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.

 


 

RESEARCH AREAS

(Please click image for more details)

Protein
Science
Drug
Discovery
Infectious
Disease
Modeling
Nano / Bio
Interface
Molecular
Neuroscience

 

 


 

REPRESENTATIVE PUBLICATIONS

  • 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

 


 

BOOKS

  • 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)

 

 

 

 

 

 

 

 

 

 




Members


Alumni

  • 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