Computer Simulation of Chemical and Biochemical Interactions

Abstract: 

Computer Simulation of Chemical and Biochemical Interactions

The Gao group is continuing their investigations in several areas, including: the dynamics and mechanism of enzymatic reactions: the development of a quantal force field, called X-Pol, for biomolecular simulations; the simulation and modeling of macromolecular assembly and diffusion in cells; and solvent effects on chemical reactions and interactions in condensed phases. The researchers’ approach is based on statistical mechanical Monte Carlo and molecular dynamics (MD) simulations, making use of combined quantum mechanical and molecular mechanical (QM/MM) potentials.

The first project area involves MD simulations of enzymatic reactions, including the demethylation reactions catalyzed by a FAD-dependent enzyme and a class of metalloenzymes employing a non-heme high-valent Iron-oxo intermediate, the final step in nucleotide UMP biosynthesis by OMP decarboxylase, and proton-coupled electron transfer processes in ribonucleotide reductase and in photosystem II. These studies will provide a deeper understanding of the reaction mechanism and the origin of catalysis. The researchers have 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 the explicit polarization (X-Pol) potential as a next-generation and quantal force field for biomolecular and materials simulations. This work represents a novel approach 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 the 2013 Nobel Prize in Chemistry

The third project is aimed at developing a simulation system to understand protein diffusion processes in cellular environment. This is a relatively new project involving methodology and software development.

The final project area focuses on development of novel computational techniques including mixed molecular orbital and valence bond (MOVB) and block-localized density functional theory (BLDFT) and applications to modeling solvent effects on SN2 reactions and the choice of geometrical and energy-gap solvent reaction coordinates in potential of mean force calculations.

A bibliography of this group's publications acknowledging MSI is attached.

Group name: 
gaoj
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