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http://dx.doi.org/10.12989/imm.2013.6.4.395

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))
Publication Information
Interaction and multiscale mechanics / v.6, no.4, 2013 , pp. 395-409 More about this Journal
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.
Keywords
model order reduction; radial basis function represented potentials and inter-atomic forces; full MD simulation; ds-DNA molecules;
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