Molecular Dynamics Simulation of Chemical and Biochemical Processes

Abstract: 

Molecular Dynamics Simulation of Chemical and Biochemical Processes

The Gao group is continuing their investigations in several areas, including the interplay between protein dynamics and mechanism of enzymatic reactions; the development of novel quantum mechanical methods for studying energy and charge transfer processes in chemical and biological macromolecular systems; the simulation and modeling of vibrational Stoke shifts of probe molecules in proteins; and solvent effects on chemical reactions and interactions in condensed phases.

The group's approach is based on statistical mechanical Monte Carlo and molecular dynamics simulations, making use of combined quantum mechanical and molecular mechanical (QM/MM) potentials. The first project area involves molecular dynamics simulations of enzymatic reactions including the demethylation reactions catalyzed by an FAD-dependent enzyme and metalloenzymes, the final step in nucleotide UMP biosynthesis by OMP decarboxylase, thiamine-dependent enzymes, and proton-coupled electron transfer (PCET) processes in ribonucleotide reductase and in photosystem II. These studies will provide a deeper understanding of the reaction mechanism and the origin of catalysis. In addition, the group has initiated a study of the ultraviolet-8 activated dimer dissociation of UVR8, which triggers cellular response in plants.

The second project aims at the development of multistate density functional theory for charge transfer, and the explicit polarization (X-Pol) potential as a next-generation and quantum force field for biomolecular and materials simulations. These methods represents novel approaches to describe molecular systems and to determine the potential energy surface, and it goes beyond the so-called combined QM/MM approach, which was awarded by the 2013 Nobel Prize in Chemistry.

The third project is aimed at developing a simulation system to understand the electrostatic environment inside of an enzyme's active site.

The final project area focuses on development of novel computational techniques including mixed molecular orbital and valence bond (MOVB) and an X-Pol based reactive force field and applications to modeling solvent effects on a variety of chemical reactions and reaction networks.

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Group name: 
gaoj