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Fangqiang Zhu Ph.D.
Assistant Professor, Physics
2004 Ph.D., Phyiscs, University of Illinois at Urbana-Champaign
2003 M.S., Computer Science, University of Illinois at Urbana-Champaign
1999 M.S., Phyiscs, Tsinghua University, China
1997 B.S., Physics, Tsinghua University, China
My general research interest lies in theoretical and computational biophysics. Throughout my scientific career, my research activities include simulations of nanotubes, modeling of G-protein coupled receptors, algorithm design in chemoinformatics, numerical methods for free energy calculations, as well as scientific software development. Particularly, a main theme in my past and current research is the study of membrane proteins such as channels and transporters.
Hao Sha and Fangqiang Zhu. Parameter optimization for interaction between C-terminal domains of HIV-1 capsid protein. Journal of Chemical Information and Modeling, 57:1134-1141, 2017.
Hamed Meshkin and Fangqiang Zhu. Thermodynamics of protein folding studied by umbrella sampling along a reaction coordinate of native contacts. Journal of Chemical Theory and Computation, 13:2086-2097, 2017.
Hyun Deok Song and Fangqiang Zhu. Finite temperature string method with umbrella sampling: application on a side chain flipping in Mhp1 transporter. The Journal of Physical Chemistry B, 121:3376-3386, 2017.
Fangqiang Zhu. Calculating transition rates from durations of transition paths. The Journal of Chemical Physics, 146:124128, 2017.
Jaekyun Jeon, Xin Qiao, Ivan Hung, Alok K. Mitra, Ambroise Desfosses, Daniel Huang, Peter L. Gor'kov, Rebecca C. Craven, Richard L. Kingston, Zhehong Gan, Fangqiang Zhu, and Bo Chen. Structural model of the tubular assembly of the Rous sarcoma virus capsid protein. Journal of the American Chemical Society, 139:2006-2013, 2017.
Fangqiang Zhu and Bo Chen. Monte Carlo simulations of HIV capsid protein homodimer. Journal of Chemical Information and Modeling, , 55:1361-1368, 2015.
Hyun Deok Song and Fangqiang Zhu. Conformational changes in two inter-helical loops of Mhp1 membrane transporter. PLoS One, 10:e0133388, 2015.
Fangqiang Zhu and Matthias Clauss. Evaluating membrane affinity by integrating protein orientations. Journal of Molecular Graphics and Modelling, 54:141-147, 2014.
Fangqiang Zhu. How does water pass through a sugar transporter? Biophysical Journal, 106:1229-1230, 2014.
Hyun Deok Song and Fangqiang Zhu. Conformational dynamics of a ligand-free adenylate kinase. PLoS One, 8:e68023, 2013.
Yingting Liu and Fangqiang Zhu. Collective diffusion model for ion conduction through microscopic channels. Biophysical Journal, 104:368-376, 2013.
Fangqiang Zhu and Gerhard Hummer. Drying transition in the hydrophobic gate of the GLIC channel blocks ion conduction. Biophysical Journal, 103:219-227, 2012.
Fangqiang Zhu and Gerhard Hummer. Theory and simulation of ion conduction in the pentameric GLIC channel. Journal of Chemical Theory and Computation, 8:3759-3768, 2012.
Fangqiang Zhu and Gerhard Hummer. Convergence and error estimation in free energy calculations using the weighted histogram analysis method. Journal of Computational Chemistry, 33:453-465, 2012.
Fangqiang Zhu and Gerhard Hummer. Pore opening and closing of a pentameric ligand-gated ion channel. Proceedings of the National Academy of Sciences USA (edited by J.-P. Changeux), 107:19814-19819, 2010.
Fangqiang Zhu and Gerhard Hummer. Gating transition of pentameric ligand-gated ion channels. Biophysical Journal, 97:2456-2463, 2009.
Fangqiang Zhu and Dimitris K. Agrafiotis. Recursive distance partitioning algorithm for common pharmacophore identification. Journal of Chemical Information and Modeling, 47:1619-1625, 2007.
Fangqiang Zhu and Dimitris K. Agrafiotis. Self-organizing superimposition algorithm for conformational sampling. Journal of Computational Chemistry, 28:1234-1239, 2007.
Fangqiang Zhu, Emad Tajkhorshid, and Klaus Schulten. Collective diffusion model for water permeation through microscopic channels. Physical Review Letters, 93:224501, 2004.
Fangqiang Zhu, Emad Tajkhorshid, and Klaus Schulten. Theory and simulation of water permeation in aquaporin-1. Biophysical Journal, 86:50-57, 2004.
Fangqiang Zhu and Klaus Schulten. Water and proton conduction through carbon nanotubes as models for biological channels. Biophysical Journal, 85:236-244, 2003.