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Research Abstracts Online
January 2010 - March 2011

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University of Minnesota Twin Cities
College of Science and Engineering
Department of Chemistry

PI: Jiali Gao, Fellow

Computer Simulation of Chemical and Biochemical Interactions

The Gao group is continuing their multi-faceted research concerning the dynamics and mechanism of enzyme reactions, the development of quantal force fields for biomolecular systems, the simulation and modeling of molecular assembly and diffusion in cells, and solvent effects on chemical reactions and interactions in condensed phases. Their approach is based on statistical Monte Carlo and MD simulations, making use of combined quantum mechanical and molecular mechanical (QM/MM) potentials.

The group is involved in several project areas. These include: MD simulations of enzymatic reactions, including phosphate hydrolysis reactions by dehalogenases for bioremediation of contaminated water, the decarboxylation reactions of L-dopa to dopamine, the demethylation reactions involved in histone modification, and the final step in nucleotide UMP biosynthesis by OMP decarboxylase; development of the explicit polarization (X-Pol) potential as a next-generation and quantal force field for biomolecular and materials simulations, which represents a novel approach to describe molecular systems and to determine the potential energy surface; developing a simulation system to understand protein diffusion processes in a cellular environment; and 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.

Group Members

Peng Bao, Research Associate
Kwok Siang Beh, Undergraduate Student
Alessandro Cembran, Research Associate
Jorge M. Estevez, Graduate Student
Jaebeom Han, Graduate Student
Jennifer Hirschi, Research Associate
Miho Isegawa, Research Associate
Pinsker Yen-lin Lin, Graduate Student
Shuhua Ma, Research Associate
Dan T. Major, Research Associate
Michael J. Mazack, Graduate Student
Yirong Mo, Department of Chemistry, Western Michigan University, Kalamazoo, Michigan
Kwangho Nam, Graduate Student
Sten O. Nilsson Lill, Research Associate
Apirak Payaka, Research Associate
Makenzie Provorse, Graduate Student
Jingzhi Pu, Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts
Charlie T. Seto, Graduate Student
Lingchun Song, Research Associate
Yingjie Wang, Graduate Student
Supachai Wanprakhon, Staff
Kin-Yiu Wong, Graduate Student
Wangshen Xie, Graduate Student
Yong Tiger Zhang, Department of Biochemistry, Albert Einstein College of Medicine, New York, New York
Peng Zhang, Graduate Student
Yan Zhou, Graduate Student