E. coli bacterium near corrugated surfaces: near-surface swimming, escape, and hydrodynamic trapping.

Bacteria often swim in complex environments where surfaces are ubiquitous and rarely flat. Surface topography and curvature can strongly affect bacterial motility, with important consequences for surface exploration, adhesion, and biofilm formation. Here, we investigate the swimming of a non-tumbling Escherichia coli bacterium near an undulating no-slip surface using hydrodynamic simulations of a detailed model bacterium. The latter is described by a rigid spherocylindrical cell body and flexible flagella modeled with the Kirchhoff rod theory, while the surrounding fluid is simulated using the method of multi-particle collision dynamics. At low curvatures of the sinusoidal surface modulations, the bacterium exhibits persistent near-surface swimming and clockwise trajectories, consistent with the known behavior near flat no-slip walls. As the curvature increases, bacteria swimming toward a ridge can escape from the surface, which we use to estimate a critical curvature where surface detachment is more likely. At larger curvatures, we find that the surface geometry promotes oscillatory swimming along the groove direction, which reduces escape opportunities and, therefore, enhances bacterial trapping. Indeed, the confinement around the groove reverses the swimming of the bacterium from clockwise to counter-clockwise, as we demonstrate by two minimal models. Thus our work highlights the importance of the three-dimensional surface topography in bacterial surface exploration.