Atomic-resolution simulations of biomolecular motions

Many biological processes require activated transitions and thus occur on time scales that are long compared to those accessible with atomistic simulations. A number of techniques, such as transition path sampling developed by the Chandler Group at UC Berkeley, enable simulation of transitions that are rare but rapid. Many biomolecular events, however, such as the association of two viral capsid proteins, are highly diffusive and thus challenging to simulate with traditional rare event techniques.

We are working to develop more efficient methods with which to sample diffusive dynamical transitions. Although part of the motivation for developing these methods is to simulate assembly reactions, we are also working with Dorothee Kern’s group in the Brandeis University biochemistry department to study enzymatic conformational transitions.