A knotted polymer chain passing through a pore

Abstract

A knotted polymer chain passing through a pore is investigated by molecule dynamics method. In this paper, we take 31 knot as an example. It is found that, during the process of translocation, the size of the knot fluctuates until the knot is unknotted. In addition, the effect of the knot on the translocation velocity of the knotted chain is also discussed. For the given external force, the average translocation time τ satisfies the scaling relation:τ～N α, and the scaling exponent α increases with the external force f. For short knotted polymer chains, the average translocation time τ decreases when the external force f increases. However, for very long knotted polymer chains, the average translocation time τ increases when the external force f increases. In the meantime, the position of knot in a knotted polymer chain also affects the average translocation time τ strongly. The closer the knot approaches the first translocated monomer, the longer the average translocation time. This investigation can provide some insights into the translocation of knotted polymer chains (especially knotted DNA) through the nanopore, and help us understand the translocation behavior of biomacromolecules.