Dynamics of polymer translocation into an anisotropic confinement

Abstract

Using Langevin dynamics simulations, we investigate the dynamics of the translocation of a flexible polymer into a confined area under a driving force through a nanopore. We choose an ellipsoidal shape for the confinement and consider the dependence of the asymmetry of the ellipsoid measured by the aspect ratio on the translocation time. Compared with an isotropic confinement (sphere), an anisotropic confinement (ellipsoid) with the same volume slows down the translocation, and the translocation time increases with increasing the aspect ratio of the ellipsoid. We further find that it takes different lengths of time for polymer translocation into the same ellipsoid through the major axis and minor axis directions, depending on the average density of the whole chain in the ellipsoid, ϕ. For ϕ lower than a critical value ϕ_c, the translocation through the minor axis is faster, and vice versa. These complicated behaviors are interpreted by the degree of the confinement and the anisotropic confinement induced folding of the translocated chain.