We develop new tools to analyze interactions between solvated (bio-)molecules and their solvent, specifically water. Our 3D-2PT software package uses classical molecular dynamics simulations to generate 3D maps of local water structure, dynamics, and contributions to the solvation free energy. We use this information to study water-mediated forces in protein complexes and driving forces in novel bioanalytical methods such as protein dielectrophoresis.
Vibrations & Dynamics
Anharmonic low-frequency vibrations are thermally excited at room temperature and thus determine many properties of biomolecules. So far our understanding of these often collective motions has been limited by harmonic approximations in theoretical models. We develop the FRESEAN mode analysis, which eliminates the need for any approximations in the analysis of molecular vibrations and provides unique insights into the dynamics of complex molecules.
Many experiments are performed on proteins in dilute solution. However, the relevant physiological environment for protein function is the intracellular medium, which boasts a mass concentration of biomolecules on the order of 30-50%. We develop new Monte Carlo simulation tools to allow computer simulations of such complex biomolecular systems in atomistic detail at moderate computational costs.
National Science Foundation
EAGER: Desyn-C3 1844327