Simulation of Bacterial Motion in Sterically Complex Environments

Abstract

Many species of bacteria navigate complex and heterogeneous environments to search for metabolic resources and avoid toxins. Common among such complexities is steric structure – solid objects whose surface curvature alters bacterial trajectories upon impact. In previous experiments, we characterized scattering of bacteria from vertical pillars of different radii, which provides the basis for understanding how impact with a solid, curved object alters bacterial motion. However, it remains poorly understood how multiple interactions affect bacterial trajectories and whether distinct object curvatures or length-scales of separation between steric objects have qualitatively distinct effects on bacterial motion. We address this question using agent-based computer simulations of cells moving within 2D environments. Each environment presents simulated cells with steric objects (i.e. circular pillars) of radius 8.3µm and a controlled separation between pillars of µm, where  is a parameter of the simulation. Cells then diffuse through this environment, scattering with pillars they encounter. By measuring the mean squared displacement (MSD) of the ensemble of trajectories in time for different values of , we are able to quantify precisely how the length-scales of separation between steric structures affect bacterial trajectories. These MSD measurements will also allow us to compare our results with future experimental work. Ultimately, we hope that our results may contribute to a more realistic model of the behavior of motile cells in natural environments such as soils or a mammalian gut.