Space- and Time-resolved Simulations of Processes in Biofilm Systems on a Microscale

Abstract

New experimental and analytical techniques such as confocal laser scanning microscopy (CSLM) or the use of RNA-targeted probes have provided insight into the morphology, architecture, and function of biofilm cultures. The different observations made there suggest that more attention has to be paid to a detailed study of microscale processes such as flow and transport phenomena as well as to the development of the biofilm's primary components, i.e., microbial cells and extracellular polymeric substances (EPS). For that, numerical simulations are a promising approach. However, due to the large variety of different effects and influence factors, strong multiscale characteristics with respect to both time and space, and the need for an explicit high spatial resolution in order to capture the occurring changes of the underlying geometry because of biomass growth 3D simulations have hardly been tackled so far. Actually, most existing simulation tools for biofilm systems are based on strongly simplified model assumptions that have turned out to be not valid in general. In this work, we report on the first steps towards microscale simulations of flow, transport, reactive, and growth processes in 3D biofilm geometries obtained from CLSM images of a small and defined monoculture biofilm setup. The basic framework is the finite volume CFD solver Nast++, to which transport equations (convection-diffusion in the fluid phase, diffusion-reaction in the biofilm) and the cellular automaton CAsim for capturing biomass growth are coupled. Some numerical results of realized simulations as well as strategies for an increased numerical efficiency are presented.