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

November 1, 2019

Lattices of Hydrodynamically Interacting Flapping Swimmers

A. U. Oza, L. Ristroph, M. Shelley

Fish schools and bird flocks exhibit complex collective dynamics whose self-organization principles are largely unknown. The influence of hydrodynamics on…

Physical Review X

October 25, 2019

Relating Rheotaxis and Hydrodynamic Actuation using Asymmetric Gold-Platinum Phoretic Rods

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

We explore the behavior of micron-scale autophoretic Janus (Au / Pt) rods, having various Au / Pt length ratios, swimming…

Physical Review Letters

October 3, 2019

Rotating Membrane Inclusions Crystallize Through Hydrodynamic and Steric Interactions

N. Oppenheimer, D. Stein, M. Shelley

We show that rotating membrane inclusions can crystallize due to combined hydrodynamic and steric interactions. Alone, steric repulsion of unconfined…

Physical Review Letters

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

December 2019

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

January 2020

06 Mon
- Meeting 10:00 AM - 12:00 PM
  Biophysical Modeling Group Meeting
13 Mon
- Meeting 10:00 AM - 12:00 PM
  Biophysical Modeling Group Meeting
20 Mon
- Meeting 10:00 AM - 12:00 PM
  Biophysical Modeling Group Meeting
27 Mon
- Meeting 10:00 AM - 12:00 PM
  Biophysical Modeling Group Meeting

February 2020

03 Mon
- Meeting 10:00 AM - 12:00 PM
  Biophysical Modeling Group Meeting
10 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.