Simulating Mechanical Response of Bacterial Biofilms
In nature bacteria have a dual mode of existence. Bacteria exist either in individual free-floating (or planktonic) form or as sessile communities on moist surfaces, known as biofilms. The biofilm mode of existence has been found to be the dominant one for bacteria in nature (more than 99%). While these biofilms are helpful in natural geochemical cycling of essential elements and nutrients in nature, they are a nuisance in variety of engineered systems. The scientific community woefully lacks the expertise to be able to control bacterial biofilms. Therefore, the Hozalski research group studies the mechanical properties of bacterial biofilms, devising strategies to measure the biofilm properties and performing related simulations in order to get a better understanding of biofilm control. Specifically, they are working with biofilm cohesive strength data collected in their laboratory and applying it in real-world systems (such as water distribution pipelines) to understand the stability of biofilms in engineered systems. To this end, they conduct Monte Carlo simulations in MATLAB to predict aggregate response of biofilms under various shear conditions in pipelines. Specifically they are looking at biomass eroded as a function of wall shear stress for different biofilm thicknesses, and conducting time-lapse studies under different flow conditions.
Another aspect of this research with involves conducting FEM-based Abaqus simulations of micro-cantilever test to determine cohesive strength and other properties. While the experiments assume homogenous stress and strain fields along with cylindrical shape assumption about the biofilm specimen, the FEM modeling allows the researchers to test the validity of their assumptions and derive realistic stress and strain fields with different biofilm specimen shapes in the micro-cantilever test. Many of these simulations in MATLAB and Abaqus are extremely complicated and time-consuming, requiring the use of MSI resources.