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New experimental and analytical techniques like 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 the microscale
processes like flow and transport phenomena as well as to the
development of the bofilm'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
due to the need for an explicit high spatial resolution in order to
capture the occurring changes of the underlying geometry because of
biomass growth, for example, 3D simulations have hardly been tackled
so far. Actually, most existing simulation tools for biofilm systems
are based on strongly simplified model assumptions that turned out
to be not valid in general.
In this work, we report on 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.
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