Uniform description of polymer ejection dynamics from capsid with and without hydrodynamics

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Abstract

We use stochastic rotation dynamics (SRD) to examine the dynamics of the ejection of an initially strongly confined flexible polymer from a spherical capsid with and without hydrodynamics. The results obtained using stochastic rotation dynamics (SRD) are compared to similar Langevin simulations. Inclusion of hydrodynamic modes speeds up the ejection but also allows the part of the polymer outside the capsid to expand closer to equilibrium. This shows as higher values of radius of gyration when hydrodynamics are enabled. By examining the waiting times of individual polymer beads, we find that the waiting time t(w) grows with the number of ejected monomers s as a sum of two exponents. When approximate to 63% of the polymer has ejected, the ejection enters the regime of slower dynamics. The functional form of t(w) versus s is universal for all ejection processes starting from the same initial monomer densities. Inclusion of hydrodynamics only reduces its magnitude. Consequently, we define a universal scaling function h such that the cumulative waiting time t = N(0)h(s/N-0) for large N-0. Our unprecedentedly precise measurements of force indicate that this form for t(w) (s) originates from the corresponding force toward the pore decreasing superexponentially at the end of the ejection. Our measured t(w) (s) explains the apparent superlinear scaling of the ejection time with the polymer length for short polymers. However, for asymptotically long polymers, t(w) (s) predicts linear scaling.

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Original languageEnglish
Article number052418
Pages (from-to)1-12
Number of pages12
JournalPhysical Review E
Volume95
Issue number5
Publication statusPublished - 26 May 2017
MoE publication typeA1 Journal article-refereed

    Research areas

  • PERSISTENCE LENGTH, MOLECULAR-DYNAMICS, DNA, MODEL, TRANSLOCATION, BACTERIOPHAGE, FORCE, FLOW

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