Zheng, Lianqing

Lianqing Zheng, Ph.D.

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



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.


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


  • 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.