Polymer ejection from strong spherical confinement

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Polymer ejection from strong spherical confinement. / Piili, Joonas; Linna, Riku P.

In: Physical Review E, Vol. 92, No. 6, 062715, 2015, p. 1-6.

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@article{d1ff01c10ace4148a9cde5ee624e797e,
title = "Polymer ejection from strong spherical confinement",
abstract = "We examine the ejection of an initially strongly confined flexible polymer from a spherical capsid through a nanoscale pore. We use molecular dynamics for unprecedentedly high initial monomer densities. We show that the time for an individual monomer to eject grows exponentially with the number of ejected monomers. By measurements of the force at the pore we show this dependence to be a consequence of the excess free energy of the polymer due to confinement growing exponentially with the number of monomers initially inside the capsid. This growth relates closely to the divergence of mixing energy in the Flory-Huggins theory at large concentration. We show that the pressure inside the capsid driving the ejection dominates the process that is characterized by the ejection time growing linearly with the lengths of different polymers. Waiting time profiles would indicate that the superlinear dependence obtained for polymers amenable to computer simulations results from a finite-size effect due to the final retraction of polymers' tails from capsids.",
keywords = "bacteriophage, capsid ejection, polymer physics, stochastic rotation dynamics, virus capsid, bacteriophage, capsid ejection, polymer physics, stochastic rotation dynamics, virus capsid, bacteriophage, capsid ejection, polymer physics, stochastic rotation dynamics, virus capsid",
author = "Joonas Piili and Linna, {Riku P.}",
note = "VK: Lampinen, J.; TRITON; CSC",
year = "2015",
doi = "10.1103/PhysRevE.92.062715",
language = "English",
volume = "92",
pages = "1--6",
journal = "Physical Review E",
issn = "2470-0045",
publisher = "American Physical Society",
number = "6",

}

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TY - JOUR

T1 - Polymer ejection from strong spherical confinement

AU - Piili, Joonas

AU - Linna, Riku P.

N1 - VK: Lampinen, J.; TRITON; CSC

PY - 2015

Y1 - 2015

N2 - We examine the ejection of an initially strongly confined flexible polymer from a spherical capsid through a nanoscale pore. We use molecular dynamics for unprecedentedly high initial monomer densities. We show that the time for an individual monomer to eject grows exponentially with the number of ejected monomers. By measurements of the force at the pore we show this dependence to be a consequence of the excess free energy of the polymer due to confinement growing exponentially with the number of monomers initially inside the capsid. This growth relates closely to the divergence of mixing energy in the Flory-Huggins theory at large concentration. We show that the pressure inside the capsid driving the ejection dominates the process that is characterized by the ejection time growing linearly with the lengths of different polymers. Waiting time profiles would indicate that the superlinear dependence obtained for polymers amenable to computer simulations results from a finite-size effect due to the final retraction of polymers' tails from capsids.

AB - We examine the ejection of an initially strongly confined flexible polymer from a spherical capsid through a nanoscale pore. We use molecular dynamics for unprecedentedly high initial monomer densities. We show that the time for an individual monomer to eject grows exponentially with the number of ejected monomers. By measurements of the force at the pore we show this dependence to be a consequence of the excess free energy of the polymer due to confinement growing exponentially with the number of monomers initially inside the capsid. This growth relates closely to the divergence of mixing energy in the Flory-Huggins theory at large concentration. We show that the pressure inside the capsid driving the ejection dominates the process that is characterized by the ejection time growing linearly with the lengths of different polymers. Waiting time profiles would indicate that the superlinear dependence obtained for polymers amenable to computer simulations results from a finite-size effect due to the final retraction of polymers' tails from capsids.

KW - bacteriophage

KW - capsid ejection

KW - polymer physics

KW - stochastic rotation dynamics

KW - virus capsid

KW - bacteriophage

KW - capsid ejection

KW - polymer physics

KW - stochastic rotation dynamics

KW - virus capsid

KW - bacteriophage

KW - capsid ejection

KW - polymer physics

KW - stochastic rotation dynamics

KW - virus capsid

UR - http://dx.doi.org/10.1103/PhysRevE.92.062715

U2 - 10.1103/PhysRevE.92.062715

DO - 10.1103/PhysRevE.92.062715

M3 - Article

VL - 92

SP - 1

EP - 6

JO - Physical Review E

JF - Physical Review E

SN - 2470-0045

IS - 6

M1 - 062715

ER -

ID: 2030371