  We study the transport of bacteria in a porous media modeled by a square
channel containing one cylindrical obstacle via molecular dynamics simulations
coupled to a lattice Boltzmann fluid. Our bacteria model is a rod-shaped rigid
body which is propelled by a force-free mechanism. To account for the behavior
of living bacteria, the model also incorporates a run-and-tumble process. The
model bacteria are capable of hydrodynamically interacting with both of the
channel walls and the obstacle. This enables the bacteria to get reoriented
when experiencing a shear-flow. We demonstrate that this model is capable of
reproducing the bacterial accumulation on the rear side of an obstacle, as has
recently been experimentally observed by [G. L. Mino, et al., Advances in
Microbiology 8, 451 (2018)] using E.coli bacteria. By systematically varying
the external flow strength and the motility of the bacteria, we resolve the
interplay between the local flow strength and the swimming characteristics that
lead to the accumulation. Moreover, by changing the geometry of the channel, we
also reveal the important role of the interactions between the bacteria and the
confining walls for the accumulation process.
