Ion fluxes through nanopores and transmembrane channels

Detalhes bibliográficos
Autor(a) principal: Bordin, José Rafael
Data de Publicação: 2012
Outros Autores: Diehl, Alexandre, Barbosa, Marcia Cristina Bernardes, Levin, Yan
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da UFRGS
Texto Completo: http://hdl.handle.net/10183/101828
Resumo: We introduce an implicit solvent Molecular Dynamics approach for calculating ionic fluxes through narrow nanopores and transmembrane channels. The method relies on a dual-control-volume grand-canonical molecular dynamics (DCV-GCMD) simulation and the analytical solution for the electrostatic potential inside a cylindrical nanopore recently obtained by Levin [Europhys. Lett. 76, 163 (2006)]. The theory is used to calculate the ionic fluxes through an artificial transmembrane channel which mimics the antibacterial gramicidin A channel. Both current-voltage and current-concentration relations are calculated under various experimental conditions. We show that our results are comparable to the characteristics associated to the gramicidin A pore, especially the existence of two binding sites inside the pore and the observed saturation in the current-concentration profiles.
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spelling Bordin, José RafaelDiehl, AlexandreBarbosa, Marcia Cristina BernardesLevin, Yan2014-08-26T09:26:16Z20121539-3755http://hdl.handle.net/10183/101828000836641We introduce an implicit solvent Molecular Dynamics approach for calculating ionic fluxes through narrow nanopores and transmembrane channels. The method relies on a dual-control-volume grand-canonical molecular dynamics (DCV-GCMD) simulation and the analytical solution for the electrostatic potential inside a cylindrical nanopore recently obtained by Levin [Europhys. Lett. 76, 163 (2006)]. The theory is used to calculate the ionic fluxes through an artificial transmembrane channel which mimics the antibacterial gramicidin A channel. Both current-voltage and current-concentration relations are calculated under various experimental conditions. We show that our results are comparable to the characteristics associated to the gramicidin A pore, especially the existence of two binding sites inside the pore and the observed saturation in the current-concentration profiles.application/pdfengPhysical review. E, Statistical, nonlinear, and soft matter physics. Vol. 85, no. 3 (Mar. 2012), 031914, 7 p.BiofísicaDinâmica molecularMicroorganismosFenômeno bioelétricoBiomembranasProcessos de transporteIon fluxes through nanopores and transmembrane channelsEstrangeiroinfo:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da UFRGSinstname:Universidade Federal do Rio Grande do Sul (UFRGS)instacron:UFRGSORIGINAL000836641.pdf000836641.pdfTexto completo (inglês)application/pdf292703http://www.lume.ufrgs.br/bitstream/10183/101828/1/000836641.pdf9106d6b3a702c52c88a933c7c1b4b190MD51TEXT000836641.pdf.txt000836641.pdf.txtExtracted Texttext/plain31406http://www.lume.ufrgs.br/bitstream/10183/101828/2/000836641.pdf.txtb52d6cdf0b8a28145eaf241698fa5f80MD52THUMBNAIL000836641.pdf.jpg000836641.pdf.jpgGenerated Thumbnailimage/jpeg2183http://www.lume.ufrgs.br/bitstream/10183/101828/3/000836641.pdf.jpg33bc41e8489c585a78b2b6599e4585ceMD5310183/1018282024-02-07 06:01:29.269383oai:www.lume.ufrgs.br:10183/101828Repositório de PublicaçõesPUBhttps://lume.ufrgs.br/oai/requestopendoar:2024-02-07T08:01:29Repositório Institucional da UFRGS - Universidade Federal do Rio Grande do Sul (UFRGS)false
dc.title.pt_BR.fl_str_mv Ion fluxes through nanopores and transmembrane channels
title Ion fluxes through nanopores and transmembrane channels
spellingShingle Ion fluxes through nanopores and transmembrane channels
Bordin, José Rafael
Biofísica
Dinâmica molecular
Microorganismos
Fenômeno bioelétrico
Biomembranas
Processos de transporte
title_short Ion fluxes through nanopores and transmembrane channels
title_full Ion fluxes through nanopores and transmembrane channels
title_fullStr Ion fluxes through nanopores and transmembrane channels
title_full_unstemmed Ion fluxes through nanopores and transmembrane channels
title_sort Ion fluxes through nanopores and transmembrane channels
author Bordin, José Rafael
author_facet Bordin, José Rafael
Diehl, Alexandre
Barbosa, Marcia Cristina Bernardes
Levin, Yan
author_role author
author2 Diehl, Alexandre
Barbosa, Marcia Cristina Bernardes
Levin, Yan
author2_role author
author
author
dc.contributor.author.fl_str_mv Bordin, José Rafael
Diehl, Alexandre
Barbosa, Marcia Cristina Bernardes
Levin, Yan
dc.subject.por.fl_str_mv Biofísica
Dinâmica molecular
Microorganismos
Fenômeno bioelétrico
Biomembranas
Processos de transporte
topic Biofísica
Dinâmica molecular
Microorganismos
Fenômeno bioelétrico
Biomembranas
Processos de transporte
description We introduce an implicit solvent Molecular Dynamics approach for calculating ionic fluxes through narrow nanopores and transmembrane channels. The method relies on a dual-control-volume grand-canonical molecular dynamics (DCV-GCMD) simulation and the analytical solution for the electrostatic potential inside a cylindrical nanopore recently obtained by Levin [Europhys. Lett. 76, 163 (2006)]. The theory is used to calculate the ionic fluxes through an artificial transmembrane channel which mimics the antibacterial gramicidin A channel. Both current-voltage and current-concentration relations are calculated under various experimental conditions. We show that our results are comparable to the characteristics associated to the gramicidin A pore, especially the existence of two binding sites inside the pore and the observed saturation in the current-concentration profiles.
publishDate 2012
dc.date.issued.fl_str_mv 2012
dc.date.accessioned.fl_str_mv 2014-08-26T09:26:16Z
dc.type.driver.fl_str_mv Estrangeiro
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dc.identifier.uri.fl_str_mv http://hdl.handle.net/10183/101828
dc.identifier.issn.pt_BR.fl_str_mv 1539-3755
dc.identifier.nrb.pt_BR.fl_str_mv 000836641
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dc.language.iso.fl_str_mv eng
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dc.relation.ispartof.pt_BR.fl_str_mv Physical review. E, Statistical, nonlinear, and soft matter physics. Vol. 85, no. 3 (Mar. 2012), 031914, 7 p.
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