Dynamic looping of a free-draining polymer

DOI10.1137/17M1127260MaRDI QIDQ3130412zbMATH OpenOpenAlexFDO

Authors Felix X.-F. Ye, Panos Stinis, Hong Qian

Publication date 22 January 2018

Published in SIAM Journal on Applied Mathematics (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1704.04361

zbMATH Keywords

first passage timeperturbation theorypolymer loopingstochastic process

Mathematics Subject Classification ID

Estimates of eigenvalues in context of PDEs (35P15) Perturbation theory of linear operators (47A55) Generalized stochastic processes (60G20) Applications of Brownian motions and diffusion theory (population genetics, absorption problems, etc.) (60J70) Statistical mechanics of polymers (82D60)

Abstract: We revisit the celebrated Wilemski-Fixman (WF) treatment for the looping time of a free-draining polymer. The WF theory introduces a sink term into the Fokker-Planck equation for the $3(N+1)$-dimensional Ornstein-Uhlenbeck process of the polymer dynamics, which accounts for the appropriate boundary condition due to the formation of a loop. The assumption for WF theory is considerably relaxed. A perturbation method approach is developed that justifies and generalizes the previous results using either a Delta sink or a Heaviside sink. For both types of sinks, we show that under the condition of a small dimensionless $epsilon$, the ratio of capture radius to the Kuhn length, we are able to systematically produce all known analytical and asymptotic results obtained by other methods. This includes most notably the transition regime between the $N^2$ scaling of Doi, and $NsqrtN/epsilon$ scaling of Szabo, Schulten, and Schulten. The mathematical issue at play is the non-uniform convergence of $epsilono0$ and $Noinfty$, the latter being an inherent part of the theory of a Gaussian polymer. Our analysis yields a novel term in the analytical expression for the looping time with small $epsilon$, which is previously unknown. Monte Carlo numerical simulations corroborate the analytical findings. The systematic method developed here can be applied to other systems modeled by multi-dimensional Smoluchowski equations.

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Cited in

(5)

• Understanding looping kinetics of a long polymer molecule in solution. Exact solution for delta function sink model
• Analysis of the mean first looping time of a rod-polymer
• Dynamic simulation of freely draining flexible polymers in steady linear flows
• Kinetics of escape of ssDNA molecules from \(\alpha \)-hemolysin nanopores: a dynamic disorder study
• First passage time of loop formation in chromatin chains

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