“Monte Carlo Simulation of Static and Dynamic Properties of Ring and Linear Polymers in a Crowded Environment”

Abstract

In this paper we investigate Monte Carlo (MC) simulation of static and dynamic properties of linear and ring polymers in the presence of obstacles. To this end we used the bond fluctuation method (BFM) to study the translocation process of a polymer chain of length N in two dimensions. To overcome the entropic barrier, we placed the middle monomers of the two polymers in the middle of the pore which is placed between ordered (cis) and disordered (trans) obstacles. We studied the static properties of the polymers by calculating the average square of radius of gyration of both polymers and mean square end-to-end distance of linear polymer, and we found that the scaling relations of mean square end-to-end distance hR2 i and average square of radius of gyration hR2 g i as a function of polymer length N are nonuniversal, they strongly depend on the area fraction of crowding agents φ. The dynamic proper ties have also been studied by investigating the translocation of the polymers. Our present work shows that the escape time τ changes with a change of area fraction φ. Moreover, the power-law relation of escape time τ as a function of polymer length N, the scaling exponent (α), is nonuniversal. And also, we found that the diffusion of the polymers is subdiffusion in the presence of obstacles. From our simulation study, we also observe that the polymers prefer to translocate towards the disordered obstacles.