Our group aims to address important questions and problems in soft matter, particularly biomaterials, where physics meets chemistry meets biology. We cover a wide range of research activities, ranging from computational structural biology, biomolecular dynamics, DNA nanopore sequencing, proteomics, to petrochemical modeling, using high performance computing (HPC) such as IBM Blue Gene supercomputers. The group pursues a broad but well grounded approach to leverage and expand upon our existing techniques for scientific and technological advancement.

• Molecular Modeling of Avian Flu
• GPCR Activation Mechanisms
• Protein Folding with Molecular Dynamics
• Nanoscale Dewetting in Physical and Biological Systems
• Protein-Ligand Binding: HIV/AIDS
• Protein Misfolding and Aggregation
• Water Nanopore Design, Molecular Signal Transduction, and Nanotoxicity
• Proteomics and Biomarker Discovery
• Protein-Nanoparticle Interactions (Nanotoxicity/Nanomedicine)
• DNA Transistor Modeling
• Smectic Clay Modeling

• Ruhong Zhou (Manager)
• Alan Grossfield (Visiting Professor)
• Binquan Luan (Research Staff Scientist)
• Bruce Berne (Visiting Professor)
• Frank Suits (Research Staff Scientist)
• Jacinta Wubben (PhD Student)
• Matteo Castelli (PhD Student)
• Mike Kuiper (Visiting Scientist)
• Mike Pitman (Research Staff Scientist)
• Payel Das (Research Staff Scientist)
• Raul Araya Secchi (PhD Student)
• Seung-gu Kang (Postdoctoral Fellow)
• Tien Huynh (Sr. Software Engineer)
• Zhen Xia (PhD Student)

• 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

• P. Ntziachristos, A. Tsirigos, P. Van Vlierberghe, J. Nedjic, T. Trimarchi, M. Sol Flaherty, D. Ferres-Marco, V. da Ros, Z. Tang, J. Siegle, P. Asp, M. Hadler, I. Rigo, K. D. Keersmaecker, J. Patel, T. Huynh, F. Utro, S. Poglio, J. B. Samon, E. Paietta, J. Racevskis, J. M. Rowe, R. Rabadan, R. L. Levine, S. Brown, F. Pflumio, M. Dominguez, A. Ferrando, and I. Aifantis, Genetic inactivation of the polycomb repressive complex 2 in T cell acute lymphoblastic leukemia, Nature Medicine, 18, 298–303, 2012

• 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, Scientific Reports, 2, 569, 2012

• 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. Zhou and H. Fang, Water-mediated signal multiplication with Y-shaped carbon nanotubes, Proc. Natl. Acad. Sci. 106, 18120-18124, 2009
• Z. Xia, J. Gu, J. Zhu and R. Zhou, Using a Mutual Information Based Site Transition Network to Map the Genetic Evolution of Influenza A/H3N2 Virus, Bioinformatics, 25, 2309-2317, 2009
• L. Hua, R. Zhou, D. Thirumalai, B. J. Berne, Urea denaturation by stronger dispersion interactions with proteins than water implies a 2-stage unfolding, Proc. Natl. Acad. Sci., 105, 16928-16933, 2008
• J. Li, X. Gong, H. Lu, D. Li, H. Fang and R. Zhou, Electrostatic Gating of a Nanometer Water Channel, Proc. Natl. Acad. Sci., 104, 3687-3692, 2007
• Miranda, K., T. Huynh, Y. Tay, Y.-S. Ang, W.-L. Tam, A. Thomson, B. Lim, I. Rigoutsos, A pattern-based method for the identification of micro-RNA target sites and their corresponding heteroduplexes, Cell, 126, 1203-1217, September 2006
• A. Grossfield, S. E. Feller, and M. C. Pitman, A role for direct interactions in the modulation of rhodopsin by ω-3 polyunsaturated lipids, Proc. Nat. Acad. Sci. 103, 4888-4893, 2006

• P. Liu, X. Huang, R. Zhou and B. J. Berne, Drying and Hydrophobic Collapse of Melittin Tetramer, Nature, 437, 159-162, 2005
• R. Zhou, X. Huang, C. Margulius and B. J. Berne, Hydrophobic Collapse in Multi-domain Protein Folding, Science, 305, 1605-1609, 2004
• R. Zhou, Trp-cage: Folding Free Energy Landscape in Explicit Water, Proc. Natl. Acad. Sci.,100, 13280-13285, 2003