Free energy evaluation in polymer translocation via Jarzynski equality

Detalhes bibliográficos
Autor(a) principal: Mondaini, Felipe
Data de Publicação: 2014
Outros Autores: Moriconi, Luca
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da UFRJ
Texto Completo: http://hdl.handle.net/11422/8524
Resumo: We perform, with the help of cloud computing resources, extensive Langevin simulations, which provide free energy estimates for unbiased three-dimensional polymer translocation. We employ the Jarzynski equality in its rigorous setting, to compute the variation of the free energy in single monomer translocation events. In our three-dimensional Langevin simulations, the excluded-volume and van der Waals interactions between beads (monomers and membrane atoms) are modeled through a repulsive Lennard-Jones (LJ) potential and consecutive monomers are subject to the Finite-Extension Nonlinear Elastic (FENE) potential. Analysing data for polymers with different lengths, the free energy profile is noted to have interesting finite-size scaling properties.
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spelling Free energy evaluation in polymer translocation via Jarzynski equalityPolymer translocationStatistical ensemblesCloud computingEnergy variationCNPQ::CIENCIAS EXATAS E DA TERRA::FISICA::AREAS CLASSICAS DE FENOMENOLOGIA E SUAS APLICACOES::DINAMICA DOS FLUIDOSWe perform, with the help of cloud computing resources, extensive Langevin simulations, which provide free energy estimates for unbiased three-dimensional polymer translocation. We employ the Jarzynski equality in its rigorous setting, to compute the variation of the free energy in single monomer translocation events. In our three-dimensional Langevin simulations, the excluded-volume and van der Waals interactions between beads (monomers and membrane atoms) are modeled through a repulsive Lennard-Jones (LJ) potential and consecutive monomers are subject to the Finite-Extension Nonlinear Elastic (FENE) potential. Analysing data for polymers with different lengths, the free energy profile is noted to have interesting finite-size scaling properties.Indisponível.ElsevierBrasilNúcleo Interdisciplinar de Dinâmica dos Fluidos2019-06-25T18:17:19Z2023-12-21T03:06:04Z2014-05-02info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article0375-9601http://hdl.handle.net/11422/852410.1016/j.physleta.2014.04.055engPhysics Letters AMondaini, FelipeMoriconi, Lucainfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da UFRJinstname:Universidade Federal do Rio de Janeiro (UFRJ)instacron:UFRJ2023-12-21T03:06:04Zoai:pantheon.ufrj.br:11422/8524Repositório InstitucionalPUBhttp://www.pantheon.ufrj.br/oai/requestpantheon@sibi.ufrj.bropendoar:2023-12-21T03:06:04Repositório Institucional da UFRJ - Universidade Federal do Rio de Janeiro (UFRJ)false
dc.title.none.fl_str_mv Free energy evaluation in polymer translocation via Jarzynski equality
title Free energy evaluation in polymer translocation via Jarzynski equality
spellingShingle Free energy evaluation in polymer translocation via Jarzynski equality
Mondaini, Felipe
Polymer translocation
Statistical ensembles
Cloud computing
Energy variation
CNPQ::CIENCIAS EXATAS E DA TERRA::FISICA::AREAS CLASSICAS DE FENOMENOLOGIA E SUAS APLICACOES::DINAMICA DOS FLUIDOS
title_short Free energy evaluation in polymer translocation via Jarzynski equality
title_full Free energy evaluation in polymer translocation via Jarzynski equality
title_fullStr Free energy evaluation in polymer translocation via Jarzynski equality
title_full_unstemmed Free energy evaluation in polymer translocation via Jarzynski equality
title_sort Free energy evaluation in polymer translocation via Jarzynski equality
author Mondaini, Felipe
author_facet Mondaini, Felipe
Moriconi, Luca
author_role author
author2 Moriconi, Luca
author2_role author
dc.contributor.author.fl_str_mv Mondaini, Felipe
Moriconi, Luca
dc.subject.por.fl_str_mv Polymer translocation
Statistical ensembles
Cloud computing
Energy variation
CNPQ::CIENCIAS EXATAS E DA TERRA::FISICA::AREAS CLASSICAS DE FENOMENOLOGIA E SUAS APLICACOES::DINAMICA DOS FLUIDOS
topic Polymer translocation
Statistical ensembles
Cloud computing
Energy variation
CNPQ::CIENCIAS EXATAS E DA TERRA::FISICA::AREAS CLASSICAS DE FENOMENOLOGIA E SUAS APLICACOES::DINAMICA DOS FLUIDOS
description We perform, with the help of cloud computing resources, extensive Langevin simulations, which provide free energy estimates for unbiased three-dimensional polymer translocation. We employ the Jarzynski equality in its rigorous setting, to compute the variation of the free energy in single monomer translocation events. In our three-dimensional Langevin simulations, the excluded-volume and van der Waals interactions between beads (monomers and membrane atoms) are modeled through a repulsive Lennard-Jones (LJ) potential and consecutive monomers are subject to the Finite-Extension Nonlinear Elastic (FENE) potential. Analysing data for polymers with different lengths, the free energy profile is noted to have interesting finite-size scaling properties.
publishDate 2014
dc.date.none.fl_str_mv 2014-05-02
2019-06-25T18:17:19Z
2023-12-21T03:06:04Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.uri.fl_str_mv 0375-9601
http://hdl.handle.net/11422/8524
10.1016/j.physleta.2014.04.055
identifier_str_mv 0375-9601
10.1016/j.physleta.2014.04.055
url http://hdl.handle.net/11422/8524
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv Physics Letters A
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Elsevier
Brasil
Núcleo Interdisciplinar de Dinâmica dos Fluidos
publisher.none.fl_str_mv Elsevier
Brasil
Núcleo Interdisciplinar de Dinâmica dos Fluidos
dc.source.none.fl_str_mv reponame:Repositório Institucional da UFRJ
instname:Universidade Federal do Rio de Janeiro (UFRJ)
instacron:UFRJ
instname_str Universidade Federal do Rio de Janeiro (UFRJ)
instacron_str UFRJ
institution UFRJ
reponame_str Repositório Institucional da UFRJ
collection Repositório Institucional da UFRJ
repository.name.fl_str_mv Repositório Institucional da UFRJ - Universidade Federal do Rio de Janeiro (UFRJ)
repository.mail.fl_str_mv pantheon@sibi.ufrj.br
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