Laboratory for Computational Life Sciences (LCLS) Left graph courtesy of Structure-Based Drug Design group, Pfizer Inc.; Generated using RasMol.

Our research focuses on application of high-performance computational methods to biomolecular computing, with a special interest on parallel, multiscale algorithms for molecular dynamics. Simulations of biomolecules are an area of great potential, both to understand cellular processes at an atomic level, and to drive important applications such as drug design. One difficulty is the size of the simulations needed (hundreds of thousands of atoms) and the fact that stability of the numerical algorithms severely limits the step size used to solve the systems of ordinary differential equations that arise in these simulations. We attempt to construct both better algorithms that are able to take longer time steps and efficient parallel implementations that exploit the multiple time and space scales present present in biological systems. These methods are driven by specific applications, such as limb formation, protein folding, and drug design.