l  Ruhong Zhou*, X. Huang, C. Margulius and B. J. Berne*, Hydrophobic Collapse in Multi-domain Protein Folding,Science,305, 1605-1609, 2004 

l  Ruhong Zhou, G. Krilov and B. J. Berne*, Comment on 'Can a continuum solvent model reproduce the free energy landscape of a beta-hairpin folding in water?': The Poisson-Boltzman Model,J. Phys. Chem. B 108, 7528-7530, 2004

l  W. Swope, J. Pitera, F. Suits, M. Pitman, M. Eleftheriou, B. Fitch, R. Germain, A. Rayshubskiy, T. J. C. Ward, Y. Zhestkov, and Ruhong Zhou*, Describing Protein Folding Kinetics by Molecular Dynamics Simulations: II. Application to a beta-hairpin Peptide, J. Phys. Chem. B 108, 6582-6594, 2004 

l  Ruhong Zhou, Sampling Protein Folding Free Energy Landscape: Coupling Replica Exchange Method with P3ME/RESPA Algorithm, J. Mol. Grap. Model. 22, 451-463, 2004 

l  Ruhong Zhou*, G. Dent, A. Royyuru, and P. Athma, Assessment of Protein Structure Refinement with Replica exchange Method, Eds, A. Gramada, P. E. Bourne, RECOMB2004 - Currents in Computational Molecular Biology, 390-391, 2004 

l  Ruhong Zhou*, A. Royyuru, P. Athma, and B. D. Silverman, Hydrophobicity of Multi-domain Proteins: Spatially Profiling their Distribution,Eds, A. Gramada, P. E. Bourne, RECOMB2004 - Currents in Computational Molecular Biology, 441-442, 2004 

l   J. Feng, L. Parida, and Ruhong Zhou*, Protein Folding Trajectory Analysis using Patterned Clusters,Ed. Y. P. Chen and L. S. Wong, Proc. 3^rdAsia-Pac. Bioinfo. Conf., p95-99, Imperial College Press, London, UK, 2004