Abstract
The elasticity and extensibility behaviors of sequence-dependent single stranded and double stranded DNA (ssDNAdsDNA) under various external loading conditions are studied by the clustered atomistic-continuum mechanics (CACM). The proposed numerical CACM is based on the finite element method, and it comprises both the atomistic-continuum and clustered atomistic-continuum (the clustered atoms are treated as a single super atom) mechanics. Through the CACM simulation, the transient mechanical response of the DNA could be revealed, including the stretching and rotating of the DNA backbone. Moreover, good agreement was achieved between the numerical simulation and single molecule experimental results. © 2006 American Institute of Physics.