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Biomolecular Simulations, Free Energy and NMR Calculations

  1. She Zhang, Jeff P. Thompson, Junchao Xia, Anthony T. Bogetti, Forrest York, Geoffrey A. Skillman, Lillian T. Chong, and David N. LeBard, " Mechanistic Insights into Passive Membrane Permeability of Drug-like Molecules from a Weighted Ensemble of Trajectories," J. Chem. Inf. Model. 62, 1891 (2022).
  2. John D. Russo, She Zhang, Jeremy M. G. Leung, Anthony T. Bogetti, Jeff P. Thompson, Alex J. DeGrave, Paul A. Torrillo, A. J. Pratt, Kim F. Wong, Junchao Xia, Jeremy Copperman, Joshua L. Adelman, Matthew C. Zwier, David N. LeBard, Daniel M. Zuckerman, and Lillian T. Chong " WESTPA 2.0: High-Performance Upgrades for Weighted Ensemble Simulations and Analysis of Longer-Timescale Applications," J. Chem. Theory Comput. 18, 638 (2022).
  3. Nanjie Deng, Junchao Xia, Lauren Wickstrom, Clement Lin, Kaibo Wang, Peng He, Yunting Yin, and Danzhou Yang, " Ligand Selectivity in the Recognition of Protoberberine Alkaloids by Hybrid-2 Human Telomeric G-Quadruplex: Binding Free Energy Calculation, Fluorescence Binding, and NMR Experiments," Molecules 24. 1574 (2019).
  4. Junchao Xia, William Flynn, Emilio Gallicchio, Keith Uplinger, Jonathan D. Armstrong, Stefano Forli, Arthur J. Olson, and Ronald M. Levy, " Massive-Scale Binding Free Energy Simulations of HIV Integrase Complexes Using Asynchronous Replica Exchange Framework Implemented on the IBM WCG distributed network," J. Chem. Info. Model. 59, 1382 (2019).
  5. Junchao Xia, William Flynn, and Ronald Levy, " Improving prediction accuracy of binding free energies and poses of HIV integrase complexes using the binding energy distribution analysis method with flattening potentials," J. Chem. Info. Model. 58, 1356 (2018).
  6. Nanjie Deng, Di Cui, Bin W. Zhang, Junchao Xia, Jeffrey Cruz and Ronald Levy, " Comparing alchemical and physical pathway methods for computing the absolute binding free energy of charged ligands," Phys. Chem. Chem. Phys. 20, 17081 (2018).
  7. Jill J. Bouchard, Junchao Xia, David A. Case, and Jeffrey W. Peng, " Enhanced sampling of interdomain motion using map-restrained langevin dynamics and NMR: Application to Pin 1," J. Mol. Biol. 430, 2164 (2018).
  8. Rajat Kumar Pal, Kamran Haider, Divya Kaur, William F. Flynn, Junchao Xia, Ronald M. Levy, Tetiana Taran, Lauren Wickstrom,Tom Kurtzman, Emilio Gallicchio, " A combined treatment of hydration and dynamical effects for the modeling of host-guest binding thermodynamics: The SAMPL5 blinded challenge," J. Comput. Aided Mol. Des. 31, 29 (2017).
  9. Nanjie Deng, William F. Flynn, Junchao Xia, R. S. K. Vijayan, Baofeng Zhang, Peng He, Ahmet Mantes, Emilio Gallicchio, Ronald M. Levy, " Large scale free energy calculations for blind predictions of protein-ligand Binding: The D3R grand challenge," J. Comput. Aided Mol. Des. 30, 743 (2016)
  10. Ahmet Mentes, Nan-jie, Deng, Vijayan, Suyambu Kesava Vijayan, Junchao Xia, Emilio Gallicchio and Ronald M. levy, " Binding Energy Distribution Analysis Method (BEDAM): Hamiltonian replica exchange with torsional flattening for binding mode prediction and binding free energy estimation," J. Chem. Theory Comput. 12 2459 (2016).
  11. Bin W. Zhang, Wei Dai, Emilio Gallicchio, Peng He, Junchao Xia, Zhiqiang Tan, and Ronald M. Levy, " Simulating replica exchange: Markov state models, proposal schemes and the infinite swapping limit," J. Phys. Chem. B 120, 8289 (2016).
  12. Zhiqiang Tan, Junchao Xia, Bin W. Zhang, and Ronald M. Levy, " Locally weighted histogram analysis and stochastic solution for large-scale multi-state free energy estimation," J. Chem. Phys. 144, 034107 (2016).
  13. Bin W. Zhang, Junchao Xia, Zhiqiang Tan, and Ronald M. Levy, " A stochastic solution to the unbinned WHAM equations," J. Phys. Chem. Lett. 6, 3834 (2015).
  14. Emilio Gallicchio, Junchao Xia, William F. Flynn, Baofeng Zhang, Sade Samlalsingh, Ahmet Mentes, and Ronald M. Levy, " Asynchronous replica exchange software for grid and heterogeneous computing," Comput. Phys. Comm. 196, 236 (2015).
  15. Junchao Xia, William F. Flynn, Emilio Gallicchio, Bin W. Zhang, Peng He, Zhiqiang Tan, and Ronald M. Levy, " Large scale asynchronous and distributed multi-dimensional replica exchange molecular simulations and efficiency analysis," J. Comput. Chem. 36, 1772 (2015).
  16. Junchao Xia and Ronald M. Levy, " Molecular dynamics of the proline switch and its role in Crk signaling," J. Phys. Chem. B 118, 4535 (2014).
  17. Junchao Xia, Nan-jie Deng, and Ronald M. Levy, " NMR relaxation in proteins with fast internal motions and slow conformational exchange: model-free framework and Markov state simulations," J. Phys. Chem. B 117, 6625 (2013).
  18. Junchao Xia and David A. Case, " Sucrose in aqueous solution revisited, Part 2: Adaptively biased molecular dynamics simulations and computational analysis of NMR relaxation," Biopolymers 97, 289 (2012).
  19. Junchao Xia and David A. Case, " Sucrose in aqueous solution revisited, Part 1: Molecular dynamics simulations and direct and indirect dipolar coupling analysis," Biopolymers 97, 276 (2012).
  20. Junchao Xia, Claudio J. Margulis, and David A. Case, " Searching and optimizing structure ensembles for complex flexible sugars," J. Am. Chem. Soc.(Communication) 133, 15252 (2011).
  21. Soumya Ganguly, Junchao Xia, Claudio Margulis, Liz Stanwyck, and C. Allen Bush, " Measuring the magnitude of internal motion in a complex hexasaccharide," Biopolymers 95, 39 (2011).
  22. Junchao Xia and Claudio J. Margulis, “ Computer study of the conformational structures of saccharides in solution based on J couplings and the 'Fast Sugar Structure Prediction software',” Biomacromolecules 10, 3081 (2009).
  23. Sai Kumar Ramadugu, Ying-Hua Chung, Junchao Xia and Claudio J. Margulis, “ When sugars get wet. A comprehensive study of the behavior of water on the surface of oligosaccharides,” J. Phys. Chem. B 113, 11003 (2009).
  24. Junchao Xia and Claudio J. Margulis, “ A tool for the prediction of structures of complex sugars,” J. Biomol. NMR 42, 241 (2008).
  25. Harsha V. R. Annapureddy, Zhonghan Hu, Junchao Xia, and Claudio J. Margulis, “ How does water affect the dynamics of the room temperature ionic liquid 1-hexyl-3-methylimidazolium hexauorophosphate and the fluorescence spectroscopy of Coumarin-153 when dissolved in it?” J. Phys. Chem. B 112, 1770 (2008).
  26. Ying-hua Chuang, Junchao Xia and Claudio J. Margulis, “ Diffusion and residence time of hydrogen peroxide and water in crowded protein environments,” J. Phys. Chem. B. 111, 13336 (2007).
  27. Junchao Xia, Ryan P Daly, Feng-Chuan Chuang, Laura Parker, Jan H. Jensen, and Claudio J. Margulis, “ Sugar folding: A novel structural prediction tool for oligosaccharides and polysaccharides 2,” J. Chem. Theory Comput. 3, 1629 (2007).
  28. Junchao Xia, Ryan P Daly, Feng-Chuan Chuang, Laura Parker, Jan H. Jensen, and Claudio J. Margulis, “ Sugar folding: A novel structural prediction tool for oligosaccharides and polysaccharides 1,” J. Chem. Theory Comput. 3, 1620(2007).

Simulations of Non-Equilibrium Driven Dissipative Systems: Earthquake Models

  1. W. Klein, Junchao Xia, C. D. Ferguson, H. Gould, K. F. Tiampo, and J. B. Rundle, “ Models of earthquake faults: Ergodicity and Forecasting,” Int. J. Mod. Phys. B 23, 5553 (2009).
  2. Junchao Xia, Harvey Gould, W. Klein, and J. Rundle, “ Near mean-field behavior in the generalized Burridge-Knopoff model of earthquakes with variable range stress transfer,” Phys. Rev. E 77, 031132 (2008).
  3. Junchao Xia, Harvey Gould, W. Klein, and J. Rundle, “ Simulation of the Burridge-Knopoff model of earthquakes with variable range stress transfer,” Phys. Rev. Lett. 95, 248501 (2005).

Simulations of Materials: Liquid Metals and Semiconductors

  1. C. S. Liu, Junchao Xia, Z. G. Zhu, and D. Y. Sun, “ The cooling rate dependence of crystallization for liquid copper: A molecular dynamics study,” J. Chem. Phys. 114, 7506 (2001).
  2. C. S. Liu, Z. G. Zhu, Junchao Xia, and D. Y. Sun, “ Cooling rate dependence of structural properties of aluminium during rapid solidification,” J. Phys.: Condens. Matter 13, 1873 (2001).
  3. Chang-Song Liu, Zhen-Gang Zhu, Jun-Chao Xia, and D. Y. Sun, “ Different cooling rate dependences of different microstructure units in aluminium glass by molecular dynamics simulation,” Chin. Phys. Lett. 17, 34 (2000).
  4. C. S. Liu, Z. G. Zhu, Junchao Xia, and D. Y. Sun, “ Molecular dynamics simulation of the local inherent structure of liquid silicon at different temperatures,” Phys. Rev. B 60, 3194 (1999).
  5. Jun-Chao Xia, Zhen-Gang Zhu, and Chang-Song Liu, “ Final structures of crystallization of liquid copper studied by molecular dynamics simulation,” Chin. Phys. Lett. 16, 850 (1999).

Published in Conference Proceedings

  1. Junchao Xia, Harvey Gould, and W. Klein, "Simulations of the Burridge-Knopoff model," Third International APEC Cooperation for Earthquake Simulation (ACES) Meeting, May 5-10, 2002, Maui, Hawaii, US.

Theses

  1. Ph.D. Thesis in Condensed Matter Physics: "Computer simulations of statistical models of earthquakes," Clark University, 2006, with Professor Harvey Gould at Clark University and William Klein at Boston University.
  2. M.S. Thesis in Condensed Matter Physics: "Microstructure evolution of liquid metals during ultra-fast solidification," Institute of Solid State Physics, Chinese Academy of Sciences, 1999, with Professor Zhengang Zhu and Changsong Liu.