Effects of static and temporally fluctuating tensions on semiflexible polymer looping

Abstract

Biopolymer looping is a dynamic process that occurs ubiquitously in cells for gene regulation, protein folding, etc. In cellular environments, biopolymers are often subject to tensions which are either static, or temporally fluctuating far away from equilibrium. We study the dynamics of semiflexible polymer looping in the presence of such tensions by using Brownian dynamics simulation combined with an analytical theory. We show a minute tension dramatically changes the looping time, especially for long chains. Considering a dichotomically flipping noise as a simple example of the nonequilibrium tension, we find the phenomenon of resonant activation, where the looping time can be the minimum at an optimal flipping time. We discuss our results in connection with recent experiments.

7 pages, 8 figures, accepted in the Journal of Chemical Physics

References in corpus (3)

• Kinetics of Interior Loop Formation in Semiflexible Chains
• Langevin dynamics with dichotomous noise; direct simulation and applications
• Polymer Escape from a Metastable Kramers potential: Path Integral Hyperdynamics Study

Cited by in corpus (4)

• Kinetics of polymer looping with macromolecular crowding: effects of volume fraction and crowder size
• Polymer translocation under time-dependent driving forces: resonant activation induced by attractive polymer-pore interactions
• Weak temporal signals can synchronize and accelerate the transition dynamics of biopolymers under tension
• Facilitation of DNA loop formation by protein-DNA non-specific interactions