Biophysical Modeling

The Biophysical Modeling group focuses on the modeling and simulation of complex systems that arise in biology and soft condensed matter physics.

Areas of interest include the dynamics of complex and active materials, and aspects of collective behavior and self-assembly in both natural systems (e.g., inside the cell) and synthetic ones. Our approach is based on mathematical modeling and analysis, the development and application of software tools for large-scale biophysical simulation, and close collaboration with experimentalists.

Research Highlights

September 1, 2020

A scalable computational platform for Stokes suspensions

W. Yan, E. Corona, D. Malhotra, S. Veerapaneni, M. Shelley

We describe a computational framework for simulating suspensions of rigid particles in Newtonian Stokes flow. One central building block is…

Journal of Computational Physics

August 27, 2020

Swirling Instability of the Microtubule Cytoskeleton

D. Stein, G. De Canio, E. Lauga, M. Shelley, R. E. Goldstein

In the cellular phenomena of cytoplasmic streaming, molecular motors carrying cargo along a network of microtubules entrain the surrounding fluid.…

BioRxiv: 2020.08.27.268318

August 12, 2020

Metallic Microswimmers Driven up the Wall by Gravity

Q. Brosseau, F. Balboa Usabiaga, E. Lushi, Y. Wu, L. Ristroph, M. D. Ward, M. Shelley, J. Zhang

As a natural and functional behavior, various microorganisms exhibit gravitaxis by orienting and swimming upwards against gravity. Swimming autophoretic nanomotors…

arXiv:2008.05273

News & Announcements

December 03, 2019

Unexpected Forces Cause Rotor Proteins to Self-Organize By Susan Reslewic Keatley

September 02, 2019

Mystery Solved About the Machines That Move Your Genes By Thomas Sumner

March 05, 2019

Swimming Microbes Steer Themselves into Mathematical Order, University of Wisconsin-Madison

Upcoming Events

No events are scheduled in March.

Group Members

Michael Shelley, Ph.D.

Director, CCB

Michael Shelley joined the Simons Foundation in 2016 to work on the modeling and simulation of complex systems arising in physics and biology.

Brato Chakrabarti, Ph.D.

Flatiron Research Fellow, Biophysical Modeling

Brato Chakrabarti joined the Center for Computational Biology’s Biophysical Modeling Group in March 2020.

XinXin Du, Ph.D.

Associate Research Scientist, Biophysical Modeling

XinXin Du joined the Center for Computational Biology at the Flatiron Institute in August, 2019.

Reza Farhadifar, Ph.D.

Research Scientist, Biophysical Modeling

Reza Farhadifar joined the foundation in 2017 as a research scientist reporting to Michael Shelley in the Biophysical Modeling Group. Previously, Farhadifar was a postdoctoral researcher in experimental and theoretical biophysics at Harvard University.

Sebastian Fürthauer, Ph.D.

Research Scientist, Biophysical Modeling

Sebastian Fürthauer joined the Center for Computational Biology in June 2016. Fürthauer is interested in the physics of cellular scale processes, such as cell division and cell motility and their role in developmental biology.

Leroy Jia, Ph.D.

Flatiron Research Fellow, Biophysical Modeling

Leroy Jia joined the Biophysical Modeling group in the Center for Computational Biology at the Flatiron Institute in October, 2018.

Gokberk Kabacaoglu, Ph.D.

Flatiron Research Fellow, Biophysical Modeling joint with CCM

Gokberk Kabacaoglu joined the foundation in 2019 as a joint member of Center for Computational Biology and Center for Computational Mathematics.

Adam Lamson, Ph.D.

Flatiron Research Fellow, Biophysical Modeling

Adam Lamson joined the Simons Foundation in 2020 as part of CCB’s biophysical modeling group.

Daniel Needleman, Ph.D.

Senior Research Scientist, Biophysical Modeling

Daniel Needleman joined the Center for Computational Biology as a Senior Research Scientist in September 2020.

Michael O’Brien

Associate Research Analyst, Biophysical Modeling

Michael joined the Biophysical Modeling group in the Center for Computational Biology in June 2020.

Aleksandra Plochocka, Ph.D.

Flatiron Research Fellow, Biophysical Modeling joint with CCM

Aleks Plochocka joined the foundation in 2019 as a joint member of Center for Computational Biology and Center for Computational Mathematics. Aleks earned her Ph.D. in mathematics at the Maxwell Institute Graduate School in Analysis & its Applications joint between the University of Edinburgh and…

Alex Rautu, Ph.D.

Flatiron Research Fellow, Biophysical Modeling

Alex Rautu joined the foundation in 2020 as a member of the Biophysical Modeling group. His research focuses on theoretical problems in soft matter and biology, and particularly on the biophysics of cellular processes.

David Stein, Ph.D.

Research Scientist, Biophysical Modeling

David Stein joined the foundation in 2016 as a Flatiron research fellow at the Center for Computational Biology in the biophysical modeling group. His research interests are in the dynamics of complex fluids and fluid suspensions, and in numerical methods for studying these fluids in…

Wen Yan, Ph.D.

Research Scientist, Biophysical Modeling

Wen Yan joined the Simons Foundation in 2016 as part of CCB’s biophysical modeling group. His research focuses on the development and simulation of mathematical models pertaining to phenomena in biophysics and active materials and the development of simulations of suspensions of such active objects.