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Atomistic to Continuum Modeling of DNA Molecules

Thursday, December 15, 3:30PM – 5PM
ACE 6.304

Chung-Hao Lee

The mechanical properties of DNA have very important biological implication. For example, the bending and twisting rigidities of DNA affect how it wraps around histones to form chromosomes, bends upon interactions with proteins, supercoils during replication process, and packs into the confined space within a virus. Many biologically important processes involving DNA are accompanied by the deformations of double helical structure of DNA. We proposed a multi-scale coarse graining method and multi-level homogenization formulation [1] for numerical simulation of DNA subjected to complex forms of deformation. We developed wavelet-based multiscale formulation [2] for the first level homogenization of potential function for representation of superatoms. Based on superatom molecular structures, we introduced second level homogenization by constructing an equivalent continuum strain energy density function of the DNA to yield a continuum hyperelastic multi-scale beam formulation for continuum modeling of DNA molecules [3]. A hybrid multi-scale computational framework, including atomistic-continuum representations of DNA molecules and POD-based reduced order model of lac repressor protein, has also been developed to the investigation of protein-mediated DNA loop formation spanning from the atomistic scale to continuum level. Numerical predictions have demonstrated that the proposed coupled MD-continuum models is capable of capturing the protein-DNA interactions during DNA loop formation process yields more accurate solutions than the single-scale continuum model. References: [1] Chen, J. S., Teng, H., and Nakano, A., “Wavelet based multi-scale coarse graining approach for DNA molecules,” Finite Elements in Analysis and Design, 43, pp. 246-260, 2007. [2] Mehraeen, S. and Chen, J.S., “Wavelet-based multi-scale projection method in homogenization of heterogeneous media,” Finite Elements in Analysis and Design, 40, pp. 1685-1679, 2004. [3] Teng H, Lee CH, Chen JS “On the continuum formulation for modeling DNA loop formation,” Interact Multiscale Mech, 4: 219-237, 2011. Short Bio: Chung-Hao Lee holds B.S. and M.S. degrees in Civil Engineering from National Taiwan University and Ph.D. in Civil Engineering from the University of California at Los Angeles. He has received the first place for the Dimitris N. Chorafas Foundation Awards (2011), UCLA Dissertation Year Fellowship (2010-2011), and Travel Awards for the 10th U.S. National Congress for Computational Mechanics (USNCCM-10, 2009). His research interests focus on the development of advanced finite element methods and meshfree methods, computational bio-mechanics, multi-scale modeling of DNA molecules, and computational mechanics for large deformation and fragment-impact problems.

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