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Junchao Xia, Ph.D. - Publications

Affiliations: 
2006 Clark University, Worcester, MA, United States 
Area:
Condensed Matter Physics, Geophysics
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25 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Xia J, Flynn W, Gallicchio E, Uplinger K, Armstrong JD, Forli S, Olson AJ, Levy RM. Massive-Scale Binding Free Energy Simulations of HIV Integrase Complexes Using Asynchronous Replica Exchange Framework Implemented on the IBM WCG Distributed Network. Journal of Chemical Information and Modeling. PMID 30758197 DOI: 10.1021/Acs.Jcim.8B00817  0.378
2018 Xia J, Flynn WF, Levy RM. On Improving Prediction Accuracy of Binding Free Energies and Poses of HIV Integrase Complexes Using the Binding Energy Distribution Analysis Method with Flattening Potentials. Journal of Chemical Information and Modeling. PMID 29927237 DOI: 10.1021/Acs.Jcim.8B00194  0.375
2018 Deng N, Cui D, Zhang BW, Xia J, Cruz J, Levy R. Comparing alchemical and physical pathway methods for computing the absolute binding free energy of charged ligands. Physical Chemistry Chemical Physics : Pccp. PMID 29896599 DOI: 10.1039/C8Cp01524D  0.313
2016 Pal RK, Haider K, Kaur D, Flynn W, Xia J, Levy RM, Taran T, Wickstrom L, Kurtzman T, Gallicchio E. A combined treatment of hydration and dynamical effects for the modeling of host-guest binding thermodynamics: the SAMPL5 blinded challenge. Journal of Computer-Aided Molecular Design. PMID 27696239 DOI: 10.1007/S10822-016-9956-6  0.345
2016 Deng N, Flynn WF, Xia J, Vijayan RS, Zhang B, He P, Mentes A, Gallicchio E, Levy RM. Large scale free energy calculations for blind predictions of protein-ligand binding: the D3R Grand Challenge 2015. Journal of Computer-Aided Molecular Design. PMID 27562018 DOI: 10.1007/S10822-016-9952-X  0.3
2016 Zhang BW, Dai W, Gallicchio E, He P, Xia J, Tan Z, Levy RM. Simulating Replica Exchange: Markov State Models, Proposal Schemes and the Infinite Swapping Limit. The Journal of Physical Chemistry. B. PMID 27079355 DOI: 10.1021/Acs.Jpcb.6B02015  0.376
2016 Mentes A, Deng NJ, Vijayan RS, Xia J, Gallicchio E, Levy RM. Binding Energy Distribution Analysis Method (BEDAM): Hamiltonian replica exchange with torsional flattening for binding mode prediction and binding free energy estimation. Journal of Chemical Theory and Computation. PMID 27070865 DOI: 10.1021/Acs.Jctc.6B00134  0.36
2016 Tan Z, Xia J, Zhang BW, Levy RM. Locally weighted histogram analysis and stochastic solution for large-scale multi-state free energy estimation. The Journal of Chemical Physics. 144: 034107. PMID 26801020 DOI: 10.1063/1.4939768  0.36
2015 Gallicchio E, Xia J, Flynn WF, Zhang B, Samlalsingh S, Mentes A, Levy RM. Asynchronous Replica Exchange Software for Grid and Heterogeneous Computing. Computer Physics Communications. 196: 236-246. PMID 27103749 DOI: 10.1016/J.Cpc.2015.06.010  0.341
2015 Zhang BW, Xia J, Tan Z, Levy RM. A Stochastic Solution to the Unbinned WHAM Equations. The Journal of Physical Chemistry Letters. 6: 3834-3840. PMID 26722879 DOI: 10.1021/Acs.Jpclett.5B01771  0.35
2015 Xia J, Flynn WF, Gallicchio E, Zhang BW, He P, Tan Z, Levy RM. Large-scale asynchronous and distributed multidimensional replica exchange molecular simulations and efficiency analysis. Journal of Computational Chemistry. PMID 26149645 DOI: 10.1002/Jcc.23996  0.363
2014 Xia J, Levy RM. Molecular dynamics of the proline switch and its role in Crk signaling. The Journal of Physical Chemistry. B. 118: 4535-45. PMID 24702481 DOI: 10.1021/Jp5013297  0.308
2013 Xia J, Deng NJ, Levy RM. NMR relaxation in proteins with fast internal motions and slow conformational exchange: model-free framework and Markov state simulations. The Journal of Physical Chemistry. B. 117: 6625-34. PMID 23638941 DOI: 10.1021/Jp400797Y  0.38
2012 Xia J, Case DA. Sucrose in aqueous solution revisited, Part 1: molecular dynamics simulations and direct and indirect dipolar coupling analysis. Biopolymers. 97: 276-88. PMID 22189655 DOI: 10.1002/Bip.22017  0.357
2012 Xia J, Case DA. Sucrose in aqueous solution revisited, Part 2: adaptively biased molecular dynamics simulations and computational analysis of NMR relaxation. Biopolymers. 97: 289-302. PMID 22058066 DOI: 10.1002/Bip.22004  0.363
2011 Xia J, Margulis CJ, Case DA. Searching and optimizing structure ensembles for complex flexible sugars. Journal of the American Chemical Society. 133: 15252-5. PMID 21863822 DOI: 10.1021/Ja205251J  0.328
2011 Ganguly S, Xia J, Margulis C, Stanwyck L, Bush CA. Measuring the magnitude of internal motion in a complex hexasaccharide. Biopolymers. 95: 39-50. PMID 20683925 DOI: 10.1002/Bip.21532  0.338
2009 Klein W, Xia J, Ferguson CD, Gould H, Tiampo KF, Rundle JB. Models of earthquake faults: Ergodicity and forecasting International Journal of Modern Physics B. 23: 5553-5569. DOI: 10.1142/S0217979209063857  0.483
2008 Xia J, Margulis C. A tool for the prediction of structures of complex sugars. Journal of Biomolecular Nmr. 42: 241-56. PMID 18953494 DOI: 10.1007/S10858-008-9279-6  0.344
2008 Xia J, Gould H, Klein W, Rundle JB. Near-mean-field behavior in the generalized Burridge-Knopoff earthquake model with variable-range stress transfer. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 77: 031132. PMID 18517354 DOI: 10.1103/Physreve.77.031132  0.553
2008 Xia J, Gould H, Klein W, Rundle JB. Near-mean-field behavior in the generalized Burridge-Knopoff earthquake model with variable-range stress transfer Physical Review E - Statistical, Nonlinear, and Soft Matter Physics. 77. DOI: 10.1103/PhysRevE.77.031132  0.525
2007 Xia J, Daly RP, Chuang FC, Parker L, Jensen JH, Margulis CJ. Sugar Folding:  A Novel Structural Prediction Tool for Oligosaccharides and Polysaccharides 2. Journal of Chemical Theory and Computation. 3: 1629-43. PMID 26633232 DOI: 10.1021/Ct700034Q  0.369
2007 Xia J, Daly RP, Chuang FC, Parker L, Jensen JH, Margulis CJ. Sugar Folding:  A Novel Structural Prediction Tool for Oligosaccharides and Polysaccharides 1. Journal of Chemical Theory and Computation. 3: 1620-8. PMID 26633231 DOI: 10.1021/Ct700033Y  0.361
2005 Xia J, Gould H, Klein W, Rundle JB. Simulation of the Burridge-Knopoff model of earthquakes with variable range stress transfer. Physical Review Letters. 95: 248501. PMID 16384429 DOI: 10.1103/Physrevlett.95.248501  0.551
2000 Liu C, Zhu Z, Xia J, Sun D. Different Cooling Rate Dependences of Different Microstructure Units in Aluminium Glass by Molecular Dynamics Simulation Chinese Physics Letters. 17: 34-36. DOI: 10.1088/0256-307X/17/1/012  0.311
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