Simulating biofilm initiation and growth in porous media flow

Biofilms are colonies of sessile bacteria attached to surfaces. They are often encountered in confined geometries where also an external flow is present. Biofilms can be detrimental, e.g. in filtration systems, or beneficial, e.g. for remediation of brittle materials by microbially induced calcite precipitation (MICP). In any case, the interplay between bacterial motility, biofilm growth and external flow in confined geometries needs to be understood, starting at the scale of individual cells.

We present a bacterial model based on coupling single cells to a surrounding flow. Bacteria are simulated as molecular dynamics particles, the fluid dynamics problem is solved using the lattice Boltzmann method. The two algorithms are connected via a point-friction coupling.
We are able to determine likely locations for biofilm initiation by explicitly taking into account bacterial motility. During the biofilm growth phase, the external flow field determines the shape of the biofilm. On the other hand, the growing biofilm restricts the fluid flow.
By applying our model to a simple porous structure, we show how flow paths can be altered or even blocked.