My research is concerned with the dynamics of large biomolecules and in particular with protein dynamics, folding, and misfolding. Novel simulation and theoretical methods are developed as needed to address specific problems. A strong emphasis is placed on making a connection with experiment, both in using experimental data to help improve simulation methodology or sampling, and simulations as a tool to assist the interpretation of results.
Recent work has focused on the following:
- the optimization of protein force fields using empirical data for peptides and macromolecules in solution;
- interpretation of single-molecule fluorescence or pulling experiments using simulation and theory;
- coarse-grained master equations as a tool for interpreting peptide dynamics in simulations;
- diffusion models of protein folding;
- the binding mechanism of intrinsically disordered proteins;
- the influence of molecular chaperonins on folding and misfolding;
- the mechanism of substrate transport in hydrogenase enzymes; and
- methods for identifying cryptic binding pockets in proteins.