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.

We are developing a suite of tools that enable us to understand adsorbate-surface interactions and quantify the energies of elementary reaction steps. This information is used to simulate the vast array of competing elementary reactions steps on the surface, follow the temporal surface structure, and model material performance. We can then tie tunable atomic structural and compositional changes to the overall process chemistry and performance. This provides a framework to manipulate the atomic scale features, such as defect sites, alloys, and solvents, toward the design of new materials. The computational tools that we are using/developing range from ab initio density functional theory and ab initio molecular dynamics methods to calculate the detailed electronic structure to first-principles based kinetic Monte Carlo simulation in order to follow the reaction kinetics.

The most important problem in the atomic-level modeling of polymers, macromolecules, and other complicated dense fluids is our ability to accurately measure and observe all the structural and conformational sampling in physical phenomena. Without sufficient physical sampling, it is impossible even to verify if models are sufficiently faithful to experiment, let alone explore behavior of either long time scales or of larger molecular systems.  It is currently only possible to simulate the equivalent of a few microseconds of all but the smallest biological systems, with some heroically expensive extensions to milliseconds with large supercomputers.  We are making important contributions to efficient analysis of free energy calculations and other thermophysical and structural data.