Bacteria often form biofilms in porous environments where an external flow is present, such as soil or filtration systems. To understand the initial stages of biofilm formation, one needs to study the interactions between cells, the fluid and the confining geometries. Here, we present an agent based numerical model for bacteria that takes into account the planktonic stage of motile cells as well as surface attachment and biofilm growth in a lattice Boltzmann fluid. In the planktonic stage we show the importance of the interplay between complex flow and cell motility when determining positions of surface attachment. In the growth stage we show the applicability of our model by investigating how external flow and biofilm stiffness determine qualitative colony morphologies as well as quantitative measurements of, e.g., permeability.
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