Logo eprints

Kinetics of Loop Formation in Polymer Chains

Toan, Ngo Minh and Morrison, Greg and Hyeon, Changbong and Thirumalai, D. Kinetics of Loop Formation in Polymer Chains. Journal of Physical Chemistry B, 112 (19). pp. 6094-6106. ISSN 1520-6106 (2008)

Full text not available from this repository.


We investigate the kinetics of loop formation in ideal flexible polymer chains (the 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 τc τ0N2 (where τ0 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, τc Nατ, where 1.5 < ατ ≤ 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 τc that fits the simulation results well. The kinetics of contact formation between the ends of the chain are profoundly effected when interactions between monomers are taken into account. Remarkably, for N < 100, the values of τc decrease by more than 2 orders of magnitude when the solvent quality changes from good to poor. Fits of the simulation data for τc to a power law in N (τc Nατ) show that ατ varies from about 2.4 in a good solvent to about 1.0 in poor solvents. The effective exponent ατ decreases as the strength of the attractive monomer−monomer interactions increases. 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. The time for contact formation between beads that are interior to the chain in good solvents changes nonmonotonically as the loop length varies. In contrast, the variation in interior loop closure time is monotonic in poor solvents. The implications of our results for contact formation in polypeptide chains, RNA, and single-stranded DNA are briefly outlined.

Item Type: Article
Identification Number: 10.1021/jp076510y
Subjects: Q Science > QD Chemistry
Research Area: Economics and Institutional Change
Depositing User: Ms T. Iannizzi
Date Deposited: 04 Oct 2013 09:27
Last Modified: 04 Oct 2013 09:52
URI: http://eprints.imtlucca.it/id/eprint/1818

Actions (login required)

Edit Item Edit Item