Loop exponent in DNA bubble dynamics

DOI10.1088/1751-8113/47/31/315003zbMATH Open1346.92049arXiv1402.1622OpenAlexW3105755012MaRDI QIDQ2877409FDOQ2877409

Authors: Vojtěch Kaiser, Tomáš Novotný 

Publication date: 22 August 2014

Published in: Journal of Physics A: Mathematical and Theoretical (Search for Journal in Brave)

Abstract: Dynamics of DNA bubbles are of interest for both statistical physics and biology. We present exact solutions to the Fokker-Planck equation governing bubble dynamics in the presence of a long-range entropic interaction. The complete meeting time and meeting position probability distributions are derived from the solutions. Probability distribution functions reflect the value of the loop exponent of the entropic interaction. Our results extend previous results which concentrated mainly on the tails of the probability distribution functions and open a way to determining the strength of the entropic interaction experimentally which has been a matter of recent discussions. Using numerical integration, we also discuss the influence of the finite size of a DNA chain on the bubble dynamics. Analogous results are obtained also for the case of subdiffusive dynamics of a DNA bubble in a heteropolymer, revealing highly universal asymptotics of meeting time and position probability functions.

Full work available at URL: https://arxiv.org/abs/1402.1622

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zbMATH Keywords

Fokker-Planck equationvicious walkersDNA bubble breathing

Mathematics Subject Classification ID

Protein sequences, DNA sequences (92D20) Fokker-Planck equations (35Q84) Stochastic methods (Fokker-Planck, Langevin, etc.) applied to problems in time-dependent statistical mechanics (82C31)

Cited In (4)

• Solution of the Fokker-Planck equation with a logarithmic potential and mixed eigenvalue spectrum
• Bubble dynamics in DNA
• Ab initio bubble-driven denaturation of double-stranded DNA: self-mechanical theory
• A unified view of transport equations

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