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 14, 2019

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…

arXiv:1909.06623

September 9, 2019

The odd free surface flows of a colloidal chiral fluid

V. Soni, E.S. Bililign, S. Magkiriadou, S. Sacanna, M. Shelley, W. Irvine

In simple fluids, such as water, invariance under parity and time-reversal symmetry imposes that the rotation of constituent ‘atoms’ is…

Nature Physics

September 2, 2019

Self-straining of actively crosslinked microtubule networks

S. Fürthauer, B. Lemma, P. J. Foster, S. C. Ems-McClung, C.-H. Yu, C. E. Walczak, Z. Dogi, D. Needleman, M. Shelley

Cytoskeletal networks are foundational examples of active matter and central to self-organized structures in the cell. In vivo, these networks…

Nature Physics

News & Announcements

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)

September 17, 2018

Particles Surf Their Own Waves, Reveal How Microbes and Cells Move Through Human Body By Thomas Sumner

Featured Events

December 2019

Conference
Universality: Turbulence Across Vast Scales

December 2-6, 2019
8:00 AM - 5:00 PM

162 5th Avenue
2nd Floor Auditorium

Upcoming Events

October 2019

21 Mon
- Meeting 10:00 AM - 12:00 PM
  Biophysical Modeling Group Meeting
28 Mon
- Meeting 10:00 AM - 12:00 PM
  Biophysical Modeling Group Meeting

November 2019

04 Mon
- Meeting 10:00 AM - 12:00 PM
  Biophysical Modeling Group Meeting
11 Mon
- Meeting 10:00 AM - 12:00 PM
  Biophysical Modeling Group Meeting
18 Mon
- Meeting 10:00 AM - 12:00 PM
  Biophysical Modeling Group Meeting
25 Mon
- Meeting 10:00 AM - 12:00 PM
  Biophysical Modeling Group Meeting

December 2019

02 Mon
- Meeting 10:00 AM - 12:00 PM
  Biophysical Modeling Group Meeting
09 Mon
- Meeting 10:00 AM - 12:00 PM
  Biophysical Modeling Group Meeting
16 Mon
- Meeting 10:00 AM - 12:00 PM
  Biophysical Modeling Group Meeting
23 Mon
- Meeting 10:00 AM - 12:00 PM
  Biophysical Modeling Group Meeting

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.

Florencio Balboa Usabiaga, Ph.D.

Flatiron Research Fellow, Biophysical Modeling

Florencio Balboa Usabiaga joined the foundation in 2017 as a member of the Biophysical Modeling group. He is interested in the development of tools for fluctuating hydrodynamics and Brownian dynamics simulations. At the foundation, he works to extend these methods to explore relevant biophysical phenomena,…

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

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.

Naomi Oppenheimer, Ph.D.

Visiting Scholar

Naomi Oppenheimer was a research fellow at the Flatiron Institute in the Center for Computational Biology. Her research interests are in fluid dynamics, elasticity and the interplay between them.

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.

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.