在分子動(dòng)力學(xué)模擬蛋白質(zhì)結(jié)構(gòu)，功能，以及動(dòng)態(tài)過(guò)程、納米尺度水的生物效應(yīng)、以及納米顆粒與生物分子的相互作用等研究領(lǐng)域成就顯著。擁有或已申請(qǐng)14項(xiàng)美國(guó)專(zhuān)利。在權(quán)威學(xué)術(shù)刊物發(fā)表學(xué)術(shù)論文102篇，SCI引用3200余次。應(yīng)邀在世界各地大學(xué)、研究機(jī)構(gòu)和國(guó)際學(xué)術(shù)會(huì)議上做邀請(qǐng)報(bào)120余次，是期刊《Nanoscale》、《Current Physical Chemistry》客座主編， 也是 《Current Bioinformatics》等6家國(guó)際期刊的編委。

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. P. 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　　3. 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　　4. 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 u2018seed-lessu2019 targets, Scientific Reports, 2, 569, 2012　　5. 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, in press, 2012　　6. 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)　　7. P. Das, J. A. King, and R. H. Zhou, Aggregation of ?D-Crystallin Associated with Human Cataracts via Domain Swapping at the C-terminal ?-strands, Proc. Natl. Acad. Sci. 108, 10514-10519, 2011 (featured article)　　8. 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　　9. 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 　　10. 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　　11. 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　　12. R. H. Zhou, Trp-cage: Folding Free Energy Landscape in Explicit Water, Proc. Natl. Acad. Sci., 100, 13280， -13285, 2003 　　13. 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 　　14. 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

1. CAREER Award for Researchers “most likely to have the greatest scientific impact for IBM and the world” (at most five scientists chosen each year among eight IBM Labs worldwide), IBM Research, May, 2012

2. IBM Outstanding Innovation Award (OIA), IBM Corp. 2012　　3. IBM Research Division Award, IBM Research (2012)　　4. William E. Schiesser Lecture, Lehigh University, April 2012　　5. Elected to AAAS Fellow (American Association of Advancement of Science), 2011 　　6. Elected to APS Fellow (American Physical Society), 2011 　　7. Part of the IBM BlueGene Team who won 2009 National Medal on Innovation and Technology (presented by President Obama), 2009　　8. IBM Invention Plateau Achievement Award, IBM Corporation (2009) 　　9. IBM Outstanding Technical Achievement Award (OTAA, the highest technical award of IBM), IBM Corp. (2008)　　10. IBM Outstanding Technical Achievement Award (OTAA), IBM Corp. (2005)　　11. IBM Research Division Award, IBM Research (2005)　　12. IBM Invention Plateau Achievement Award, IBM Corporation (2004) 　　13. IBM Invention Achievement Award, IBM Corporation (2002) 　　14. The Hammett Award for Best Ph.D. Graduates, Columbia University (1997)　　15. ACS Award on Computational Chemistry (DEC Award), American Chemical Society (1995)　　16. Faculty Fellowship, Columbia University (1994-1997)　　17. Second Prize, Research in Science & Technology, China Ministry of Education (1993)　　18. Best Paper Award for Outstanding Research, Zhejiang University (1993)　　19. Award for Outstanding Research, Zhejiang University (1992)

1. Bruce J. Berne and Ruhong Zhou, Fast methods for simulating biomolecular systems with long-range electrostatic interactions by molecular dynamics, US patent No. 5,915,230, Jun 22, 1999

2. Ruhong Zhou, Huafeng Xu, Ed Harder, and Bruce J. Berne, System and Method for Molecular Dynamics Simulation , US patent, No. 7,096,167 B2, August 22, 2006

3. Prasanna Athma, Ajay Royyuru, David Silverman and Ruhong Zhou, Method and apparatus for protein structure analysis, US Patent, No. 7,499,805, March 3, 2009

4. Ruhong Zhou, David Silverman, Ajay Royyuru, and Prasanna Athma, Hydrophobic Moment of Multi-domain Proteins, United States, US patent No. 7,877,214, Jan, 25, 2011

5. Ruhong Zhou, David Silverman, Ajay Royyuru, and Prasanna Athma, Hydrophobic Dipole Orientational Analysis for Multi-domain Protein Structures, US patent No. 8,010,332, Jan, 2012

6. Ruhong Zhou, and David Silverman, Method and Apparatus for Protein Structure Analysis, US patent filed (IBM Docket No. YOR920020224US1), Nov. 15, 2002

7. David Silverman, Ruhong Zhou and Ajay Royyuru, Hydrophobic Fourier Transform for Protein Structure Prediction Validation, US patent search (IBM Docket No. YOR820030692), September, 2003

8. Laxmi Parida and Ruhong Zhou, Pattern Discovery Analysis for Protein Folding Trajectories, US patent search (IBM Docket No. YOR820040227), April, 2004

9. Laxmi Parida and Ruhong Zhou, Clustering of Multidimentional Real-valued Data Using Signature Patterns, US patent (IBM Docket No. YOR820040321), May, 2004

10. Laxmi Parida and Ruhong Zhou, Visual Analysis of Pattern Landscape Animation, US patent (IBM Docket No. YOR920060233US1), March, 2006

11. Zhen Xia and Ruhong Zhou, Prediction of Influenza A Virus’ Genetic Evolution with a Mutual Information Based Site Transition Network, IBM Docket No. YOR820090279, July 1, 2009

12. Payel Das and Ruhong Zhou, A biomimetic nano-pump for automatic separation of urea from water, DISCLOSURE NO. YOR820101155, November 12, 2010

13. Zhen Xia, Tien Hyunh, and Ruhong Zhou, Weighted mutual information method and automatic web server for influenza genetic variation prediction, DISCLOSURE NO. YOR820101065, October 18, 2010

14. James Kozloski, Cliff Pickover, Jacinta Wubben and Ruhong Zhou, System and Method for Competitive Binding of Sequence Annotations and Analysis Tools to Sequences in a Biological Data Repository, YOR820110975, October, 2011

15. Binquan Luan and Ruhong Zhou, Base-by-base Ratcheting DNA in a Y-shaped Carbon Nanotube, YOR820120589, May, 2012

16. Binquan Luan and Ruhong Zhou, Nanopore-Based Sensors for Detecting Nanotoxicity of a Carbon Nanotube to Proteins, YOR820120951, July, 2012