Research Interests

    My major research interests are in the methodological development of multiscale models and their application to biological systems.
  • Development of a protein model at a hybrid resolution
  • Coarse-grained (CG) models can considerably extend the ability of molecular dynamics (MD) simulations to very large systems and long timescale. A residue-based CG model, known as MARTINI forcefield, is able to model membrane systems at a speed of over three order of magnitude faster than all-atom (AA) MD, allowing people to to study biological events such as membrane fusion and pore formation. However, the ability of MARTINI is limited by its discription of proteins in a too coarse way. For this reason, I have developed a united-atom protein model and embedded it into MARTINI. Compared to original MARTINI, simulations of proteins are much improved. I am now implementating the hybrid-resolution model into NAMD and benchmarking it on various membrane protein systems.

  • Multiscale modeling of peptide aggregation
  • Many diseases, such as Alzheimer's Disease, Parkingson's Disease and type II diabetes, are related to the aggregation of intrinsically disordered peptides. Recent studies show that the oligomers are very toxic, probably because of their ability to disrupt membrane. Despite decades of study, it still remains illusive how the peptides oligomerize and what are the olgiomeric structures, mainly due to the extreme difficulty for experimental charaterization when peptides aggregate. Although all-atom MD simulations can provide invaluable structural information, their application is hindered by the long timescale of peptide aggregation. Therefore, I am now employing combined CG and AA apporaches to study the oligomeric structures of the peptides as well as their interaction with membrane.


  • PACE Force Field for Protein Simulations. 1. Full Parameterization of Version 1 and Verification
  • Han, W.; Wan, C.-K.; Jiang, F.; Wu, Y.-D. Journal of Chemical Theory and Computation, 2010, 6, 3373.

  • PACE Force Field for Protein Simulations. 2. Folding Simulations of Peptides
  • Han, W.; Wan, C.-K.; Wu, Y.-D. Journal of Chemical Theory and Computation, 2010, 6, 3390.

  • Influence of Side Chain Conformations on Local Conformational Features of Amino Acids and Implication for Force Field Development
  • Jiang, F.; Han, W.; Wu, Y.-D. Journal of Physical Chemistry B, 2010, 114, 5840.

  • Toward a Coarse-Grained Protein Model Coupled with a Coarse-Grained Solvent Model: Solvation Free Energies of Amino Acid Side Chains
  • Han, W.; Wan, C.-K.; Wu, Y.-D. Journal of Chemical Theory and Computation, 2008, 4, 1891.

  • Theoretical Analysis of Secondary Structures of beta-Peptides
  • Wu, Y.-D.; Han, W.; Wang, D. P.; Gao, Y.; Zhao, Y. L. Account of Chemical Research, 2008, 41, 1418.

  • In silico study on the effect of F19T mutation on amyloid-beta peptide (10-35)
  • Han, W.; Xiong, H.; Wu, Y.-D. Frontier in Bioscience, 2008, 13, 3951.

  • Coarse-grained protein model coupled with a coarse-grained water model: Molecular dynamics study of polyalanine-based peptides
  • Han, W.; Wu, Y.-D. Journal of Chemical Theory and Computation, 2007, 3, 2146.

  • Molecular dynamics studies of hexamers of amyloid-beta peptide (16-35) and its mutants: Influence of charge states on amyloid formation
  • Han, W.; Wu, Y.-D. Proteins-Structure Function and Bioinformatics, 2007, 66, 575.

  • A strand-loop-strand structure is a possible intermediate in fibril elongation: Long time simulations of amylold-beta peptide (10-35)
  • Han, W.; Wu, Y.-D. Journal of the American Chemical Society, 2005, 127, 15408.