Variable viscosity and density biofilm simulations using an immersed boundary method, part II: Experimental validation and the heterogeneous rheology-IBM

The goal of this work is to develop a numerical simulation that accurately captures the biomechanical response of bacterial biofilms and their associated extracellular matrix (ECM). In this, the second of a two-part effort, the primary focus is on formally presenting the heterogeneous rheology Immersed Boundary Method (hrIBM) and validating our model against experimental results. With this extension of the Immersed Bounadry Method (IBM), we use the techniques originally developed in Part I, (Hammond et al. [15]) to treat the biofilm as a viscoelastic fluid possessing variable rheological properties anchored to a set of moving locations (i.e., the bacteria locations). We validate our modeling approach from Part I by comparing dynamic moduli and compliance moduli computed from our model to data from mechanical characterization experiments on Staphylococcus epidermidis biofilms. The experimental setup is described in Pavlovsky et al. (2013) [22] in which biofilms are grown and tested in a parallel plate rheometer. Matlab code used to produce results in this paper will be available at https://github.com/MathBioCU/BiofilmSim.