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No Access Submitted: 04 February 2005 Accepted: 31 March 2005 Published Online: 17 June 2005

  • Topological coarse graining of polymer chains using wavelet-accelerated Monte Carlo. I. Freely jointed chains

J. Chem. Phys. 122, 234901 (2005); https://doi.org/10.1063/1.1924480
Ahmed E. Ismail, Gregory C. Rutledgea), and George Stephanopoulos
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  • Ahmed E. Ismail
  • Gregory C. Rutledge
  • George Stephanopoulos
  • See also: The Journal of Chemical Physics 122 (23), 234902 (2005)
    • ABSTRACT
    We introduce a new, topologically-based method for coarse-graining polymer chains. Based on the wavelet transform, a multiresolution data analysis technique, this method assigns a cluster of particles to a coarse-grained bead located at the center of mass of the cluster, thereby reducing the complexity of the problem by dividing the simulation into several stages, each with a fraction of the number of beads as the overall chain. At each stage, we compute the distributions of coarse-grained internal coordinates as well as potential functions required for subsequent simulation stages. In this paper, we present the basic algorithm, and apply it to freely jointed chains; the companion paper describes its applications to self-avoiding chains.

    ACKNOWLEDGMENTS

    This work was supported by the Department of Energy Computational Science Graduate Fellowship Program of the Office of Scientific Computing and Office of Defense Programs in the Department of Energy under Contract No. DE-FG02-97ER25308. This work was also supported by the Engineering Research Centers Programs of the National Science Foundation under NSF Award No. EEC-9731680. Any opinions, findings, conclusions, or recommendations expressed in this material are those of the authors and do not necessarily reflect those of the National Science Foundation.

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