Ring polymer translocation through nanopore in a crowded environment

Abstract

In this paper, we use a Monte Carlo (MC) simulation method in two dimensions with a bond fluctuation model (BFM) to investigate the translocation of a ring polymer through a nanopore in a crowded environment . We put the two middle monomers in the center of the pore, to con- quer the entropic obstruction caused by the presence of an mpenetrable membrane wall. In our system, a fixed size and same density of crowding agents (φ ) are populated orderly on the left (cis) side and randomly on the right (trans) side of the wall. As the translocation of macromolecules is an important process to study the properties of polymers, we explored the static property of the polymer which is characterized by a radius of gyration and the dynamic properties, characterized by mean square displacement and escape time. We found that the scaling exponents of the average square of radius of gyration as a function of size of the polymer N varies with density of the obstacle beads, φ . Our current investigation appears that the universal power-law relation of escape time τ as a function of polymer size (τ ∼ N 2.50 ) is influenced by the density of the crowding agents. Furthermore, our research shows that the size of the polymer, the size of the pore, and the density of the obstacles all have a significant impact on polymer diffusion.

Unbiased counting of whole proteins with nanopores over the full dynamic range of a proteome: a computational study

“…In [24] D for a confined polymer with N = 12 residues has an upper bound of 0.5-10 ×10 -12 m 2 /s, which is at least 2 orders of magnitude smaller than the bulk diffusion coefficient for a single strand of DNA with the same number of bases. See [25] for a log-log plot of D versus polymer chain length N = 23, 31, 45, 57, and 73, the plot has a slope of -0.93. For a rigid rod of length L and radius R, the hydrodynamic radius is given by…”