Abstract
A novel atomistic-continuum method (ACM) based on the transient finite element theory is proposed herein to simulate the dynamic structural transitions of the double strand DNA (dsDNA) under external loading. Moreover, the meso-mechanics of dsDNA molecules is then studied via the ACM model, including the base-stacking interaction between DNA adjacent nucleotide base pairs, the hydrogen bond of complementary base-pairs and electrostatic interactions along DNA backbones. In this research, an atomistic-continuum mechanics 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. To describe the material properties of the spring in dsDNA structure, the Cornell's second generation force field potential energy and Universal force field are utilized to simulate the bond stretching and bond angle energy terms. The method proposed here would be used to study the mechanical behavior in DNA packaging and release form viral capsids in the future.