A criterion to identify the equilibration time in lipid bilayer simulations

Autores
Porasso, Rodolfo Daniel; Lopez Cascales, Jose Javier
Año de publicación
2012
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
With the aim of establishing a criterion for identifying when a lipid bilayer has reached steady state using the molecular dynamics simulation technique, lipid bilayers of different composition in their liquid crystalline phase were simulated in aqueous solution in presence of CaCl 2 as electrolyte, at different concentration levels. In this regard, we used two different lipid bilayer systems: one composed by 288 DPPC (DiPalmitoylPhosphatidylCholine) and another constituted by 288 DPPS (DiPalmitoylPhosphatidylSerine). In this sense, for both type of lipid bilayers, we have studied the temporal evolution of some lipids properties, such as the surface area per lipid, the deuterium order parameter, the lipid hydration and the lipid-calcium coordination. From their analysis, it became evident how each property has a different time to achieve equilibrium. The following order was found, from faster property to slower property: coordination of ions ≈ deuterium order parameter > area per lipid ≈ hydration. Consequently, when the hydration of lipids or the mean area per lipid are stable, we can ensure that the lipid membrane has reached the steady state.
Fil: Porasso, Rodolfo Daniel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Luis. Instituto de Matemática Aplicada de San Luis "Prof. Ezio Marchi". Universidad Nacional de San Luis. Facultad de Ciencias Físico, Matemáticas y Naturales. Instituto de Matemática Aplicada de San Luis "Prof. Ezio Marchi"; Argentina
Fil: Lopez Cascales, Jose Javier. Universidad Politécnica de Cartagena; España
Materia
LIPID BILAYER
CALCIUM IONS
MOLECULAR DINAMICS
STEADY STATE
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/211176
Acceder
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network_name_str CONICET Digital (CONICET)
spelling A criterion to identify the equilibration time in lipid bilayer simulationsPorasso, Rodolfo DanielLopez Cascales, Jose JavierLIPID BILAYERCALCIUM IONSMOLECULAR DINAMICSSTEADY STATEhttps://purl.org/becyt/ford/1.3https://purl.org/becyt/ford/1With the aim of establishing a criterion for identifying when a lipid bilayer has reached steady state using the molecular dynamics simulation technique, lipid bilayers of different composition in their liquid crystalline phase were simulated in aqueous solution in presence of CaCl 2 as electrolyte, at different concentration levels. In this regard, we used two different lipid bilayer systems: one composed by 288 DPPC (DiPalmitoylPhosphatidylCholine) and another constituted by 288 DPPS (DiPalmitoylPhosphatidylSerine). In this sense, for both type of lipid bilayers, we have studied the temporal evolution of some lipids properties, such as the surface area per lipid, the deuterium order parameter, the lipid hydration and the lipid-calcium coordination. From their analysis, it became evident how each property has a different time to achieve equilibrium. The following order was found, from faster property to slower property: coordination of ions ≈ deuterium order parameter > area per lipid ≈ hydration. Consequently, when the hydration of lipids or the mean area per lipid are stable, we can ensure that the lipid membrane has reached the steady state.Fil: Porasso, Rodolfo Daniel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Luis. Instituto de Matemática Aplicada de San Luis "Prof. Ezio Marchi". Universidad Nacional de San Luis. Facultad de Ciencias Físico, Matemáticas y Naturales. Instituto de Matemática Aplicada de San Luis "Prof. Ezio Marchi"; ArgentinaFil: Lopez Cascales, Jose Javier. Universidad Politécnica de Cartagena; EspañaCentro Atómico Bariloche2012-11info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/211176Porasso, Rodolfo Daniel; Lopez Cascales, Jose Javier; A criterion to identify the equilibration time in lipid bilayer simulations; Centro Atómico Bariloche; Papers in Physics; 4; 40005; 11-2012; 1-51852-4249CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.4279/pip.040005info:eu-repo/semantics/altIdentifier/url/https://www.papersinphysics.org/papersinphysics/article/view/112info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-10-22T11:37:13Zoai:ri.conicet.gov.ar:11336/211176instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-10-22 11:37:13.373CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv A criterion to identify the equilibration time in lipid bilayer simulations
title A criterion to identify the equilibration time in lipid bilayer simulations
spellingShingle A criterion to identify the equilibration time in lipid bilayer simulations
Porasso, Rodolfo Daniel
LIPID BILAYER
CALCIUM IONS
MOLECULAR DINAMICS
STEADY STATE
title_short A criterion to identify the equilibration time in lipid bilayer simulations
title_full A criterion to identify the equilibration time in lipid bilayer simulations
title_fullStr A criterion to identify the equilibration time in lipid bilayer simulations
title_full_unstemmed A criterion to identify the equilibration time in lipid bilayer simulations
title_sort A criterion to identify the equilibration time in lipid bilayer simulations
dc.creator.none.fl_str_mv Porasso, Rodolfo Daniel
Lopez Cascales, Jose Javier
author Porasso, Rodolfo Daniel
author_facet Porasso, Rodolfo Daniel
Lopez Cascales, Jose Javier
author_role author
author2 Lopez Cascales, Jose Javier
author2_role author
dc.subject.none.fl_str_mv LIPID BILAYER
CALCIUM IONS
MOLECULAR DINAMICS
STEADY STATE
topic LIPID BILAYER
CALCIUM IONS
MOLECULAR DINAMICS
STEADY STATE
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.3
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv With the aim of establishing a criterion for identifying when a lipid bilayer has reached steady state using the molecular dynamics simulation technique, lipid bilayers of different composition in their liquid crystalline phase were simulated in aqueous solution in presence of CaCl 2 as electrolyte, at different concentration levels. In this regard, we used two different lipid bilayer systems: one composed by 288 DPPC (DiPalmitoylPhosphatidylCholine) and another constituted by 288 DPPS (DiPalmitoylPhosphatidylSerine). In this sense, for both type of lipid bilayers, we have studied the temporal evolution of some lipids properties, such as the surface area per lipid, the deuterium order parameter, the lipid hydration and the lipid-calcium coordination. From their analysis, it became evident how each property has a different time to achieve equilibrium. The following order was found, from faster property to slower property: coordination of ions ≈ deuterium order parameter > area per lipid ≈ hydration. Consequently, when the hydration of lipids or the mean area per lipid are stable, we can ensure that the lipid membrane has reached the steady state.
Fil: Porasso, Rodolfo Daniel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Luis. Instituto de Matemática Aplicada de San Luis "Prof. Ezio Marchi". Universidad Nacional de San Luis. Facultad de Ciencias Físico, Matemáticas y Naturales. Instituto de Matemática Aplicada de San Luis "Prof. Ezio Marchi"; Argentina
Fil: Lopez Cascales, Jose Javier. Universidad Politécnica de Cartagena; España
description With the aim of establishing a criterion for identifying when a lipid bilayer has reached steady state using the molecular dynamics simulation technique, lipid bilayers of different composition in their liquid crystalline phase were simulated in aqueous solution in presence of CaCl 2 as electrolyte, at different concentration levels. In this regard, we used two different lipid bilayer systems: one composed by 288 DPPC (DiPalmitoylPhosphatidylCholine) and another constituted by 288 DPPS (DiPalmitoylPhosphatidylSerine). In this sense, for both type of lipid bilayers, we have studied the temporal evolution of some lipids properties, such as the surface area per lipid, the deuterium order parameter, the lipid hydration and the lipid-calcium coordination. From their analysis, it became evident how each property has a different time to achieve equilibrium. The following order was found, from faster property to slower property: coordination of ions ≈ deuterium order parameter > area per lipid ≈ hydration. Consequently, when the hydration of lipids or the mean area per lipid are stable, we can ensure that the lipid membrane has reached the steady state.
publishDate 2012
dc.date.none.fl_str_mv 2012-11
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/211176
Porasso, Rodolfo Daniel; Lopez Cascales, Jose Javier; A criterion to identify the equilibration time in lipid bilayer simulations; Centro Atómico Bariloche; Papers in Physics; 4; 40005; 11-2012; 1-5
1852-4249
CONICET Digital
CONICET
url http://hdl.handle.net/11336/211176
identifier_str_mv Porasso, Rodolfo Daniel; Lopez Cascales, Jose Javier; A criterion to identify the equilibration time in lipid bilayer simulations; Centro Atómico Bariloche; Papers in Physics; 4; 40005; 11-2012; 1-5
1852-4249
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/doi/10.4279/pip.040005
info:eu-repo/semantics/altIdentifier/url/https://www.papersinphysics.org/papersinphysics/article/view/112
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Centro Atómico Bariloche
publisher.none.fl_str_mv Centro Atómico Bariloche
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
_version_ 1846782018861400064
score 12.982451

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