2007 NSTI Nanotechnology Conference and Trade Show - Nanotech 2007 - 10th Annual

Investigation of dsDNA Molecule Mechanical Behavior using Atomistic Continuum Mechanics Method

C-N Han, C-Y Chou, C-J Wu and K-N Chiang
Advanced Microsystem Packaging and Nano-Mechanics Research Laboratory, National Tsing Hua University, Taiwan, TW

Keywords:
dsDNA, atomistic continuum mechanics, CAM method, worm-like rod chain, WLRC

Abstract:
In this research, an atomistic continuum model of dsDNA based on equivalent-spring method would be first conducted and the simulation result would be further validated by the experimental result. A spring element is chosen to represent the covalent bond between neighbor atoms of backbone in dsDNA. The Conrell’s second generation force field potential energy which includes the bond stretching and bond angle energy term is adopted to describe the material properties of the spring in dsDNA backbone structure. Moreover, using the hydrogen bond to define the force occurred in base-pairs that in the separate backbones and using the stacking force to describe the reciprocal effect between adjoin base-pairs in the same backbone. The method proposed here would be used to study the mechanical behavior in DNA packaging and release form viral capsids in the future.

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