Chemotactic clusters in confined run-and-tumble bacteria: a numerical investigation.

We present a simulation study of pattern formation in an ensemble of chemotactic run-and-tumble bacteria, focussing on the effect of spatial confinement, either within traps or inside a maze. These geometries are inspired by previous experiments probing pattern formation in chemotactic strains of E. coli under these conditions. Our main result is that a microscopic model of chemotactic run-and-tumble particles which themselves secrete a chemoattractant is able to reproduce the main experimental observations, namely the formation of bacterial aggregates within traps and in dead ends of a maze. Our simulations also demonstrate that stochasticity plays a key role and leads to a hysteretic response when the chemotactic sensitivity is varied. We compare the results of run-and-tumble particles with simulations performed with a simplified version of the model where the active particles are smooth swimmers which respond to chemotactic gradients by rotating towards the source of chemoattractant. This class of models leads again to aggregation, but with quantitative and qualitative differences in, for instance, the size and shape of clusters.