Semiflexible polymer dynamics with a bead-spring model

DOI10.1088/1742-5468/2014/11/P11008MaRDI QIDQ3301789zbMATH OpenOpenAlexFDO

Authors G. T. Barkema, J. M. J. van Leeuwen, Debabrata Panja

Publication date 11 August 2020

Published in Journal of Statistical Mechanics: Theory and Experiment (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1410.0139

Mathematics Subject Classification ID

Statistical mechanics of plasmas (82D10) Protein sequences, DNA sequences (92D20)

Abstract: We study the dynamical properties of semiflexible polymers with a recently introduced bead-spring model. We focus on double-stranded DNA. The two parameters of the model, $T^{\ast }$ and $u$, are chosen to match its experimental force-extension curve. The bead-spring Hamiltonian is approximated in the first order by the Hessian that is quadratic in the bead positions. The eigenmodels of the Hessian provide the longitudinal (stretching) and transverse (bending) eigenmodes of the polymer, and the corresponding eigenvalues match well with the established phenomenology of semiflexible polymers. Using the longitudinal and transverse eigenmodes, we obtain analytical expressions of (i) the autocorrelation function of the end-to-end vector, (ii) the autocorrelation function of a bond (i.e., a spring, or a tangent) vector at the middle of the chain, and (iii) the mean-square displacement of a tagged bead in the middle of the chain, as sum over the contributions from the modes. We also perform simulations with the full dynamics of the model. The simulations yield numerical values of the correlation functions (i-iii) that agree very well with the analytical expressions for the linearized dynamics. We also study the mean-square displacement of the longitudinal component of the end-to-end vector that showcases strong nonlinear effects in the polymer dynamics, and we identify at least an effective $t^{7/8}$ power-law regime in its time-dependence. Nevertheless, in comparison to the full mean-square displacement of the end-to-end vector the nonlinear effects remain small at all times --- it is in this sense we state that our results demonstrate that the linearized dynamics suffices for dsDNA fragments that are shorter than or comparable to the persistence length. Our results are consistent with those of the wormlike chain (WLC) model, the commonly used descriptive tool of semiflexible polymers.

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Cites work

• A model for the dynamics of extensible semiflexible polymers
• scientific article; zbMATH DE number 3076473 (Why is no real title available?)

Cited in

(8)

• Brownian dynamics simulation of finitely extensible bead-spring chains
• Rheological modeling with Hookean bead-spring cubes (SC, BCC and FCC)
• A mathematical analysis for the Brownian dynamics of a DNA tether
• A model for the dynamics of extensible semiflexible polymers
• Dynamical eigenmodes of a polymerized membrane
• Review on the Brownian dynamics simulation of bead-rod-spring models encountered in computational rheology
• A finitely extensible bead-spring chain model for dilute polymer solutions
• Large scale behavior of semiflexible heteropolymers

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