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Zhenyu Lu, Ph.D. - Publications

Affiliations: 
2005 Duke University, Durham, NC 
Area:
quantum mechanical simulations of biological systems and nanostructures
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19 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
2014 Zhou N, Lu Z, Wu Q, Zhang Y. Improved parameterization of interatomic potentials for rare gas dimers with density-based energy decomposition analysis. The Journal of Chemical Physics. 140: 214117. PMID 24908000 DOI: 10.1063/1.4881255  0.612
2011 Lu Z, Zhou N, Wu Q, Zhang Y. Directional Dependence of Hydrogen Bonds: a Density-based Energy Decomposition Analysis and Its Implications on Force Field Development. Journal of Chemical Theory and Computation. 7: 4038-4049. PMID 22267958 DOI: 10.1021/Ct2003226  0.622
2011 Wu R, Lu Z, Cao Z, Zhang Y. A Transferable Non-bonded Pairwise Force Field to Model Zinc Interactions in Metalloproteins. Journal of Chemical Theory and Computation. 7: 433-443. PMID 21552372 DOI: 10.1021/Ct100525R  0.564
2011 Wu R, Lu Z, Cao Z, Zhang Y. Zinc chelation with hydroxamate in histone deacetylases modulated by water access to the linker binding channel. Journal of the American Chemical Society. 133: 6110-3. PMID 21456530 DOI: 10.1021/Ja111104P  0.503
2009 Lu Z, Lai J, Zhang Y. Importance of charge independent effects in readout of the trimethyllysine mark by HP1 chromodomain. Journal of the American Chemical Society. 131: 14928-31. PMID 19788305 DOI: 10.1021/Ja904951T  0.509
2008 Lu Z, Zhang Y. Interfacing ab initio Quantum Mechanical Method with Classical Drude Osillator Polarizable Model for Molecular Dynamics Simulation of Chemical Reactions. Journal of Chemical Theory and Computation. 4: 1237-48. PMID 19221605 DOI: 10.1021/Ct800116E  0.63
2008 Hu H, Lu Z, Parks JM, Burger SK, Yang W. Quantum mechanics/molecular mechanics minimum free-energy path for accurate reaction energetics in solution and enzymes: sequential sampling and optimization on the potential of mean force surface. The Journal of Chemical Physics. 128: 034105. PMID 18205486 DOI: 10.1063/1.2816557  0.728
2007 Hu H, Lu Z, Yang W. Fitting Molecular Electrostatic Potentials from Quantum Mechanical Calculations. Journal of Chemical Theory and Computation. 3: 1004-13. PMID 26627419 DOI: 10.1021/Ct600295N  0.562
2007 Hu H, Lu Z, Yang W. QM/MM Minimum Free Energy Path: Methodology and Application to Triosephosphate Isomerase. Journal of Chemical Theory and Computation. 3: 390-406. PMID 19079734 DOI: 10.1021/Ct600240Y  0.602
2007 Hu H, Lu Z, Elstner M, Hermans J, Yang W. Simulating water with the self-consistent-charge density functional tight binding method: from molecular clusters to the liquid state. The Journal of Physical Chemistry. A. 111: 5685-91. PMID 17474727 DOI: 10.1021/Jp070308D  0.504
2006 Zhang Q, Lu Z, Hu H, Yang W, Marszalek PE. Direct detection of the formation of V-amylose helix by single molecule force spectroscopy. Journal of the American Chemical Society. 128: 9387-93. PMID 16848474 DOI: 10.1021/Ja057693+  0.485
2006 Lu Z, Hu H, Yang W, Marszalek PE. Simulating force-induced conformational transitions in polysaccharides with the SMD replica exchange method. Biophysical Journal. 91: L57-9. PMID 16829559 DOI: 10.1529/Biophysj.106.090324  0.524
2006 Wang M, Lu Z, Yang W. Nuclear quantum effects on an enzyme-catalyzed reaction with reaction path potential: proton transfer in triosephosphate isomerase. The Journal of Chemical Physics. 124: 124516. PMID 16599706 DOI: 10.1063/1.2181145  0.559
2005 Cisneros GA, Liu H, Lu Z, Yang W. Reaction path determination for quantum mechanical/molecular mechanical modeling of enzyme reactions by combining first order and second order "chain-of-replicas" methods. The Journal of Chemical Physics. 122: 114502. PMID 15836224 DOI: 10.1063/1.1860560  0.678
2004 Lu Z, Nowak W, Lee G, Marszalek PE, Yang W. Elastic properties of single amylose chains in water: a quantum mechanical and AFM study. Journal of the American Chemical Society. 126: 9033-41. PMID 15264836 DOI: 10.1021/Ja031940X  0.552
2004 Liu H, Lu Z, Cisneros GA, Yang W. Parallel iterative reaction path optimization in ab initio quantum mechanical/molecular mechanical modeling of enzyme reactions. The Journal of Chemical Physics. 121: 697-706. PMID 15260596 DOI: 10.1063/1.1759318  0.688
2004 Wang M, Lu Z, Yang W. Transmission coefficient calculation for proton transfer in triosephosphate isomerase based on the reaction path potential method. The Journal of Chemical Physics. 121: 101-7. PMID 15260526 DOI: 10.1063/1.1757437  0.575
2004 Lu Z, Yang W. Reaction path potential for complex systems derived from combined ab initio quantum mechanical and molecular mechanical calculations. The Journal of Chemical Physics. 121: 89-100. PMID 15260525 DOI: 10.1063/1.1757436  0.604
2003 Hasegawa J, Ishida M, Nakatsuji H, Lu Z, Liu H, Yang W. Energetics of the Electron Transfer from Bacteriopheophytin to Ubiquinone in the Photosynthetic Reaction Center ofRhodopseudomonas Viridis:  Theoretical Study The Journal of Physical Chemistry B. 107: 838-847. DOI: 10.1021/Jp022334B  0.527
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