Abstract
A novel single-stranded DNA (ssDNA) model based on the clustered atomistic method is conducted to simulate the meso-mechanics of ssDNA molecule. Through the validation of the single molecular experiment, the proposed ssDNA model could represent the ssDNA molecule in different counter length, and the mechanical characteristic of the ssDNA molecule in external tensile loading could be elucidated. Furthermore, the characteristic of the validated ssDNA model is adapted in the double-stranded DNA (dsDNA) model. The simulation result of the dsDNA model under external loading reveals mechanical behavior of the dsDNA B-S structural transition. Good agreement is achieved between the numerical simulation and single molecular manipulation experimental result, and the mechanical behavior of stretching nicked dsDNA could be revealed.