Publications

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  1. P. L. Cao, R. Zhou and X. Zhou, Interaction among adsorbed Li atoms on Si(100) and phase change of surface structure, Phys. Lett. A 159, 179, 1991

  2. R. Zhou and P. L. Cao, Theoretical study of CN chemisorbed on Pd(111) surface, Surf. Sci. 243, L49, 1991

  3. S. B. Fu, R. Zhou and P. L. Cao, Investigation of the Chemisorption process of nitric oxide on Si(100)-2x1 , Surf. Sci. 247, L224, 1991

  4. R. Zhou, P. L. Cao and S. B. Fu, Adsorption of Ammonia on Si(100) and Si(111) surface: a theoretical approach , Surf. Sci. 249, 129, 1991,

  5. R. Zhou and P. L. Cao, Theoretical Investigation of the Ammonia Adsorption Process on Si(100)-2x1 Surface, Chin. Phys. Lett. 8, 94, 1991

  6. P. L. Cao, X. Zhou and R. Zhou, Mechanism of the Phase Change of Li/Si(100)-2x1 structure , ACTA PHYSICA SINICA, 40, 1116, 1991

  7. R. Zhou and P. L. Cao, Strong Chemisorption and Dissociation of N2 on Cr(110) Surfaces, ACTA PHYSICA SINICA, 41, 295, 1992

  8. R. Zhou and P. L. Cao, Mechanism of the formation of Ag linear chains in the early stage of Ag deposition on Si(100), Proc. Intl. Symp. on Vac. Sci. & Tech. 92 (ISVST92), Wuxi, China, September 1992

  9. R. Zhou and P. L. Cao, Molecular Cluster Analysis of O2 adsorption and dissociation on Pt(111), Phys. Lett. A 169 , 167, 1992

  10. R. Zhou and P. L. Cao, pi-bonded N2 on Cr(110) as a precursor for dissociation: Molecular orbital theory, J. Phys. Cond. Matt. 4, 2429, 1992

  11. R. Zhou and P. L. Cao, Atom superposition and Electron delocalization--Molecular Orbital theoretical study of Oxygen chemisorption on Pt(111) surface, ACTA PHYSICA SINICA, 42, 470, 1993

  12. P. L. Cao and R. Zhou, Bonding characterization of Br on Si(100), J. Phys. Cond. Matt. 5, 2897, 1993

  13. R. Zhou and P. L. Cao, Ethylene adsorption and decomposition on Si(100)-2x1: a semi-empirical quantum chemical study, J. Phys. Cond. Matt. 5, 2887, 1993

  14. R. Zhou, P. L. Cao and L. Q. Lee, Total-energy calculation for acetylene adsorption and decomposition on Si(100)-2x1, Phys. Rev. B 47, 10601, 1993

  15. R. Zhou, P. L. Cao and L. Q. Lee, Cluster models study of Ag bonding, migration and interaction on Si(100), Surf. Sci. Lett. 290, L649, 1994

  16. P. L. Cao, L. Q. Lee, J. Dai, and R. Zhou, Adsorption and dissociation of PH3 on Si(100)-2x1 and Si(111)-7x7: theoretical study , J. Phys. Cond. Matt. 6, 6103, 1994

  17. R. Zhou and B. J. Berne, A new molecular dynamics method combing the reference system propagator algorithm with a fast multipole method for simulating proteins , J. Chem. Phys. 103, 9444, 1995

  18. S. J. Stuart, R. Zhou and B. J. Berne, Molecular Dynamics with Multiple Timescales: The Selection of Efficient Reference System Propagators , J. Chem. Phys. 105, 1426, 1996

  19. R. Zhou, S. J. Stuart and B. J. Berne, Molecular Dynamics for nonequilibrium systems in which there are a small number of very hot particles in a cold bath: Reference System Propagator Methods , J. Chem. Phys. 105, 235, 1996

  20. F. Figueirido, R. Zhou, B. J. Berne, and R. M. Levy, Large Scale simulation of macromolecules in solution: Combining the periodic Fast Multipole Method with multiple time step integrators , J. Chem. Phys. 106, 9835, 1997

  21. R. Zhou, Novel methods for efficient sampling of conformation space of proteins , PhD thesis, Columbia University Press, July 1997

  22. F. Figueirido, R. M. Levy, R. Zhou, and B. J. Berne, Erratum: "Large Scale simulation of macromolecules in solution: Combining the periodic Fast Multipole Method with multiple time step integrators", J. Chem. Phys. 107, 7002, 1997

  23. R. Zhou and B. J. Berne, Smart Walking: a new method for Boltzmann sampling of protein conformations, J. Chem. Phys. 107, 9185, 1997

  24. R. Zhou and B. J. Berne, Large scale simulation of solvated proteins: Combining a multiple time step integrator with a periodic fast multipole method , in P. Deuflhard, J. Hermans, B. Leimkuhler, A. Mark, S. Reich, R. D. Skeel editors, Computational Molecular Dynamics: Challenges, Methods, Ideas, Volume 4 of Lecture Notes in Computational Science and Engineering, Springer-Verlag, Nov 1998

  25. J. Banks, G. Kirminski, R. Zhou, B. J. Berne, and R. A. Friesner, Parametrizing a Polarizable Force Field from ab initio Data. I: The Fluctuating Point Charge Model , J. Chem. Phys. 110, 741-754, 1999

  26. B. J. Berne and R. Zhou, Fast methods for simulating biomolecular systems with long-range electrostatic interactions by molecular dynamics, US patent No. 5915230, Jun 22, 1999

  27. M. Friedrich, R. Zhou, S. Edinger, and R. A. Friesner, Poisson-Boltzmann Analytical Gradients for Molecular Modeling Calculations, J. Phys. Chem. 103, 3057-3061, 1999

  28. H. A. Stern, G. Kirminski, J. Banks, R. Zhou, B. J. Berne, R. A. Friesner, Fluctuating charge, polarizable dipole, and combined models: Parameterization from ab initio quantum chemistry, J. Phys. Chem. B103, 4730-4737, 2000

  29. F. Allen, G. Almasi, W. Andreoni, D. Beece, B. J. Berne, A. Bright, J. Brunheroto, C. Cascaval, J. Castanos, P. Coteus, P. Crumley, A. Curioni, M. Denneau, W. Donath, M. Eleftheriou, B. Fitch, B. Fleischer, C. J. Georgiou, R. Germain, M. Giampapa, D. Gresh, M. Gupta, R. Haring, H. Ho, P. Hochschild, S. Hummel, T. Jonas, D. Lieber, G. Martyna, K. Maturu, J. Moreira, D. Newns, M. Newton, R. Philhower, T. Picunko, J. Pitera, M. Pitman, R. Rand, A. Royyuru, V. Salapura, A. Sanomiya, R. Shah, Y. Sham, S. Singh, M. Snir, F. Suits, R. Swetz, W. C. Swope, N. Vishnumurthy, T. J. C. Ward, H. Warren, and R. Zhou, Blue Gene: A vision for protein science using a petaflop supercomputer, IBM Systems Journal 40, 310-327, 2001

  30. R. Zhou, E. Harder, H. Xu and B. J. Berne, Efficient multiple time step method for use with Ewald and Particle-Mesh Ewald for large biomolecular systems , J. Chem. Phys. 115, 2348-2358, 2001

  31. R. Zhou, R. A. Friesner, A. Ghosh, R. C. Rizzo, W. L. Jorgensen, and R. M. Levy, New Linear Interaction Method for Binding Affinity Calculations using a Continuum Solvent Model, J. Phys. Chem. B105, 10388-10397, 2001

  32. R. Zhou, B. J. Berne and R. Germain, Free energy landscape of a beta-hairpin folding in explicit water, Proc. Natl. Acad. Sci. 98, 14931-14936, 2001

  33. R. Zhou and B. D. Silverman, Detecting native protein folds among large decoy sets with hydrophobic moments profiling, Proc. Paci. Symp. Biocomp. 2002, Eds. R. B. Altman, A. K. Dunker, L. Hunter, K. Lauderdale and T. E. Klein, p673-684, World Scientific, Singapore, 2002

  34. G. A. Kaminski, H. A. Stern, B. J. Berne, R. A. Friesner, Y. Cao, R. B. Murphy, R. Zhou, and T. A. Halgren, Development of a Polarizable Force Field for Proteins via ab initio Quantum Chemistry: First Generation Model and Gas phase Tests, J. Comp. Chem. 23, 1515-1531, 2002

  35. R. Zhou and B. J. Berne, Can a continuum solvent model reproduce the free energy landscape of a beta-hairpin folding in water?, Proc. Natl. Acad. Sci. 99, 12777-12782, 2002

  36. G. Kaminski, R. A. Friesner and R. Zhou, A computationally inexpensive modification of the point dipole electrostatic polarization model for molecular simulation, J. Comp. Chem. 24, 267-276, 2003

  37. R. Zhou, B. D. Silverman, A. Royyuru, and P. Athma, Spatial Profiling of Protein Hydrophobicity: Native vs. Decoy Structures , Proteins, 52, 561-572, 2003

  38. R. Zhou, Folding free energy landscape of protein folding in water: explicit vs. implicit solvent, Proteins 53, 148-161, 2003

  39. B. G. Fitch, R. S. Germain, M. Mendell, J. Pitera, M. Pitman, A. Rayshubskiy, Y. Sham, F. Suits, W. Swope, T. J. C. Ward, Y. Zhestkov, and R. Zhou, Blue Matter, An Application Framework for Molecular Simulation on Blue Gene , J. Parallel & Distrib. Comput. 63, 759-773, 2003

  40. R. Zhou, Trp-cage: Folding Free Energy Landscape in Explicit Water, Proc. Natl. Acad. Sci., 100, 13280-13285, 2003

  41. R. Zhou, Exploring Protein Folding Free Energy Landscape: Replica Exchange Monte Carlo , Eds, J. E. Gubernatis, The Monte Carlo Method in the Physical Sciences, Celebrating the 50th Anniversary of the Metropolis Algorithm, AIP Conf. Proc. Vol 690, 406-408, 2003

  42. R. Zhou, Sampling Protein Folding Free Energy Landscape: Coupling Replica Exchange Method with P3ME/RESPA Algorithm , J. Mol. Grap. Model. 22, 451-463, 2004

  43. R. Zhou, G. Dent, A. Royyuru, and P. Athma, Assessment of Protein Structure Refinement with Replica exchange Method, Eds, A. Gramada, P. E. Bourne, RECOMB2004 - Currents in Computational Molecular Biology, 390-391, 2004

  44. R. Zhou, A. Royyuru, P. Athma, and B. D. Silverman, Hydrophobicity of Multi-domain Proteins: Spatially Profiling their Distribution, Eds, A. Gramada, P. E. Bourne, RECOMB2004 - Currents in Computational Molecular Biology, 441-442, 2004

  45. R. Zhou, G. Krilov and B. J. Berne, Comment on "Can a continuum solvent model reproduce the free energy landscape of a beta-hairpin folding in water?": The Poisson-Boltzman Model, J. Phys. Chem. B 108, 7528 - 7530, 2004

  46. W. Swope, J. Pitera, F. Suits, M. Pitman, M. Eleftheriou, B. Fitch, R. Germain, A. Rayshubskiy, T. J. C. Ward, Y. Zhestkov, and R. Zhou, Describing Protein Folding Kinetics by Molecular Dynamics Simulations: II. Application to a beta-hairpin Peptide, J. Phys. Chem. B 108, 6582-6594, 2004

  47. R. Zhou, X. Huang, C. Margulius and B. J. Berne, Hydrophobic Collapse in Multi-domain Protein Folding, Science, 305, 1605-1609, 2004

  48. J. Feng, R. Zhou, and L. Parida, Pattern Discovery Analysis for Protein Folding Trajectories, Ed. Y. P. Chen and L. S. Wong, Proc. 3rd Asia-Pac. Bioinfo. Conf., p95-99, Imperial College Press, London, UK, 2004

  49. X. Huang, R. Zhou, and B. J. Berne, Drying and Hydrophobic Collapse of Paraffin Plates, J. Phys. Chem. B 109, 3546-3552, 2005

  50. L. Parida and R. Zhou, Combinatorial Pattern Discovery Approach for the Folding Trajectory Analysis of a beta-hairpin, PLoS Comp. Biol. 1, 32-40, 2005

  51. J. Li, H. Chen, T. Liu, L. Ye, H. Fang, X. Tang, Z. Wu and R. Zhou, Water Hydration Near Graphite-CH3 and Graphite-COOH Surfaces, J. Phys. Chem. B 109, 13639-13648, 2005

  52. P. Liu, X. Huang, R. Zhou and B. J. Berne, Drying and Hydrophobic Collapse of Melittin Tetramer, Nature, 437, 159-162, 2005

  53. Y. Lei, J. Li, T. Liu, Z. Wu and R. Zhou, Wavelets approach for protein trajectory analysis, J. Bioinfo. Comp. Biol., 3, 1351-1370, 2005

  54. R. Zhou, Protein Folding with Parallel Replica Exchange Molecular Dynamics Method,, Ed. Albert Zomaya, "Parallel Computing for Bioinformatics and Computational Biology", p397-425, John Wiley & Sons Publisher, New Jersey, 2006

  55. H. Lan, X. Huang, R. Zhou and B. J. Berne, Water dynamics in the salvation shell of a multi-domain protein, J. Phys. Chem. B. 110, 3704-3711, 2006

  56. R. Zhou, A. Royyuru, P. Athma, F. Suits and B. D. Silverman, Magnitude and Spatial Orientation of the Hydrophobic Moments of Multi-Domain Proteins, Int. J. Bioinfo. Res. Appl., 2, 161-176, 2006

  57. T. Z. Lwin, R. Zhou and R. Luo, Is Poisson-Boltzmann theory insufficient for protein folding simulations? J. Chem. Phys. 124, 34902-34907, 2006

  58. M. Eleftheriou, A. Rayshubski, J. Pitera, B. Fitch, R. Zhou, R. Germain, Parallel Implementation of the Replica Exchange Molecular Dynamics Algorithm on Blue Gene/L, International Parallel and Distributed Processing Symposium HiCOMB 2006.

  59. M. Eleftheriou, A. Rayshubski, J. Pitera, B. Fitch, R. Zhou, R. Germain, Large Scale Parallel Implementation of Replica Exchange on Blue Gene/L, SIAM Conference on Parallel Processing for Scientific Computing San Francisco, California, USA February 22-24, 2006

  60. B. Fitch, A. Rayshubskiy, M. Eleftheriou, T.J. C. Ward, Mark Giampapa, Yuri Zhestkov, M. Pitman, F. Suits, A. Grossfield, J. Pitera, W. Swope, R. Zhou, R. Germain. S. Feller, Blue Matter: Strong Scaling of Molecular Dynamcis on Blue Gene/L, International Parallel and Distributed Processing Symposium, 2006

  61. P. Liu, X. Huang, R. Zhou and B. J., Berne, Hydrophobic Aided Replica Exchange Method for Protein Folding, J. Phys. Chem. B, 110, 19018-19022, 2006

  62. M. Eleftheriou, R. Germain, A. Royyuru and R. Zhou, Thermal denaturing of mutant lysozyme with both OPLSAA and CHARMM force fields, J. Am. Chem. Soc. 128, 13388-13395, 2006

  63. T. Liu, L. Ye, H. Chen, J. Li, Z. Wu and R. Zhou, A Combined Steepest Descent and Genetic Algorithm (SD/GA) Approach for the Optimization of Solvation Parameters, Mol. Simul. 32, 427-435, 2006

  64. X. Li, J. Li and M. Eleftheriou and R. Zhou, Hydration and Dewetting near Fluorinated Superhydrophobic Plates, J. Am. Chem. Soc. 128, 12439-12447, 2006

  65. R. Zhou, Replica Exchange Molecular Dynamics Method for Protein Folding,, Methods Mol. Biol. 350, 205-223, 2006

  66. R. Zhou, L. Parida, K. Kapila, and S. Mudur, PROTERAN: Animated Terrain Evolution for Visual Analysis of Patterns in Protein Folding Trajectory, Bioinformatics, 23, 99-106, 2007

  67. R. Zhou, M. Eleftheriou, A. Royyuru, B. J. Berne, Destruction of long-range interactions by a single mutation in lysozyme, Proc. Natl. Acad. Sci., 104, 5824-5829, 2007

  68. X. Huang, M. Hagen, B. Kim, R. A. Friesner, R. Zhou, and B. J. Berne, Replica Exchange with Solute Tempering: Efficiency in Large Scale Systems, J. Phys. Chem. B 111, 5405-5410, 2007

  69. L. Hua, X. Huang, P. Liu, R. Zhou, and B. J. Berne, Nanoscale Dewetting Transition in Protein Complex Folding, J. Phys. Chem. B 111, 9069-9077, 2007

  70. J. Li, X. Gong, H. Lu, D. Li, H. Fang and R. Zhou, Electrostatic Gating of a Nanometer Water Channel, Proc. Natl. Acad. Sci., 104,3687-3692, 2007

  71. J. Li, Z. Yang, H. Fang, R. Zhou and X. Tang, Effect of the Carbon Nanotube Length on the Water Permeability, Chinese Phys. Lett., 24, 2710-2713, 2007

  72. J. L. Lorieau, R. Zhou, and A. E. McDermott,Tertiary Structure and Charge Effects on the Catalysis of Yeast Triosephosphate Isomerase Using Molecular Dynamics Simulations, J. Mol. Biol., 2007

  73. L. Yei, T. Liu, Z. Wu and R. Zhou, Sequence-based protein domain boundary prediction using BP neural network with various property profiles, Proteins, 71,300-307, 2008

  74. L. Hua, R. Zhou, D. Thirumalai, B. J. Berne, Urea denaturation by stronger dispersion interactions with proteins than water implies a 2-stage unfolding, Proc. Natl. Acad. Sci., 105, 16928-16933, 2008

  75. M. G. Krone, L. Hua, P. Soto, R. Zhou, B. J. Berne, and J-E. Shea, Role of Water in Mediating the Assembly of Alzheimer Amyloid-beta Ab16-22 Protofilaments, J. Am. Chem. Soc. 130, 11066-11072, 2008

  76. R. Zhou, M. Eleftheriou, C.-C. Hon, R. S. Germain, A. K. Royyuru, and B. J. Berne, Massively parallel molecular dynamics simulations of lysozyme unfolding, IBM J. Res. Dev. 52, 19-30, 2008

  77. R. Zhou, P. Das, A. K. Royyuru, Single Mutation Induced H3N2 Hemagglutinin Antibody Neutralization: A Free Energy Perturbation Study, Cover article, J. Phys. Chem. B 112, 15813-15820, 2008

  78. R. Zangi, R. Zhou, and B. J. Berne, Urea's Action on Hydrophobic Interactions, J. Am. Chem. Soc. 131, 1535-1541, 2009
  79. B. J. Berne, J. D.Weeks, and R. Zhou, Dewetting and Hydrophobic Interaction in Physical and Biological Systems, Annu. Rev. Phys. Chem. 2009, 60, 85–103

  80. Z. Xia, Z. Zhu, J. Zhu, and R. Zhou, Recognition Mechanism of siRNA by Viral p19 Suppressor of RNA Silencing: A Molecular Dynamics Study, Biophys. J. 96, in press, 2009

  81. P. Das, J. Li, A. K. Royyuru, and R. Zhou, A Double Mutation Can Alter Receptor Specificity of Avian H5N1 Virus Hemagglutinin: A Free Energy Simulation Study, J. Comp. Chem. Special Issue on Free Energy Perturbation, 2009