School of Engineering
Showing 51-73 of 73 Results
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Grant M. Rotskoff
Assistant Professor of Chemistry
BioGrant Rotskoff studies the nonequilibrium dynamics of living matter with a particular focus on self-organization from the molecular to the cellular scale. His work involves developing theoretical and computational tools that can probe and predict the properties of physical systems driven away from equilibrium. Recently, he has focused on characterizing and designing physically accurate machine learning techniques for biophysical modeling. Prior to his current position, Grant was a James S. McDonnell Fellow working at the Courant Institute of Mathematical Sciences at New York University. He completed his Ph.D. at the University of California, Berkeley in the Biophysics graduate group supported by an NSF Graduate Research Fellowship. His thesis, which was advised by Phillip Geissler and Gavin Crooks, developed theoretical tools for understanding nonequilibrium control of the small, fluctuating systems, such as those encountered in molecular biophysics. He also worked on coarsegrained models of the hydrophobic effect and self-assembly. Grant received an S.B. in Mathematics from the University of Chicago, where he became interested in biophysics as an undergraduate while working on free energy methods for large-scale molecular dynamics simulations.
Research Summary
My research focuses on theoretical and computational approaches to "mesoscale" biophysics. Many of the cellular phenomena that we consider the hallmarks of living systems occur at the scale of hundreds or thousands of proteins. Processes like the self-assembly of organelle-sized structures, the dynamics of cell division, and the transduction of signals from the environment to the machinery of the cell are not macroscopic phenomena—they are the result of a fluctuating, nonequilibrium dynamics. Experimentally probing mesoscale systems remains extremely difficult, though it is continuing to benefit from advances in cryo-electron microscopy and super-resolution imaging, among many other techniques. Predictive and explanatory models that resolve the essential physics at these intermediate scales have the power to both aid and enrich the understanding we are presently deriving from these experimental developments.
Major parts of my research include:
1. Dynamics of mesoscale biophysical assembly and response.— Biophysical processes involve chemical gradients and time-dependent external signals. These inherently nonequilibrium stimuli drive supermolecular organization within the cell. We develop models of active assembly processes and protein-membrane interactions as a foundation for the broad goal of characterizing the properties of nonequilibrium biomaterials.
2. Machine learning and dimensionality reduction for physical models.— Machine learning techniques are rapidly becoming a central statistical tool in all domains of scientific research. We apply machine learning techniques to sampling problems that arise in computational chemistry and develop approaches for systematically coarse-graining physical models. Recently, we have also been exploring reinforcement learning in the context of nonequilibrium control problems.
3. Methods for nonequilibrium simulation, optimization, and control.— We lack well-established theoretical frameworks for describing nonequilibrium states, even seemingly simple situations in which there are chemical or thermal gradients. Additionally, there are limited tools for predicting the response of nonequilibrium systems to external perturbations, even when the perturbations are small. Both of these problems pose key technical challenges for a theory of active biomaterials. We work on optimal control, nonequilibrium statistical mechanics, and simulation methodology, with a particular interest in developing techniques for importance sampling configurations from nonequilibrium ensembles. -
Amin Saberi
Professor of Management Science and Engineering
BioAmin Saberi is Professor of Management Science and Engineering at Stanford University. He received his B.Sc. from Sharif University of Technology and his Ph.D. from Georgia Institute of Technology in Computer Science. His research interests include algorithms, design and analysis of social networks, and applications. He is a recipient of the Terman Fellowship, Alfred Sloan Fellowship and several best paper awards.
Amin was the founding CEO and chairman of NovoEd Inc., a social learning environment designed in his research lab and used by universities such as Stanford as well as non-profit and for-profit institutions for offering courses to hundreds of thousands of learners around the world. -
Julia Salzman
Associate Professor of Biomedical Data Science, of Biochemistry and, by courtesy, of Statistics and of Biology
Current Research and Scholarly Interestsstatistical computational biology focusing on splicing, cancer and microbes
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Michael Saunders
Professor (Research) of Management Science and Engineering, Emeritus
BioSaunders develops mathematical methods for solving large-scale constrained optimization problems and large systems of equations. He also implements such methods as general-purpose software to allow their use in many areas of engineering, science, and business. He is co-developer of the large-scale optimizers MINOS, SNOPT, SQOPT, PDCO, the dense QP and NLP solvers LSSOL, QPOPT, NPSOL, and the linear equation solvers SYMMLQ, MINRES, MINRES-QLP, LSQR, LSMR, LSLQ, LNLQ, LSRN, LUSOL.
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Eric S.G. Shaqfeh
Lester Levi Carter Professor and Professor of Mechanical Engineering
Current Research and Scholarly InterestsI have over 25 years experience in theoretical and computational research related to complex fluids following my PhD in 1986. This includes work in suspension mechanics of rigid partlcles (rods), solution mechanics of polymers and most recently suspensions of vesicles, capsules and mixtures of these with rigid particles. My research group is internationally known for pioneering work in all these areas.
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Aaron Sidford
Associate Professor of Management Science and Engineering and of Computer Science
Current Research and Scholarly InterestsMy research interests lie broadly in the optimization, the theory of computation, and the design and analysis of algorithms. I am particularly interested in work at the intersection of continuous optimization, graph theory, numerical linear algebra, and data structures.
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Andrew Spakowitz
Tang Family Foundation Chair of the Department of Chemical Engineering, Professor of Chemical Engineering and of Materials Science and Engineering
Current Research and Scholarly InterestsTheory and computation of biological processes and complex materials
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Jenny Suckale
Associate Professor of Geophysics and, Senior Fellow, by courtesy, at the Woods Institute for the Environment
BioMy research group studies disasters to reduce the risk they pose. We approach this challenge by developing customized mathematical models that can be tested against observational data and are informed by community needs through a scientific co-production process. We intentionally work on extremes across different natural systems rather than focusing on one specific natural system to identify both commonalities in the physical processes driving extremes and in the best practices for mitigating risk at the community level. Our current research priorities include volcanic eruptions, ice-sheet instability, permafrost disintegration, induced seismicity and flood-risk mitigation. I was recently awarded the Presidential Early Career Awards for Scientists and Engineers, the highest honor bestowed by the United States Government on science and engineering professionals in the early stages of their independent research careers and the CAREER award from the National Science Foundation.
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Hamdi Tchelepi
Professor of Energy Science Engineering and Senior Fellow at the Precourt Institute for Energy
Current Research and Scholarly InterestsCurrent research activities: (1) model and simulate unstable miscible and immiscible fluid flow in heterogeneous porous media, (2) develop multiscale numerical solution algorithms for coupled mechanics and multiphase fluid flow in large-scale subsurface formations, and (3) develop stochastic solution methods that quantify the uncertainty associated with predictions of fluid-structure dynamics in porous media.
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Madeleine Udell
Assistant Professor of Management Science and Engineering and, by courtesy, of Electrical Engineering
Current Research and Scholarly InterestsProfessor Udell develops new techniques to accelerate and automate data science,
with a focus on large-scale optimization and on data preprocessing,
and with applications in medical informatics, engineering system design, and automated machine learning. -
Johan Ugander
Associate Professor of Management Science and Engineering
BioProfessor Ugander's research develops algorithmic and statistical frameworks for analyzing social networks, social systems, and other large-scale data-rich contexts. He is particularly interested in the challenges of causal inference and experimentation in these complex domains. His work commonly falls at the intersections of graph theory, machine learning, statistics, optimization, and algorithm design.
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Benjamin Van Roy
Professor of Electrical Engineering, of Management Science and Engineering
BioBenjamin Van Roy is a Professor at Stanford University, where he has served on the faculty since 1998. His current research focuses on reinforcement learning. Beyond academia, he leads a DeepMind Research team in Mountain View, and has also led research programs at Unica (acquired by IBM), Enuvis (acquired by SiRF), and Morgan Stanley.
He is a Fellow of INFORMS and IEEE and has served on the editorial boards of Machine Learning, Mathematics of Operations Research, for which he co-edited the Learning Theory Area, Operations Research, for which he edited the Financial Engineering Area, and the INFORMS Journal on Optimization. He received the SB in Computer Science and Engineering and the SM and PhD in Electrical Engineering and Computer Science, all from MIT, where his doctoral research was advised by John N. Tstitsiklis. He has been a recipient of the MIT George C. Newton Undergraduate Laboratory Project Award, the MIT Morris J. Levin Memorial Master's Thesis Award, the MIT George M. Sprowls Doctoral Dissertation Award, the National Science Foundation CAREER Award, the Stanford Tau Beta Pi Award for Excellence in Undergraduate Teaching, the Management Science and Engineering Department's Graduate Teaching Award, and the Lanchester Prize. He was the plenary speaker at the 2019 Allerton Conference on Communications, Control, and Computing. He has held visiting positions as the Wolfgang and Helga Gaul Visiting Professor at the University of Karlsruhe, the Chin Sophonpanich Foundation Professor and the InTouch Professor at Chulalongkorn University, a Visiting Professor at the National University of Singapore, and a Visiting Professor at the Chinese University of Hong Kong, Shenzhen. -
Andras Vasy
Robert Grimmett Professor of Mathematics
Current Research and Scholarly InterestsMy research concentrates on topics in two broad areas of applications of microlocal analysis in which, partly with collaborators, I introduced new ideas in recent years: non-elliptic linear and non-linear partial differential equations (PDE), typically concerning wave propagation or other related phenomena, and inverse problems for X-ray type transforms along geodesics and related problems for determining the metric tensor from boundary measurements.
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Wing Hung Wong
Stephen R. Pierce Family Goldman Sachs Professor of Science and Human Health and Professor of Biomedical Data Science
Current Research and Scholarly InterestsCurrent interest centers on the application of statistics to biology and medicine. We are particularly interested in questions concerning gene regulation, genome interpretation and their applications to precision medicine.
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Lei Xing
Jacob Haimson and Sarah S. Donaldson Professor and Professor, by courtesy, of Electrical Engineering
Current Research and Scholarly Interestsartificial intelligence in medicine, medical imaging, Image-guided intervention, molecular imaging, biology guided radiation therapy (BGRT), treatment plan optimization
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Yinyu Ye
Kwoh-Ting Li Professor in the School of Engineering and Professor, by courtesy, of Electrical Engineering
Current Research and Scholarly InterestsMy current research interests include Continuous and Discrete Optimization, Algorithm Development and Analyses, Algorithmic Game/Market Theory and Mechanism-Design, Markov Decision Process and Reinforcement Learning, Dynamic/Online Optimization and Resource Allocation, and Stochastic and Robust Decision Making. These areas have been the unique and core disciplines of MS&E, and extended to new application areas in AI, Machine Learning, Data Science, and Business Analytics.
