Ruhong Zhou  Ruhong Zhou photo       

contact information

Distinguished RSM & Head, Soft Matter Science, IBM Research
AAAS Fellow, APS Fellow



  1. Ruhong Zhou, MOLECULAR MODELING AT THE ATOMIC SCALE: Methods and Applications in Quantitative Biology, Editor, CRC Press, Taylor & Francis, ISBN-10: 1466562951 | ISBN-13: 978-1466562950, 2014 (384 pages)


  2. Ruhong Zhou, Modeling of Nanotoxicity, Springer, ISBN-10:  3319153811 | ISBN-13: 978-3319153810, 2015

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


  2. R. H. 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,


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


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


  5. 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


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


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


  9. R. H. 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


  10. R. H. 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


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


  12. R. H. 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


  13. R. H. 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


  14. R. H. 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


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


  16. R. H. 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


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


  18. R. H. 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


  19. F. Figueirido, R. H. 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


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


  21. R. H. 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


  22. J. Banks, G. Kirminski, R. H. 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


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


  24. H. A. Stern, G. Kirminski, J. Banks, R. H. 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


  25. 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. H. Zhou, Blue Gene: A vision for protein science using a petaflop supercomputer, IBM Systems Journal 40, 310-327, 2001


  26. R. H. 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


  27. R. H. 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


  28. R. H. 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


  29. R. H. 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


  30. G. A. Kaminski, H. A. Stern, B. J. Berne, R. A. Friesner, Y. Cao, R. B. Murphy, R. H. 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


  31. R. H. 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


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


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


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


  35. 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. H. Zhou, Blue Matter, An Application Framework for Molecular Simulation on Blue Gene , J. Parallel & Distrib. Comput. 63, 759-773, 2003


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


  37. R. H. 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


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


  39. R. H. 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


  40. R. H. 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


  41. R. H. 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


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


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


  44. J. Feng, R. H. 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


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


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


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


  48. L. Ye, J. Li, T. Liu, Z. Wu and R. H. Zhou, Wavelets approach for protein trajectory analysis, J. Bioinfo. Comp. Biol. 3, 1351-1370, 2005


  49. P. Liu, X. Huang, R. H. Zhou and B. J. Berne, Observation of a Dewetting Transition in the Collapse of the Melittin Tetramer, Nature, 437, 159-162, 2005


  50. R. H. Zhou, Protein Folding with the 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


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


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


  53. R. H. Zhou, A. Royyuru, P. Athma, F. Suits and BD Silverman, Magnitude and Spatial Orientation of the Hydrophobic Moments of Multi-Domain Proteins, Int. J. Bioinf. Res. Appl. 2, 161-176, 2006


  54. M. Eleftheriou, A. Rayshubski, J. Pitera, B. Fitch, R. H. 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


  55. B. G. Fitch, A. Rayshubskiy, M. Eleftheriou, T.J. C. Ward, M. Giampapa, Y. Zhestkov, M. C. Pitman, F. Suits, A. Grossfield, J. Pitera, W. Swope, R. H. Zhou, S. Feller, and R. S. Germain. Blue Matter: Strong scaling of molecular dynamics on Blue Gene/L. In V. Alexandrov, D. van Albada, P. Sloot, and J. Dongarra, editors, International Conference on Computational Science (ICCS 2006), volume 3992 of LNCS, pages 846–854. Springer-Verlag, 2006.


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


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


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


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


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


  61. R. H. Zhou, Dewetting in Nanoscale Hydrophobic Plates Collapse and Protein Complex Folding, NIC Workshop 2006,From Computational Biophysics to Systems Biology, Jan Meinke, Olav Zimmermann, Sandipan Mohanty, Ulrich H.E. Hansmann (Editors), John von Neumann Institute for Computing, Jeulich,NIC Series, Vol. 34, pp. 53-58, 2006


  62. R. H. 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


  63. R. H. 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


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


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


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


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


  68. L. Ye, Z. Wu, M. Eleftheriou, and R. H. Zhou, Single-mutation-induced stability loss in protein lysozyme, Biochem. Soc. Trans. 35, 1551-1557, 2007


  69. L. Hua, R. H. 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


  70. M. G. Krone, L. Hua, P. Soto, R. H. Zhou, B. J. Berne, and J-E. Shea, Role of Water in Mediating the Assembly of Alzheimer Amyloid-beta Abeta16-22 Protofilaments, J. Am. Chem. Soc. 130, 11066-11072, 2008


  71. R. H. 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


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


  73. R. H. 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


  74. B. J. Berne, J. D.Weeks, and R. H. Zhou, Dewetting and Hydrophobic Interaction in Physical and Biological Systems, Annu. Rev. Phys. Chem. 60, 85–103, 2009


  75. R. Zangi, R. H. Zhou, and B. J. Berne, Urea’s Action on Hydrophobic Interactions, J. Am. Chem. Soc. 131, 1535-1541, 2009


  76. Z. Xia, Z. Zhu, J. Zhu, and R. H. Zhou, Recognition Mechanism of siRNA by Viral p19 Suppressor of RNA Silencing: A Molecular Dynamics Study, Biophys. J. 96, 1761-1769, 2009


  77. P. Das, J. Li, A. K. Royyuru, and R. H. 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, Vol. 30, 1654-1633, 2009


  78. Antonios Tavlarakis and R. H. Zhou, Linear interaction energy approximation for binding affinities of nevirapine and HEPT analogues with HIV-1 reverse transcriptase, Mol. Simul. 35, 1224-1241, 2009


  79. Y. Tu, P. Xiu, R. Wan, J. Hu, R. H. Zhou and H. Fang, Water-mediated signal multiplication with Y-shaped carbon nanotubes, Proc. Natl. Acad. Sci. 106, 18120-18124, 2009


  80. Z. Xia, J. Gu, J. Zhu and R. H. Zhou, Using a Mutual Information Based Site Transition Network to Map the Genetic Evolution of Influenza A/H3N2 Virus, Bioinformatics, 25, 2309-2317, 2009


  81. P. Das, J. A. King, and R. H. Zhou, beta-strand interactions at the domain interface critical for the stability of human lens gammaD-crystallin, Prot. Sci., 19, 131-140, 2010


  82. J. Bernauer, S. C. Flores, X. Huang, S. Shin and R. H. Zhou, Multi-resolution modeling of biological macromolecules, Pacific Symposium on Biocomputing, 15, 200-204, 2010


  83. P. Das, R. H. Zhou, Urea-induced drying of carbon nanotubes, J. Phys. Chem. B 114, 5427-5430, 2010


  84. J. A. Morrone, R. H. Zhou, and B. J. Berne, Molecular dynamics with multiple time scales: How to avoid pitfalls, J. Comp. Theo. Chem., 6, 1798-1804, 2010


  85. Z. Wang, C. Wang, P. Xiu, W. Qi, Y. Tu, Y. Shen, R. H. Zhou, R. Zhang, and H. Fang, Size Dependence of Nanoscale Confinement on Chiral Transformation, Chem. Eur. J. 16, 6482-6487, 2010


  86. J. Li, P. Das, R. H. Zhou, Single mutation effects on conformational change and membrane deformation of influenza Hemagglutinin fusion peptides, J. Phys. Chem. B 114, 8799-8806, 2010


  87. Y. Tu, R. H. Zhou, and H. Fang, Signal transmission, conversion and multiplication by polar molecules confined in nanochannels, Nanoscale, 2, 1976-1983, 2010 (featured article)


  88. G. Zuo, Q. Huang, G. Wei, R. H. Zhou, and H. Fang, Plugging Into Proteins: Poisoning Protein Function by a Hydrophobic Nanoparticle, ACS Nano, 4, 7508-7514, 2010


  89. M. Gao, Z. She, and R. H. Zhou, Key residues that play a critical role in lysozyme denaturing in 8M urea, J. Phys. Chem. B 114, 15687-15693, 2010


  90. R. H. Zhou, J. Li, L. Hua, Z. Yang, and B. J. Berne, Comment on “Urea-Mediated Protein Denaturation: A Consensus View”, J. Phys. Chem. B, 115, 1323-1326, 2011


  91. P. Xiu, Z. Yang, B. Zhou, P. Das, H. P. Fang and R. H. Zhou, Urea-Induced Drying of Hydrophobic Nanotubes: Comparison of Different Urea Models, J. Phys. Chem. B, 115, 2988-2994, 2011


  92. J. Bernauer, S. C. Flores, X. Huang, S. Shin, R. H. Zhou, Introduction to Multi-Scale Modelling of Biosystems: From Molecular to Mesoscale, Pacific Symposium on Biocomputing 16:177-180, 2011


  93. G. Zuo, H. P. Fang, and R. H. Zhou, Nanotoxicity: Exploring the interactions between carbon nanotubes and proteins, Editor J. M. Marulanda, Carbon Nanotubes -Growth and Applications, pp539-564, InTech Publisher, ISBN 978-953-307-566-2, 2011


  94. Z. Xia, P. Das, T. Huynh, A. K. Royyuru, and R. H. Zhou, Modeling Mutations of Influenza Virus with IBM Blue Gene, IBM J. Res. Dev., 55, 7:1-7:11, 2011


  95. G. Zuo, W. Gu, H. P. Fang, and R. H. Zhou, Competition between a Carbon Nanotube and a Proline-Rich Motif Ligand on the Binding Pocket of SH3 Domain, J. Phys. Chem. C, 12322-12328, 2011


  96. P. Das, J. A. King, and R. H. Zhou, Aggregation of Partially Folded gamma-Crystallin Associated with Human Cataracts via Domain Swapping at the C-terminal beta-strands, Proc. Natl. Acad. Sci, 108, 10514-10519, 2011 (featured article)


  97. C. Ge, J. F. Du, L. Zhao, L. Wang, Y. Liu, D. H. Li, Y. Yang, R. H. Zhou, Y. L. Zhao, Z. F. Chai, C. Y. Chen, Binding of human serum proteins on single-wall carbon nanotubes reduces cytotoxicity, Proc. Natl. Acad. Sci. 108, 16968-16973, 2011 (featured article)


  98. Z. X. Yang, B. Y. Shi, H. J. Lu, P. Xiu, and R. H. Zhou, Dewetting transitions in the self-assembly of two amyloidogenic β-sheets and the importance of matching surfaces, J. Phys. Chem. B 115, 11137-11144, 2011


  99. G. Zuo, X Zhou, Q Huang, H. P. Fang, and R. H. Zhou, Adsorption of Villin Headpiece onto Graphene, Carbon Nanotube and C60: Effect of Contacting Surface Curvatures on Binding Affinity, J. Phys. Chem. C 115, 23323-23328, 2011


  100. P. Xiu, Y. Tu, X. L. Tian, H. P. Fang, and R. H. Zhou, Molecular Wire of Urea in Carbon Nanotube: A Molecular Dynamics Study, Nanoscale, 4, 652-658, 2012


  101. R. H. Zhou, Protein folding: Bridging the gap between theory and experiment, Editorial for Hot-topic Special Issue, Curr. Phys. Chem., 2, 2-3, 2012


  102. G. Zuo, P. Xiu, X. Zhou, R. H. Zhou, and H. P. Fang, Protein conformational changes upon binding with carbon nanotubes, Curr. Phys. Chem., 2, 12-22, 2012


  103. Z. X. Yang, Z. Wang, X. L. Tian, P. Xiu, and R. H. Zhou, Amino Acid Analogues Bind to Carbon Nanotube via π-π interactions: Comparison of Molecular Mechanical and Quantum Mechanical Calculations, J. Chem. Phys. 136, 025103, 2012


  104. S. C. Flores, J. Bernauer, S. Shin, R. H. Zhou, and X. Huang, Multiscale modeling of macromolecular biosystems, Briefings in Bioinformatics, 13, 395-405, 2012


  105. W. F. Li, R. H. Zhou, and Y. G. Mu, Linking Denaturation to Salting Effects: Action of Aqueous Urea and NaCl Solutions on Protein Components, J. Phys. Chem. B 116, 1446-1451, 2012


  106. Amanda Barnard, Changming Li, R. H. Zhou, Y. L. Zhao, Modeling of nanoscale, Nanoscale, 4, 1042-1043, 2012


  107. Z. Xia, T. Huynh, S. G. Kang, and R. H. Zhou, Free Energy Simulations Reveal Both Hydrophobic and Polar Interactions are Important to Influenza Hemagglutinin Antibody Binding, Biophys. J. 102, 1453-1461, 2012


  108. C. Guo, Y. Luo, R. H. Zhou, and G. H. Wei, Dissecting the self-assembly pathway of diphenylalanine-based nanovesicles and nanotubes, ACS Nano, 6, 3907-3918, 2012


  109. T. Y. Yoo, A. Adhikari, Z. Xia, T. Huynh, K. F. Freed, R. H. Zhou, T. R. Sosnick, The folding transition state of protein L is extensive with non-native interactions, J. Mol. Biol. 420, 220-234, 2012


  110. X. Y. Li, Y. C. Shi, Y. L. Yang, H. L. Du, R. H. Zhou, and Y. L. Zhao, How does water-nanotube interaction influence water flow through the nanochannel? J. Chem. Phys. 136, 175101, 2012


  111. L. Zhao, Y. L. Zhao, and R. H. Zhou, Novel design of a nanoflowmeter based on carbon nanotubes, J. Phys. Chem. C, 116, 13429-13434, 2012


  112. Z. Xia, P. Xiu, and R. H. Zhou, Small Molecules and Peptides inside Carbon Nanotubes: Impact of Nanoscale Confinement, Editor A. Lazinica, Recent Progress in Carbon Nanotube Research, ISBN 980-953-307-485-1, InTech Publisher, 2012


  113. Z. X. Yang, P. Xiu, B. Y. Shi, L. Hua, and R. H. Zhou, A coherent microscopic picture for urea-induced denaturation of proteins, J. Phys. Chem. B 116, 8856-8862, 2012


  114. L. Cong, R. H. Zhou, Y. C. Kuo, M. Cunniff, and F. Zhang, Comprehensive Interrogation of Natural TALE DNA Binding Modules and Transcriptional Repressor Domains, Nature Commun. 3, 968, 2012


  115. Z. Xia, P. Clark, T. Huynh, P. Loher, Y. Zhao, H.W. Chen, P. Y. Ren, I. Rigoutsos, and R. H. Zhou, Molecular dynamics simulations of Ago silencing complexes reveal a large repertoire of admissible ‘seed-less’ targets, (Nature) Sci. Rep. 2, 569, 2012


  116. B. Q. Luan and R. H. Zhou, Nanopore Sensor for Detecting Nanotoxicity of a Carbon Nanotube to Proteins, J. Phys. Chem. Lett. 3, 2337-2341, 2012


  117. S. G. Kang, G. Q. Zhou, P. Yang, Y. Liu, B. Y. Sun, T. Huynh, H. Meng, L. Zhao, G. M. Xing, C. Y. Chen, Y. L. Zhao, R. H. Zhou, Molecular Mechanism of Pancreatic Tumor Metastases Inhibition by Metallofullerenol Gd@C82(OH)22: Implication for de novo Design of Nanomedicine, Proc. Natl. Acad. Sci., 109, 15431-15436, 2012 (featured article)


  118. S.G. Kang, H. Li, T. Huynh, F. Zhang, Z. Xia, Y. Zhang and R. H. Zhou, Molecular Mechanism of Surface-Assisted Epitaxial Self-Assembly of Amyloid-like Peptides, ACS Nano, 6, 9276-9282, 2012


  119. C. J. Tian, P. Xiu, Y. Meng, W. Y. Zhao, Z. G. Wang, and R. H. Zhou, Mechanism of Chiral Inversion of Thalidomide and the Role of Water and Hydroxide Ion, Chem. Eur. J. 18, 14305-14313, 2012 (cover article)


  120. B. Q. Luan, D. Q. Wang, R. H. Zhou, S. Harrer, H. B. Peng, and G. Stolovitzky, Dynamics of DNA Translocation in a Solid-State Nanopore Immersed in Aqueous Glycerol, Nanotechnology, 23, 455102, 2012


  121. Z. Xia, P. Das, E. I. Shakhnovich, and R. H. Zhou, Collapse of Unfolded Proteins in a Mixture of Denaturants, J. Am. Chem. Soc. 134, 18266-18274, 2012


  122. S. G. Kang, T. Huynh, and R. H. Zhou, Metallofullerenol Gd@C82(OH)22 Non-destructively Inhibits Signal Transduction Pathway of WW domain, (Nature) Sci. Rep. 2, 957, 2012


  123. G. H. Zuo, S. G. Kang, P. Xiu, Y. L. Zhao, and R. H. Zhou, Interactions between Proteins and Carbon-Based Nanoparticles: Exploring the Origin of Nanotoxicity at Molecular Level, Small 9, 1546-1556, 2013


  124. Y. Tu , H. Lu, Y. Z. Zhang, T. Huynh, and R. H. Zhou, Capability of Charge Signal Conversion and Transmission by Water Chains Confined inside Y-Shaped Carbon Nanotubes, J. Chem. Phys. 138, 015104, 2013


  125. Z. Xia, T. Huynh, P. Y. Ren and R. H. Zhou, Large Domain Motions in Ago Protein Controlled by the Guide Strand Seed Region Determine the Ago Silencing Complex Recognition Process, PLoS ONE 8, e54620, 2013


  126. S. G. Kang, T. Huynh, and R. H. Zhou, Metallofullerenol Gd@C82(OH)22 Distracts Proline-Rich-Motif from Putative Binding on SH3 domain, Nanoscale 5, 2703-2712, 2013


  127. X. Yin, L. Zhao, S. G. Kang, J. Pan, Y. Song, M. Zhang, G. Xing, F. Wang, J. Y. Li, R. H. Zhou, Y. L. Zhao, Impacts of Fullerene Derivatives to Regulate the Structure and Assembly of Collagen Molecules, Nanoscale 5, 7341-7348, 2013


  128. P. Das, D. Kapoor, K. T. Halloran, R. H. Zhou, and C. R. Matthews, Interplay between Drying and Stability of a TIM Barrel Protein: A Combined Simulation-Experimental Study, J. Am. Chem. Soc. 135, 1882-1890, 2013


  129. S. G. Kang, T. Huynh, Z. Xia, Y. Zhang, H. P. Fang, G. H. Wei and R. H. Zhou, Hydrophobic Interaction Drives Surface-Assisted Epitaxial Assembly of Amyloid-like Peptides, J. Am. Chem. Soc. 135, 3150-3157, 2013


  130. X. P. Ren, C. L. Wang, B. Zhou, H. P. Fang, J. Hu, and R. H. Zhou, Ethanol Promotes Dewetting Transition at Low Concentrations, Soft Matter, 9, 4655-4660, 2013


  131. B. Y. Shi, G. H. Zuo, P. Xiu, and R. H. Zhou, Binding Preference of Carbon Nanotube Over Proline-Rich Motif Ligand on SH3-domain: A Comparison with Different Force Fields, J. Phys. Chem. B 117, 3541-3547, 2013


  132. P. Das, Z. Xia, R. H. Zhou, Collapse of A Hydrophobic Polymer in Mixture of Denaturants, Langmuir 29, 4877-4882, 2013


  133. Y. Tu, M. Lv, P. Xiu, T. Huynh, M. Zhang, M. Castelli, Z. R. Liu, Q. Huang, C. H. Fan, H. P. Fang, and R. H. Zhou, Destructive Extraction of Phospholipids from E. Coli Membrane by a Graphene Nanosheet, Nature Nanotech. 8, 594-601, 2013


  134. B. Dai, S. G. Kang, T. Huynh, H. Z. Lei, M. Castelli, J. Hu, Y. Zhang and R. H. Zhou, Salts Drive Controllable Multi-Layered Upright Assembly of Amyloid-like Peptides at Mica/Water Interface, Proc. Natl. Acad. Sci. 110, 8543-8548, 2013


  135. Z. Xia, Z. X. Yang, T. Huynh, J. A. King, and R. H. Zhou, UV-radiation Induced Disruption of Tightly Packed Dry Cavities in Human γD-crystallin Results in Decreased Stability and Faster Unfolding, (Nature) Sci. Rep. 3, 1560, 2013


  136. X. Y. Zhou, C. L. Wang, F. Wu, M. Feng, J. Y. Li, H. J. Lu, R. H. Zhou, The Ice-like Water Monolayer near the Wall Makes Inner Water Shells Diffuse Faster inside a Charged Nanotube, J. Chem. Phys. 138, 204710, 2013


  137. Z. X. Yang, S. G. Kang, and R. H. Zhou, Nanomedicine: De Novo Design of Nanodrugs, Nanoscale 6, 663-677, 2014


  138. Z. X. Yang, Z. Xia, T. Huynh, J. A. King, and R. H. Zhou, Dissecting the contributions of beta-hairpin tyrosine pair to the folding and stability of long-lived human gammaD-crystallins, Nanoscale 6, 1797-1807, 2014


  139. X. H. Huang, R. H. Zhou, and B. J. Berne, Introduction to Molecular Dynamics and Enhanced Sampling Algorithms, in MOLECULAR MODELING AT THE ATOMIC SCALE: Methods and Applications in Quantitative Biology (Editor Ruhong Zhou), CRC Press, Taylor & Francis, ISBN-10: 1466562951 | ISBN-13: 978-1466562950, 2014


  140. S. G. Kang and R. H. Zhou, Protein and Nanoparticle Interactions: Perspectives of Nanomedicine and Nanotoxicity, in MOLECULAR MODELING AT THE ATOMIC SCALE: Methods and Applications in Quantitative Biology (Editor Ruhong Zhou), CRC Press, Taylor & Francis, ISBN-10: 1466562951 | ISBN-13: 978-1466562950, 2014


  141. Z. Xia and R. H. Zhou, Protein and Nucleic Acid Interactions with Molecular Dynamics Simulations, in MOLECULAR MODELING AT THE ATOMIC SCALE: Methods and Applications in Quantitative Biology (Editor Ruhong Zhou), CRC Press, Taylor & Francis, ISBN-10: 1466562951 | ISBN-13: 978-1466562950, 2014


  142. R. H. Zhou, Biological Water under Confinement: Nanoscale Dewetting, in MOLECULAR MODELING AT THE ATOMIC SCALE: Methods and Applications in Quantitative Biology (Editor Ruhong Zhou), CRC Press, Taylor & Francis, ISBN-10: 1466562951 | ISBN-13: 978-1466562950, 2014


  143. Y. Meng, P. Xiu, B. L. Huang, Z. G. Wang, R. Q. Zhang and R. H. Zhou, A unique feature of chiral transition of a difluorobenzo[c]phenanthrene molecule confined in a boron-nitride nanotube based on molecular dynamics simulations, Chem. Phys. Lett. 591, 265-267, 2014


  144. Z. W. Cai, J. Q. Li, C. J. Yin, Z. X. Yang, J. L. Wu, and R. H. Zhou, Effect of Urea Concentration on Aggregation of Amyloidogenic Hexapeptides (NFGAIL), J. Phys. Chem. B 118, 48-57, 2014


  145. C. Guo, Y. Luo, R. H. Zhou, and G. H. Wei, Triphenylalanine peptides self-assemble into nanospheres and nanorods that are different from the nanovesicles and nanotubes formed by diphenylalanine peptides, Nanoscale, 6, 2800-2811, 2014


  146. Z. Xia, H. B. Chen, S. G. Kang, T. Huynh, J. W. Fang, P. A. Lamothe, B. D. Walker, and R. H. Zhou, The complex and specific pMHC interactions with diverse HIV-1 TCR clonotypes reveal a structural basis for alterations in CTL function, (Nature) Sci. Rep. 4, 4087, 2014


  147. Guillaume Stirnemann, Seung-Gu Kang, R. H. Zhou, and B. J. Berne, How Force Unfolding Differs from Chemical Denaturation, Proc. Natl. Acad. Sci. 111, 3413-3418, 2014


  148. Seung-gu Kang, Payel Das, Scott J. McGrane, Alan J. Martin, Tien Huynh, Ajay K. Royyuru, Andrew J. Taylor, Paul G. Jones, R. H. Zhou, Molecular Recognition of Metabotropic Glutamate Receptor Type 1 (mGluR1): Synergistic Understanding with Free Energy Perturbation and Linear Response Modeling, J. Phys. Chem. B 118, 6393-6404, 2014


  149. W. Li, L. Nordenski, R. H. Zhou, and Y. G. Mu, Conformation-dependent DNA Attraction, Nanoscale, 6, 7085-7092, 2014
  150. Seung-gu Kang, Raul Araya-Secchi, Deqiang Wang, Bo Wang, Tien Huynh, R. H. Zhou, Dual Inhibitory Pathways of Metallofullerenol Gd@C82(OH)22 on Matrix Metalloproteinase-2: Molecular insight into drug-like nanomedicine, (Nature) Sci. Rep. 4, 4775, 2014
  151. B. Song, Q. Sun, H. Li, B. S. Ge, J. S. Pan, A. T. S. Wee, R. H. Zhou, X. Y. Gao, F. Huang, and H. P. Fang, Irreversible Denaturation of Proteins due to Aluminum-induced Formation of Ring Structures, Angew. Chem. Intl. Ed., 53, 6358-6363, 2014
  152. Raul Araya-Secchi, Tomas Perez-Acle, Seung-gu Kang, Tien Huynh, Alejandro Bernardin, Agustin D. Martinez, Juan C. Saez, , R. H. Zhou, Characterization of a novel water pocket inside the human Cx26 hemi-channel structure, Biophys J. 106, 599-609, 2014
  153. Camilo A. Jimenez-Cruz, Seung-gu Kang, and R. H. Zhou, Large Scale Molecular Simulations of Nanotoxicity, WIREs Sys. Biol. Med., 6, 329-343, 2014
  154. R. H. Zhou and H. J. Gao, Cytotoxicity of Graphene: Recent Advances and Future PerspectiveNanotoxicity, WIREs Nanomed. Nanobiotech. 6, 452-474, 2014
  155. Yang Gao, Bo Zhou, Seung-gu Kang, Minsi Xin, Ping Yang, Xing Dai, Zhigang Wang, and R.H. Zhou, Effect of Ligands on Characteristics of (CdSe)13 Quantum Dot, RSC Advances, 4, 27146-27151, 2014
  156. Xiankai Jiang, Jun Gao, Tien Huynh, Ping Huai, Chunhai Fan, R. H. Zhou*, and Bo Song*, An Improved DNA Force Field for ssDNA Interactions with Gold Nanoparticles, J. Chem. Phys. 140, 234102, 2014
  157. J. Y. Li, X. F. Wang, X. F. Gao, Y. L. Zhao and R. H. Zhou, Rotation Motion of Designed Nano-Turbine, (Nature) Sci. Rep. 4, 5846, 2014
  158. Binquan Luan, Bo Zhou, Tien Huynh, and R. H. Zhou, Controlled Transport of DNA through a Y-shaped Carbon Nanotube in a Solid Membrane, Nanoscale, 6, in press, 2014
  159. Yang Gao, Xing Dai, Seung-gu Kang, Camilo A. Jimenez-Cruz, Minsi Xin, Yan Meng, Jie Han, Zhigang Wang, and R. H. Zhou, Structural and electronic properties of uranium-encapsulated Au14 cage, (Nature) Sci. Rep. 4, 5862, 2014
  160. Minsi Xin, Xing Dai, Jie Han, Mingxing Jin, Camilo A. Jimenez-Cruz, Dajun Ding, Zhigang Wang, and R. H. Zhou, Carbon nanotubes adsorb U atoms differently in their inner and outer surfaces, RSC Advances, 4, 30074-30080, 2014
  161. Yuxing Peng, Zhen Cao, R. H. Zhou, and Gregory A. Voth, Path Integral Coarse-graining Replica Exchange Method for Enhanced Sampling, J. Comp. Theo. Chem., 10, 3634-3640, 2014
  162. Jian Gao, Liming Wang, Seung-gu Kang, Lina Zhao, Mingjuan Ji, Chunying Chen, Yuliang Zhao, R. H. Zhou, and Jingyuan Li, Size-Dependent Impact of CNT on Dynamical Properties of Calmodulin, Nanoscale, 6, 12828-12837, 2014
  163. Jiajia Liu, Zaixing Yang, Haotian Li, Zonglin Gu, Jose A. Garate, and R. H. Zhou, Dewetting transition assisted clearance of (NFGAILS) amyloid fibrils from cell membranes by graphene, J. Chem. Phys. 141, 22D520, 2014
  164. Yuanzhao Zhang, Camilo A. Jimenez-Cruz, Jian Wang, Bo Zhou, Zaixing Yang and R. H. Zhou, Bio-mimicking of Proline-Rich Motif Applied to Carbon Nanotube Reveals Unexpected Subtleties Underlying Nanoparticle Functionalization, Sci. Rep. 4, 7229, 2014
  165. Xing Dai, Yang Gao, Minsi Xin, Zhigang Wang, R. H. Zhou, The ground state and electronic structure of Gd@C82: A systematic theoretical investigation of first principle density functionals, J. Chem. Phys. 141, 244306, 2014
  166. Ruixia Song, Wei Feng, Camilo A. Jimenez-Cruz, Bo Wang, Wanrun Jiang, Zhigang Wang, R. H. Zhou, Water Film inside Graphene Nanosheets: Electron Transfer Reversal between Water and Graphene via Tight Nano-confinement, RSC Adv. 5, 274-280, 2015
  167. Binquan Luan, Tien Huynh, Lin Zhao, R. H. Zhou, Potential Toxicity of Graphene to Cell Functions via Disrupting Protein-Protein Interactions, ACS Nano, 9, 663-669, 2015
  168. Yuxing Peng, Jessica M. Swanson, Seung-gu Kang, R. H. Zhou, and Gregory A. Voth, Hydrated Excess Protons Can Create Their Own Water Wires, J. Phys. Chem. B 119, 9212-9218, 2015
  169. Binquan Luan , Tien Huynh , and R. H. Zhou, Nanopore-based Sensors for Ligand-Receptor Lead-Optimization, J. Phys. Chem. Lett., 6, 331-337, 2015
  170. Weifeng Li, Lushan Wang, R. H. Zhou, Yuguang Mu, Ionic liquid induced inactivation of cellobiohydrolase I from Trichoderma reesei, Green Chem. 17, 1618-1625, 2015
  171. Cuicui Ge, Jian Tian, Yuliang Zhao, Chunying Chen, R. H. Zhou, and Zhifang Chai, Towards understanding of nanoparticle-protein corona, Arch. Tox. 89, 519-539, 2015
  172. Zonglin Gu, Zaixing Yang, Lingle Wang, Hong Zhou, Camilo A. Jimenez-Cruz, and R. H. Zhou, The role of basic residues in the adsorption of blood proteins onto the graphene surface, Sci. Rep. 5, 10873, 2015
  173. Zonglin Gu, Zaixing Yang, Yu Chong, Cuicui Ge, Jeffrey K. Weber, David R. Bell and R. H. Zhou, Surface Curvature Relation to Protein Adsorption for Carbon-based Nanomaterials, Sci. Rep. 5, 10886, 2015
  174. Binquan Luan, Tien Huynh, R. H. Zhou, Simplified TiO2 force fields for studies of its interaction with biomolecules, J. Chem. Phys. 142, 234102, 2015
  175. Michael C. Baxa, Wookyung Yu, Aashish N. Adhikari, Liang Ge, Zhen Xia, R. H. Zhou, Karl F. Freed, Tobin R. Sosnick, Even with non-native interactions, the updated folding transition states of the homologs Protein G & L are extensive and similar, Proc. Natl. Acad. Sci. 112, 8302-8307, 2015
  176. Y Chong, C Ge, Z Yang, JA Garate, Z Gu, JK Weber, J Liu, R. H. Zhou, Reduced Cytotoxicity of Graphene Nanosheets Mediated by Blood-Protein Coating, ACS Nano 9, 5713-5724, 2015
  177. Yuanming Pan, Liming Wang, Seung-gu Kang, Chengdu Sun, Youyong Lu, Zaixing Yang, Tien Huynh, Chunying Chen, R. H. Zhou*, Yuliang Zhao*, and Mingzhou Guo*, Gd-Metallofullerenol Nanomaterial Suppresses Pancreatic Cancer Metastasis by Inhibiting the Interaction of Histone Deacetylase 1 and Metastasis-Associated Protein 1, ACS Nano, 9, 6826-6836, 2015
  178. Deyi An, Jiguo Su, Jeffrey K. Weber, Xueyun Gao, R. H. Zhou*, Jingyuan Li*, A peptide-coated gold nanocluster exhibits unique behavior in protein activity inhibition, J. Am. Chem. Soc. 137, 8412-8418, 2015
  179. Wei Zhang, Tien Huynh, Peng Xiu, Bo Zhou, Chao Ye, Binquan Luan, R. H. Zhou, Revealing the importance of surface morphology of nanomaterials to biological responses: Adsorption of the villin headpiece onto graphene and phosphorene, Carbon, 94, 895-902, 2015
  180. Guangxin Duan, Seung-gu Kang, Xin Tian, Jose Antonio Garate, Lin Zhao, Cuicui Ge, H. Zhou, Protein corona mitigates the cytotoxicity of graphene oxide by reducing its physical interaction with cell membrane, Nanoscale, 7, 15214-15224, 2015
  181. Xiaofeng Wang, Jeffrey K. Weber, Lei Liu,  Mingdong Dong,  H. Zhou*, and   Jingyuan Li*, A novel form of β-strand assembly observed in Aβ33–42 adsorbed onto graphene, Nanoscale, 7, 15341-15348, 2015
  182. Hua Yue, Wei Wei, Zonglin Gu, Dezhi Ni, Nana Luo, Zaixing Yang, Lin Zhao,   Jose Antonio Garate, R. H. Zhou*, Zhiguo Su*, Guanghui Ma*, Exploration of graphene oxide as intelligent platform for cancer vaccine,  Nanoscale, 7, 19949-19957, 2015
  183. Angelique Hölzemer, Christina F. Thobakgale, Camilo A. Jimenez-Cruz, Wilfredo F. Garcia-Beltran, Jonathan M. Carlson, Nienke H. van Teijlingen, Jaclyn K. Mann, Manjeetha Jaggernath, Seung-gu Kang, Christian Körner, Amy W. Chung, Jamie L. Schafer, David T. Evans, Galit Alter, Bruce D. Walker, Philip J. Goulder, Mary Carrington, Pia Hartmann, Thomas Pertel, H. Zhou, Thumbi Ndung’u, Marcus Altfeld, Selection of an HLA-C*03:04-Restricted HIV-1 p24 Gag Sequence Variant Is Associated with Viral Escape from KIR2DL3+ Natural Killer Cells: Data from an Observational Cohort in South Africa, PLoS Medicine, 12, e1001900, 2015
  184. Zaixing Yang, Cuicui Ge, Jiajia Liu, Yu Chong, Zonglin Gu, Camilo A. Jimenez-Cruz, Zhifang Chai, H. Zhou, Destruction of amyloid fibrils by graphene through penetration and extraction of peptides, Nanoscale 7, 18725-18737, 2015
  185. Binquan Luan, Tien Huynh, Jingyuan Li, H. Zhou, Nanomechanics of Protein Unfolding Outside a Generic Nanopore, ACS Nano 10, 317-323, 2016
  186. Weifeng Li, Yanmei Yang, Jeffrey K. Weber, Gang Zhang, and H. Zhou, Tunable, Strain-Controlled Nanoporous MoS2 Filter for Water Desalination, ACS Nano 10, 1829-1835, 2016
  187. Zonglin Gu, Yuanzhao Zhang, Binquan Luan, H. Zhou, DNA translocation through single-layer boron nitride nanopores, Soft Matter 12, 817-823, 2016
  188. Binquan Luan and H. Zhou, Wettability and Friction of Water on a MoS2 nanosheet, Appl. Phys. Lett. 108, 131601, 2016
  189. Binquan Luan, Tien Huynh, and H. Zhou, Complete Wetting of Graphene by Biological Lipids, Nanoscale 8, 5750 – 5754, 2016
  190. Zhonghe Xu, Shuang Zhang, Jeffrey K. Weber, Binquan Luan, H. Zhou*, Jingyuan Li,* Sequential protein unfolding through a carbon nanotube pore, Nanoscale 8, 12143-12151, 2016
  191. Xuan-Yu Meng, Baoyu Li, Shengtang Liu, Hongsuk Kang, Lin Zhao, H. Zhou, EGCG in Green Tea Induces Aggregation of HMGB1 Protein through Large Conformational Changes with Polarized Charge Redistribution, Sci. Rep. 6, 22128, 2016
  192. Binquan Luan, Tien Huynh, and H. Zhou, Potential Interference of Protein-Protein Interactions by Graphyne, J. Phys. Chem. B 120, 2124-2131, 2016
  193. Ramy El-Sayed, Zonglin Gu, Zaixing Yang, Jeffrey K. Weber, Hu Li, Klaus Leifer, Muhammet S. Toprak, H. Zhou*, and Bengt Fadeel*, Single-Walled Carbon Nanotubes Inhibit the Cytochrome P450 Enzyme, CYP3A4, Sci. Rep. 6, 21316, 2016
  194. Qingming Deng, Jun Pan, Xiaohui Yin, Xiaofeng Wang, Lina Zhao, Seung-gu Kang, Camilo A. Jimenez-Cruz, H. Zhou, Jingyuan Li, Toward High Permeability, Selectivity and Controllability of Water Desalination with FePc Nanopores, Phys. Chem. Chem. Phys. 18, 8140-8147, 2016
  195. Yang Ling, Zonglin Gu, Seung-gu Kang, Judong Luo, R. H. Zhou, Structural damage of a β-sheet protein upon adsorption onto Molybdenum Disulfide nanotubes, J. Phys. Chem. C 120 , 6796-6803, 2016
  196. Yuanzhao Zhang, Jeffrey K. Weber, H. Zhou, Folding and Stabilization of Native-Sequence-Reversed Proteins, Sci. Rep. 6, 25138, 2016
  197. Yuanchao Zhang, Jingquan Liu, Da Li, Xing Dai, Fuhua Yan, H. Zhou, Xavier A. Conlan, Colin J. Barrow, Jin He, Xin Wang, Wenrong Yang, Self-Assembled Core-Satellite Gold Nanoparticle Networks for Ultrasensitive Detection of Chiral Molecules by Recognition Tunneling, ACS Nano, 10, 5096-5103, 2016
  198. Zonglin Gu, Weifeng Li, Linbi Hong, H. Zhou, Exploring Biological Effects of MoS2 Nanosheets on Native Structures of α-helical Peptides, J. Chem. Phys. 144, 175103, 2016
  199. Dongling Cao, Jinlin He, Jiaying Xu, Mingzu Zhang, Lin Zhao, Guangxin Duan, Youwen Cao, H. Zhou*, and Peihong Ni*, Polymeric prodrugs conjugated with reduction-sensitive dextran-camptothecin and pH-responsive dextran-doxorubicin: An effective combinatorial drug delivery platform for cancer therapy, Poly. Chem. 7, 4198-4212, 2016
  200. Mei Feng, Hongsuk Kang, Zaixing Yang, Binquan Luan, H. Zhou, Potential Disruption of Protein-Protein Interactions by Graphene Oxide, J. Chem. Phys. 144, 225102, 2016
  201. Yerko Escalona, Jose A. Garate, Raul Araya-Secchi, Tien Huynh, H. Zhou, Tomas Perez-Acle, Exploring the membrane potential of simple dual-membrane systems as models for Gap-junction channels, Biophys. J. 110, 2678-2688, 2016
  202. Zonglin Gu, Zaixing Yang, Seung-gu Kang, Jerry R. Yang, Judong Luo, H. Zhou, Robust Denaturation of Villin Headpiece by MoS2 Nanosheet: Potential Molecular Origin of the Nanotoxicity, Sci. Rep. 6, 28252, 2016
  203. Xuan-Yu Meng, Shengtang Liu, Meng Cui, H. Zhou, and Diomedes Logothetis, The Molecular Mechanism of Opening the Helix Bundle Crossing (HBC) Gate of a Kir Channel, Sci. Rep. 6, 29399, 2016
  204. Motilal Mathesh, Binquan Luan, Taiwo Akanbia, Jeffrey K. Weber, Jingquan Liu, Colin J. Barrow, H. Zhou* and Wenrong Yang*, Opening Lids: Modulation of Lipase Immobilization by Graphene Oxides, ACS Catalysis, 6, 4760-4768, 2016
  205. Binquan Luan, Kai Loon Chen, and H. Zhou, Mechanism of Divalent-Ion-Induced Charge Inversion of Bacterial Membrane, J. Phys. Chem. Lett. 7, 2434-2438, 2016
  206. Shengtang Liu, Xuan-Yu Meng, Jose Manuel Perez-Aguilar, and H. Zhou, An In Silico study of TiO2 nanoparticles interaction with twenty standard amino acids in aqueous solution, Sci. Rep. 6, 37761, 2016
  207. Wei Zhang, Chao Ye, Linbi Hong, Zaixing Yang, and H. Zhou, Molecular Structure and Dynamics of Water on Pristine and Strained Phosphorene: Wetting and Diffusion at Nanoscale, Sci. Rep. 6, 38327, 2016
  208. Nana Luo, Jeffrey K. Weber, Shuang Wang, Binquan Luan, Hua Yue, Xiaobo Xi, Jing Du, Zaixing Yang, Wei Wei, H. Zhou, Guanghui Ma, PEGylated Graphene Oxide Elicits Strong Immunological Responses Despite Surface Passivation, Nature Communications, 8, 14537, 2017
  209. Phil De Luna, Sahar Mahshid, Jagotamoy Das, Binquan Luan, Edward H Sargent, Shana O Kelley, H. Zhou, High-Curvature Nanostructuring Enhances Probe Display for Biomolecular Detection, Nano Lett. 17, 1289–1295, 2017
  210. Xin Tian, Zaixing Yang, Guangxin Duan, Anqing Wu, Zonglin Gu, Leili Zhang, Chunying Chen, Zhifang Chai, Cuicui Ge, and H. Zhou, Graphene Oxide Nanosheets Retard Cellular Migration via Disruption of Actin Cytoskeleton, Small, 13, 1602133, 2017
  211. Baoyu Li, Weifeng Li, Jose Manuel Perez‐Aguilar, H. Zhou, Mild Binding of Protein to C2N Monolayer Reveals Its Suitable Biocompatibility, Small, 13, 1603685, 2017
  212. Zonglin Gu, Phil De Luna, Zaixing Yang, H. Zhou, Structural Influence of Proteins Upon Adsorption to MoS2 Nanomaterials: Comparison of MoS2 Force Field Parameters, Phys. Chem. Chem. Phys. 19, 3039-3045, 2017
  213. Wei Zhang, Chao Ye, Phil De Luna and H. Zhou, Snatching the Ligand or Destroying the Structure: Disruption of WW Domain by Phosphorene, J. Phys. Chem. C, 121, 1362–1370, 2017
  214. Zonglin Gu, Zaixing Yang, Binquan Luan, Xifa Zhou, Linbi Hong, Hong Zhou, Judong Luo, H. Zhou, Membrane Insertion and Phospholipids Extraction by Graphyne Nanosheets, J. Phys. Chem. C, 121, 2444–2450, 2017
  215. Duan, Y. Zhang, B. Luan, J. K. Weber, R. W. Zhou, Z. X. Yang, L. Zhao, J. Xu, J. Luo, and R. H. Zhou, Graphene-Induced Pore Formation on Cell Membranes, Sci. Rep. 7, 42767, 2017
  216. Zheng, Z. X. Yang, D. Gui, Z. Liu, X. Wang, X. Dai, S. Liu, L. Zhang, Y. Gao, L. Chen, D. Sheng, Y. Wang, J. Diwu, J. Wang, R. H. Zhou, Z. F. Chai, T. E. Albrecht-Schmitt, and S. Wang, Overcoming the crystallization and designability issues in the ultrastable zirconium phosphonate framework system, Nature Communications 8, 15369, 2017
  217. Zonglin Gu, Lin Zhao, Shengtang Liu, Guangxin Duan, Jose M. Perez-Aguilar, Judong Luo, Weifeng Li , and H. Zhou, Orientational Binding of DNA Guided by the C2N Template, ACS Nano, 11, 3198–3206, 2017
  218. Liu, X. Dai, Z. Bai, Y. Wang, Z. X. Yang, L. Zhang, L. Xu, L. Chen, Y. Li, D. Gui, J. Diwu, J. Wang, R. H. Zhou, Z. F. Chai, and S. Wang, Highly Sensitive and Selective Uranium Detection in Natural Water Systems Using a Luminescent Mesoporous Metal–Organic Framework Equipped with Abundant Lewis Basic Sites: A Combined Batch, X-ray Absorption Spectroscopy, and First Principles Simulation Investigation, Environ. Sci. Technol., 51, 3911–3921, 2017
  219. Mei Feng, David R. Bell, Judong Luo and  H. Zhou, Impact of graphyne on structural and dynamical properties of calmodulin, Phys. Chem. Chem. Phys., 19, 10187-10195, 2017
  220. Zhonghe Xu, Yang Sun, Jeffrey K. Weber, Yi Cao, Wei Wang, Daniel Jasinski, Peixuan Guo, H. Zhou, and Jingyuan Li, Directional mechanical stability of Bacteriophage ϕ29 motor’s 3WJ-pRNA: extraordinary robustness along portal axis, Science Advances, 3, e1601684, 2017
  221. Leili Zhang, Hongsuk Kang, Francisco X. Vázquez, Leticia Toledo-Sherman, Binquan Luan, and R. H. Zhou, Molecular Mechanism on Stabilizing Huntingtin N17 Helical Structure in Micelle Environment, J. Phys. Chem. B 121, in press, 2017