Targeted Grants in the Mathematical Modeling of Living Systems Awardees

The Simons Foundation congratulates the investigators who were awarded a Targeted Grant in the Mathematical Modeling of Living Systems.

 

 

Vijay Balasubramanian

University of Pennsylvania

Adaptive Molecular Sensing in the Olfactory and Immune Systems

Vijay Balasubramanian was born in Bombay (Mumbai) and grew up in India and Indonesia. He earned degrees in Physics (B.Sc.) and Computer Science (B.Sc. and M.Sc.) at Massachusetts Institute of Technology (MIT) and a Ph.D. in Physics from Princeton University. After holding a postdoctoral fellowship as a Junior Fellow of the Harvard Society of Fellows, he joined the faculty in the Department of Physics and Astronomy of the University of Pennsylvania, where he is currently the Cathy and Marc Lasry Professor. He spent the 2012–2013 year at the École normale supérieure in Paris on a fellowship from the Fondation Pierre-Gilles de Gennes. He has been a visiting professor at the City University of New York Graduate Center, Rockefeller University, the International Center for Theoretical Physics in Trieste, Italy, and the Vrije Universiteit Brussel (Free University of Brussels) in Belgium. As a biophysicist, he seeks to explain the fundamental principles that govern the information-processing architectures of living systems. Balasubramanian has also addressed problems in statistical inference and Occam’s razor — the trade-off between simple and accurate mathematical models — and has written extensively as a string theorist on problems in theoretical physics, such as the question of whether black holes destroy information.

 

Sam Brown, Howard Weiss & William Ratcliff

Georgia Institute of Technology

Collective Bacterial Decision-Making

Sam Brown is an evolutionary microbiologist, with a B.A. and Ph.D. from the University of Cambridge. Brown is a pioneer in the study of bacterial social interactions and their consequences for disease. His theoretical and experimental work integrates molecular microbiology with ecology, epidemiology and evolution, and centers on two themes: the evolution of sociality and the evolution of virulence. These two themes combine strongly when applied to microbial pathogens, as microbes must often communicate, coordinate and cooperate in order to successfully grow within and transmit among their hosts.

Howard Weiss is a professor of mathematics at Georgia Institute of Technology. He is also an adjunct professor of biology and global health at Emory University. His current research projects include studying the bacterial genetics and pharmacodynamics of antibiotics for bacteria growing in physically structured habitats, studying the transmission of infectious diseases in an airplane cabin and studying the dynamics of the bacterial community in the gut. Previously, Weiss made many significant contributions to the mathematical theory of dynamical systems. His most recent honors include being selected as a Georgia Power Professor of Excellence and a fellow of the American Association of Arts and Sciences. In recent years, he has taught courses in virus dynamics, population genetics, mathematical biology, dynamical systems and probability statistics.

William Ratcliff uses experimental evolution and computational approaches to study the dynamics of microbial collectives, with a specific focus on cooperation/conflict, bet hedging and the evolution of multicellularity. He obtained his bachelor’s degree in plant biology in 2004 from the University of California, Davis, and his Ph.D. in 2010 in ecology, evolution and behavior from the University of Minnesota, where he worked on the legume-rhizobium mutualism. As a postdoc at the University of Minnesota, he developed a novel model system (“snowflake yeast”) for studying the evolutionary origin of multicellularity. In 2014, he began a faculty position at the Georgia Institute of Technology.

 

Jané Kondev

Brandeis University

Building a Proportional Cell: Design Principles of Biological Size Control

Jané Kondev is a theoretical physicist whose research focuses on cells, with the overarching goal of uncovering mathematical laws that govern living systems. He studied physics and mathematics in Serbia at the Mathematical High School and at the University of Belgrade. His research career began at Cornell University, where he obtained his Ph.D. in theoretical condensed matter physics. After postdoctoral research at Brown University and the Institute for Advanced Study at Princeton, he joined the faculty at Brandeis University as a professor of physics. There, initially he led a research group that focused on problems in fluctuating geometries, glassy systems and the quantum Hall effect. Subsequently he became interested in problems in cell biology and eventually his research focus completely shifted to living systems. These days his group combines theoretical and experimental approaches to study fundamental biological processes such as the transcription of genes, the assembly of cytoskeleton structures and the dynamics of chromosomes. He is one of the authors of the textbook Physical Biology of the Cell and is an Howard Hughes Medical Institute professor.

 

Simon A. Levin

Princeton University

A New Framework for Ecological Kinetics in Natural Environments

Simon A. Levin is the George M. Moffett Professor of Biology at Princeton University and the director of the Center for BioComplexity in the Princeton Environmental Institute. His research examines the structure and functioning of ecosystems, the dynamics of disease and the coupling of ecological and socioeconomic systems. Levin is a fellow of the American Academy of Arts and Sciences and the American Association for the Advancement of Science, a member of the National Academy of Sciences and the American Philosophical Society, and a foreign member of the Istituto Veneto di Scienze, Lettere ed Arti and the Istituto Lombardo Accademia di Scienze e Lettere (Milan). He has over 500 publications and is the editor of the Encyclopedia of Biodiversity and the Princeton Guide to Ecology. Levin’s awards include the Heineken Prize for Environmental Sciences, Kyoto Prize in Basic Sciences, Ramon Margalef Prize for Ecology, the Ecological Society of America’s MacArthur and Eminent Ecologist Awards, the Luca Pacioli Prize (Ca’ Foscari University of Venice), the Tyler Prize for Environmental Achievement, and most recently, the National Medal of Science.

 

Pankaj Mehta

Boston University

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Alvaro Sanchez

Yale University

What Constrains Microbial Diversity? Deriving New Ecological Principles for the Microbial World

(Funded in conjunction with the Scialog program of the Research Corporation for Science Advancement and the Gordon and Betty Moore Foundation; see here for more information.)

Pankaj Mehta works on theoretical problems at the interface of physics and biology with a focus on how large-scale, collective behavior observed in biological systems emerges from the interaction of many individual biological elements. He has a B.S. in mathematics from California Institute of Technology and a Ph.D. in theoretical condensed matter physics from Rutgers University, and did his postdoctoral work in the theoretical biophysics group at Princeton University. Since 2010, he has been a faculty member in the Department of Physics at Boston University.

Alvaro Sanchez is an assistant professor of Ecology and Evolutionary Biology at Yale University. His laboratory uses a combination of mathematical modeling and experimental evolution to investigate the fundamental principles that govern the behavior of microbial communities. His current work is focused on understanding how the structure of microbial communities, and particularly the interactions between bacteria, determines the collective properties of these communities. His group has recently been able to domesticate hundreds of large and very diverse bacterial communities in defined minimal media, leading to a new line of work in trying to elucidate the functional roles played by the rare species in these communities. From 2013 to 2016, he was a Rowland Junior Fellow at Harvard, where his work focused on the eco-evolutionary dynamics of microbial communities. His previous appointments include a two-year postdoc at Massachusetts Institute of Technology and graduate work at Brandeis, where he graduated with a Ph.D. in biophysics in 2011.

 

 

Christopher Klausmeier & Elena Litchman

Michigan State University

Microscopic foundations for macroecological patterns

Christopher Klausmeier is a theoretical ecologist, with a B.S. in mathematics from Harvey Mudd College and a Ph.D. in ecology from the University of Minnesota. His research uses mathematical and computational models to uncover the principles that structure ecological communities, with a focus on plankton communities. Particular topics of interest include spatial and temporal dynamics, ecological stoichiometry and eco-evolutionary interactions using adaptive dynamics.

Elena Litchman is an experimental and conceptual ecologist, focusing on phytoplankton communities. She received her undergraduate degree in biology from Moscow State University, Russia, and Ph.D. in ecology from the University of Minnesota. She is a pioneer in the application of trait-based approaches to plankton ecology, combining lab experiments with meta-analyses and modeling.

 

M. Cristina Marchetti

Syracuse University

Models of collective cell migration and sorting

M. Cristina Marchetti is a theoretical physicist with a background in nonequilibrium statistical mechanics and soft matter physics. She obtained her Ph.D. in physics from the University of Florida, Gainesville, and has been on the physics faculty at Syracuse University since 1987. In the last ten years, she has applied ideas and tools from statistical physics to problems of biological relevance, especially in the emerging field of active matter. The name refers to nonequilibrium materials composed of many interacting units that individually consume energy and collectively generate motion or mechanical stresses. Examples include bacterial suspensions, the cell cytoskeleton and living tissues. Marchetti has contributed to the quantitative understanding of the structure and rheology of in vitro gels and suspensions of motor proteins and cytoskeletal filaments and has formulated predictive theories of force transmissions among cells and of cells with their environment.

 

Massimo Vergassola

University of California, San Diego

Learning how living systems navigate turbulent environments

Massimo Vergassola studied theoretical physics at the University of Rome and received his Ph.D. in 1993 at the University of Nice. After a postdoc at Princeton University, he obtained a tenured research position at the French CNRS for work on the statistical physics of turbulence. In 2001, he was a visiting research associate at Rockefeller University and went on in 2005 to the Pasteur Institute in Paris to head the Physics of Biological Systems group. In 2013, he moved to his present position as professor of physics at the University of California, San Diego. His main current research interest is in the sensing and processing of environmental information by living organisms, namely for their behavior in conditions of strong fluctuations as in the olfactory searches by insects and the soaring of birds.

 

Kalin Vetsigian

University of Wisconsin-Madison

Role of higher-order interactions for stability of microbial communities

Kalin Vetsigian combines theory and experiment to study ecological and evolutionary dynamics in multi-species microbial communities. He obtained bachelor degrees in physics and mathematics from MIT and went on to receive a Ph.D. in physics at the University of Illinois at Urbana-Champaign in 2005. After a postdoc at the Department of Systems Biology at Harvard Medical School, he became a professor in the Department of Bacteriology at the University of Wisconsin-Madison in 2012.

 

Stanislas Leibler

Institute for Advanced Study and The Rockefeller University

Acquisition, Storage and Inheritance of Information in Dynamical Living Matter

The enormous diversity of phenomena in biology implies that a large variety of topics are being tackled by biological research. In the tradition of theoretical approaches in physics, Stanislas Leibler and his collaborators at the Simons Center for Systems Biology (Institute for Advanced Study) and at the Laboratory of Living Matter (Rockefeller University) are striving to find common mechanisms that could operate across different length and time scales and across different organizational levels in biological systems.

One direction these efforts take is to search for relevant collective variables in biological dynamics. Subjects studied range from the internal dynamics of proteins to the population dynamics of microbial ecosystems and the behavioral dynamics of interacting animals, such as flies, worms or ants. All these dynamical systems are characterized by complex, time-dependent interactions between their numerous microscopic components, which are impossible to characterize or control in detail. Finding possible collective “modes” characterizing these dynamics is arguably the only way to establish a quantitative, predictive description of such systems.

Leibler and his colleagues are also interested in the flow of information in biological systems. In particular, they study the role played by information about the environment and memory of previous experience in the survival strategies of simple organisms, such as microbes. In related studies, they are trying to establish a theoretical framework to classify different modes of heredity (acting on different time scales) and to tackle the evolution of heredity itself.

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Stanislas Leibler studied physics as an undergraduate at the University of Warsaw. He went on to earn three degrees from the University of Paris: an M.S. in theoretical physics in 1979, a Ph.D. in theoretical physics in 1981 and another Ph.D. in physics in 1984. Dr. Leibler spent a year at the École Normale Supérieure and became a tenured research fellow at the le Centre CEA de Saclay in 1984, staying until 1992. He was also a visiting research associate at Cornell University from 1985 to 1987 and a visiting professor at the École Supérieure de Physique et de Chimie Industrielles from 1989 to 1991. In 1992, Dr. Leibler moved to Princeton University as a professor in the department of physics, also becoming a professor in the department of molecular biology in 1993. He spent a year from 1997 to 1998 as a visiting scientist at the European Molecular Biological Laboratory in Heidelberg, Germany.

In 2001, Dr. Leibler moved to Rockefeller University, where he is the Gladys T. Perkin Professor at the Center for Studies in Physics and Biology. In 2009, he also joined the Institute for Advanced Study (IAS) as a professor in the Simons Center for Systems Biology, at the School of Natural Sciences. Since 2009, Dr. Leibler has headed the IAS–Rockefeller Joint Initiative in Quantitative Biology.

 

 

Terence Hwa

University of California, San Diego

Coarse-Graining Bacterial Metabolic Network: From Molecules to Growth Physiology

Hwa applies concepts and tools from statistical physics to study the organizing principles of living systems. In recent years, he pionnered the use of quantitative phenomenology (growth laws) to formulate predictive theories of bacterial physiology, particularly in the areas of metabolic coordination and antibiotic resistance. He is credited with building a comprehensive educational and research program in quantitative biology at the University of California, San Diego.

 

Boris Shraiman

University of California, Santa Barbara

&

Daniel E. Gottschling

Fred Hutchinson Cancer Research Center

Natural Selection in Rapidly Mutating Populations and Mitochondrial Aging

Boris Shraiman is a theoretical physicist with a background in statistical physics. He received his Ph.D. in 1983 at Harvard University. In 2004, Shraiman moved to his present position as a permanent member of the Kavli Institute for Theoretical Physics and a professor in the Department of Physics at the University of California, Santa Barbara. His current research interests are in morphogenesis, addressing the problem of “growth and form” in animal development, and statistical genetics, which aims to quantitatively describe evolutionary dynamics in populations.

Daniel E. Gottschling received his Ph.D. in chemistry in 1984 at the University of Colorado. He moved to his present position as a member of the Basic Sciences Division, Fred Hutchinson Cancer Research Center in 1996. Gottschling pioneered methods for analyzing fundamental biological processes in yeast, with which he elucidated the relationship between telomeres and transcriptional silencing, facilitating a mechanistic understanding of eukaryotic epigenetic regulation; and discovered yeast telomerase RNA, novel modes of chromatin regulation, links between aging and genomic instability, and nuclear protein quality control. His current research focuses on understanding how organelles decline with age and how interconnectivity between organelles modulates the aging process.

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