Publications

• H.-J. Woo, J. Jiang, E. M. Lafer, and R. Sousa, ATP induced conformational changes in Hsp70: Molecular dynamics and experimental validation of an in silico predicted conformation, submitted (2009) (closing transition movie of Hsp70 NBD).
  
• H.-J. Woo, Relaxation dynamics near nonequilibrium stationary states in Brownian ratchets, Phys. Rev. E 79, 021101 (2009).
  
• H.-J. Woo, Y. Liu, and R. Sousa, Molecular dynamics studies of the energetics of translocation in model T7 RNA polymerase elongation complexes, Proteins 73, 1021-1036 (2008) (biased sampling movie1 and movie2 of T7 RNAP).
• M. J. Harris and H.-J. Woo, Energetics of subdomain movements and fluorescence probe solvation environment change in ATP-bound myosin, Eur. Biophys. J. 38, 1-12 (2008).
  
• H.-J. Woo, Calculation of absolute protein-ligand binding constants with the molecular dynamics free energy perturbation method, in Molecular Modeling of Proteins, edited by A. Kukol, Methods in molecular biology 443, 109-120, Springer, New York (2008).
  
• H.-J. Woo, Exploration of the conformational space of myosin recovery stroke via molecular dynamics,  Biophys. Chem. 125, 127-137 (2007).
• R. Valiullin, S. Naumov, P. Galvosas, J. Kärger, H.-J. Woo, F. Porcheron, and P. A. Monson, Exploration of molecular dynamics during transient sorption of fluids in mesoporous materials, Nature 443, 965-968 (2006).
  
• H.-J. Woo, Analytical theory of the nonequilibrium stationary distribution of RNA polymerase translocations, Phys. Rev. E 74, 011907 (2006).
• Y. Liu, M. Scolari, W. Im, and H.-J. Woo, Protein-protein interactions in actin-myosin binding and structural effects of R405Q mutation: A molecular dynamics study, Proteins 64, 156-166 (2006).
• H.-J. Woo and C. L. Moss, Analytical theory of the stochastic dynamics of the power stroke in nonprocessive motor proteins, Phys. Rev. E 72, 051924 (2005).