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Research Abstracts Online
January 2008 - March 2009

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 study of molecular transport through membrane channels and the structure of membrane proteins; 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

Cristobal Alhambra, AstraZeneca Pharmaceuticals LP, Wilmington, Delaware
Kyoungrim Byun, Life Science Research Center, SK Chemicals, Republic of Korea
Alessandro Cembran, Research Associate
Jun Kyung Chung, Graduate Student
Jorge M. Estevez, 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
Pinsker Yen-lin Lin, Graduate Student
Minkui Luo, Department of Biochemistry, Albert Einstein College of Medicine, Yeshiva University, Bronx, New York
Yirong Mo, Department of Chemistry, Western Michigan University, Kalamazoo, Michigan
Suwipa Saen-oon, Department of Physiology and Biophysics, Albert Einstein College of Medicine, Yeshiva University, Bronx, New York
Lingchun Song, Supercomputing Institute Research Scholar
Kin-Yiu (Kiniu) Wong, Research Associate
Wangshen Xie, Graduate Student
Yan Zhou, Graduate Student