Segregation Kinetics of Topologically Modified (DNA-)Polymers in Confinement

Abstract

It is known that when two self-avoiding polymers are confined in a cylindrical space, they spontaneously evolve towards a state in which the polymers are segregated along the long axis of the cylinder. In such a segregated state, the conformational entropy of both polymers is higher than that of a state where they are mixed. In this computational work, we systematically study the effect of topological modifications to the polymer contour on the segregation speed of these polymers via simulations. The simplest topology we consider is a ring, and we introduce modifications by adding smaller loops to this ring contour. We observe that the speed of the entropic segregation increases with increasing the number of loops of the topology while keeping the total length of the contour constant. The effect of such smaller loops could be relevant for the DNA present in simple bacteria such as E. coli. Additionally, we hope that such topological modifications can be harnessed by synthetic polymers for industrial applications.