Optimal motility strategies for self-propelled agents to explore porous media

Abstract

Micro-robots for, e.g., biomedical applications, need to be equipped with motility strategies that enable them to navigate through complex environments. Inspired by biological microorganisms we investigate motility patterns such as run-and-reverse, run-and-tumble or run-reverse-flick applied to active rod-like particles in silico. We investigate their capability to efficiently explore disordered porous environments with various porosities and mean pore sizes ranging down to the scale of the active particle. By calculating the effective diffusivity for the different patterns, we can predict the optimal one for each porous sample geometry. We find that providing the agent with the ability to sense position for a certain time and to make a decision based on its observation yields a motility pattern outperforming the biologically inspired patterns for all investigated porous samples.

Influence of bacterial swimming and hydrodynamics on infection by phages

“…Our model for the bacterium builds on previous studies of microswimmers [34–37], extended to also explicitly consider the cell and flagellum geometry. Specifically, we represent the bacterium by a rigid collection of three different types of particles denoted by τ to model the rod-like shape of flagellated bacteria like E. coli, B. subtilis , and S. enterica .…”

“…Each simulation is repeated N ensemble times with different seeds, i.e., different initial conditions and noise realisations, to obtain the standard error of the mean of the quantities reported below. We choose N ensemble ≥ 5, the exact numbers for each reported result can be found in the data set [42] that accompanies this work.…”

“…( 1)-( 12) numerically using the development version of the ESPResSo simulation package [39] with the waLBerla [40,41] library for lattice Boltzmann hydrodynamics. Exact software versions as well as our custom code are freely available; details are provided in [42].…”

Influence of bacterial swimming and hydrodynamics on attachment of phages

“…Exact software versions as well as our custom code are freely available; details are provided in ref. 43.…”

A novel model for biofilm initiation in porous media flow

“…The data that support the findings of this study as well as the source code are publicly available. 48…”