A microscale model of bacterial swimming, chemotaxis and substrate transport

In this paper, we introduce a mathematical and computational model at the microscale level of bacterial motility and chemotaxis coupled with the advection and diffusion of a biologically reacting substrate. The hydrodynamic interaction of a small bacterial population is explicitly modelled through the use of discrete representations of individual microbes. We use the immersed boundary method to couple microbial motion and the advection-diffusion of substrate with the full incompressible Navier-Stokes equations. Simulations using a preliminary two-dimensional model are presented, demonstrating the mutual dependence through the fluid media of several swimming bacteria. A run and tumble mechanism is introduced for simulating the chemotaxis of swimming bacteria.