Research Areas

Additional Information

Group Members

  • Ruhong Zhou (Manager)
  • Bruce Berne
  • Payel Das
  • Tien Huynh
  • Camilo Jimenez
  • Seung-gu Kang
  • Binquan Luan
  • Frank Suits


  • Matteo Castelli
  • Yuxing Peng
  • Michael Pitman
  • Raul Araya Secchi
  • Jacinta Wubben
  • Zhen Xia


  • Gordon Conferences
  • Telluride Workshops
  • ACS National Meetings
  • APS March Meetings
  • BPS Annual Meetings
  • Pacific Symposium on Biocomputing

  • Project Name

    Soft Matter Theory and Simulation

    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.



    • R. Zhou, X. Huang, C. Margulius and B. J. Berne,
      Hydrophobic Collapse in Multi-domain Protein Folding,
      Science, 305, 1605-1609, 2004
    • P. Liu, X. Huang, R. Zhou and B. J. Berne,
      Drying and Hydrophobic Collapse of Melittin Tetramer,
      Nature, 437, 159-162, 2005
    • 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
    • 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
    • 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
    • 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)
    • 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)
    • 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)
    • 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
    • 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
    • A. Grossfield, S. E. Feller, and M. C. Pitman,
      A role for direct interactions in the modulation of rhodopsin by ?-3 polyunsaturated lipids,
      Proc. Nat. Acad. Sci., 103, 4888-4893, 2006
    • R. Zhou,
      Trp-cage: Folding Free Energy Landscape in Explicit Water,
      Proc. Natl. Acad. Sci.,100, 13280-13285, 2003
    • L. Laurent, E. Wong, G. L. Li, T. Huynh, A. Tsirigos, C. T. Ong, H. M. Low, K. W. K. Sung, I. Rigoutsos, J. Loring, C. L. Wei,
      Dynamic changes in the human methylome during differentiation
      Genome Research 20 (3), 320-331, 2010
    • 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