An iterative, fast, linear-scaling method for computing induced charges on arbitrary dielectric boundaries
Autor(a) principal: | |
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Data de Publicação: | 2010 |
Outros Autores: | , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UFRGS |
Texto Completo: | http://hdl.handle.net/10183/205060 |
Resumo: | Simulating coarse-grained models of charged soft-condensed matter systems in presence of dielectric discontinuities between different media requires an efficient calculation of polarization effects. This is almost always the case if implicit solvent models are used near interfaces or large macromolecules. We present a fast and accurate method (ICC⋆) that allows to simulate the presence of an arbitrary number of interfaces of arbitrary shape, each characterized by a different dielectric permittivity in one-, two-, and three-dimensional periodic boundary conditions. The scaling behavior and accuracy of the underlying electrostatic algorithms allow to choose the most appropriate scheme for the system under investigation in terms of precision and computational speed. Due to these characteristics the method is particularly suited to include nonplanar dielectric boundaries in coarse-grained molecular dynamics simulations. |
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Tyagi, SandeepSüzen, MehmetSega, MarcelloBarbosa, Marcia Cristina BernardesKantorovich, SofiaHolm, Christian2020-01-30T04:09:06Z20100021-9606http://hdl.handle.net/10183/205060000749472Simulating coarse-grained models of charged soft-condensed matter systems in presence of dielectric discontinuities between different media requires an efficient calculation of polarization effects. This is almost always the case if implicit solvent models are used near interfaces or large macromolecules. We present a fast and accurate method (ICC⋆) that allows to simulate the presence of an arbitrary number of interfaces of arbitrary shape, each characterized by a different dielectric permittivity in one-, two-, and three-dimensional periodic boundary conditions. The scaling behavior and accuracy of the underlying electrostatic algorithms allow to choose the most appropriate scheme for the system under investigation in terms of precision and computational speed. Due to these characteristics the method is particularly suited to include nonplanar dielectric boundaries in coarse-grained molecular dynamics simulations.application/pdfengThe journal of chemical physics. New York. Vol. 132, no. 15 (Apr. 2010), 154112, 9 p.Física da matéria condensadaPolarização dieletricaDinâmica molecularPermissividadeEquação de Poisson-BoltzmannAn iterative, fast, linear-scaling method for computing induced charges on arbitrary dielectric boundariesEstrangeiroinfo: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:UFRGSTEXT000749472.pdf.txt000749472.pdf.txtExtracted Texttext/plain51172http://www.lume.ufrgs.br/bitstream/10183/205060/2/000749472.pdf.txt187dd9f822a7254caba67dd761aa4c78MD52ORIGINAL000749472.pdfTexto completo (inglês)application/pdf632500http://www.lume.ufrgs.br/bitstream/10183/205060/1/000749472.pdf6261ecb6bec97331af9c1a71c777ab62MD5110183/2050602024-02-07 05:59:05.520489oai:www.lume.ufrgs.br:10183/205060Repositório de PublicaçõesPUBhttps://lume.ufrgs.br/oai/requestopendoar:2024-02-07T07:59:05Repositório Institucional da UFRGS - Universidade Federal do Rio Grande do Sul (UFRGS)false |
dc.title.pt_BR.fl_str_mv |
An iterative, fast, linear-scaling method for computing induced charges on arbitrary dielectric boundaries |
title |
An iterative, fast, linear-scaling method for computing induced charges on arbitrary dielectric boundaries |
spellingShingle |
An iterative, fast, linear-scaling method for computing induced charges on arbitrary dielectric boundaries Tyagi, Sandeep Física da matéria condensada Polarização dieletrica Dinâmica molecular Permissividade Equação de Poisson-Boltzmann |
title_short |
An iterative, fast, linear-scaling method for computing induced charges on arbitrary dielectric boundaries |
title_full |
An iterative, fast, linear-scaling method for computing induced charges on arbitrary dielectric boundaries |
title_fullStr |
An iterative, fast, linear-scaling method for computing induced charges on arbitrary dielectric boundaries |
title_full_unstemmed |
An iterative, fast, linear-scaling method for computing induced charges on arbitrary dielectric boundaries |
title_sort |
An iterative, fast, linear-scaling method for computing induced charges on arbitrary dielectric boundaries |
author |
Tyagi, Sandeep |
author_facet |
Tyagi, Sandeep Süzen, Mehmet Sega, Marcello Barbosa, Marcia Cristina Bernardes Kantorovich, Sofia Holm, Christian |
author_role |
author |
author2 |
Süzen, Mehmet Sega, Marcello Barbosa, Marcia Cristina Bernardes Kantorovich, Sofia Holm, Christian |
author2_role |
author author author author author |
dc.contributor.author.fl_str_mv |
Tyagi, Sandeep Süzen, Mehmet Sega, Marcello Barbosa, Marcia Cristina Bernardes Kantorovich, Sofia Holm, Christian |
dc.subject.por.fl_str_mv |
Física da matéria condensada Polarização dieletrica Dinâmica molecular Permissividade Equação de Poisson-Boltzmann |
topic |
Física da matéria condensada Polarização dieletrica Dinâmica molecular Permissividade Equação de Poisson-Boltzmann |
description |
Simulating coarse-grained models of charged soft-condensed matter systems in presence of dielectric discontinuities between different media requires an efficient calculation of polarization effects. This is almost always the case if implicit solvent models are used near interfaces or large macromolecules. We present a fast and accurate method (ICC⋆) that allows to simulate the presence of an arbitrary number of interfaces of arbitrary shape, each characterized by a different dielectric permittivity in one-, two-, and three-dimensional periodic boundary conditions. The scaling behavior and accuracy of the underlying electrostatic algorithms allow to choose the most appropriate scheme for the system under investigation in terms of precision and computational speed. Due to these characteristics the method is particularly suited to include nonplanar dielectric boundaries in coarse-grained molecular dynamics simulations. |
publishDate |
2010 |
dc.date.issued.fl_str_mv |
2010 |
dc.date.accessioned.fl_str_mv |
2020-01-30T04:09:06Z |
dc.type.driver.fl_str_mv |
Estrangeiro info:eu-repo/semantics/article |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://hdl.handle.net/10183/205060 |
dc.identifier.issn.pt_BR.fl_str_mv |
0021-9606 |
dc.identifier.nrb.pt_BR.fl_str_mv |
000749472 |
identifier_str_mv |
0021-9606 000749472 |
url |
http://hdl.handle.net/10183/205060 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.ispartof.pt_BR.fl_str_mv |
The journal of chemical physics. New York. Vol. 132, no. 15 (Apr. 2010), 154112, 9 p. |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
application/pdf |
dc.source.none.fl_str_mv |
reponame:Repositório Institucional da UFRGS instname:Universidade Federal do Rio Grande do Sul (UFRGS) instacron:UFRGS |
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UFRGS |
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UFRGS |
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Repositório Institucional da UFRGS |
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Repositório Institucional da UFRGS |
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