Polymer escape from a metastable Kramers potential: Path integral hyperdynamics study
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School of Science |
A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
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Date
2010
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Language
en
Pages
184902
Series
The Journal of Chemical Physics, Volume 133, Issue 18
Abstract
We study the dynamics of flexible, semiflexible, and self-avoiding polymer chains moving under a Kramers metastable potential. Due to thermal noise, the polymers, initially placed in the metastable well, can cross the potential barrier, but these events are extremely rare if the barrier is much larger than thermal energy. To speed up the slow rate processes in computer simulations, we extend the recently proposed path integral hyperdynamics method to the cases of polymers. We consider the cases where the polymers’ radii of gyration are comparable to the distance between the well bottom and the barrier top. We find that, for a flexible polymers, the crossing rate (R) monotonically decreases with chain contour length (L), but with the magnitude much larger than the Kramers rate in the globular limit. For a semiflexible polymer, the crossing rate decreases with L but becomes nearly constant for large L. For a fixed L, the crossing rate becomes maximum at an intermediate bending stiffness. For the self-avoiding chain, the rate is a nonmonotonic function of L, first decreasing with L, and then, above a certain length, increasing with L. These findings can be instrumental for efficient separation of biopolymers.Description
Keywords
bending, polymers, thermal noise, free energy, activation energies, Brownian dynamics, biopolymers
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Citation
Shin, Jaeoh & Ikonen, Timo & Khandkar, Mahendra D. & Ala-Nissilä, Tapio & Sung, Wokyung. 2010. Polymer escape from a metastable Kramers potential: Path integral hyperdynamics study. The Journal of Chemical Physics. Volume 133, Issue 18. 184902. 1089-7690 (electronic). 0021-9606 (printed). DOI: 10.1063/1.3493292.
