Weitao Yang

Department of Chemistry

Duke University, Durham, NC

Simulation of Structures and Functions of Biological Systems with Linear-Scale and Multi-Scale Approaches

The development of linear-scaling and multi-scale methodologies and their applications to biological systems will be presented. These methods extend the realm of quantum mechanical theory to complex systems, which are otherwise beyond the reach of conventional approaches. Simulations of the complex mechanics of polymers in single-molecule atomic force microscopy experiments (AFM) and simulations of chemical reactions in enzymes will be featured.

References:

Zhenyu Lu, Wieslaw Nowak, Gwangrog Lee, Piotr E. Marszalek, and Weitao Yang. Complex mechanics of sugar rings in water revealed by quantum mechanics simulations. J. Am. Chem. Soc., 126: 9033, 2004.

G. Andres Cisneros, Haiyan Liu, Yingkai Zhang, and Weitao Yang. Ab initio qm/mm study shows that there is no general acid in the reaction catalized by 4?oxalocrotonate tautomerase. J. Am. Chem. Soc., 125: 10384, 2003.

Gerardo A. Cisneros, Min Wang, Peter. Silinski, Michael C. Fitzgerald, and Weitao Yang. The protein backbone makes important contributions to 4-oxalocrotonate tautomerase enzyme catalysis: Understanding from theory

and experiment. Biochemistry, 43: 6885, 2004.

Zhenyu Lu and Weitao Yang. Reaction path potential for complex systems derived from ab initioqm/mm calculations. J. Chem. Phys., 121: 89, 2004.

Mingliang Wang, Zhenyu Lu, and Weitao Yang. Transmission coefficient calculation for proton transfer in triosephosphate isomerase on the reaction path potential generated from ab initio qm/mm calculations. J. Chem. Phys., 121: 101, 2004.