Lianqing Zheng, Ph.D.

Research Assistant Professor
Dr. Wei Yang’s Group
Office – KLB 408
Email – lzheng@fsu.edu

RESEARCH INTERESTS

My current research focuses on the methodology development for free energy simulations for biomolecular systems. I am particularly interested in protein-ligand/protein-protein binding affinity predictions, protein functional conformation transitions, and protein folding. With our new method (orthogonal space tempering), we are able to use molecular dynamics simulations to achieve long-time scale events in biomolecules through actively overcoming both explicit and implicit barriers in the systems; this, in turn, allows us to achieve robust, accurate, and precise free energy calculations.

EDUCATION

Ph.D. (2004) Mechanical Engineering, University of Rochester
B.S. (1998) Applied Mechanics, University of Science and Technology of China

SELECTED PUBLICATIONS

• Zheng, L., & Yang, W. (2012). Practically efficient and robust free energy calculations: Double-integration orthogonal space tempering. Journal of Chemical Theory and Computation, 8(3), 810-823.
• Lv, C., Zheng, L., & Yang, W. (2012). Generalized essential energy space random walks to more effectively accelerate solute sampling in aqueous environment. Journal of Chemical Physics, 136(4), 044103.
• Al-Hariri, L. A., Zheng, L., Yang, W., & Schlenoff, J. B. (2011). Thermal elimination of precursors to poly(phenylenevinylene) with a macrocounterion versus a small sounterion: A coordinated experimental and simulation study. Macromolecules, 44(17), 6663-6668.
• Riera, T. V., Zheng, L., Josephine, H. R., Min, D., Yang, W., & Hedstrom, L. (2011). Allosteric activation via kinetic control: potassium accelerates a conformational change in IMP dehydrogenase. Biochemistry, 50(39), 8508-8518.
• Min, D., Zheng, L., Harris, W., Chen, M., Lv, C., & Yang, W. (2010). Practically efficient QM/MM alchemical free energy simulations: The orthogonal space random walk strategy. Journal of Chemical Theory and Computation, 6(8), 2253-2266.
• Zheng, L., Chen, M., & Yang, W. (2009). Simultaneous escaping of explicit and hidden free energy barriers: Application of the orthogonal space random walk strategy in generalized ensemble based conformational sampling. Journal of Chemical Physics, 130(23), 234105.
• Zheng, L., Chen, M., & Yang, W. (2008). Random walk in orthogonal space to achieve efficient free-energy simulation of complex systems. Proceedings of the National Academy of Sciences of the United States of America, 105(51), 20227-20232.
• Zheng, L., Carbone, I., Lugovskoy, A., Berg, B., & Yang, W. (2008). A hybrid recursion method to robustly ensure convergence efficiencies in the simulated scaling based free energy simulations. Journal of Chemical Physics, 129(3), 034105.
• Zheng, L., & Yang, W. (2008). Essential energy space random walks to accelerate molecular dynamics simulations: Convergence improvements via an adaptive-length self-healing strategy. Journal of Chemical Physics, 129(1), 014105.
• Zheng, L., & Yang, W. (2008). On the simulated scaling based free energy simulations: Adaptive optimization of the scaling parameter intervals. Journal of Chemical Physics, 129(12), 124107.
• Zheng, L., An, Q., Xie, Y., & Luo, S. N. (2007). Homogeneous nucleation and growth of melt in copper. Journal of Chemical Physics, 127, 164503.
• Zheng, L., Luo, S. N., & Thompson, D. L. (2006). Molecular dynamics simulations of melting and the glass transition of nitromethane. Journal of Chemical Physics, 124(15), 154504.
• Zheng, L., Lambropoulos, J. C., & Schmid, A. W. (2005). Molecular dynamics study of UV-laser-induced densification of fused silica. II. Effects of laser pulse duration, pressure, and temperature, and comparison with pressure-induced densification. Journal of Non-crystalline Solids, 351, 3271-3278.
• Zheng, L., Lambropoulos, J. C., & Schmid, A. W. (2004). UV-laser-induced densification of fused silica: a molecular dynamics study. Journal of Non-crystalline Solids, 347, 144-152.