Iso-Flux Tension Propagation Theory of Driven Polymer Translocation: The Role of Initial Configurations

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Journal Title
Journal ISSN
Volume Title
School of Science | A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
Date
2014
Major/Subject
Mcode
Degree programme
Language
en
Pages
214907-1-9
Series
The Journal of Chemical Physics, Volume 141, Number 21
Abstract
We investigate the dynamics of pore-driven polymer translocation by theoretical analysis and molecular dynamics (MD) simulations. Using the tension propagation theory within the constant flux approximation we derive an explicit equation of motion for the tension front. From this we derive a scaling relation for the average translocation time τ, which captures the asymptotic result τ∝N1+ν0 , where N 0 is the chain length and ν is the Flory exponent. In addition, we derive the leading correction-to-scaling term to τ and show that all terms of order N2ν0 exactly cancel out, leaving only a finite-chain length correction term due to the effective pore friction, which is linearly proportional to N 0. We use the model to numerically include fluctuations in the initial configuration of the polymer chain in addition to thermal noise. We show that when the cis side fluctuations are properly accounted for, the model not only reproduces previously known results but also considerably improves the estimates of the monomer waiting time distribution and the time evolution of the translocation coordinate s(t), showing excellent agreement with MD simulations.
Description
Keywords
Polymer translocation, Polymer dynamics, DNA sequencing
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Citation
Sarabadani, J. & Ikonen, T. & Ala-Nissilä, Tapio. 2014. Iso-Flux Tension Propagation Theory of Driven Polymer Translocation: The Role of Initial Configurations. The Journal of Chemical Physics. Volume 141, Number 214907. P. 214907-1-9. ISSN 0021-9606 (printed). DOI: 10.1063/1.4903176.