Departmental WebPage

Dr. Wei Yang
Faculty

Dr. Wei Yang

Associate Professor

Ph.D.(2001) State University of New York at Stony Brook

Contact Information
Email:yang [at] sb.fsu.edu
Office:850.645.6884
   Lab:850.645.6885
Location Information
Office:418 KLB
Lab:418 KLB
Chemistry Research
 Biochemistry
Research Website
2 Graduate; 0 Postdocs

Research Interest

Although experimental biochemical & biophysical measurements have been developed rapidly, understanding and designing complex biomolecular systems is still quite challenging. Computer simulation based on captured biopolymer structures (by X-ray, NMR etc.) can be an essential complementary technique to catalyze our exploration of microscopic world. Due to the complexity of biological systems in both length scale and time scale, biomolecular simulation need to be both functional and efficient; facing this challenge, my research interest targets the development and application of state-of-art multi-spectrum atomistic simulation techniques including QM/MM calculation, free energy simulation, conformation path simulation, motion analysis etc., to understand the hidden nature of complex biological phenomena. Specifically, my research program includes three directions:

1. First principle based protein and ligand design;

2. Simulation study of multi-timescale biochemical & biophysical events such as DNA repair, motion- coupled biomolecular recognition, and enzymatic reactions; (Figure below shows one of systems studied previously)

3. Development of simulation techniques to describe complex systems and enhance efficiency of biomolecular simulations.

Faculty Interview




Publications

Zheng, L. and Yang, W.* Practically efficient and robust free energy calculations: Double integration orthogonal space tempering. J. Chem. Theor. Comput. 2011, in press
Riera, T. V., Zheng, L. Q., Josephine, H. R., Min, D., Yang, W.*, and Hedstrom, L.* Allosteric activation via kinetic control: Potassium accelerates a conformational change in IMP Dehydrogenase. Biochemistry 2011, 50:85088518
Min, D. H., Chen, M. E., Zheng, L. Q., Jin, Y. H., Schwartz, M. A., Sang, Q. X. A., and Yang, W.* QM/MM molecular dynamics sampling in explicit environments via an orthogonal space random walk based strategy. J. Phys. Chem. B 2011, 115, 3924-3935
Lee, S., Chen, M., Yang, W.*, and Richards, N. G. J.* Sampling Long Timescale Protein Motions: OSRW Simulation of Active Site Loop Conformational Free Energies in Formyl-CoA:Oxalate CoA Transferase. J. Am. Chem. Soc. 2010, 132, 7252-7253
Zheng, L., Chen, M., and Yang, W.* Random walk in orthogonal space to achieve efficient free energy simulation of complex systems. Proc. Natl. Acad. Sci. USA 2008, 51, 20227-20232