Architectures and Algorithms for Biomolecular Simulation

Many important outstanding questions in the fields of biology, chemistry, and medicine could in principle be answered through the atomic-level simulation of biologically significant molecules. Current technology and algorithms, however, fall several orders of magnitude short of the power that would be required to do so. This talk describes the state of the art in biomolecular simulation and explores the potential role of high-performance computing technologies in extending current capabilities. Efforts within our own lab to develop novel architectures and algorithms for the acceleration of molecular dynamics simulations by several orders of magnitude will be described.