Studies of bacteria motility in environments with flowing fluids have shown their ability to swim against fluid flows. Concerningly, this enables them to infiltrate vital areas such as medical devices, filtration systems, and biological tissues. Often, these settings consist of complex arrangements of pores and obstacles, where local flow variations strongly influence bacterial transport. Understanding this behavior is essential for predicting and controlling contamination and infection.

Physical experiments on bacterial systems, while informative, are limited by fabrication complexity, material costs, and waiting time. Computational modeling offers a convenient alternative, enabling rapid exploration of varied geometries and flow fields with virtually unlimited size and complexity. Here, we present the process of building and interpreting simulations examining:

(I) bacterial density transport in circular pillar arrays under varying flow strengths, (II) trajectory responses to flow direction in triangular porous media, (III) and motility patterns in pillar arrays with systematically varied pore radius and separation.

These results provide insight into how geometry and flow interact to guide bacterial motion in porous environments all without experimenting on physical systems.