This project began as a hobby side-project to model bacteria as active rod-shaped agents and study their migration in porous environments. Some of this work has been published in Phys. Rev. Lett. 128, 144501.

Collective Motion of Bacteria

One of the long-term goals was to investigate collective motion of bacteria in these settings. As a first step, here’s a simulation I built using the jax-md package—partly to test its cool features: