Kinetics of Loop Formation in Polymer Chains

Abstract

We investigate the kinetics of loop formation in flexible ideal polymer chains (Rouse model), and polymers in good and poor solvents. We show for the Rouse model, using a modification of the theory of Szabo, Schulten, and Schulten, that the time scale for cyclization is $τ_c\sim τ_0 N^2$ (where $τ_0$ is a microscopic time scale and $N$ is the number of monomers), provided the coupling between the relaxation dynamics of the end-to-end vector and the looping dynamics is taken into account. The resulting analytic expression fits the simulation results accurately when $a$, the capture radius for contact formation, exceeds $b$, the average distance between two connected beads. Simulations also show that, when $a < b$, $τ_c\sim N^{α_τ}$, where $1.5<{α_τ}\le 2$ in the range $7<N<200$ used in the simulations. By using a diffusion coefficient that is dependent on the length scales $a$ and $b$ (with $a<b$), which captures the two-stage mechanism by which looping occurs when $a < b$, we obtain an analytic expression for $τ_c$ that fits the simulation results well. The kinetics of contact formation between the ends of the chain are profoundly affected when interactions between monomers are taken into account. Remarkably, for $N < 100$ the values of $τ_c$ decrease by more than two orders of magnitude when the solvent quality changes from good to poor. Fits of the simulation data for $τ_c$ to a power law in $N$ ($τ_c\sim N^{α_τ}$) show that $α_τ$ varies from about 2.4 in a good solvent to about 1.0 in poor solvents. Loop formation in poor solvents, in which the polymer adopts dense, compact globular conformations, occurs by a reptation-like mechanism of the ends of the chain.

30 pages, 9 figures. Revised version includes a new figure (8) and minor changes to the text