Simulation & Complex Systems Research

Monte Carlo methods can be used to for predicting how bacteria that have been released into the groundwater supply will spread to nearby drinking water sources. Pictured here is a path traced out by a swimming bacterium as it navigates its way through a maze of sand grains.  We also model the fluid flow and bacterial swimming paths as they migrate towards a chemical signal within a microfluidic device, and then compared to direct experimental observations.

All-atom molecular dynamics simulations are used to study the structure and dynamics of molecular interactions; specifically, the analyses often include intra- and inter-molecular conformational sampling of proteins, diffusional association of protein molecules within a solvated system, and recognition events (i.e. conformational rearrangement and binding/unbinding events) of a biomolecular system. The picture illustrates a designer protein engineered to undergo temperature-dependent conformational changes inside a water box. We apply this computational approach, alongside experimentation, in the design of engineered extracellular matrix proteins for constructing stimuli-responsive and biocompatible materials in drug delivery, tissue engineering, and regenerative medicine.