Viscoelastic Properties of Bacterial Biofilms Using Coarse-Grained Molecular Dynamics Simulations

Bacterial biofilms are aggregates of bacteria surrounded by polymeric extracellular matrix (ECM) that colonize biotic and abiotic surfaces.  Primarily composed of polysaccharides, ECM plays a multifunctional role throughout the lifecycle of the biofilm by supporting the bacterial colony through a three-dimensional structural scaffold. Viscoelsatic properties of ECM are crucial in supporting the biofilm because although ECM is mechanically resistant but it tends to fragment when subjected to shear stress. To calculate the viscoelastic properties, we have developed a systematic framework for the hierarchical computational modeling of common extracellular bacterial polysaccharide-Dextran. Based on our initial atomistic modeling, we have developed a coarse grained methodology derived from the MARTINI model that allows for four-to-one mapping of the heavy atoms to a single interaction center. Structural properties such as persistence length, radial distribution functions, and radius of gyration have been used to benchmark the coarse grained model against the all-atom system. The coarse grained system has been used to calculate structural and the dynamical properties such as end-to-end autocorrelation function, relaxation times, stress and elastic modulus of polysaccharide matrix. The characterization of the physical and mechanical properties of these polysaccharides is being used to understand the dynamics in the flow-induced fragmentation process of the biofilms.    

This financial support for this research project has been provided by the National Science Foundation under grant PHYS-1049489, and the computational resources were provided in part by the Brookhaven National Laboratory.