Driven polymer translocation through a nanopore from a confining channel

Abstract

We consider the dynamics of pore-driven polymer translocation through a nanopore to a two-dimensional semi-infinite space when the chain is initially confined and equilibrated in a narrow channel. To this end, we use Langevin dynamics (LD) simulations and iso-flux tension propagation (IFTP) theory to characterize local and global dynamics of the translocating chain. The dynamics of the process can be described by the IFTP theory in very good agreement with the LD simulations for all values of confinement in the channel. The theory reveals that for channels with a size comparable to or less than the end-to-end distance of the unconfined chain, in which the blob theory works, the scaling form of the translocation time depends on both the chain contour length and the channel width. Conversely, for a very narrow channel, the translocation time only depends on the chain contour length and is similar to that of a rod due to the absence of spatial chain fluctuations.