Soft Matter Science - overview

The department 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, multiscale modeling of bio-nano interface, 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.




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Nano / Bio





  • 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. 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




  • 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)
  • Ruhong Zhou,
    Modeling of Nanotoxicity,
    Springer, ISBN-10: 3319153811 | ISBN-13: 978-3319153810, 2015 (201 pages)













  • Otitoaleke G. Akinola
  • David R. Bell
  • Matteo Castelli
  • Camilo Jimenez
  • Yuxing Peng
  • Michael Pitman
  • Raul Araya Secchi
  • Frank Suits
  • Jacinta Wubben
  • Zhen Xia
  • Payel Das