Polymer escape from a confining potential

Harri Mökkönen (Corresponding Author), Timo Ikonen, Hannes Jónsson, Tapio Ala-Nissila

Research output: Contribution to journalArticleScientificpeer-review

3 Citations (Scopus)

Abstract

The rate of escape of polymers from a two-dimensionally confining potential well has been evaluated using self-avoiding as well as ideal chain representations of varying length, up to 80 beads. Long timescale Langevin trajectories were calculated using the path integral hyperdynamics method to evaluate the escape rate. A minimum is found in the rate for self-avoiding polymers of intermediate length while the escape rate decreases monotonically with polymer length for ideal polymers. The increase in the rate for long, self-avoiding polymers is ascribed to crowding in the potential well which reduces the free energy escape barrier. An effective potential curve obtained using the centroid as an independent variable was evaluated by thermodynamic averaging and Kramers rate theory then applied to estimate the escape rate. While the qualitative features are well reproduced by this approach, it significantly overestimates the rate, especially for the longer polymers. The reason for this is illustrated by constructing a two-dimensional effective energy surface using the radius of gyration as well as the centroid as controlled variables. This shows that the description of a transition state dividing surface using only the centroid fails to confine the system to the region corresponding to the free energy barrier and this problem becomes more pronounced the longer the polymer is. A proper definition of a transition state for polymer escape needs to take into account the shape as well as the location of the polymer.
Original languageEnglish
Number of pages7
JournalJournal of Chemical Physics
Volume140
Issue number5
DOIs
Publication statusPublished - 2014
MoE publication typeA1 Journal article-refereed

Fingerprint

confining
escape
Polymers
polymers
centroids
Free energy
free energy
crowding
Energy barriers
gyration
Interfacial energy
beads
surface energy
Trajectories
trajectories
Thermodynamics
thermodynamics
radii
curves
estimates

Cite this

Mökkönen, H., Ikonen, T., Jónsson, H., & Ala-Nissila, T. (2014). Polymer escape from a confining potential. Journal of Chemical Physics, 140(5). https://doi.org/10.1063/1.4863920
Mökkönen, Harri ; Ikonen, Timo ; Jónsson, Hannes ; Ala-Nissila, Tapio. / Polymer escape from a confining potential. In: Journal of Chemical Physics. 2014 ; Vol. 140, No. 5.
@article{dfca848746b84caf9cc4d0294b452edd,
title = "Polymer escape from a confining potential",
abstract = "The rate of escape of polymers from a two-dimensionally confining potential well has been evaluated using self-avoiding as well as ideal chain representations of varying length, up to 80 beads. Long timescale Langevin trajectories were calculated using the path integral hyperdynamics method to evaluate the escape rate. A minimum is found in the rate for self-avoiding polymers of intermediate length while the escape rate decreases monotonically with polymer length for ideal polymers. The increase in the rate for long, self-avoiding polymers is ascribed to crowding in the potential well which reduces the free energy escape barrier. An effective potential curve obtained using the centroid as an independent variable was evaluated by thermodynamic averaging and Kramers rate theory then applied to estimate the escape rate. While the qualitative features are well reproduced by this approach, it significantly overestimates the rate, especially for the longer polymers. The reason for this is illustrated by constructing a two-dimensional effective energy surface using the radius of gyration as well as the centroid as controlled variables. This shows that the description of a transition state dividing surface using only the centroid fails to confine the system to the region corresponding to the free energy barrier and this problem becomes more pronounced the longer the polymer is. A proper definition of a transition state for polymer escape needs to take into account the shape as well as the location of the polymer.",
author = "Harri M{\"o}kk{\"o}nen and Timo Ikonen and Hannes J{\'o}nsson and Tapio Ala-Nissila",
year = "2014",
doi = "10.1063/1.4863920",
language = "English",
volume = "140",
journal = "Journal of Chemical Physics",
issn = "0021-9606",
publisher = "American Institute of Physics AIP",
number = "5",

}

Mökkönen, H, Ikonen, T, Jónsson, H & Ala-Nissila, T 2014, 'Polymer escape from a confining potential', Journal of Chemical Physics, vol. 140, no. 5. https://doi.org/10.1063/1.4863920

Polymer escape from a confining potential. / Mökkönen, Harri (Corresponding Author); Ikonen, Timo; Jónsson, Hannes; Ala-Nissila, Tapio.

In: Journal of Chemical Physics, Vol. 140, No. 5, 2014.

Research output: Contribution to journalArticleScientificpeer-review

TY - JOUR

T1 - Polymer escape from a confining potential

AU - Mökkönen, Harri

AU - Ikonen, Timo

AU - Jónsson, Hannes

AU - Ala-Nissila, Tapio

PY - 2014

Y1 - 2014

N2 - The rate of escape of polymers from a two-dimensionally confining potential well has been evaluated using self-avoiding as well as ideal chain representations of varying length, up to 80 beads. Long timescale Langevin trajectories were calculated using the path integral hyperdynamics method to evaluate the escape rate. A minimum is found in the rate for self-avoiding polymers of intermediate length while the escape rate decreases monotonically with polymer length for ideal polymers. The increase in the rate for long, self-avoiding polymers is ascribed to crowding in the potential well which reduces the free energy escape barrier. An effective potential curve obtained using the centroid as an independent variable was evaluated by thermodynamic averaging and Kramers rate theory then applied to estimate the escape rate. While the qualitative features are well reproduced by this approach, it significantly overestimates the rate, especially for the longer polymers. The reason for this is illustrated by constructing a two-dimensional effective energy surface using the radius of gyration as well as the centroid as controlled variables. This shows that the description of a transition state dividing surface using only the centroid fails to confine the system to the region corresponding to the free energy barrier and this problem becomes more pronounced the longer the polymer is. A proper definition of a transition state for polymer escape needs to take into account the shape as well as the location of the polymer.

AB - The rate of escape of polymers from a two-dimensionally confining potential well has been evaluated using self-avoiding as well as ideal chain representations of varying length, up to 80 beads. Long timescale Langevin trajectories were calculated using the path integral hyperdynamics method to evaluate the escape rate. A minimum is found in the rate for self-avoiding polymers of intermediate length while the escape rate decreases monotonically with polymer length for ideal polymers. The increase in the rate for long, self-avoiding polymers is ascribed to crowding in the potential well which reduces the free energy escape barrier. An effective potential curve obtained using the centroid as an independent variable was evaluated by thermodynamic averaging and Kramers rate theory then applied to estimate the escape rate. While the qualitative features are well reproduced by this approach, it significantly overestimates the rate, especially for the longer polymers. The reason for this is illustrated by constructing a two-dimensional effective energy surface using the radius of gyration as well as the centroid as controlled variables. This shows that the description of a transition state dividing surface using only the centroid fails to confine the system to the region corresponding to the free energy barrier and this problem becomes more pronounced the longer the polymer is. A proper definition of a transition state for polymer escape needs to take into account the shape as well as the location of the polymer.

U2 - 10.1063/1.4863920

DO - 10.1063/1.4863920

M3 - Article

VL - 140

JO - Journal of Chemical Physics

JF - Journal of Chemical Physics

SN - 0021-9606

IS - 5

ER -

Mökkönen H, Ikonen T, Jónsson H, Ala-Nissila T. Polymer escape from a confining potential. Journal of Chemical Physics. 2014;140(5). https://doi.org/10.1063/1.4863920