  Biofilms are bacterial aggregates encased in a self-produced polymeric matrix
which attach to moist surfaces and are extremely resistant to chemicals and
antibiotics. Recent experiments show that their structure is defined by the
interplay of elastic deformations and liquid transport within the biofilm, in
response to the cellular activity and the interaction with the surrounding
environment. We propose a poroelastic model for elastic deformation and liquid
transport in three dimensional biofilms spreading on agar surfaces. The motion
of the boundaries can be described by the combined use of Von Karman type
approximations for the agar/biofilm interface and thin film approximations for
the biofilm/air interface. Bacterial activity informs the macroscopic
continuous model through source terms and residual stresses, either
phenomenological or derived from microscopic models. We present a procedure to
estimate the structure of such residual stresses, based on a simple cellular
automata description of bacterial activity. Inspired by image processing, we
show that a filtering strategy effectively smooths out the rough tensors
provided by the stochastic cellular automata rules, allowing us to insert them
in the macroscopic model without numerical instability.
