l  X. Li, J. Li, M. Eleftheriou and Ruhong Zhou*, Hydration and Dewetting near Fluoronated Superhydrophobic Plates,J. Am. Chem. Soc. 128, 12439-12447, 2006

l  M. Eleftheriou, R. Germain, A. Royyuru and Ruhong Zhou*, Thermal denaturing of mutant lysozyme with both OPLSAA and CHARMM force fields, J. Am. Chem. Soc. 128, 13388-13395, 2006

l  H. Lan, X. Huang, Ruhong Zhouand B. J. Berne*, Water dynamics in the salvation shell of a multi-domain protein,J. Phys. Chem. B., 110, 3704-3711, 2006

l   P. Liu, X. Huang, Ruhong Zhouand B. J., Berne*, Hydrophobic Aided Replica Exchange Method for Protein Folding, J. Phys. Chem. B 110, 19018 - 19022, 2006

l   T. Z. Lwin, Ruhong Zhouand R. Luo*, Is Poisson-Boltzmann theory insufficient for protein folding simulations,J. Chem. Phys. 124, 34902-34907, 2006

l   T. Liu, L. Ye, H. Chen, J. Li, Z. Wu and Ruhong Zhou*, A Combined Steepest Descent and Genetic Algorithm (SD/GA) Approach for the Optimization of Solvation Parameters, Mol. Simul. 32, 427-435, 2006

l  Ruhong Zhou, A. Royyuru, P. Athma, F. Suits and BD Silverman, Magnitude and Spatial Orientation of the Hydrophobic Moments of Multi-Domain Proteins,Int. J. Bioinf. Res. Appl. 2, 161-176, 2006

l  M. Eleftheriou, A. Rayshubski, J. Pitera, B. Fitch, Ruhong Zhou, R. Germain, Large Scale Parallel Implementation of Replica Exchange on Blue Gene/L, SIAM Conference on Parallel Processing for Scientific Computing San Francisco, California, USA February 22-24, 2006

l  Ruhong Zhou, Protein Folding with the Parallel Replica Exchange Molecular Dynamics Method,Ed. Albert Zomaya, 'Parallel Computing for Bioinformatics and Computational Biology', p397-425, John Wiley & Sons Publisher, New Jersey, 2006

l  B. G. Fitch, A. Rayshubskiy, M. Eleftheriou, T.J. C. Ward, M. Giampapa, Y. Zhestkov, M. C. Pitman, F. Suits, A. Grossfield, J. Pitera, W. Swope, Ruhong Zhou, S. Feller, and R. S. Germain.Blue Matter: Strong scaling of molecular dynamics on Blue Gene/L.In V. Alexandrov, D. van Albada, P. Sloot, and J. Dongarra, editors, International Conference on Computational Science (ICCS 2006), volume 3992 of LNCS, pages 846–854. Springer-Verlag, 2006. 

l  Ruhong Zhou, Dewetting in Nanoscale Hydrophobic PlatesCollapse and Protein Complex Folding, NIC Workshop 2006, From Computational Biophysics to Systems Biology, Jan Meinke, Olav Zimmermann,Sandipan Mohanty, Ulrich H.E. Hansmann (Editors), John von Neumann Institute for Computing, Jeulich, NIC Series, Vol. 34, pp. 53-58, 2006