is to relate the cell’s current state to its past history,” Weissman says. “Being able to do that in an unperturbed human sample lets us watch the dynamics of the blood production process and understand functional differences in hematopoietic stem cells in a way that has just not been possible before.”

Using this approach, the researchers made several interesting discoveries about blood production.

Blood cell lineage diversity shrinks with age

The researchers mapped the family trees of blood cells derived from each HSC. Each one of these lineages is called a clonal group. Researchers have had various hypotheses about how clonal groups work: Perhaps they are interchangeable, with each stem cell producing equivalent numbers and types of blood cells. Perhaps they are specialized, with one stem cell producing red blood cells, and another producing white blood cells. Perhaps they work in shifts, with some HSCs lying dormant while others produce blood cells. The researchers found that in healthy, young individuals, the answer is somewhere in the middle: Essentially every stem cell produced every type of blood cell, but certain lineages had biases toward producing one type of cell over another. The researchers took two samples from each test subject four months apart, and found that these differences between the lineages were stable over time.

Next, the researchers took blood samples from people of older age. They found that as humans age, some clonal groups begin to dominate and produce a significantly above-average percent of the total blood cells. When a clonal group outcompetes others like this, it is called expansion. Researchers knew that in certain diseases, a single clonal group containing a disease-related mutation could expand and become dominant. They didn’t know that clonal expansion was pervasive in aging even in seemingly healthy individuals, or that it was typical for multiple clonal groups to expand. This complicates the understanding of clonal expansion but sheds light on how blood production changes with age: The diversity of clonal groups decreases. The researchers are working on figuring out the mechanisms that enable certain clonal groups to expand over others. They are also interested in testing clonal groups for disease markers to understand which expansions are caused by or could contribute to disease.

ReDeeM enabled the researchers to make a variety of additional observations about blood production, many of which are consistent with previous research. This is what they hoped to see: the fact that the tool efficiently identified known patterns in blood production validates its efficacy. Now that the researchers know how well the method works, they can apply it to many different questions about the relationships between cells and what mechanisms drive changes in cell behavior. They are already using it to learn more about autoimmune disorders, blood cancers, and the origins of certain types of blood cells.

The researchers hope that others will use their method to ask questions about cell dynamics in many scenarios in health and disease. Sankaran, who is a practicing hematologist, also hopes that the method one day revolutionizes the patient data to which clinicians have access.

“In the not-too-distant future, you could look at a patient chart and see that this patient has an abnormally low number of HSCs, or an abnormally high number, and that would inform how you think about their disease risk,” Sankaran says. “ReDeeM provides a new lens through which to understand the clone dynamics of blood production, and how they might be altered in human health and diseases. Ultimately, we will be able to apply those lessons to patient care.”

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Imaging method reveals new cells and structures in human brain tissue

Using a novel microscopy technique, MIT and Brigham and Women’s Hospital/Harvard Medical School researchers have imaged human brain tissue in greater detail than ever before, revealing cells and structures that were not previously visible.

Among their findings, the researchers discovered that some “low-grade” brain tumors contain more putative aggressive tumor cells than expected, suggesting that some of these tumors may be more aggressive than previously thought.

The researchers hope that this technique could eventually be deployed to diagnose tumors, generate more accurate prognoses, and help doctors choose treatments.

“We’re starting to see how important the interactions of neurons and synapses with the surrounding brain are to the growth and progression of tumors. A lot of those things we really couldn’t see with conventional tools, but now we have a tool to look at those tissues at the nanoscale and try to understand these interactions,” says Pablo Valdes, a former MIT postdoc who is now an assistant professor of neuroscience at the University of Texas Medical Branch and the lead author of the study.

Edward Boyden, the Y. Eva Tan Professor in Neurotechnology at MIT; a professor of biological engineering, media arts and sciences, and brain and cognitive sciences; a Howard Hughes Medical Institute investigator; and a member of MIT’s McGovern Institute for Brain Research and Koch Institute for Integrative Cancer Research; and E. Antonio Chiocca, a professor of neurosurgery at Harvard Medical School and chair of neurosurgery at Brigham and Women’s Hospital, are the senior authors of the study, which appears today in Science Translational Medicine.

Making molecules visible

The new imaging method is based on expansion microscopy, a technique developed in Boyden’s lab in 2015 based on a simple premise: Instead of using powerful, expensive microscopes to obtain high-resolution images, the researchers devised a way to expand the tissue itself, allowing it to be imaged at very high resolution with a regular light microscope.

The technique works by embedding the tissue into a polymer that swells when water is added, and then softening up and breaking apart the proteins that normally hold tissue together. Then, adding water swells the polymer, pulling all the proteins apart from each other. This tissue enlargement allows researchers to obtain images with a resolution of around 70 nanometers, which was previously possible only with very specialized and expensive microscopes such as scanning electron microscopes.

In 2017, the Boyden lab developed a way to expand preserved human tissue specimens, but the chemical reagents that they used also destroyed the proteins that the researchers were interested in labeling. By labeling the proteins with fluorescent antibodies before expansion, the proteins’ location and identity could be visualized after the expansion process was complete. However, the antibodies typically used for this kind of labeling can’t easily squeeze through densely packed tissue before it’s expanded.

So, for this study, the authors devised a different tissue-softening protocol that breaks up the tissue but preserves proteins in the sample. After the tissue is expanded, proteins can be labelled with commercially available fluorescent antibodies. The researchers then can perform several rounds of imaging, with three or four different proteins labeled in each round. This labelling of proteins enables many more structures to be imaged, because once the tissue is expanded, antibodies can squeeze through and label proteins they couldn’t previously reach.

“We open up the space between the proteins so that we can get antibodies into crowded spaces that we couldn’t otherwise,” Valdes says. “We saw that we could expand the tissue, we could decrowd the proteins, and we could image many, many proteins in the same tissue by doing multiple rounds of staining.”

Working with MIT Assistant Professor Deblina Sarkar, the researchers demonstrated a form of this “decrowding” in 2022 using mouse tissue.

The new study resulted in a decrowding technique for use with human brain tissue samples that are used in clinical settings for pathological diagnosis and to guide treatment decisions. These samples can be more difficult to work with because they are usually embedded in paraffin and treated with other chemicals that need to be broken down before the tissue can be expanded.

In this study, the researchers labeled up to 16 different molecules per tissue sample. The molecules they targeted include markers for a variety of structures, including axons and synapses, as well as markers that identify cell types such as astrocytes and cells that form blood vessels. They also labeled molecules linked to tumor aggressiveness and neurodegeneration.

Using this approach, the researchers analyzed healthy brain tissue, along with samples from patients with two types of glioma — high-grade glioblastoma, which is the most aggressive primary brain tumor, with a poor prognosis, and low-grade gliomas, which are considered less aggressive.

“We wanted to look at brain tumors so that we can understand them better at the nanoscale level, and by doing that, to be able to develop better treatments and diagnoses in the future. At this point, it was more developing a tool to be able to understand them better, because currently in neuro-oncology, people haven't done much in terms of super-resolution imaging,” Valdes says.

A diagnostic tool

To identify aggressive tumor cells in gliomas they studied, the researchers labeled vimentin, a protein that is found in highly aggressive glioblastomas. To their surprise, they found many more vimentin-expressing tumor cells in low-grade gliomas than had been seen using any other method.

“This tells us something about the biology of these tumors, specifically, how some of them probably have a more aggressive nature than you would suspect by doing standard staining techniques,” Valdes says.

When glioma patients undergo surgery, tumor samples are preserved and analyzed using immunohistochemistry staining, which can reveal certain markers of aggressiveness, including some of the markers analyzed in this study.   

“These are incurable brain cancers, and this type of discovery will allow us to figure out which cancer molecules to target so we can design better treatments. It also proves the profound impact of having clinicians like us at the Brigham and Women’s interacting with basic scientists such as Ed Boyden at MIT to discover new technologies that can improve patient lives,” Chiocca says. 

The researchers hope their expansion microscopy technique could allow doctors to learn much more about patients’ tumors, helping them to determine how aggressive the tumor is and guiding treatment choices. Valdes now plans to do a larger study of tumor types to try to establish diagnostic guidelines based on the tumor traits that can be revealed using this technique.

“Our hope is that this is going to be a diagnostic tool to pick up marker cells, interactions, and so on, that we couldn’t before,” he says. “It’s a practical tool that will help the clinical world of neuro-oncology and neuropathology look at neurological diseases at the nanoscale like never before, because fundamentally it’s a very simple tool to use.”

Boyden’s lab also plans to use this technique to study other aspects of brain function, in healthy and diseased tissue.

“Being able to do nanoimaging is important because biology is about nanoscale things — genes, gene products, biomolecules — and they interact over nanoscale distances,” Boyden says. “We can study all sorts of nanoscale interactions, including synaptic changes, immune interactions, and changes that occur during cancer and aging.”

The research was funded by K. Lisa Yang, the Howard Hughes Medical Institute, John Doerr, Open Philanthropy, the Bill and Melinda Gates Foundation, the Koch Institute Frontier Research Program, the National Institutes of Health, and the Neurosurgery Research and Education Foundation.

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3 Questions: What can graduate students expect from MIT’s newest grad housing option?

In October 2017, MIT made a commitment to add 950 on-campus beds for graduate students as part of the Volpe zoning agreement with the City of Cambridge that allows the Institute to develop a 10-acre parcel in Kendall Square. Since then, MIT opened the Graduate Tower at Site 4 residential community in Kendall Square with about 250 net-new beds for graduate students and families, and reallocated the 135 beds in 70 Amherst Street to graduate students.

In December 2020, MIT entered into a partnership with American Campus Communities (ACC) to build and operate a graduate housing complex on Vassar Street, adjacent to Simmons Hall. Owned by MIT but operated by American Campus Communities, this MIT-affiliated community fulfills the Volpe commitment and introduces a new residential option for graduate students and families. Named “Graduate Junction,” the residence is split between two buildings framing a gateway to Fort Washington Park and the Cambridgeport neighborhood. Flanking a central plaza and green space, the buildings will rise in five- and six-story sections and then progress to a 10-story segment as it extends beyond the park. Housing options will include efficiencies and one-, two-, and four-bedroom units that will be licensed by ACC to individuals, couples, and families.

With the addition of 676 beds at the new Graduate Junction and the beds gained by the reconfiguration of rooms in other buildings, the Institute has now exceeded the original commitment with a total of 1,076 new graduate beds. With Graduate Junction due to open this August, David Friedrich, senior associate dean for housing and residential services, shared some important project updates and perspectives on what potential residents can expect from the newest graduate residence on MIT’s campus.

Q: How is the Graduate Junction project going, and when will it open?

A: You can already see the buildings taking shape on Vassar Street and the construction timeline puts us on target for an August 2024 opening. This is a product of years of collaborative work with students and campus stakeholders, who teamed up to design an option to fill gaps in the student housing market. It is thrilling to see it near completion. 

The project is also going well thanks to our productive relationship with ACC. ACC is an experienced student housing company and has built or managed more than 100,000 beds on more than 90 campuses across the U.S., including graduate residences at peer institutions. As we add this new MIT-affiliated housing option to our portfolio of residences, we’re actively working with the leadership of ACC to onboard the team that will manage the property. Kendra Lowery, the general manager of Graduate Junction, is a dynamic and thoughtful partner with a breadth of experience managing student housing. She will be an excellent resource for Graduate Junction residents.

We are pleased to meet the recommendations of the 2018 Graduate Housing Working Group to add beds while providing students with additional cost-effective options for their residential experience. The Working Group — composed of students, staff, and faculty — was instrumental in shaping the project and provided substantive data to inform an optimal combination of unit types and amenities desirable to graduate students. In the coming weeks, we will highlight Graduate Junction alongside the Institute’s existing eight graduate residences to help students select the housing option that best suits their needs.

Q: How will living in Graduate Junction differ from living in MIT-operated residences?

A: Graduate Junction offers a new approach that combines apartment-style living with proximity to main campus — an off-campus experience with an on-campus location. Our partner ACC will be responsible for the housing license process, maintenance, building access, and IT infrastructure. While student residents will have access to MIT’s student support resources and can participate in on-campus social events, there will not be a faculty head of house or resident governance structure. Instead, ACC will directly work with Graduate Junction residents to address needs and answer questions. 

Residents of Graduate Junction will enjoy the same flexibility and pricing of an on-campus housing license and will not need to pay first and last months' rent, security deposit, or a broker fee — all upfront costs typical of off-campus properties. Instead, Graduate Junction will have a utility-inclusive rental rate for furnished apartments set by MIT. Since this partnership with ACC provides a different model for managing on-campus residences at the Institute, this approach is also a pilot to test if partners like ACC can help the Institute manage the demand for graduate housing.

Q: What would you say to incoming graduate students considering Graduate Junction or other on-campus residences?

A: The MIT housing system is designed to offer students choices so they can determine their own residential experience. We want to make living on campus the first and best option and do so by careful analysis that prices our units at below market rates. Combined with the Institute’s support for students and families through the Office of Graduate Education, the on-campus experience is tailored to fit graduate student needs. 

Graduate Junction responds to what students say is most important — location, unit configuration, all-inclusive payments, and flexibility in securing or leaving their housing arrangements. Bordering Cambridgeport, Graduate Junction is proximate to Cambridge public schools, local grocery stores, and neighborhood parks and playgrounds.

It joins a range of housing options available to students, and there are residences to fit a diverse array of budgets. With the added benefit of close proximity to labs and classes, student support, campus services, and other amenities, on-campus residences remain a great value. We invite graduate students to review the new rate sheet for 2024-25 and consider living on campus.

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

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.

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.

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.

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.

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New MIT.nano equipment to accelerate innovation in “tough tech” sectors

A new set of advanced nanofabrication equipment will make MIT.nano one of the world’s most advanced research facilities in microelectronics and related technologies, unlocking new opportunities for experimentation and widening the path for promising inventions to become impactful new products.

The equipment, provided by Applied Materials, will significantly expand MIT.nano’s nanofabrication capabilities, making them compatible with wafers — thin, round slices of semiconductor material — up to 200 millimeters, or 8 inches, in diameter, a size widely used in industry. The new tools will allow researchers to prototype a vast array of new microelectronic devices using state-of-the-art materials and fabrication processes. At the same time, the 200-millimeter compatibility will support close collaboration with industry and enable innovations to be rapidly adopted by companies and mass produced.

MIT.nano’s leaders say the equipment, which will also be available to scientists outside of MIT, will dramatically enhance their facility’s capabilities, allowing experts in the region to more efficiently explore new approaches in “tough tech” sectors, including advanced electronics, next-generation batteries, renewable energies, optical computing, biological sensing, and a host of other areas — many likely yet to be imagined.

“The toolsets will provide an accelerative boost to our ability to launch new technologies that can then be given to the world at scale,” says MIT.nano Director Vladimir Bulović, who is also the Fariborz Maseeh Professor of Emerging Technology. “MIT.nano is committed to its expansive mission — to build a better world. We provide toolsets and capabilities that, in the hands of brilliant researchers, can effectively move the world forward.”

The announcement comes as part of an agreement between MIT and Applied Materials, Inc. that, together with a grant to MIT from the Northeast Microelectronics Coalition (NEMC) Hub, commits more than $40 million of estimated private and public investment to add advanced nano-fabrication equipment and capabilities at MIT.nano.

“We don’t believe there is another space in the United States that will offer the same kind of versatility, capability, and accessibility, with 8-inch toolsets integrated right next to more fundamental toolsets for research discoveries,” Bulović says. “It will create a seamless path to accelerate the pace of innovation.”

Pushing the boundaries of innovation

Applied Materials is the world’s largest supplier of equipment for manufacturing semiconductors, displays, and other advanced electronics. The company will provide at MIT.nano several state-of-the-art process tools capable of supporting 150- and 200-millimeter wafers and will enhance and upgrade an existing tool owned by MIT. In addition to assisting MIT.nano in the day-to-day operation and maintenance of the equipment, Applied Materials engineers will develop new process capabilities to benefit researchers and students from MIT and beyond.

“This investment will significantly accelerate the pace of innovation and discovery in microelectronics and microsystems,” says Tomás Palacios, director of MIT’s Microsystems Technology Laboratories and the Clarence J. Lebel Professor in Electrical Engineering. “It’s wonderful news for our community, wonderful news for the state, and, in my view, a tremendous step forward toward implementing the national vision for the future of innovation in microelectronics.”

Nanoscale research at universities is traditionally conducted on machines that are less compatible with industry, which makes academic innovations more difficult to turn into impactful, mass-produced products. Jorg Scholvin, associate director for MIT.nano’s shared fabrication facility, says the new machines, when combined with MIT.nano’s existing equipment, represent a step-change improvement in that area: Researchers will be able to take an industry-standard wafer and build their technology on top of it to prove to companies it works on existing devices, or to co-fabricate new ideas in close collaboration with industry partners.

“In the journey from an idea to a fully working device, the ability to begin on a small scale, figure out what you want to do, rapidly debug your designs, and then scale it up to an industry-scale wafer is critical,” Scholvin says. “It means a student can test out their idea on wafer-scale quickly and directly incorporate insights into their project so that their processes are scalable. Providing such proof-of-principle early on will accelerate the idea out of the academic environment, potentially reducing years of added effort. Other tools at MIT.nano can supplement work on the 200-millimeter wafer scale, but the higher throughput and higher precision of the Applied equipment will provide researchers with repeatability and accuracy that is unprecedented for academic research environments. Essentially what you have is a sharper, faster, more precise tool to do your work.”

Scholvin predicts the equipment will lead to exponential growth in research opportunities.

“I think a key benefit of these tools is they allow us to push the boundary of research in a variety of different ways that we can predict today,” Scholvin says. “But then there are also unpredictable benefits, which are hiding in the shadows waiting to be discovered by the creativity of the researchers at MIT. With each new application, more ideas and paths usually come to mind — so that over time, more and more opportunities are discovered.”

Because the equipment is available for use by people outside of the MIT community, including regional researchers, industry partners, nonprofit organizations, and local startups, they will also enable new collaborations.

“The tools themselves will be an incredible meeting place — a place that can, I think, transpose the best of our ideas in a much more effective way than before,” Bulović says. “I’m extremely excited about that.”

Palacios notes that while microelectronics is best known for work making transistors smaller to fit on microprocessors, it’s a vast field that enables virtually all the technology around us, from wireless communications and high-speed internet to energy management, personalized health care, and more.

He says he’s personally excited to use the new machines to do research around power electronics and semiconductors, including exploring promising new materials like gallium nitride, which could dramatically improve the efficiency of electronic devices.

Fulfilling a mission

MIT.nano’s leaders say a key driver of commercialization will be startups, both from MIT and beyond.

“This is not only going to help the MIT research community innovate faster, it’s also going to enable a new wave of entrepreneurship,” Palacios says. “We’re reducing the barriers for students, faculty, and other entrepreneurs to be able to take innovation and get it to market. That fits nicely with MIT’s mission of making the world a better place through technology. I cannot wait to see the amazing new inventions that our colleagues and students will come out with.”

Bulović says the announcement aligns with the mission laid out by MIT’s leaders at MIT.nano’s inception.

"We have the space in MIT.nano to accommodate these tools, we have the capabilities inside MIT.nano to manage their operation, and as a shared and open facility, we have methodologies by which we can welcome anyone from the region to use the tools,” Bulović says. “That is the vision MIT laid out as we were designing MIT.nano, and this announcement helps to fulfill that vision.”

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MIT, Applied Materials, and the Northeast Microelectronics Coalition Hub to bring 200mm advanced research capabilities to MIT.nano

The following is a joint announcement from MIT and Applied Materials, Inc.

MIT and Applied Materials, Inc., announced an agreement today that, together with a grant to MIT from the Northeast Microelectronics Coalition (NEMC) Hub, commits more than $40 million of estimated private and public investment to add advanced nano-fabrication equipment and capabilities to MIT.nano, the Institute’s center for nanoscale science and engineering. The collaboration will create a unique open-access site in the United States that supports research and development at industry-compatible scale using the same equipment found in high-volume production fabs to accelerate advances in silicon and compound semiconductors, power electronics, optical computing, analog devices, and other critical technologies.

The equipment and related funding and in-kind support provided by Applied Materials will significantly enhance MIT.nano’s existing capabilities to fabricate up to 200-millimeter (8-inch) wafers, a size essential to industry prototyping and production of semiconductors used in a broad range of markets including consumer electronics, automotive, industrial automation, clean energy, and more. Positioned to fill the gap between academic experimentation and commercialization, the equipment will help establish a bridge connecting early-stage innovation to industry pathways to the marketplace.

“A brilliant new concept for a chip won’t have impact in the world unless companies can make millions of copies of it. MIT.nano’s collaboration with Applied Materials will create a critical open-access capacity to help innovations travel from lab bench to industry foundries for manufacturing,” says Maria Zuber, MIT’s vice president for research and the E. A. Griswold Professor of Geophysics. “I am grateful to Applied Materials for its investment in this vision. The impact of the new toolset will ripple across MIT and throughout Massachusetts, the region, and the nation.”

Applied Materials is the world’s largest supplier of equipment for manufacturing semiconductors, displays, and other advanced electronics. The company will provide at MIT.nano several state-of-the-art process tools capable of supporting 150 and 200mm wafers and will enhance and upgrade an existing tool owned by MIT. In addition to assisting MIT.nano in the day-to-day operation and maintenance of the equipment, Applied engineers will develop new process capabilities that will benefit researchers and students from MIT and beyond.

“Chips are becoming increasingly complex, and there is tremendous need for continued advancements in 200mm devices, particularly compound semiconductors like silicon carbide and gallium nitride,” says Aninda Moitra, corporate vice president and general manager of Applied Materials’ ICAPS Business. “Applied is excited to team with MIT.nano to create a unique, open-access site in the U.S. where the chip ecosystem can collaborate to accelerate innovation. Our engagement with MIT expands Applied’s university innovation network and furthers our efforts to reduce the time and cost of commercializing new technologies while strengthening the pipeline of future semiconductor industry talent.”

The NEMC Hub, managed by the Massachusetts Technology Collaborative (MassTech), will allocate $7.7 million to enable the installation of the tools. The NEMC is the regional “hub” that connects and amplifies the capabilities of diverse organizations from across New England, plus New Jersey and New York. The U.S. Department of Defense (DoD) selected the NEMC Hub as one of eight Microelectronics Commons Hubs and awarded funding from the CHIPS and Science Act to accelerate the transition of critical microelectronics technologies from lab-to-fab, spur new jobs, expand workforce training opportunities, and invest in the region’s advanced manufacturing and technology sectors.

The Microelectronics Commons program is managed at the federal level by the Office of the Under Secretary of Defense for Research and Engineering and the Naval Surface Warfare Center, Crane Division, and facilitated through the National Security Technology Accelerator (NSTXL), which organizes the execution of the eight regional hubs located across the country. The announcement of the public sector support for the project was made at an event attended by leaders from the DoD and NSTXL during a site visit to meet with NEMC Hub members.

“The installation and operation of these tools at MIT.nano will have a direct impact on the members of the NEMC Hub, the Massachusetts and Northeast regional economy, and national security. This is what the CHIPS and Science Act is all about,” says Ben Linville-Engler, deputy director at the MassTech Collaborative and the interim director of the NEMC Hub. “This is an essential investment by the NEMC Hub to meet the mission of the Microelectronics Commons.”

MIT.nano is a 200,000 square-foot facility located in the heart of the MIT campus with pristine, class-100 cleanrooms capable of accepting these advanced tools. Its open-access model means that MIT.nano’s toolsets and laboratories are available not only to the campus, but also to early-stage R&D by researchers from other academic institutions, nonprofit organizations, government, and companies ranging from Fortune 500 multinationals to local startups. Vladimir Bulović, faculty director of MIT.nano, says he expects the new equipment to come online in early 2025.

“With vital funding for installation from NEMC and after a thorough and productive planning process with Applied Materials, MIT.nano is ready to install this toolset and integrate it into our expansive capabilities that serve over 1,100 researchers from academia, startups, and established companies,” says Bulović, who is also the Fariborz Maseeh Professor of Emerging Technologies in MIT’s Department of Electrical Engineering and Computer Science. “We’re eager to add these powerful new capabilities and excited for the new ideas, collaborations, and innovations that will follow.”

As part of its arrangement with MIT.nano, Applied Materials will join the MIT.nano Consortium, an industry program comprising 12 companies from different industries around the world. With the contributions of the company’s technical staff, Applied Materials will also have the opportunity to engage with MIT’s intellectual centers, including continued membership with the Microsystems Technology Laboratories.

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