When Physics and Math Go Viral

With more viruses on Earth than stars in the observable universe, researchers like Raunak Dey may never run out of work.

As a physics Ph.D. student at the University of Maryland, Dey designs theoretical and mathematical models to understand how viruses interact in vast microbial communities. Part of the challenge is that these communities are crowded: A drop of water, a gram of soil and the human gut each harbors millions or billions of microbes and viruses.

“Some viruses can be useful, and some viruses can be harmful,” Dey said. “The beauty of it is that the knowledge you learn from these model systems can be translated into applications.”

Dey’s research intersects with a growing interest in phage therapy, which uses phages—viruses that only infect and replicate in bacterial cells—to treat antibiotic-resistant infections in humans. Much is still unknown about how phages interact with bacteria, but Dey’s problem-solving research fuses math, biology and computational physics to help demystify these processes.

“I don’t see myself as a physics or biology person,” Dey said. “I only see myself as a scientist who will use all the tools at our disposal to solve challenging problems.” Raunak Dey gesturing to a screen with information about one-step growth cruve data Raunak Dey's research aims to solve inverse and optimization problems using time series data. Image courtesy of Raunak Dey. Raunak Dey gesturing to a screen with information about one-step growth cruve data Raunak Dey's research aims to solve inverse and optimization problems using time series data. Image courtesy of Raunak Dey.

‘Mathematical modeling for good’

Driven by a desire to “understand how things work,” Dey enrolled in a dual bachelor’s and master’s degree program in physical sciences at the Indian Institute of Science Education and Research Kolkata, where he studied the random motions of tiny particles. 

After graduating in 2020, Dey moved to the U.S. to pursue a physics Ph.D. at Georgia Tech. As he watched the global pandemic unfold, he realized he wanted to conduct research that would directly benefit people.

“I had this philosophical feeling that the frontline workers were working so hard,” Dey said, “and I wanted to be doing research where I could apply my math aptitude to something useful to society.”

That’s when Dey started using “mathematical modeling for good” to study COVID-19 and its health implications with Joshua Weitz, now a professor in UMD’s Department of Biology and the University of Maryland Institute for Health Computing.

“The same class of models—compartmental differential equations—that we use to describe how viruses like COVID spread in the human population can be used to describe how viruses infect microbes,” Dey explained.

When Weitz moved to UMD in 2023, Dey followed. He wanted to continue what he started, and he also valued the interdisciplinary collaborations happening at UMD and the proximity to federal agencies like the National Institutes of Health. 

“I'm very appreciative of the environment UMD has provided,” Dey said. “There are a lot of projects with professors across departments that allowed me to make connections, which I'm grateful for.”

Capturing complexity

While working with Weitz, Dey also joined a national research project called the Simons Collaboration on Ocean Processes and Ecology (SCOPE) that’s aimed at understanding marine microbial processes. In his work with SCOPE, Dey helps quantify the role of phages in ocean ecosystems, where “good” viruses might help maintain balance by killing microbes and recycling nutrients back into the ocean.

Dey’s ongoing research uses models to understand how different species of viruses and microbes might interact—a process that reveals just how complex these microbial communities can be. 

“One of the fundamental things I’ve learned is that things in biology are really complicated, and we don’t know all the knobs that are turning to make something happen—you just see the output,” Dey said. “In our modeling framework, we try to capture a lot of these complexities, but it's not possible to capture everything.”

Viruses that live in the gut microbiome can be just as complex, but, if harnessed or managed well, can help to improve human health. As a fellow with UMD’s Center of Excellence in Microbiome Sciences, Dey said he’s looking for ways to “translate microbiome science research into policies” that will have an impact on people’s lives. 

In recognition of his research collaborations, Dey received the 2024 Thomas G. Mason Interdisciplinary Physics Fund award from UMD’s Department of Physics, which supports doctoral students who work with professors in other departments.

“Interdisciplinary science is necessary and hard, and sometimes it's frustrating because of how long it takes,” Dey said, “but it’s also rewarding and hopefully useful.”

Making science accessible

When he isn’t conducting research, Dey is passionate about making science accessible to more people—especially budding scientists in his home country, India.

“Many people from underrepresented communities never get a fair shot at trying science,” he said. “This needs to change, and I want to be a part of that positive change by reducing the barrier of entry for science.”

Over the last two years, Dey has been writing tutorials and gathering resources to provide a “good starting point” for students interested in learning more about his area of research. He also mentors other Ph.D. and undergraduate students, adding that this “fulfilling experience” has helped him tailor his teaching to different audiences.

In the future, Dey wants to dive deeper into biomedical research that leverages artificial intelligence (AI) and machine learning. While he doesn’t know exactly where his career might take him after graduation, he feels that UMD has prepared him for whatever challenges await. 

“I don’t know what the future holds, but I want to keep working on innovative and challenging problems that directly contribute to society,” Dey said. “That’s why I wanted to do science in the first place.”

Original story: https://cmns.umd.edu/news-events/news/raunak-dey-makes-physics-and-math-go-viral

UMD-Led Team Wins Major NSF Grant to Pioneer “High-Entropy” Quantum Materials

A University of Maryland–led research team has been awarded a highly competitive grant from the National Science Foundation’s Designing Materials to Revolutionize and Engineer our Future (DMREF) program to launch a bold new frontier in quantum materials science: High-Entropy Quantum Materials.

The $2 million, four-year award brings together scientists from UMD, the University of British Columbia (UBC), the University of North Texas (UNT), and national labs including NIST and the National High Magnetic Field Laboratory. Their mission is to harness “configurational entropy”—the mixing of multiple elements in a single crystal structure—to discover and control new forms of magnetism, superconductivity, and topological states of matter.

“Traditionally, materials scientists try to eliminate disorder when making new compounds,” said Johnpierre Paglione, UMD physics professor and director of the Maryland Quantum Materials Center, who is leading the project. “We’re flipping that idea around—embracing disorder as a way to stabilize entirely new phases of matter.”Approach of high entropy materials stabilization.Approach of high entropy materials stabilization.

High-entropy materials, first discovered in metallic alloys, contain five or more elements randomly distributed across a lattice site. This chemical “chaos” can give rise to surprising stability and novel properties. The UMD-UBC team aims to extend this concept into the quantum realm, coining a new class: High-Entropy Quantum Materials.

“As a chemist, I’m excited by the chance to explore how we can use entropy as a new design principle for building quantum materials,” said co-lead Efrain Rodriguez, UMD professor of chemistry and biochemistry and co-lead on the project. “By mixing multiple elements into a single structure, we’re creating an almost limitless playground for discovering unexpected electronic and magnetic behaviors. It’s a fundamentally new way to think about how chemistry can drive quantum science forward.”

The project will integrate theory, machine learning, and high-throughput synthesis to rapidly identify promising compounds, guided by the AFLOW computational platform and sped up by the use of combinatorial thin-film libraries. “This award allows us to couple cutting-edge computation with rapid experimentation, giving us a chance to accelerate discovery on an unprecedented scale,” said Ichiro Takeuchi, UMD materials scientist and co-lead on the project.

Beyond research, the team will contribute to quantum workforce development by expanding UMD’s Quantum Materials Winter School and Machine Learning for Materials Boot Camp, training the next generation of scientists in synthesis, computation, and quantum technologies.

The collaboration also includes building a public data repository in collaboration with the NSF-funded UC Santa Barbara Quantum Foundry to share results with the broader scientific community, amplifying the project’s impact through the Materials Genome Initiative.

“With this effort, we’re opening a whole new landscape for discovery,” said Paglione. “High-entropy quantum materials could unlock fundamental properties and quantum technologies we haven’t even imagined yet—we are excited to launch this new field of research.”

Srinivasan Named NIST Co-Director of JQI

Adjunct Professor Kartik Srinivasan has been appointed the newest National Institute of Standards and Technology (NIST) Co-Director of JQI. He assumed the role on Sept. 8, 2025 and will be working with Jay Sau who has been the University of Maryland (UMD) Co-Director of JQI since 2022.

“The JQI is central to quantum science research at NIST and UMD,” says Srinivasan. “I look forward to helping it continue to be successful.”

Srinivasan has been a project leader at NIST since 2007 and became a JQI Fellow and NIST Fellow in 2019. In these roles, he has researched integrated photonics—a field that studies how light and its particles (photons) behave and can be manipulated in structures made on compact semiconductor chips. Much of his research has explored ways that light can interact with matter to produce unique phenomena that reveal novel physics and may lead to practical technologies for quantum computing, metrology and sensing. Kartik Srinivasan Kartik Srinivasan

In recent years, Srinivasan and his colleagues have been developing chip-scale frequency combs—devices that produce laser light at a series of evenly spaced frequencies. Frequency combs are valuable tools for precisely measuring light, and smaller versions could help miniaturize high-performance atomic clocks and improve GPS resilience. Srinivasan’s team has also been studying ways to create low-noise, chip-scale laser sources in colors that are useful for quantum information science. In 2024, he and his collaborators developed a way to generate lasers across the green-yellow-orange-red spectral region using compact devices. Low-noise lasers in these colors are generally hard to produce with compact devices, and they are useful for driving quantum transitions in many important atomic and solid-state quantum systems. 

Srinivasan has been an Optica Fellow since 2018 and has received multiple awards, including the Presidential Early Career Award in Science and Engineering in 2010, the NIST Department of Commerce Gold Medal in 2021, and the NIST Samuel Wesley Stratton Award in 2022.

He is taking over the role of NIST Co-Director from JQI Fellow Gretchen Campbell, who had held the position since 2016. Campbell was recently appointed the associate vice president for quantum research and education at the University of Maryland. Sau, the UMD JQI Co-Director, expressed gratitude for Campbell’s stewardship of the institute and looks forward to working more closely with Srinivasan.

"It has been a pleasure to have worked with Gretchen as the NIST co-director of JQI,” says Sau, who is also an associate professor of physics at UMD and a member of the Condensed Matter Theory Center. “We are really excited that Kartik is able to step into the role and bring to bear his experience of exemplary collaborations within JQI."

Original story by Bailey Bedford: https://jqi.umd.edu/news/srinivasan-named-nist-co-director-jqi

Maryland Quantum-Thermodynamics Hub Secures Funding for Three More Years

Watch housingResearchers at the pioneering Maryland Quantum-Thermodynamics Hub meld 19th century physics with the modern techniques and tools of quantum information science. Since 2022, they have plumbed the intriguing depths of this disciplinary fusion, uncovering a deeper understanding of how the everyday world emerges from the quantum realm of tiny particles.

Now, new funding will catapult the hub into the next three years, enabling the addition of new team members and a renewed focus on answering open research questions that might lead to better quantum computers and even alter our fundamental understanding of the nature of time.

The hub launched three years ago with a $2 million grant from the John Templeton Foundation. New funding for the next three years includes a recommitment from Templeton that will match support from the state via Gov. Wes Moore’s Capital of Quantum Initiative and University of Maryland campus sponsors like the National Quantum Laboratory, the Brin Mathematics Research Center and the Institute for Physical Science and Technology. Several private companies, including Fidelity Investments and Normal Computing, will provide additional support. Altogether the new funding totals more than $5 million and will support team members at UMD as well as the University of Maryland, Baltimore County (UMBC); the University of Southern California; the University of Arizona; Los Alamos National Laboratory in New Mexico; the University of Rochester in New York; and University College Dublin.

“The intention is to make Maryland a lodestone for quantum thermodynamics in North America,” says Nicole Yunger Halpern, an adjunct assistant professor of physics at UMD and a co-leader of the hub who is also a physicist at the National Institute of Standards and Technology and a Fellow of the Joint Center for Quantum Information and Computer Science.

Hub researchers mix the old with the new, combining three fields of physics from different centuries. The oldest is thermodynamics, which emerged from the industrial revolution in the 19th century and investigates, among other things, how machines transform energy into work and heat. Next is quantum physics, which was founded in the 20th century and provides our most fundamental understanding of nature at the level of atoms, electrons and other tiny constituents of matter and energy. Finally, quantum information science, which has become a major field in the early 21st century, applies the rules of quantum physics to information processing and has led to new applications like quantum computing, quantum networking and quantum sensing. Quantum thermodynamics seeks to combine the best tools and insights from all these areas to answer both deep and practical questions about the physical world. While fusing these fields together over the past three years, researchers at the hub have published more than 60 journal articles, conference papers and preprints, and the hub has supported five Ph.D. theses.

“I'm excited that we've obtained funding to build on the success of our first three years,” says Distinguished University Professor Christopher Jarzynski, a co-leader of the hub who is also a professor of physics and a professor of chemistry and biochemistry at UMD. “The hub has firmly placed Maryland on the map as a center for innovative quantum thermodynamics research, education and outreach.”

Research at the hub broadly investigates how quantum systems, such as collections of atoms, interact with their environments and the variety of ways that quantum features either frustrate or facilitate thermodynamic processes like energy or information exchange. Energy exchange between a system and its environment helps explain how physical systems thermalize, or end up at a shared temperature. Information exchange explains how the values of quantum measurements—typically of just a few quantum particles—are imprinted in much larger measurement devices.

One particular mystery energizes many scientists at the hub—a nagging problem at the heart of physics that researchers refer to as the arrow of time. The gist of the problem is that although the detailed microscopic theories of physics look the same whether time is running forwards or backwards, the much larger scale of everyday reality seems to have an unmistakable direction. We never see an egg unscramble itself or smoldering ash and smoke reassemble into a log. Somewhere between the reversible rules of microscopic physics and our common experience of the world, there is a transition, an emergent effect that causes time to flow toward the future.

“The big goal of the hub has been to identify how, from microscopic quantum physics, our classical objective reality emerges thermodynamically,” says Yunger Halpern. “Thermodynamics traditionally has addressed large numbers of particles, and it stems from the actions of many, many small particles. So thermodynamics kind of bridges scales and helps us understand how large-scale macroscopic phenomena emerge, such as the arrow of time.”

Some hub researchers have been motivated by questions about which quantum phenomena hinder quantum systems from experiencing the arrow of time. One example turned out to be the exchange of incompatible quantities between a quantum system and its environment. These incompatible quantities are quantum properties that, thanks to the uncertainty principle, cannot be simultaneously known.

For instance, researchers can check if the quantum spin of a particle is pointing up or down along any direction, but the spin along some other direction is an incompatible quantity. If a quantum system is exchanging spin with its environment along two incompatible directions, it hinders certain features of thermalization and impedes the system’s experience of time. Understanding more about which quantum phenomena interact with time’s arrow could have applications to error correction in quantum computing, which fights against the march of time and preserves quantum information by monitoring for and removing heat and disorder.

“We found some tensions in this, though,” says Yunger Halpern. “We found some ways that this exchange of incompatible quantities hinders some facets of thermalization, but also some ways that it enhances some facets. In the next three years, we hope to get a unified picture.”

The hub will use its next three years to refine the questions it has been asking, seeking to clarify the tensions that cropped up during the first three years. In addition to investigating how certain quantum phenomena impact the arrow of time, they will also consider new models of information exchange between quantum systems and their environments. They even plan to add an entirely new kind of question to the mix: How might the continuous fabric of space and time in Einstein’s general theory of relativity emerge from a microscopic network of discrete quantum systems?

Beyond research, the hub has also become a nexus for community building and outreach in the field, hosting an annual gathering to foster collaboration and innovation and organizing a short story contest in 2023. Part of the hub’s mission, Yunger Halpern says, is to share the adventure of quantum thermodynamics with the general public and inspire the next generation of quantum thermodynamicists.

The new funding will allow the hub to expand its team, adding new spokes. New team members will join from UMD, UMBC, and the University of Rochester, but the hope is that the growth won’t stop there.

“If anyone else would like to partner with us, we’d be happy to hear from them,” says Yunger Halpern.

Story by Chris Cesare