Molecular dynamics simulations of the monomer density profiles of knotted ring polymer chains confined in a slit of two parallel walls with one attractive and another repulsive surface

2023
journal article
article
dc.abstract.enWe have used Molecular Dynamics simulations to obtain the monomer density profiles for real linear and ring polymer chains of 360 monomers length with different topological structures such as simple knots: 3$_{1}$, 6$_{1}$, 9$_{1}$, 10$_{124}$, complex knots 3$_{1}$ 3$_{1}$ 5$_{1}$ and twisted knots with n = 10 and n = 20 in a slit geometry of two parallel walls with one attractive and another repulsive surface. We have used Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) software to perform simulations with the Verlet integration algorithm. The interactions between monomers were simulated as Lennard-Jones 12-6 potential, for bonds we have used Finitely Extensible Nonlinear Elastic (FENE) potential and the interaction with the walls was taken into account via Lennard-Jones 9-3 potential. We observed that topologically complex polymers have lower monomer density profiles near the attractive wall, but at some distance in the direction to the repulsive wall this tendency changes to the opposite. We showed that most complex twisted knots have two maxima in narrow slits. In the wide slits we do not observe such relation for twisted knots at higher temperatures. These results are important for better understanding the nature of the depletion forces which arise in a slit geometry of two parallel walls with one attractive and one repulsive wall.
dc.affiliationWydział Fizyki, Astronomii i Informatyki Stosowanej : Instytut Fizyki Teoretycznej
dc.contributor.authorKuterba, Piotr - 117409
dc.contributor.authorChristiansen, H.
dc.contributor.authorDanel, Z.
dc.contributor.authorJanke, W.
dc.date.accessioned2025-10-16T13:51:34Z
dc.date.available2025-10-16T13:51:34Z
dc.date.createdat2025-10-03T09:00:43Zen
dc.date.issued2023
dc.date.openaccess0
dc.description.accesstimew momencie opublikowania
dc.description.number1
dc.description.versionostateczna wersja wydawcy
dc.description.volume2436
dc.identifier.articleid012031
dc.identifier.doi10.1088/1742-6596/2436/1/012031
dc.identifier.eissn1742-6596
dc.identifier.issn1742-6588
dc.identifier.projectDRC AI
dc.identifier.urihttps://ruj.uj.edu.pl/handle/item/563031
dc.languageeng
dc.language.containereng
dc.rightsUdzielam licencji. Uznanie autorstwa 3.0
dc.rights.licenceCC-BY
dc.rights.urihttp://creativecommons.org/licenses/by/3.0/legalcode
dc.share.typeotwarte czasopismo
dc.subtypeArticle
dc.titleMolecular dynamics simulations of the monomer density profiles of knotted ring polymer chains confined in a slit of two parallel walls with one attractive and another repulsive surface
dc.title.journalJournal of Physics: Conference Series
dc.title.volume22nd International School on Condensed Matter Physics : State of the Art in Functional Materials & Technologies (ISCMP 2022) 28/08/2022 - 02/09/2022 VARNA, Bulgaria
dc.typeJournalArticle
dspace.entity.typePublicationen
dc.abstract.en
We have used Molecular Dynamics simulations to obtain the monomer density profiles for real linear and ring polymer chains of 360 monomers length with different topological structures such as simple knots: 3$_{1}$, 6$_{1}$, 9$_{1}$, 10$_{124}$, complex knots 3$_{1}$ 3$_{1}$ 5$_{1}$ and twisted knots with n = 10 and n = 20 in a slit geometry of two parallel walls with one attractive and another repulsive surface. We have used Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) software to perform simulations with the Verlet integration algorithm. The interactions between monomers were simulated as Lennard-Jones 12-6 potential, for bonds we have used Finitely Extensible Nonlinear Elastic (FENE) potential and the interaction with the walls was taken into account via Lennard-Jones 9-3 potential. We observed that topologically complex polymers have lower monomer density profiles near the attractive wall, but at some distance in the direction to the repulsive wall this tendency changes to the opposite. We showed that most complex twisted knots have two maxima in narrow slits. In the wide slits we do not observe such relation for twisted knots at higher temperatures. These results are important for better understanding the nature of the depletion forces which arise in a slit geometry of two parallel walls with one attractive and one repulsive wall.
dc.affiliation
Wydział Fizyki, Astronomii i Informatyki Stosowanej : Instytut Fizyki Teoretycznej
dc.contributor.author
Kuterba, Piotr - 117409
dc.contributor.author
Christiansen, H.
dc.contributor.author
Danel, Z.
dc.contributor.author
Janke, W.
dc.date.accessioned
2025-10-16T13:51:34Z
dc.date.available
2025-10-16T13:51:34Z
dc.date.createdaten
2025-10-03T09:00:43Z
dc.date.issued
2023
dc.date.openaccess
0
dc.description.accesstime
w momencie opublikowania
dc.description.number
1
dc.description.version
ostateczna wersja wydawcy
dc.description.volume
2436
dc.identifier.articleid
012031
dc.identifier.doi
10.1088/1742-6596/2436/1/012031
dc.identifier.eissn
1742-6596
dc.identifier.issn
1742-6588
dc.identifier.project
DRC AI
dc.identifier.uri
https://ruj.uj.edu.pl/handle/item/563031
dc.language
eng
dc.language.container
eng
dc.rights
Udzielam licencji. Uznanie autorstwa 3.0
dc.rights.licence
CC-BY
dc.rights.uri
http://creativecommons.org/licenses/by/3.0/legalcode
dc.share.type
otwarte czasopismo
dc.subtype
Article
dc.title
Molecular dynamics simulations of the monomer density profiles of knotted ring polymer chains confined in a slit of two parallel walls with one attractive and another repulsive surface
dc.title.journal
Journal of Physics: Conference Series
dc.title.volume
22nd International School on Condensed Matter Physics : State of the Art in Functional Materials & Technologies (ISCMP 2022) 28/08/2022 - 02/09/2022 VARNA, Bulgaria
dc.type
JournalArticle
dspace.entity.typeen
Publication
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