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1983-1990     1991-1993     1994-1996     1997-1999     2000-2002     2003-2005     2006-2008     2009-2011

  1. Gao, Jiali; Wong, Kin-Yiu; Major, Dan T.; Cembran, Alessandro; Song, Lingchun ; Lin, Yen-lin; Fan, Yao; Ma, Shuhua; "Kinetic Isotope Effects from Hybrid Classical and Quantum Path Integral Computations." In Kinetic Isotoped Effects in Enzyme Catalysis, Eds. R. Alleman and M. Scruton, RSC Biomolecular Sciences, 2009, pp 105-131.
  2. Shi, Lei; Cembran, Alessandro; Gao, Jiali; Veglia, Gianluigi; "Tilt and Azymuthal angles of a Transmembrane Peptide: A Comparison of Molecular Dynamics Calculations and Solid-State NMR Data of Sarcolipin in Lipid Membranes." Biophysical Journal, 2009, 96, 3648-3662.
  3. Valero, Rosendo; Song, Lingchun; Gao, Jiali; Truhlar, Donald G.; "Perspective on Diabatic Models of Chemical Reactivity as Illustrated by the Gas-Phase SN2 Reaction of Acetate Ion with 1,2-Dichloroethane." Journal of Chemical Theory and Computation, 2009, 5, 1-22. Erratum: 5, 2191.
  4. Wangshen Xie, Jingzhi Pu and Jiali Gao; "A Coupled Polarization-Matrix Inversion and Iteration Approach for Accelerating the Dipole Convergence in a Polarizable Potential Function." Journal of Physical Chemistry A, 2009, 113, 2109-2116.
  5. Lingchun Song, Yirong Mo, and Jiali Gao,; "An Effective Hamiltonian Molecular Orbital-Valence Bond (MOVB) Approach for Chemical Reactions Applied to the Nucleophilic Substitution Reaction of Hydrosulfide Ion and Chloromethane". Journal of Chemical Theory and Computation, 2009, 5, 174-185.
  6. Xie, Wangshen; Orozco, Modesto; Truhlar, Donald G.; Gao, Jiali; "X-Pol Potential: An Electronic Structure Based Force Field for Molecular Dynamics Simulation of a Solvated Protein in Water." Journal of Chemical Theory and Computation, 2009, 5, 459-467.
  7. Lucia Becucci, Alessandro Cembran, Christine B. Karim, David D. Thomas, Rolando Guidelli, Jiali Gao, and Gianluigi Veglia,; "On the Function of Pentameric Phospholamban: Ion Channel or Storage Form?," Biophysical Journal (Letter), 2009, 96, L60-L62.
  8. Emilia L. Wu, Kin-Yiu Wong, Xin Zhang, Keli Ha, Jiali Gao,; "Determination of the Structure Form of the Fourth Ligand of Zinc in Acutolysin A using Combined Quantum Mechanical and Molecular Mechanical Simulation," Journal of Physical Chemistry B, 2009, 113, 2477-2485.
  9. J. Javier Ruiz-Pernia, Mireia Garcia-Viloca, Sudeep Bhattacharyya, Jiali Gao, Donald G. Truhlar, and Inaki Tunon,; "Critical Role of Substrate Conformational Change in the Proton Transfer Process Catalyzed by 4-Oxalocrotonate Tautomerase," Journal of the American Chemical Society, 2009, 131, 2687-2698.
  10. B. B. Brooks, C. L. Brooks III, A. D. MacKerell, Jr., L. Nilsson, R. J. Petrella, B. Roux, Y. D. Wong, G. Archontis, C. Bartels, S. Boresch, A. Caflisch, L. Caves, Q. Cui, A. R. Dinner, M. Feig, S. Fischer, J. Gao, M. Hodoscek, W. Im, K. Kuczera, T. Lazaridis, J. Ma, V. Ovchinnikov, E. Paci, R. W. Pastor, C. B. Post, J. Z. Pu, M. Schaefer, B. Tidor, R. M. Venable, H. L. Woodcock, X. Wu, W. Wang, D. M. York, M. Karplus,; "CHARMM: The Biomolecular Simulation Programm," Journal of Computational Chemistry, 2009, 30, 1545-1614.
  11. Kin-Yiu Wong, Lingchun Song, Wangshen Xie, Dan T. Major, Yen-lin Lin, Alessandro Cembran, Jiali Gao,; "Quantum Mechanical Methods for Biomolecular Simulations," in Multi-scale Quantum Models for Biocatalysis, D. M. York and T.-S. Lee eds. 2009, Springer Science+Business Media B. V. pp. 79-101. DOI 10.1007/078-1-4020-9956-4_4.
  12. Tai-Sung Lee, George M. Giambasu, Adam Moser, Kwangho Nam, Carlos Silva-Lopez, Francesca Guerra, Olalla Nieto-Faza, Timothy J. Giese, Jiali Gao and Darrin M. York,; "Unraveling the mechanisms of ribozyme catalysis with multi-scale simulations," in Multi-scale Quantum Models for Biocatalysis, D. M. York and T.-S. Lee eds. 2009, Springer Science+Business Media B. V. pp. 377-408.
  13. Lingchun Song, Jaebeom Han, Yen-lin Lin, Jiali Gao,; "Explicit Polarization (X-Pol) Potential Using ab initio Molecular Orbital Theory and Density Functional Theory," Journal of Physical Chemistry A, 2009, 113, 11656-11664. DOI: 10.1021/jp902710a
  14. Alessandro Cembran, Lingchun Song, Yirong Mo, and Jiali Gao,; "Block-Localized Density Functional Theory (BLDFT), Diabatic Coupling, and Their Use in Valence Bond Theory for Representing Reactive Potential Energy Surfaces". Journal of Chemical Theory and Computation, 2009, 5, 2702-2716. DOI: 10.1021/ct9002898
  15. Kin-Yiu Wong, John P. Richard, Jiali Gao,; "Theoretical Analysis of Kinetic Isotope Effects on Proton Transfer Reactions between Substituted _-Methoxystyrenes and Substituted Acetic Acids," Journal of the American Chemical Society, 2009, 131, 13963-13971.
  16. Dan T. Major, Annie Heroux, Allen M. Orville, Michael P. Valley, Paul F. Fitzpatrick, Jiali Gao,; "Differential Quantum Tunneling Contributions in Nitroalkane Oxidase Catalyzed and the Uncatalyzed Proton Transfer Reaction," Proceedings of the National Academy of Sciences, 2009, 106, 20736-20739.
  17. Yen-lin Lin, Jiali Gao,; "Protonation State of the External Pyridoxal-5«-phosphate Schiff Base in Dopa Decarboxylase," Biochemistry, 2010, 49, 84-84.
  18. Alessandro Cembran, Apirak Payaka, Yen-lin Lin, Wangshen Xie, Yirong Mo, Lingchun Song and Jiali Gao; "A Non-Orthogonal Block-Localized Effective Hamiltonian Approach for Chemical and Enzymatic Reactions," Journal of Chemical Thoery and Computation, 2010, 6, 2242-2251.
  19. Jiali Gao, Alessandro Cembran and Yirong Mo;"Generalized X-Pol Theory and Charge Delocalization States." Journal of Chemical Theory and Computation, 2010, 6, 2402-2410.
  20. DOI: 10.1021/ct100292g.
  21. Alessandro Cembran, Peng Bao, Yingjie Wang, Lingchun Song, Donald G. Truhlar and Jiali Gao"On the Interfragment Exchange in the X-Pol Method." Journal of Chemical Theory and Computation, 2010, 6, 2469-2476.
  22. DOI: 10.1021/ct100268p.
  23. Michael J. M. Mazack, Alessandro Cembran, and Jiali Gao:"Internal Dynamics of an Analytically Coarse-Grained Protein," Journal of Chemical Theory and Computation, 2010, 6, 3601-3612.
  24. DOI: 10.1021/ct100426m.
  25. Hannah R. Leverentz, Jiali Gao, and Donald G. Truhlar,"Using Multipole Point Charge Distributions to Provide the Electrostatic Potential in the Variational Explicit Polarization (X-Pol) Potential," Theoretical Chemistry Accounts, 2011, 129 3-13.
  26. DOI: 10.1007/s00214-011-0889-9
  27. Ramkumar Rajamani, Yen-lin Lin and Jiali Gao,"The Opsin Shift and Mechanism of Spectral Tuning of Rhodopsin." Journal of Computational Chemistry, 2011, 32, 854-865. On line (Oct. 12, 2010).
  28. doi/10.1002/jcc.21663.
  29. Yen-lin Lin and Jiali Gao,"Kinetic Isotope Effects of L-Dopa Decarboxylase." Journal of the American Chemical Society, 2011, 133, DOI: 10.1021/ja108209w; 4398-4403.
  30. On line (March 2, 2011)
  31. Peng Zhang, Peng Bao, and Jiali Gao,"Dipole Preserving and Polarization Consistent Charges." Journal of Computational Chemistry, 2011, 32, 2127-2139.
  32. Larry R. Masterson,, Lei Shi, Emily E. Metcalfe, Jiali Gao, Susan. S. Taylor, and Gianluigi Veglia,"Intrinsic Dynamics Encodes for Catalytically Committed, Uncommitted, and Quenched States in Protein Kinase A." Proceedings of the National Academy of Sciences, 2011, 108, 6969-6974.
  33. Lei Shi, Nathaniel J. Traaseth, Raffaello Verardi, Martin Gustavsson, Jiali Gao, and Gianluigi Veglia,"Paramagnetism-Based NMR Restraints Lift Residual Dipolar Coupling Degeneracy in Multidomain Detergent-Solubilized Membrane Proteins." Journal of the American Chemical Society, 2011, 113, 2232-2241.
  34. Yirong Mo, Peng Bao, and Jiali Gao,"Energy Decomposition Analysis Based on Block-Localized Wavefunction and Multistate Density Functional Theory." Physical Chemimistry Chemical Physics, 2011, 13, 6760-6775. DOI: 10.1039/C0CP02206C; On line (March 2, 2011); (Perspective Article).
  35. Luke Fiedler, Jiali Gao, and Donald G. Truhlar,"Polarized Molecular Orbital Theory. I. Ab Initio Foundations." Journal of Chemical Theory and Computation, 2011, 7, 852-856. Online (March 3, 2011).
  36. DOI: 10.1021/ct1006373
  37. Peng Zheng, Luke Fiedler, Hannah Leverentz, Donald G. Truhlar, and Jiali Gao," Polarized Molecular Orbital Theory. II. The PMO Method." Journal of Chemical Theory and Computation, 2011, 857-867. Online (March 3, 2011).
  38. DOI: 10.1021/ct100638g
  39. Kin-Yiu Wong and Jiali Gao," Insight into Phosphodiesterase Mechanism from Combined QM/MM Molecular Dynamics Simulations." FASB J., 2011, 278, 2579-2595
  40. Adam J. Fleisher, Justin W. Young, and David W. Pratt, Alessandro Cembran, and Jiali Gao," Flickering dipoles in the gas phase. Structures, internal dynamics, and dipole moments of beta-naphthol-H2O in its ground and excited electronic states." Journal of Chemical Physics, 2011, 134, 114304.
  41. doi:10.1063/1.3562373
  42. Rockney Atz, Shuhua Ma, Jiali Gao, Paul J. Jardine, Shelley Grimes " Role of phi29 connector channel loops in late stage DNA packaging”, " Journal of Molecular Biology, 2011, 410, 50-59.
  43. Isegawa Miho, Jiali Gao, Donald G. Truhlar " Incorporation of charge transfer into the explicit polarization fragment method by grand canonical density functional theory, " Journal of Chemical Physics, 2011, 135, 084107.
  44. Jason D. Perlmutter, William J. Drasler, Wangshen Xie, Jiali Gao, Jean-Luc Popot, Jonathan Sachs " All-atom and coarse-grained molecular dynamics simulations of a membrane protei stabilizing polymer, " Langmuir, 2011, 27, 10523-10537.
  45. Yen-Lin Lin, Jiali Gao, Amir Rubinstein, and Dan Thomas Major," Molecular Dynamics Simulations of the Intramolecular Proton Transfer and Carbanion Stabilization in the Pyridoxal 5'-Phosphate Dependent Enzymes L-Dopa Decarboxylase and Alanine Racemase." BBA - Proteins and Proteomics, 2011, 1814, 1438-1446.
  46. Jiali Gao, " Computation of Kinetic Isotope Effects for Enzymatic Reactions”, " Science China - Chemistry (Special Issue on Year of Chemistry), 2011, 54, 1841-1850.
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Revised: November 01, 2006.