Interaction and multiscale mechanics

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RBF-POD reduced-order modeling of DNA molecules under stretching and bending

  • Lee, Chung-Hao (Institute for Computational Engineering and Sciences (ICES),University of Texas at Austin) ;
  • Chen, Jiun-Shyan (Department of Structural Engineering, University of California, San Diego (UCSD))
  • Received : 2013.09.18
  • Accepted : 2013.11.12
  • Published : 2013.12.25
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Abstract

Molecular dynamics (MD) systems are highly nonlinear and nonlocal, and the conventional model order reduction methods are ineffective for MD systems. The RBF-POD method (Lee and Chen, 2013) employed a radial basis function (RBF) approximated potential energies and inter-atomic forces of MD systems under the framework of the proper orthogonal decomposition (POD) method for the reduced-order modeling of MD systems. In this work, we focus on the numerical procedures of the RBF-POD method and demonstrate how to apply this approach to the modeling of ds-DNA molecules under stretching and bending conditions.

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