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Research Abstracts Online
January 2009 - March 2010

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University of Minnesota Twin Cities
Institute of Technology
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 structure and interactions of proteins, the simulation of molecular transport through membrane channels, 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; developing a simulation system to understand protein diffusion processes in a cellular environment; the development of the explicit polarization potential as a next-generation and quantal force field for biomolecular and materials simulations; and development of novel computational techniques in combined QM/MM calculations 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

Kwok Siang Beh, Undergraduate Student
Maria Bohorquez, Department of Chemistry, University of St. Thomas, St. Paul, Minnesota
Alessandro Cembran, Research Associate
Jun Kyung Chung, Graduate Student
Jorge M. Estevez, Graduate Student
Yao Fan, Graduate Student
Qiang Gao, Graduate Student
Mireia Garcia-Viloca, Institute of Biotechnology and Biomedicine, Bellaterra, Spain
Francesca Guerra, Department of Chemistry, University of Calabria, Arcavacata di Reni, Italy
Jaebeom Han, Graduate Student
Michael J. Harris, Undergraduate Student
Paul Henriksen, Graduate Student
Christian Hensen, Graduate Student
Jennifer Hirschi, Research Associate
Petra Imhof, Visiting Researcher
Huitian Jiang, Research Associate
Gary S. Kedziora, Research Associate
Pinsker Yen-lin Lin, Graduate Student
Minkui Luo, Department of Biochemistry, Albert Einstein College of Medicine, Yeshiva University, Bronx, New York
Shuhua Ma, Research Associate
Dan Major, Research Associate
Sergio Marti, Graduate Student
Michael Mazack, Graduate Student
Yirong Mo, Department of Chemistry, Western Michigan University, Kalamazoo, Michigan
Kwangho Nam, Graduate Student
Sten O. Nilsson Lill, Research Associate
Jiayun Pang, Graduate Student
Apirak Payaka, Research Associate
Jingzhi Pu, Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts
Charlie Seto, Graduate Student
Lingchun Song, Research Associate
Kin-Yiu Wong, Graduate Student
Wangshen Xie, Graduate Student
Jiangwei Yao, Undergraduate Student
Yong Tiger Zhang, Department of Biochemistry, Albert Einstein College of Medicine, New York, New York
Yan Zhou, Graduate Student