Non-Markovian dynamics of reaction coordinate in polymer folding

Abstract

We develop a theoretical description of the critical zipping dynamics of a self-folding polymer. We use tension propagation theory and the formalism of the generalized Langevin equation applied to a polymer that contains two complementary parts which can bind to each other. At the critical temperature, the (un)zipping is unbiased and the two strands open and close as a zipper. The number of closed base pairs $n(t)$ displays a subdiffusive motion characterized by a variance growing as $⟨\Delta n^2(t)⟩\sim t^{\alpha }$ with $\alpha <1$ at long times. Our theory provides an estimate of both the asymptotic anomalous exponent $\alpha$ and of the subleading correction term, which are both in excellent agreement with numerical simulations. The results indicate that the tension propagation theory captures the relevant features of the dynamics and shed some new insights on related polymer problems characterized by anomalous dynamical behavior.

8 pages, 3 figures, submitted

References in corpus (8)

• Nonequilibrium dynamics of polymer translocation and straightening
• Physics of base-pairing dynamics in DNA
• Dynamics of forced biopolymer translocation
• Anomalous dynamics of DNA hairpin folding
• On the generalized Langevin equation for a Rouse bead in a nonequilibrium bath
• Anomalous zipping dynamics and forced polymer translocation
• Transient behaviour of a polymer dragged through a viscoelastic medium
• A lattice polymer study of DNA renaturation dynamics

Cited by in corpus (4)

• Transition path time distributions
• The influence of absorbing boundary conditions on the transition path times statistics
• Role of helicity in DNA hairping folding dynamics
• Polymer Concentration Regimes from Fractional Microrheology