Soft Matter Science     

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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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RESEARCH AREAS

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Immunology Modeling	Molecular Neuroscience	Protein Science	Nanomedicine	Ligand-receptor Binding

 

 

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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

 

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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)