Ruhong Zhou  Ruhong Zhou photo         

contact information

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



group team members


Dr. Zhou is currently a Distinguished Research Staff Scientist (DRSM) and Head of Soft Matter Science Dept, at IBM Research, as well as an Adjunct Professor at Department of Chemistry, Columbia University. He received his Ph.D. in Chemistry from Columbia University (with Prof. Bruce Berne) in 1997. His current research interests include development of novel algorithms for computational biology and bioinformatics, protein folding dynamics, protein-protein interaction, ligand-receptor binding, as well as protein-nanoparticle interactions (nanotoxicity/nanomedicine). He has published 220+ peer-reviewed papers and 26 patents, and delivered 150+ invited talks worldwide. He was part of the core IBM Blue Gene team which won the 2009 National Medal on Technology (issued by President Obama). He also won the IBM Outstanding Technical Achievement Award (OTAA), the highest IBM technical award, in 2005, 2008, 2014 and 2016,  and IBM Outstanding Innovation Award (OIA) in 2012, 2017 and the DEC Award from American Chemical Society (ACS). He serves as Editor-in-Chief of Current Physical Chemistry, Editor of (Nature) Scientific Reports, Guest Editor for Nanoscale (2011), and Editorial Board Member of 5 other international journals. He sits on the Board of Directors of Telluride Science and Research Center (TSRC), and the Scientific Advisory Board of Center for Multiscale Theory and Simulation, University of Chicago. He was elected to AAAS Fellow and APS Fellow in 2011, and IBM Distinguished RSM in 2014.

My Google Scholar Profile

Research Interests

The main research theme of my group is to understand the relationship between protein sequence, structure, and function, which is of fundamental importance in life science and the health care industry. We address important questions and problems in biophysics, structural biology, and biomolecular dynamics, using computational biology and bioinformatics approaches. In particular, we develop methodologies and techniques for molecular dynamics simulations with massively parallel supercomputers such as the IBM Blue Gene, and other high performance computing (HPC) platforms such as Cognitive Computing Cluster (CCC). The group pursues a broad but well grounded approach to leverage and expand upon our existing techniques for scientific and technological advancement.

The current research projects in my group include: (1). Development of novel methods for molecular dynamics and multi-scale modeling of complex biological systems. (2). Free energy perturbation (FEP) methods for large scale protein-protein, protein-ligand binding affinity predictions. (3) Infectious disease modeling with both statistical models and physics-based models. (4) Molecular mechanisms of protein (mis)folding, aggregation, and associated diseases such as Alzheimer's Disease (AD) and Huntington's Disease (HD). (5) Interactions of nanoparticles with macrobiomolecules such as proteins, DNA/RNAs, and membranes (nanotoxicity and nanomedicine modeling).



Conferences, Workshops Organized/Chaired

Organizer, Session Chair, and Organizing Committee Member of: KITPC Program on Algorithms for Molecular Simulations, Beijing, June 2013; Telluride workshop on Hydrophobicity and Confined Water, Telluride, June 2012; 4th International Workshop on Interfacial Water (Shanghai Water2011), Shanghai, May 2011; Pacific Symposium on Biocomputing (PSB), Hawaii, January, 2011; CECAM Workshop on Protein Folding Dynamics, Lausaane, Switzerland, 2010; Pacific Symposium on Biocomputing (PSB), Hawaii, January, 2010; 2nd International Workshop on Water at Biological Interface, Hangzhou, China, October, 2008; 3rd US-Japan Conference on Protein Folding & Design, University of Pennsylvania, Philadelphia, May 2-6, 2005; 227th National ACS Meeting, Symposium on Interplay between Theory and Experiment on Biomolecules, Anaheim, CA, 2004; 2004 Emerging Technology Conference (EITC2004), Princeton, NJ; 225th National ACS Meeting, Symposium on Continuum Solvent Models for Biological Macromolecules, Orlando, 2003


Selected Recent Papers

  • 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
  • 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


  • 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


  • 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


  • 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


  • 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


  • 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


  • 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


  • 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


  • 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)


  • 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


  • 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)


  • 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)


  • 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


  • 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


  • 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


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




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