Uniform description of polymer ejection dynamics from capsid with and without hydrodynamics
Loading...
Access rights
openAccess
publishedVersion
URL
Journal Title
Journal ISSN
Volume Title
A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
This publication is imported from Aalto University research portal.
View publication in the Research portal (opens in new window)
View/Open full text file from the Research portal (opens in new window)
View publication in the Research portal (opens in new window)
View/Open full text file from the Research portal (opens in new window)
Authors
Date
2017-05-26
Department
Major/Subject
Mcode
Degree programme
Language
en
Pages
12
Series
Physical Review E, Volume 95, issue 5, pp. 1-12
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.Description
Keywords
PERSISTENCE LENGTH, MOLECULAR-DYNAMICS, DNA, MODEL, TRANSLOCATION, BACTERIOPHAGE, FORCE, FLOW
Other note
Citation
Piili, J, Suhonen, P M & Linna, R P 2017, ' Uniform description of polymer ejection dynamics from capsid with and without hydrodynamics ', Physical Review E, vol. 95, no. 5, 052418, pp. 1-12 . https://doi.org/10.1103/PhysRevE.95.052418