Difference between revisions of "Publications"

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"Replica Exchange Molecular Dynamics Simulations of an α/β-type Small Acid Soluble Protein (SASP)," Ojeda-May, P.; '''Pu, J.''', ''Biophys. Chem.'', in press.
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"Replica Exchange Molecular Dynamics Simulations of an α/β-type Small Acid Soluble Protein (SASP)," Ojeda-May, P.; '''Pu, J.''', ''Biophys. Chem.'' '''2013''', ''184'', 17-21.
 
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Revision as of 07:38, 10 September 2013

  1. "Isotropic Periodic Sum Treatment of Long-Range Electrostatic Interactions in Combined Quantum Mechanical and Molecular Mechanical Calculations," Ojeda-May, P.; Pu, J., submitted.
  2. "Replica Exchange Molecular Dynamics Simulations of an α/β-type Small Acid Soluble Protein (SASP)," Ojeda-May, P.; Pu, J., Biophys. Chem. 2013, 184, 17-21.
  3. "H-loop Histidine Catalyzes ATP Hydrolysis in the E. coli ABC-Transporter HlyB," Zhou, Y.; Ojeda-May, P.; Pu, J. Phys. Chem. Chem. Phys., in press (DOI:10.1039/C3CP50965F; SI: movie_S1& movie_S2; see also arXiv:1304.0052 [q-bio.BM]).
  4. "All-atom Simulations of Torque Generation in F1-ATPase," Pu, J.; Nam, K.; Karplus, M., submitted.
  5. "Expanding the Horizon of the Thymine Isostere Biochemistry: Unique Dimers formed via Photoreaction between a Thymine and a Toluene residue in the Dinucleotide Framework," Liu, D.; Zhou, Y.; Pu, J.; Li, L. Chem. Eur. J. 2012, 18, 7823-7833.
  6. "Chemical Synthesis, Crystal Structure and Enzymatic Evaluation of a Dinucleotide Spore Photoproduct Analogue Containing Formacetal Linker," Lin, G.; Chen, C.-H; Pink, M.; Pu, J.; Li, L. Chem. Eur. J. 2011, 17, 9658-9668.

    --- Before IUPUI ---

  1. "How Biomolecular Motors Work: Synergy between Single Molecule Experiments and Single Molecule Simulations," Karplus, M.; Pu, J., in Springer Series in Chemical Physics 2010, 96 (Single Molecule Spectroscopy in Chemistry, Physics, and Biology), pp. 271-285.
  2. "A Coupled Polarization-Matrix Inversion and Iteration Approach for Accelerating the Dipole Convergence in a Polarizable Potential Function," Xie, W.; Pu, J.; Gao, J. J. Phys. Chem. A 2009, 113, 2109-2116.
  3. "CHARMM: The Biomolecular Simulation Program," Brooks, B. R.; Brooks III, C. L.; MacKerell, Jr., A. D.; Nilsson, L.; Petrella, R. J.; Roux, B.; Won, Y.; Archontis, G.; Bartels, C.; Boresch, S.; Caflisch, A.; Caves, L.; Cui, Q.; Dinner, A. R.; Feig, M.; Fischer, S.; Gao, J.; Hodoscek, M.; Im, W.; Kuczera, K.; Lazaridis, T.; Ma, J.; Ovchinnikov, V.; Paci, E.; Pastor, R. W.; Post, C. B.; Pu, J.; Schaefer, M.; Tidor, B.; Venable, R. M.; Woodcock, H. L.; Wu, X.; Yang, W.; York, D. M.; Karplus, M. J. Comput. Chem. 2009, 30, 1545-1614.
  4. "How Subunits Coupling Produces the Rotary Motion in F1-ATPase," Pu, J.; Karplus, M. Proc. Natl. Acad. Sci. USA 2008, 105, 1192-1197 (track II, direction submission); selected by Faculty of 1000: http://f1000.com/1102040
  5. "Development of a Polarizable Intermolecular Potential Function for Liquid Amides and Alkanes," Xie, W.; Pu, J.; MacKerell, Jr. A. D.; Gao, J. J. Chem. Theor. Comput. 2007, 3, 1878-1889.
  6. "Multi-coefficient Gaussian-3 Calculation of the Rate Constant for the OH + CH4 Reaction and its 12C/13C Kinetic Isotope Effect with Emphasis on the Effects of Coordinate System and Tensional Treatment," Ellingson, B. A.; Pu, J.; Lin, H.; Zhao, Y.; Truhlar, D. G. J. Phys. Chem. A 2007, 111, 11706-11717.
  7. "Mechanism and Free Energies of Enzymatic Reactions," Gao, J.; Ma, S.; Major, D. T.; Nam, K.; Pu, J.; Truhlar, D. G. Chem. Rev. 2006, 106, 3188-3209.
  8. "Multidimensional Tunneling, Recrossing, and Transmission Coefficient for Enzymatic Reactions," Pu, J.; Gao, J.; Truhlar, D. G. Chem. Rev. 2006, 106, 3140-3169.
  9. "Hydride Transfer Reaction Catalyzed by Hyperthermophilic Dihydrofolate Reductase is Dominated by Quantum Mechanical Tunneling and is Promoted by Both Inter- and Intramonomeric Correlated Motions," Pang, J.; Pu, J.; Gao, J.; Truhlar, D. G; Allemann, R. K. J. Am. Chem. Soc. 2006, 128, 8015-8023.
  10. "Searching for Saddle Points by Using the Nudged Elastic Band Method: An Implementation for Gas-Phase Systems," Gonzalez-Garcia, N.; Pu, J.; Gonzalez-Lafont, A.; Lluch, J. M.; Truhlar, D. G. J. Chem. Theor. Comput. 2006, 2, 895-904.
  11. "Nonperfect Synchronization of Reaction Center Rehybridization in the Transition State of the Hyrdride Transfer Catalyzed by Dihydrofolate Reductase," Pu, J.; Ma, S.; Garcia-Viloca, M.; Gao, J.; Truhlar, D. G.; Kohen, A. J. Am. Chem. Soc. 2005, 127, 14879-14886.
  12. "Generalized Hybrid Orbital Method for Combined Quantum Mechanical and Molecular Mechanical Calculations Based on Density Functional Theory and Hybrid Density Functional Theory," Pu, J.; Gao, J.; Truhlar, D. G. ChemPhysChem 2005, 6, 1853-1865.
  13. "Small Temperature Dependence of the Kinetic Isotope Effect for the Hydride Transfer Reaction Catalyzed by Escherichia coli Dihydrofolate Reductase," Pu, J.; Gao, J.; Truhlar, D. G. J. Phys. Chem. B 2005, 109, 8551-8556.
  14. "Temperature Dependence of Carbon-13 Kinetic Isotope Effects of Importance to Global Climate Change," Lin, H.; Zhao, Y.; Ellingson, B. A.; Pu, J.; Truhlar, D. G. J. Am. Chem. Soc. 2005, 127, 2830-2831.
  15. "Benchmark Calculations of Reaction Energies, Barrier Heights, and Transition State Geometries for Hydrogen Abstraction from Methanol by a Hydrogen Atom," Pu, J.; Truhlar, D. G. J. Phys. Chem. A 2005, 109, 773-778.
  16. "Use of Block Hessian for the Optimization of Molecular Geometries," Pu, J.; Truhlar, D. G. J. Chem. Theor. Comput. 2005, 1, 54-60.
  17. "Combining Self-Consistent-Charge Density-Functional Tight-Binding (SCC-DFTB) with Molecular Mechanics by the Generalized Hybrid Orbital (GHO) Method," Pu, J.; Gao, J.; Truhlar, D. G. J. Phys. Chem. A 2004, 108, 5454-5463.
  18. "Efficient Molecular Mechanics for Chemical Reactions: Multiconfiguration Molecular Mechanics using Partial Electronic Structure Hessians," Lin, H.; Pu, J.; Albu, T. V.; Truhlar, D. G. J. Phys. Chem. A 2004, 108, 4112-4124.
  19. "Tests of Second-Generation Density Functionals for Thermochemical Kinetics," Zhao, Y.; Pu, J.; Lynch, B. J. Truhlar, D. G. Phys. Chem. Chem. Phys. 2004, 6, 673-676.
  20. "Benchmark Results for Hydrogen Atom Transfer between Carbon Centers and Validation of Electronic Structure Methods for Bond Energies and Barrier Heights," Dybala-Defratyka, A.; Paneth, P.; Pu, J.; Truhlar, D. G. J. Phys. Chem. A 2004, 108, 2475-2468.
  21. "Generalized Hybrid Orbital (GHO) Method for Combining Ab Initio Hartree-Fock Wave Functions with Molecular Mechanics," Pu, J.; Gao, J.; Truhlar, D. G. J. Phys. Chem. A 2004, 108, 632-650.
  22. "Lateral Confinement of Image Electron Wavefunction by an Interfacial Dipole Lattice," G. Dutton, Pu, J.; Truhlar, D. G.; Zhu, X. -Y. J. Chem. Phys. 2003, 118, 4337.
  23. "Tests of Potential Energy Surfaces for H + CH4 → CH3 + H2: Deuterium and Muonium Kinetic Isotope Effects for the Forward and Reverse Reaction," Pu, J.; Truhlar, D. G. J. Chem. Phys. 2002, 117, 10675.
  24. "Validity of Variational Transition State Theory with Multi-dimensional Tunneling Contributions against Accurate Quantum Mechanical Dynamics for H + CH4 → CH3 + H2 in an Extended Temperature Interval," Pu, J.; Truhlar, D. G. J. Chem. Phys. 2002, 117, 1479.
  25. "Parametrized Direct Dynamics Study of Rate Constants of H with CH4 from 250 to 2400 K," Pu, J.; Truhlar, D. G. J. Chem. Phys. 2002, 116, 1468.
  26. "Test of Variational Transition State Theory with Multidimensional Tunneling Contributions Against an Accurate Full-Dimensional Rate Constant Calculation for a Six-Atom system," Pu, J.; Corchado, J. C.; Truhlar, D. G. J. Chem. Phys. 2001, 115, 6266.
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