A general theory of polymer ejection tested in a quasi two-dimensional space

Abstract A general ejection theory of polymer is developed in a two- and three-dimensional space. A polymer is confined initially in a cavity and ejects spontaneously to the outer space through a nanopore channel without the help of any external stimulus. A reflective wall boundary is set at the por...

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Autores principales:	Pai-Yi Hsiao, Wei-Yei Chen
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/73aaff358cdd4dd99afcef22dec77a85
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spelling	oai:doaj.org-article:73aaff358cdd4dd99afcef22dec77a852021-12-02T17:55:09ZA general theory of polymer ejection tested in a quasi two-dimensional space10.1038/s41598-021-94054-22045-2322https://doaj.org/article/73aaff358cdd4dd99afcef22dec77a852021-07-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-94054-2https://doaj.org/toc/2045-2322Abstract A general ejection theory of polymer is developed in a two- and three-dimensional space. A polymer is confined initially in a cavity and ejects spontaneously to the outer space through a nanopore channel without the help of any external stimulus. A reflective wall boundary is set at the pore entrance to prevent the falling of the head monomer of chain into the cavity. Three stages are distinguished in a process: (1) an entering stage, in which the head monomer enters the pore to search for a way to traverse the pore channel, (2) a main ejection stage, in which the chain body is transported from the cavity to the outer space, (3) a leaving stage, in which the tail monomer passes through and leaves the pore channel. Depending on the number of the monomers remaining in the cavity, the main ejection stage can be divided into the confined and the non-confined stages. The non-confined stage can be further split into the thermal escape and the entropic pulling stages. The Onsager’s variational principle is applied to derive the kinetics equation of ejection. The escape time is calculated from the corresponding Kramers’ escape problem. Extensive molecular dynamics simulations are then performed in a quasi two-dimensional space to verify the theory. The variation of the ejection speed is carefully examined. The decreasing behavior of the number of monomers in the cavity is studied in details. The scaling properties of the spending time at each processing stage are investigated systematically by varying the chain length, the cavity diameter, and the initial volume fraction of chain. The results of simulation support firmly the predictions of the theory, cross-checked in the studies of various topics. In combining with the previous investigations in the three-dimensional space, the generalized theory is very robust, able to explain the two seemly different phenomena, polymer ejection and polymer translocation, together under the same theoretical framework in the two space dimensions.Pai-Yi HsiaoWei-Yei ChenNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-20 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Pai-Yi Hsiao Wei-Yei Chen A general theory of polymer ejection tested in a quasi two-dimensional space
description	Abstract A general ejection theory of polymer is developed in a two- and three-dimensional space. A polymer is confined initially in a cavity and ejects spontaneously to the outer space through a nanopore channel without the help of any external stimulus. A reflective wall boundary is set at the pore entrance to prevent the falling of the head monomer of chain into the cavity. Three stages are distinguished in a process: (1) an entering stage, in which the head monomer enters the pore to search for a way to traverse the pore channel, (2) a main ejection stage, in which the chain body is transported from the cavity to the outer space, (3) a leaving stage, in which the tail monomer passes through and leaves the pore channel. Depending on the number of the monomers remaining in the cavity, the main ejection stage can be divided into the confined and the non-confined stages. The non-confined stage can be further split into the thermal escape and the entropic pulling stages. The Onsager’s variational principle is applied to derive the kinetics equation of ejection. The escape time is calculated from the corresponding Kramers’ escape problem. Extensive molecular dynamics simulations are then performed in a quasi two-dimensional space to verify the theory. The variation of the ejection speed is carefully examined. The decreasing behavior of the number of monomers in the cavity is studied in details. The scaling properties of the spending time at each processing stage are investigated systematically by varying the chain length, the cavity diameter, and the initial volume fraction of chain. The results of simulation support firmly the predictions of the theory, cross-checked in the studies of various topics. In combining with the previous investigations in the three-dimensional space, the generalized theory is very robust, able to explain the two seemly different phenomena, polymer ejection and polymer translocation, together under the same theoretical framework in the two space dimensions.
format	article
author	Pai-Yi Hsiao Wei-Yei Chen
author_facet	Pai-Yi Hsiao Wei-Yei Chen
author_sort	Pai-Yi Hsiao
title	A general theory of polymer ejection tested in a quasi two-dimensional space
title_short	A general theory of polymer ejection tested in a quasi two-dimensional space
title_full	A general theory of polymer ejection tested in a quasi two-dimensional space
title_fullStr	A general theory of polymer ejection tested in a quasi two-dimensional space
title_full_unstemmed	A general theory of polymer ejection tested in a quasi two-dimensional space
title_sort	general theory of polymer ejection tested in a quasi two-dimensional space
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/73aaff358cdd4dd99afcef22dec77a85
work_keys_str_mv	AT paiyihsiao ageneraltheoryofpolymerejectiontestedinaquasitwodimensionalspace AT weiyeichen ageneraltheoryofpolymerejectiontestedinaquasitwodimensionalspace AT paiyihsiao generaltheoryofpolymerejectiontestedinaquasitwodimensionalspace AT weiyeichen generaltheoryofpolymerejectiontestedinaquasitwodimensionalspace
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A general theory of polymer ejection tested in a quasi two-dimensional space

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