Polymer Dynamics and Protein Folding


B. Ostrovsky, G. E. Crooks, M. A. Smith, and Y. Bar-Yam: Cellular Automata for Polymer Simulation with Application to Polymer Melts and Polymer Collapse Including Implications for Protein Folding, Parallel Computing, 27, 613-641, 2001. PDF file

G. E. Crooks, B. Ostrovsky and Y. Bar-Yam: Mesostructure of Polymer Collapse and Fractal Smoothing, Phys. Rev. E 60, 4559, 1999. PDF file

B. Ostrovsky, M. A. Smith and Y. Bar-Yam: Simulations of Polymer Interpenetration in 2-D Melts, Int. J. of Mod. Physics C, 8, 931, 1997.

Y. Bar-Yam: Polymer simulation using Cellular Automata: 2-D Melts, Gel-Electrophoresis and Polymer collapse, in Some New Directions in Science on Computers, Eds. G. Bhanot, S. Chen, P. Seiden (World-Scientific, Singapore, 1996).

B. Ostrovsky, M. A. Smith and Y. Bar-Yam: Polymer Interpenetration in 2D High Density Melts, Inter. Journal of Polymers and Complex Fluids [4], 1995. PDF file

B. Ostrovsky and Y. Bar-Yam: Motion of Polymer Ends in Homopolymer and Heteropolymer Collapse, Biophysical Journal, 68, 1694-98, 1995.

B. Ostrovsky, M. A. Smith and Y. Bar-Yam: Applications of Parallel Computing to Biological Problems, Annual Review of Biophysics and Biomolecular Structure 24, 239-67, 1995.

B. Ostrovsky and Y. Bar-Yam: Irreversible Polymer Collapse in 2 and 3 Dimensions, Europhysics Letters 25, 409, 1994. PDF file

B. Ostrovsky and Y. Bar-Yam: Irreversible polymer collapse by Monte-Carlo simulations, Journal of Comp. Polymer Science, 3, 9, 1993. PDF file

B. Ostrovsky, M. A. Smith, M. Biafore, Y. Bar-Yam, Y. Rabin, N. Margolus and T. Toffoli: Massively parallel architectures and polymer simulation, in Proc. 6th SIAM Conf. on Parallel Processing for Scientific Computing, 1993. PDF file

M. A. Smith, Y. Bar-Yam, Y. Rabin, B. Ostrovsky, C. H. Bennett, N. Margolus and T. Toffoli: Parallel Processing Simulation of Polymers, Journal of Computational Polymer Science, 2, 165, 1992.

M. A. Smith, Y. Bar-Yam, Y. Rabin, C. H. Bennett, N. Margolus and T. Toffoli: Cellular Automata Simulation of Polymers, in Complex Fluids, (E. B. Sirota, D. Weitz, T. Witten and J. Israelachvili) MRS Symp. Proc. Vol. 248, 1992. PDF file

Y. Bar-Yam, Dynamics of Complex Systems, Chapters 4 and 5

 

 

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