Direct Numerical Simulation of Single-Molecule DNA by Cable Dynamics

In this paper, we present direct numerical simulation (DNS) of the transient dynamics of single-molecule DNA by modeling it as a highly flexible cable. Fully nonlinear dynamic equations are derived from the principles of conservation of momentum and angular momentum, and solved via numerical means. Compared to previous models, this cable-dynamics model enables direct physical simulation of an individual biopolymer string rather than a random-walk style statistical modeling. To validate this DNS modeling approach, the canonical DNA stretching problem is simulated. The DNS solutions are compared with published benchmark results. The DNS model is further deployed to investigate the Brownian motion of single DNA molecule, and the translocation process of a DNA molecule through a nanopore induced by the presence of an external electric field. In the latter case, our simulations have exhibited good agreement with experimental observations, including the linear dependence of the translocation time on the contour length of the molecule, the formation of "hairpins" during translocation, and back-and-forth molecule motions