Fangqiang Zhu

Contact information

Lawrence Livermore National Laboratory
7000 East Avenue, L-367
Livermore, CA 94550
email: zhu13@llnl.gov
phone: 925 423 0920
 

Education

2004 Ph.D., Physics, University of Illinois at Urbana-Champaign, USA

2003 M.S., Computer Science, University of Illinois at Urbana-Champaign, USA

1999 M.S., Physics, Tsinghua University, China

1997 B.S., Physics, Tsinghua University, China

Research

Theoretical and computational biophysics. Applications (such as simulations) as well as method development for improving the quantitative understanding of biomolecular systems.

Publications

  1. Xiaoyan Zhou and Fangqiang Zhu. Calculating single-channel permeability and conductance from transition paths. Journal of Chemical Information and Modeling, 59: 777- 785, 2019.

  2. Xiaoyan Zhou and Fangqiang Zhu. Kinetic mechanism for water in vibrating carbon nanotubes. Physical Review E, 98:032410, 2018.

  3. Xiaoling Leng, Fangqiang Zhu, and Stephen R. Wassall. Vitamin E has reduced affinity for a polyunsaturated phospholipid: an umbrella sampling molecular dynamics simulations study. The Journal of Physical Chemistry B, 122:8351-8358, 2018.

  4. 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.

  5. 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.

  6. 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.

  7. Fangqiang Zhu. Calculating transition rates from durations of transition paths. The Journal of Chemical Physics, 146:124128, 2017.

  8. 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.

  9. Xin Qiao, Jaekyun Jeon, Jeff Weber, Fangqiang Zhu, and Bo Chen. Mechanism of polymorphism and curvature of HIV capsid assemblies probed by 3D simulations with a novel coarse grain model. BBA - General Subjects, 1850:2353-2367, 2015.

  10. Xin Qiao, Jaekyun Jeon, Jeff Weber, Fangqiang Zhu, and Bo Chen. Construction of a novel coarse grain model for simulations of HIV capsid assembly to capture the backbone structure and inter-domain motions in solution. Data in Brief, 5:506-512, 2015.

  11. Fangqiang Zhu and Bo Chen. Monte Carlo simulations of HIV capsid protein homodimer. Journal of Chemical Information and Modeling, 55:1361-1368, 2015.

  12. Wenyun Wu, Jingying Yue, Dongqi Li, Xiaoyang Lin, Fangqiang Zhu, Xue Yin, Jun Zhu, Xingcan Dai, Peng Liu, Yang Wei, Jiaping Wang, Haitao Yang, Lina Zhang, Qunqing Li, Shoushan Fan, and Kaili Jiang. True-color real-time imaging and spectroscopy of carbon nanotubes on substrate by enhanced Rayleigh scattering. Nano Research, 8:2721-2732, 2015.

  13. Hyun Deok Song and Fangqiang Zhu. Conformational changes in two inter-helical loops of Mhp1 membrane transporter. PLoS One, 10:e0133388, 2015.

  14. Wenyun Wu, Jingying Yue, Dongqi Li, Xiaoyang Lin, Fangqiang Zhu, Xue Yin, Jun Zhu, Xingcan Dai, Peng Liu, Yang Wei, Jiaping Wang, Haitao Yang, Lina Zhang, Qunqing Li, Shoushan Fan, and Kaili Jiang. Interface dipole enhancement effect and enhanced Rayleigh scattering. Nano Research, 8:303-319, 2015.

  15. Fangqiang Zhu and Matthias Clauss. Evaluating membrane affinity by integrating protein orientations. Journal of Molecular Graphics and Modelling, 54:141-147, 2014.

  16. Yi Xue, Tairan Yuwen, Fangqiang Zhu, and Nikolai R. Skrynnikov. Role of electrostatic interactions in binding of peptides and intrinsically disordered proteins to their folded targets: 1. NMR and MD characterization of the complex between the c-Crk N-SH3 domain and the peptide Sos. Biochemistry, 53:6473-6495, 2014.

  17. Fangqiang Zhu. How does water pass through a sugar transporter? Biophysical Journal, 106:1229-1230, 2014.

  18. Hyun Deok Song and Fangqiang Zhu. Conformational dynamics of a ligand-free adenylate kinase. PLoS One, 8:e68023, 2013.

  19. Yingting Liu and Fangqiang Zhu. Collective diffusion model for ion conduction through microscopic channels. Biophysical Journal, 104:368-376, 2013.

  20. Fangqiang Zhu and Gerhard Hummer. Drying transition in the hydrophobic gate of the GLIC channel blocks ion conduction. Biophysical Journal, 103:219-227, 2012.

  21. 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.

  22. 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.

  23. Matthew Melillo, Fangqiang Zhu, Mark A. Snyder, and Jeetain Mittal. Water transport through nanotubes with varying interaction strength between tube wall and water. The Journal of Physical Chemistry Letters, 2: 2978-2983, 2011.

  24. Dimitris K. Agrafiotis, Huafeng Xu, Fangqiang Zhu, Deepak Bandyopadhyay, and Pu Liu. Stochastic proximity embedding: methods and applications. Molecular Informatics, 29:758- 770, 2010.

  25. 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.

  26. Fangqiang Zhu and Gerhard Hummer. Gating transition of pentameric ligand-gated ion channels. Biophysical Journal, 97:2456-2463, 2009.

  27. Pascal Bonnet, Dimitris K. Agrafiotis, Fangqiang Zhu, and Eric Martin. Conformational analysis of macrocycles: finding what common search methods miss. Journal of Chemical Information and Modeling, 49:2242-2259, 2009.

  28. Pu Liu, Fangqiang Zhu, Dmitrii N. Rassokhin, and Dimitris K. Agrafiotis. A self-organizing algorithm for modeling protein loops. PLoS Computational Biology, 5:e1000478, 2009.

  29. Youyong Li, Fangqiang Zhu, Nagarajan Vaidehi, William A. Goddard III, Felix Sheinerman, Stephan Reiling, Isabelle Morize, Lan Mu, Keith Harris, Ali Ardati, and Abdelazize Laoui. Prediction of the 3D structure and dynamics of human DP G-Protein coupled receptor bound to an agonist and an antagonist. Journal of the American Chemical Society, 129:10720-10731, 2007.

  30. Fangqiang Zhu and Dimitris K. Agrafiotis. Recursive partitioning algorithm for common pharmacophore identification. Journal of Chemical Information and Modeling, 47:1619- 1625, 2007.

  31. Dimitris K. Agrafiotis, Alan Gibbs, Fangqiang Zhu, Sergei Izrailev, and Eric Martin. Conformational sampling of bioactive molecules: a comparative study. Journal of Chemical Information and Modeling, 47:1067-1086, 2007.

  32. Fangqiang Zhu and Dimitris K. Agrafiotis. Self-organizing superimposition algorithm for conformational sampling. Journal of Computational Chemistry, 28:1234-1239, 2007.

  33. Hanning Chen, Boaz Ilan, Yujie Wu, Fangqiang Zhu, Klaus Schulten, and Gregory A. Voth. Charge delocalization in proton channels. I. The aquaporin channels and proton blockage. Biophysical Journal, 92:46-60, 2007.

  34. Dimitris K. Agrafiotis, Alan Gibbs, Fangqiang Zhu, Sergei Izrailev, and Eric Martin. Conformational boosting. Australian Journal of Chemistry, 59:874-878, 2006.

  35. Sergei Izrailev, Fangqiang Zhu, and Dimitris K. Agrafiotis. A distance geometry heuristic for expanding the range of geometries sampled during conformational search. Journal of Computational Chemistry, 27:1962-1969, 2006.

  36. Emad Tajkhorshid, Fangqiang Zhu, and Klaus Schulten. Kinetic theory and simulation of single-channel water transport. In S. Yip, editor, Handbook of Materials Modeling, Vol. I: Methods and Models, pp. 1797-1822. Springer, Netherlands, 2005.

  37. Fangqiang Zhu, Emad Tajkhorshid, and Klaus Schulten. Collective diffusion model for water permeation through microscopic channels. Physical Review Letters, 93:224501, 2004.

  38. Fangqiang Zhu, Emad Tajkhorshid, and Klaus Schulten. Theory and simulation of water permeation in aquaporin-1. Biophysical Journal, 86:50-57, 2004.

  39. Emad Tajkhorshid, Aleksij Aksimentiev, Ilya Balabin, Mu Gao, Barry Isralewitz, James C. Phillips, Fangqiang Zhu, and Klaus Schulten. Large scale simulation of protein mechanics and function. In Frederic M. Richards, David S. Eisenberg, and John Kuriyan, editors, Advances in Protein Chemistry, volume 66, pp. 195-247. Elsevier Academic Press, New York, 2003.

  40. Fangqiang Zhu and Klaus Schulten. Water and proton conduction through carbon nanotubes as models for biological channels. Biophysical Journal, 85:236-244, 2003.

  41. Fangqiang Zhu, Emad Tajkhorshid, and Klaus Schulten. Pressure-induced water transport in membrane channels studied by molecular dynamics. Biophysical Journal, 83:154-160, 2002.

  42. Fangqiang Zhu, Emad Tajkhorshid, and Klaus Schulten. Molecular dynamics study of aquaporin-1 water channel in a lipid bilayer. FEBS Letters, 504:212-218, 2001.