Wavelet-based multi-scale coarse graining approach for DNA molecules

  • Authors:

  • Jiun-Shyan Chen;Hailong Teng;Aiichiro Nakano

  • Affiliations:

  • Civil and Environmental Engineering Department, University of California, Los Angeles, CA 90095-1593, USA;Civil and Environmental Engineering Department, University of California, Los Angeles, CA 90095-1593, USA;Department of Computer Science, University of Southern California, Los Angeles, CA 90089-0242, USA

  • Venue:
  • Finite Elements in Analysis and Design
  • Year:
  • 2007

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Abstract

In this work, a coarse graining technique based on a multi-scale wavelet projection is proposed for modeling of DNA molecules. Based on the fine scale atomistic response and the Henderson's theorem, the distribution functions between centers of mass of two groups of atoms are employed to obtain the fine scale potential functions. These fine scale potential functions are then homogenized using the multi-scale wavelet projection to yield the coarse-scale effective potential functions between superatoms. Molecular dynamics simulation of DNA molecules under stretching process demonstrates that the results of fine scale model and the proposed coarse grained DNA model are in good agreement. The coarse grained simulation with a significant saving of computation time is shown to be in good agreement with the fine scale simulation. Due to the reduced spatial degrees of freedom and temporal discretization, a computational efficiency of three to four orders of magnitude is achieved in the proposed coarse grained model.