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. Diego Chowell, Luc GT Morris, Claud M Grigg, Jeffrey K Weber, Robert M Samstein, Vladimir Makarov, Fengshen Kuo, Sviatoslav M Kendall, David Requena, Nadeem Riaz, Benjamin Greenbaum, James Carroll, Edward Garon, David M Hyman, Ahmet Zehir, David Solit, Michael Berger, R. H. Zhou, Naiyer A Rizvi, Timothy A Chan, Patient HLA class I genotype influences cancer response to checkpoint blockade immunotherapy, Science, 359, 582-587,  2018
  2. Ge Fang, Weifeng Li, Xiaomei Shen, Jose Manuel Perez-Aguilar, Yu Chong, Xingfa Gao, Zhifang Chai, Chunying Chen, Cuicui Ge, and R. H. Zhou, Differential Pd-Nanocrystal Facets Demonstrate Distinct Antibacterial Activity against Gram-positive and Gram-negative Bacteria, Nature Communications, 9, 129, 2018
  3. Alok V. Joglekar, Zhe Liu, Jeffrey K. Weber, Yong Ouyang, John D. Jeppson, Won Jun Noh, Pedro A. Lamothe-Molina, Huabiao Chen, Seung-gu Kang, Michael T. Bethune, R. H. Zhou, Bruce D. Walker, David Baltimore, HIV-specific T cell receptors from patients with differential immunologic control are functionally indistinguishable, Proc. Natl. Acad. Sci., 115, in press, 2018
  4. Zonglin Gu, Leigh D. Plant, Xuan-Yu Meng, Jose Manuel Perez-Aguilar, Zegao Wang, Mingdong Dong, Diomedes E. Logothetis, and R. H. Zhou, Exploring the Nanotoxicology of MoS2: A Study on the Interaction of MoS2 Nanoflake and K+ Channels, ACS Nano, DOI: 10.1021/acsnano.7b07871, 2018
  5. Jing Liu, Seung-gu Kang, Peng Wang, Yue Wang, Xiaonan Lv, Ying Liu, Fei Wang, Zonglin Gu, Zaixing Yang, Jeffrey K Weber, Ning Tao, Zhihai Qin, Qing Miao, Chunying Chen, R. H. Zhou, Yuliang Zhao, Molecular mechanism of Gd@C82(OH)22 increasing collagen expression: Implication for encaging tumor, Biomaterials, 152, 24-36, 2018
  6. David R. Bell, Seung-gu Kang, Tien Huynh, R. H. Zhou, Concentration-dependent binding of CdSe quantum dot on SH3 domain, Nanoscale, DOI: 10.1039/C7NR06148J, 2018
  7. Dongfang Ma, Xuan-Yu Meng, David R. Bell, Shengtang Liu,  R. H. Zhou, Inhibition of CYP2C8 by metallofullerenol Gd@C82(OH)22 through blocking substrate channels and substrate recognition sites, Carbon 127, 667-675, 2018



  1. Nana Luo, Jeffrey K. Weber, Shuang Wang, Binquan Luan, Hua Yue, Xiaobo Xi, Jing Du, Zaixing Yang, Wei Wei, R. H. Zhou, Guanghui Ma, PEGylated Graphene Oxide Elicits Strong Immunological Responses Despite Surface Passivation, Nature Communications, 8, 14537, 2017
  2. 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
  3. Li, Z. Yang, Y. Wang, Z. Bai, T. Zheng, X. Dai, S. Liu, D. Gui, W. Liu, M. Chen, L. Chen, J. Diwu, L. Zhu, R. H. Zhou, Z. Chai, T. E. Albrecht-Schmitt, and S. Wang, A Robust Mesoporous Cationic Thorium Organic Framework that Rapidly Traps Large Anionic Persistent Organic Pollutants, Nature Communications, 8, 1354, 2017
  4. Zhonghe Xu, Yang Sun, Jeffrey K. Weber, Yi Cao, Wei Wang, Daniel Jasinski, Peixuan Guo, R. 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
  5. Hongsuk Kang, Francisco X. Vázquez, Leili Zhang, Payel Das, Leticia Toledo-Sherman, Binquan Luan, Michael Levitt, and R.H. Zhou, Emerging β-Sheet Rich Conformations in Supercompact Huntingtin Exon-1 Mutant Structures, J. Am. Chem. Soc. 139, 8820-8827, 2017
  6. Lin Zhu, Daopeng Sheng, Chao Xu, Xing Dai, Mark A Silver, Jie Li, Peng Li, Yaxing Wang, Yanlong Wang, Lanhua Chen, Chengliang Xiao, Jing Chen, R.H. Zhou, Chao Zhang, Omar K Farha, Zhifang Chai, Thomas E Albrecht-Schmitt, Shuao Wang, Identifying the Recognition Site for Selective Trapping of 99TcO4–in a Hydrolytically Stable and Radiation Resistant Cationic Metal–Organic Framework, J. Am. Chem. Soc. 139, 14873-14876, 2017
  7. Shen, B. Luan, H. Pei, Z. X. Yang, X. Zuo, G. Liu, J. Shi, L. Wang, R. H. Zhou, W. Cheng, C. H. Fan, Humidity-Responsive Single Nanoparticle Layer Plasmonic Films, Adv. Mater. 29, 1606796, 2017
  8. Phil De Luna, Sahar Mahshid, Jagotamoy Das, Binquan Luan, Edward H Sargent, Shana O Kelley, R.H. Zhou, High-Curvature Nanostructuring Enhances Probe Display for Biomolecular Detection, Nano Lett. 17, 1289–1295, 2017
  9. Zonglin Gu, Lin Zhao, Shengtang Liu, Guangxin Duan, Jose M. Perez-Aguilar, Judong Luo, Weifeng Li , and R.H. Zhou, Orientational Binding of DNA Guided by the C2N Template, ACS Nano, 11, 3198–3206, 2017
  10. Rui Shi, Xing Dai, Weifeng Li, Fang Lu, Yang Liu, Huihua Qu, Hao Li, Qiongyang Chen, He Tian, Enhui Wu, Yong Wang, R.H. Zhou, Shuit-Tong Lee, Yeshayahu Lifshitz, Zhenhui Kang, Jian Liu, Hydroxyl-Group-Dominated Graphite Dots Reshape Laser Desorption/Ionization Mass Spectrometry for Small Biomolecular Analysis and Imaging, ACS Nano 11, 9500-9513, 2017
  11. Binquan Luan, Shuo Zhou, Deqiang Wang, H. Zhou, Detecting Interactions between Nanomaterials and Cell Membranes by Synthetic Nanopores, ACS Nano, DOI: 10.1021/acsnano.7b07005, 2017
  12. Xin Tian, Zaixing Yang, Guangxin Duan, Anqing Wu, Zonglin Gu, Leili Zhang, Chunying Chen, Zhifang Chai, Cuicui Ge, and R.H. Zhou, Graphene Oxide Nanosheets Retard Cellular Migration via Disruption of Actin Cytoskeleton, Small, 13, 1602133, 2017
  13. Baoyu Li, Weifeng Li, Jose Manuel Perez‐Aguilar, R.H. Zhou, Mild Binding of Protein to C2N Monolayer Reveals Its Suitable Biocompatibility, Small, 13, 1603685, 2017
  14. Weifeng Li, Xing Dai, Joseph Morrone, Gang Zhang, R.H. Zhou, Thickness Dependent Semiconductor-to-Metal Transition of Two-Dimensional Polyaniline with Unique Work Functions, Nanoscale, 9, 12025-12031, 2017
  15. Fang, B. Luan, C. Ge, Y. Chong, X. Dong, J. Guo, C. Tang, R. H. Zhou, Understanding the Graphene Quantum Dots-Ubiquitin Interaction by Identifying the Interaction Sites, Carbon, 121, 285-291, 2017
  16. Zhu, C. Xiao, X. Dai, J. Li, D. Gui, D. Sheng, L. Chen, R. H. Zhou, Z. F. Chai, T. E. Albrecht-Schmitt, and S. Wang, Exceptional Perrhenate/Pertechnetate Uptake and Subsequent Immobilization by a Low-Dimensional Cationic Coordination Polymer: Overcoming the Hofmeister Bias Selectivity, Environ. Sci. Technol. Lett. 4, 316-322, 2017
  17. 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
  18. Xiuxiu Wang, Baoyu Li, David R. Bell, Weifeng Li, R.H. Zhou, Hydrogen and methane storage and release by MoS2 nanotubes for energy storage, J. Mater. Chem. A 5, 23020-23027, 2017
  19. Lin Zhao, Shengtang Liu, Jiaying Xu, Wei Li, Guangxin Duan, Haichao Wang, Huilin Yang, Zaixing Yang, R.H. Zhou, A new molecular mechanism underlying the EGCG-mediated autophagic modulation of AFP in HepG2 cells, Cell Death & Disease, 8, e3160, 2017
  20. 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
  21. Jeffrey K Weber, R.H. Zhou, Phosphatidylserine-Induced Conformational Modulation of Immune Cell Exhaustion-Associated Receptor TIM3, Sci. Rep. 7, 13579, 2017
  22. Mei Feng, David R. Bell, Judong Luo and  R.H. Zhou, Impact of graphyne on structural and dynamical properties of calmodulin, Phys. Chem. Chem. Phys., 19, 10187-10195, 2017
  23. Zonglin Gu, Phil De Luna, Zaixing Yang,  R.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
  24. Binquan Luan, R.H. Zhou, A Novel Self-Activation Mechanism of Candida antarctica Lipase B, Phys. Chem. Chem. Phys. 19, 15709-15714, 2017
  25. Wei Zhang, Chao Ye, Phil De Luna and R.H. Zhou, Snatching the Ligand or Destroying the Structure: Disruption of WW Domain by Phosphorene, J. Phys. Chem. C, 121, 1362–1370, 2017
  26. Zonglin Gu, Zaixing Yang, Binquan Luan, Xifa Zhou, Linbi Hong, Hong Zhou, Judong Luo, R.H. Zhou, Membrane Insertion and Phospholipids Extraction by Graphyne Nanosheets, J. Phys. Chem. C, 121, 2444–2450, 2017
  27. 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, 4713-4721, 2017
  28. Leili Zhang, Mei Feng, R.H. Zhou, Binquan Luan, Structural Perturbations on Huntingtin N17 Domain during its Folding on 2D-Nanomaterials, Nanotechnol. 28, 354001, 2017
  29. Xu Liu, Guangxin Duan, Weifeng Li, Zhufa Zhou, R.H. Zhou, Membrane Destruction-Mediated Antibacterial Activity of Tungsten Disulfide (WS2), RSC Adv. 7, 37873-37880, 2017


  1. Binquan Luan, Tien Huynh, Jingyuan Li, R.H. Zhou, Nanomechanics of Protein Unfolding Outside a Generic Nanopore, ACS Nano 10, 317-323, 2016
  2. Yuanchao Zhang, Jingquan Liu, Da Li, Xing Dai, Fuhua Yan, R.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
  3. Weifeng Li, Yanmei Yang, Jeffrey K. Weber, Gang Zhang, and R.H. Zhou, Tunable, Strain-Controlled Nanoporous MoS2 Filter for Water Desalination, ACS Nano 10, 1829-1835, 2016
  4. Motilal Mathesh, Binquan Luan, Taiwo Akanbia, Jeffrey K. Weber, Jingquan Liu, Colin J. Barrow, R.H. Zhou* and Wenrong Yang*, Opening Lids: Modulation of Lipase Immobilization by Graphene Oxides, ACS Catalysis, 6, 4760-4768, 2016
  5. Binquan Luan, Tien Huynh, and R.H. Zhou, Complete Wetting of Graphene by Biological Lipids, Nanoscale 8, 5750 – 5754, 2016
  6. Zhonghe Xu, Shuang Zhang, Jeffrey K. Weber, Binquan Luan, R.H. Zhou*, Jingyuan Li,* Sequential protein unfolding through a carbon nanotube pore, Nanoscale 8, 12143-12151, 2016
  7. Binquan Luan, Kai Loon Chen, and R.H. Zhou, Mechanism of Divalent-Ion-Induced Charge Inversion of Bacterial Membrane, J. Phys. Chem. Lett. 7, 2434-2438, 2016
  8. Binquan Luan and R.H. Zhou, Wettability and Friction of Water on a MoS2 nanosheet, Appl. Phys. Lett. 108, 131601, 2016
  9. Zonglin Gu, Yuanzhao Zhang, Binquan Luan, R.H. Zhou, DNA translocation through single-layer boron nitride nanopores, Soft Matter 12, 817-823, 2016
  10. Xuan-Yu Meng, Baoyu Li, Shengtang Liu, Hongsuk Kang, Lin Zhao, R.H. Zhou, EGCG in Green Tea Induces Aggregation of HMGB1 Protein through Large Conformational Changes with Polarized Charge Redistribution, Sci. Rep. 6, 22128, 2016
  11. Ramy El-Sayed, Zonglin Gu, Zaixing Yang, Jeffrey K. Weber, Hu Li, Klaus Leifer, Muhammet S. Toprak, R.H. Zhou*, and Bengt Fadeel*, Single-Walled Carbon Nanotubes Inhibit the Cytochrome P450 Enzyme, CYP3A4, Sci. Rep. 6, 21316, 2016
  12. Yuanzhao Zhang, Jeffrey K. Weber, R.H. Zhou, Folding and Stabilization of Native-Sequence-Reversed Proteins, Sci. Rep. 6, 25138, 2016
  13. Zonglin Gu, Zaixing Yang, Seung-gu Kang, Jerry R. Yang, Judong Luo, R.H. Zhou, Robust Denaturation of Villin Headpiece by MoS2 Nanosheet: Potential Molecular Origin of the Nanotoxicity, Sci. Rep. 6, 28252, 2016
  14. Xuan-Yu Meng, Shengtang Liu, Meng Cui, R.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
  15. Shengtang Liu, Xuan-Yu Meng, Jose Manuel Perez-Aguilar, and R.H. Zhou, An In Silico study of TiO2 nanoparticles interaction with twenty standard amino acids in aqueous solution, Sci. Rep. 6, 37761, 2016
  16. Wei Zhang, Chao Ye, Linbi Hong, Zaixing Yang, and R.H. Zhou, Molecular Structure and Dynamics of Water on Pristine and Strained Phosphorene: Wetting and Diffusion at Nanoscale, Sci. Rep. 6, 38327, 2016
  17. Qingming Deng, Jun Pan, Xiaohui Yin, Xiaofeng Wang, Lina Zhao, Seung-gu Kang, Camilo A. Jimenez-Cruz, R.H. Zhou, Jingyuan Li, Toward High Permeability, Selectivity and Controllability of Water Desalination with FePc Nanopores, Phys. Chem. Chem. Phys. 18, 8140-8147, 2016
  18. 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
  19. Binquan Luan, Tien Huynh, and R.H. Zhou, Potential Interference of Protein-Protein Interactions by Graphyne, J. Phys. Chem. B 120, 2124-2131, 2016
  20. Zonglin Gu, Weifeng Li, Linbi Hong,  R.H. Zhou, Exploring Biological Effects of MoS2 Nanosheets on Native Structures of α-helical Peptides, J. Chem. Phys. 144, 175103, 2016
  21. Mei Feng, Hongsuk Kang, Zaixing Yang, Binquan Luan, R.H. Zhou, Potential Disruption of Protein-Protein Interactions by Graphene Oxide, J. Chem. Phys. 144, 225102, 2016
  22. Dongling Cao, Jinlin He, Jiaying Xu, Mingzu Zhang, Lin Zhao, Guangxin Duan, Youwen Cao, R.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
  23. Yerko Escalona, Jose A. Garate, Raul Araya-Secchi, Tien Huynh, R.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


  1. 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
  2. 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
  3. 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, R.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
  4. 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
  5. Chong, C. Ge, Z. X. Yang, J. A. Garate, Z. Gu, J. K. Weber, J. Liu, R. H. Zhou, Reduced Cytotoxicity of Graphene Nanosheets Mediated by Blood-Protein Coating, ACS Nano 9, 5713-5724, 2015
  6. 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
  7. 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
  8. Zaixing Yang, Cuicui Ge, Jiajia Liu, Yu Chong, Zonglin Gu, Camilo A. Jimenez-Cruz, Zhifang Chai, R.H. Zhou, Destruction of amyloid fibrils by graphene through penetration and extraction of peptides, Nanoscale 7, 18725-18737, 2015
  9. Guangxin Duan, Seung-gu Kang, Xin Tian, Jose Antonio Garate, Lin Zhao, Cuicui Ge, R.H. Zhou, Protein corona mitigates the cytotoxicity of graphene oxide by reducing its physical interaction with cell membrane, Nanoscale, 7, 15214-15224, 2015
  10. 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
  11. 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
  12. 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
  13. Binquan Luan , Tien Huynh , and R.H. Zhou, Nanopore-based Sensors for Ligand-Receptor Lead-Optimization, J. Phys. Chem. Lett., 6, 331-337, 2015
  14. 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
  15. 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
  16. 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
  17. 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
  18. Binquan Luan, Tien Huynh, R.H. Zhou, Simplified TiO2 force fields for studies of its interaction with biomolecules, J. Chem. Phys. 142, 234102, 2015
  19. 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


  1. 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
  2. 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
  3. 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
  4. R.H. Zhou and H. J. Gao, Cytotoxicity of Graphene: Recent Advances and Future PerspectiveNanotoxicity, WIREs Nanomed. Nanobiotech. 6, 452-474, 2014
  5. X. Yang, S. G. Kang, and R. H. Zhou, Nanomedicine: De Novo Design of Nanodrugs, Nanoscale 6, 663-677, 2014
  6. X. Yang, Z. Xia, T. Huynh, J. A. King, and R. H. Zhou, Dissecting the contributions of b-hairpin tyrosine pair to the folding and stability of long-lived human gD-crystallins, Nanoscale 6, 1797-1807, 2014
  7. 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
  8. Li, L. Nordenski, R. H. Zhou, and Y. G. Mu, Conformation-dependent DNA Attraction, Nanoscale, 6, 7085-7092, 2014
  9. 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, 11479-11483, 2014
  10. 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
  11. 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
  12. 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, Sci. Rep. 4, 4087, 2014
  13. 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, Sci. Rep. 4, 4775, 2014
  14. Y. Li, X. F. Wang, X. F. Gao, Y. L. Zhao and R. H. Zhou, Rotation Motion of Designed Nano-Turbine, Sci. Rep. 4, 5846, 2014
  15. 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, Sci. Rep. 4, 5862, 2014
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. Xiankai Jiang, Jun Gao, Tien Huynh, Ping Huai, Chunhai Fan, H. Zhou*, and Bo Song*, An Improved DNA Force Field for ssDNA Interactions with Gold Nanoparticles, J. Chem. Phys. 140, 234102, 2014
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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), ISBN-10: 1466562951 | ISBN-13: 978-1466562950, 2014
  29. 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), ISBN-10: 1466562951 | ISBN-13: 978-1466562950, 2014


  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. Das, Z. Xia, R. H. Zhou, Collapse of A Hydrophobic Polymer in Mixture of Denaturants, Langmuir 29, 4877-4882, 2013
  9. 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
  10. Xia, Z. X. Yang, T. Huynh,  Jonathan 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, Sci. Rep. 3, 1560, 2013
  11. 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
  12. 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
  13. 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
  14. 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


  1. 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
  2. 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)
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. Amanda Barnard, Changming Li, H. Zhou, Y. L. Zhao, Modeling of nanoscale, Nanoscale, 4, 1042-1043, 2012
  9. C. Flores, J. Bernauer, S. Shin, R. H. Zhou, and X. H. Huang, Multiscale modeling of macromolecular biosystems, Briefings in Bioinformatics, 13, 395-405, 2012
  10. 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
  11. 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, Sci. Rep., 2, 569, 2012
  12. G. Kang, T. Huynh, and R. H. Zhou, Metallofullerenol Gd@C82(OH)22 Non-destructively Inhibits Signal Transduction Pathway of WW domain, Sci. Rep. 2, 957, 2012
  13. 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)
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. H. Zhou, Protein folding: Bridging the gap between theory and experiment, Editorial for Hot-topic Special Issue, Curr. Phys. Chem., 2, 2-3, 2012
  22. 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
  23. 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


  1. Das, J. A. King, and R. H. Zhou, Aggregation of gD-Crystallin Associated with Human Cataracts via Domain Swapping at the C-terminal b-strands, Proc. Natl. Acad. Sci. 108, 10514-10519, 2011 (featured article)
  2. 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)
  3. 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. C115, 12322-12328, 2011
  4. 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
  5. 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
  6. 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
  7. 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
  8. Xia, P. Das, T. Huynh, A. K. Royyuru, and R. H. Zhou, Modeling Mutations of Influenza Virus with Blue Gene, IBM J. Res. Dev. 55, 7:1-7:11, 2011
  9. 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
  10. 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


  1. 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
  2. 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)
  3. 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
  4. 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 (cover article)
  5. Das, R. H. Zhou, Urea-induced drying of carbon nanotubes, J. Phys. Chem. B 114, 5427-5430, 2010
  6. 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
  7. 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
  8. Das, J. A. King, and R. H. Zhou, b-strand interactions at the domain interface critical for the stability of human lens gD-crystallin, Prot. Sci., 19, 131-140, 2010
  9. 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


  1. 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
  2. Zangi, R. H. Zhou, and B. J. Berne, Urea’s Action on Hydrophobic Interactions, J. Am. Chem. Soc. 131, 1535-1541, 2009
  3. 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
  4. 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
  5. 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
  6. 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
  7. Antonios Tavlarakis and 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


  1. 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 (featured article)
  2. 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 Ab16-22 Protofilaments, J. Am. Chem. Soc. 130, 11066-11072, 2008
  3. 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
  4. 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
  5. 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


  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. Ye, Z. Wu, M. Eleftheriou, and R. H. Zhou, Single-mutation-induced stability loss in protein lysozyme, Biochem. Soc. Trans. 35, 1551-1557, 2007


  1. Li, J. Li, M. Eleftheriou and R. H. Zhou, Hydration and Dewetting near Fluoronated Superhydrophobic Plates, J. Am. Chem. Soc. 128, 12439-12447, 2006
  2. 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
  3. 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
  4. 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
  5. Z. Lwin, R. H. Zhou and R. Luo, Is Poisson-Boltzmann theory insufficient for protein folding simulations? J. Chem. Phys. 124, 34902-34907, 2006
  6. 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
  7. R.H. Zhou, Replica Exchange Molecular Dynamics Method for Protein Folding,, Methods Mol. Biol. 350, 205-223, 2006
  8. 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
  9. 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
  10. 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
  11. 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.
  12. 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


  1. Liu, X. Huang, R. H. Zhou and B. J. Berne, Observation of a dewetting transition in the collapse of melittin tetramer, Nature, 437, 159-162, 2005
  2. Li, Y. Lei, T. Liu, Z. Wu, and R. H. Zhou, Water hydration near graphite-CH3 and graphite-COOH plates, J. Phys. Chem. B. 109, 13639-13648, 2005
  3. Huang, R. H. Zhou and B. J. Berne, Drying and Hydrophobic Collapse of Paraffin Plates, J. Phys. Chem. B. 109, 3546-3552, 2005
  4. Parida and R. H. Zhou, Combinatorial Pattern Discovery for Protein Folding Trajectory Analysis, PLoS Comp. Biol., 1, 32-40, 2005
  5. 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


  1. R.H. Zhou, X. Huang, C. Margulius and B. J. Berne, Hydrophobic Collapse in Multi-domain Protein Folding, Science, 305, 1605-1609, 2004
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. Feng, L. Parida, and R. H. Zhou, Protein Folding Trajectory Analysis using Patterned Clusters, Ed. Y. P. Chen and L. S. Wong, Proc. 3rd Asia-Pac. Bioinfo. Conf., p95-99, Imperial College Press, London, UK, 2004


  1. R.H. Zhou, Trp-cage: Folding Free Energy Landscape in Explicit Water, Proc. Natl. Acad. Sci., 100, 13280-13285, 2003
  2. 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
  3. 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
  4. 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
  5. 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
  6. R.H. Zhou, Folding free energy landscape of protein folding in water: explicit vs. implicit solvent, Proteins 53, 148-161, 2003
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. Allen, et al. R. H. Zhou, Blue Gene: A vision for protein science using a petaflop supercomputer, IBM Systems Journal 40, 310-327, 2001


  1. 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
  2. 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
  3. 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, 1999
  4. 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
  5. 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
  6. R.H. Zhou and B. J. Berne, Smart Walking: a new method for Boltzmann sampling of protein conformations, J. Chem. Phys. 107, 9185, 1997
  7. 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
  8. 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
  9. 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


  1. 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
  2. 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
  3. 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
  4. L. Cao and R. H. Zhou, Bonding characterization of Br on Si(100), J. Phys. Cond. Matt. 5, 2897, 1993
  5. 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
  6. 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
  7. 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
  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, Strong Chemisorption and Dissociation of N2 on Cr(110) Surfaces, ACTA PHYSICA SINICA, 41, 295, 1992
  10. 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
  11. 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
  12. 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
  13. B. Fu, R. H. Zhou and P. L. Cao, Investigation of the Chemisorption process of nitric oxide on Si(100)-2x1 , Surf. Sci. 247, L224, 1991
  14. L. Cao, X. Zhou and R. H. Zhou, Mechanism of the Phase Change of Li/Si(100)-2x1 structure , ACTA PHYSICA SINICA, 40, 1116, 1991
  15. R.H. Zhou and P. L. Cao, Theoretical study of CN chemisorbed on Pd(111) surface, Surf. Sci. 243, L49, 1991