Theory of Biomolecular Structure and Dynamics

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New theoretical and computational methods for computer simulation studies of biomolecular systems will be developed. These methods will be applied to help explain the activity of several systems of chemical and biological interest. More specifically, effective potential energy functions that are more accurate than those in common use for molecular dynamics simulations will be created by explicit inclusion of electronic polarization. Other potential functions that are more approximate but that can be evaluated rapidly will be created by implicit treatment of solvent. Applications will be made to molecular recognition in host-receptor systems, to the dynamics of enzyme-substrate interactions, and to the kinetics of enzymatic reactions. %%% The significance of the work lies in the provision of new tools for designing drugs, enzymes, ion channels, and other molecules for practical applications; in the deepening understanding of the activity of biological molecules; and in the preparation of young scientists for research careers in this emerging field.