SUPER COMPUTER SIMULATIONS OF LIQUIDS & PROTEINS

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The research in my laboratory is centered around computer simulations of liquids and proteins. The simulations are being used to gain a better understanding of how solvation affects a variety of chemical and biochemical processes. The current focus of our liquid state simulations is twofold: (a) the development of algorithms for very large liquid state simulations on massively parallel computers which include novel methods for treating long range interactions, and (b) simulations of polarization effects. There are four ongoing protein simulations projects in my laboratory: (a) the calculation of pKa shifts in proteins from simulations with explicit solvent models, (b) characterization of the thermodynamic and structural properties of the protein solvation shell, (c) computer simulations of protein-ligand interactions, and (d) determination of protein structure and dynamics from simulations and NMR data. This is an umbrella proposal for all the projects in my laboratory.