The conformational relaxation of a polymer chain often slows down in various biological and engineering processes. The polymer, then, may stay in nonequilibrium states throughout the process such that one may not invoke the local thermal equilibrium (LTE) approximation, which has been usually employed to describe the kinetics of various processes. In this work, motivated by recent single-molecule experiments on DNA packaging into a viral capsid, we investigate how the nonequilibrium conformations and the LTE approximation would affect the packaging of a polymer chain into small confinement. We employ a simple but generic coarse-grained model and Langevin dynamics simulations to investigate the packaging kinetics. The polymer segments (both inside and outside the confinement) stay away from equilibrium under strong external force. We devise a simulation scheme to invoke the LTE approximation during packaging and find that the relaxation of nonequilibrium conformations plays a critical role in regulating the packaging rate.
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28 May 2019
Research Article|
May 22 2019
The breakdown of the local thermal equilibrium approximation for a polymer chain during packaging
Seulki Kwon
;
Seulki Kwon
a)
1
Department of Chemistry, Sogang University
, Seoul 04107, South Korea
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Seulgi Lee;
Seulgi Lee
a)
1
Department of Chemistry, Sogang University
, Seoul 04107, South Korea
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Hyun Woo Cho;
Hyun Woo Cho
1
Department of Chemistry, Sogang University
, Seoul 04107, South Korea
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Jeongmin Kim;
Jeongmin Kim
1
Department of Chemistry, Sogang University
, Seoul 04107, South Korea
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Jun Soo Kim;
Jun Soo Kim
b)
2
Department of Chemistry and Nano Science, Ewha Womans University
, Seoul 03760, South Korea
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Bong June Sung
Bong June Sung
c)
1
Department of Chemistry, Sogang University
, Seoul 04107, South Korea
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a)
Contribution: Seulki Kwon and Seulgi Lee contributed equally to this work.
b)
Electronic mail: [email protected]
c)
Electronic mail: [email protected]
J. Chem. Phys. 150, 204901 (2019)
Article history
Received:
February 26 2019
Accepted:
April 30 2019
Citation
Seulki Kwon, Seulgi Lee, Hyun Woo Cho, Jeongmin Kim, Jun Soo Kim, Bong June Sung; The breakdown of the local thermal equilibrium approximation for a polymer chain during packaging. J. Chem. Phys. 28 May 2019; 150 (20): 204901. https://doi.org/10.1063/1.5093946
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