Using Intrinsic Surfaces to Calculate the Free-Energy Change When Nanoparticles Adsorb on Membranes

Autores
Klug, Joaquín; Triguero, Carles; del Popolo, Mario Gabriel; Tribello, Gareth A.
Año de publicación
2018
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
A reaction coordinate that can be used when investigating binding to dynamical surfaces with molecular dynamics is introduced. This coordinate measures the distance between the adsorbate and an isocontour in a density field. Furthermore, the coordinate is continuous so simulation biases that are a function of this coordinate can be added to the Hamiltonian to increase the rate of adsorption/desorption. The efficacy of this new coordinates is demonstrated by performing metadynamics simulations to measure the strength with which a hydrophilic nanoparticle binds to a lipid bilayer. An investigation of the binding mechanism that is performed using the coordinate demonstrates that the lipid bilayer undergoes a series of concerted changes in structure as the nanoparticle binds.
Fil: Klug, Joaquín. The Queens University of Belfast; Irlanda. Universidad Nacional de Cuyo. Facultad de Ciencias Exactas y Naturales; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza; Argentina
Fil: Triguero, Carles. The Queens University of Belfast; Irlanda
Fil: del Popolo, Mario Gabriel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza; Argentina. Universidad Nacional de Cuyo. Facultad de Ciencias Exactas y Naturales; Argentina. The Queens University of Belfast; Irlanda
Fil: Tribello, Gareth A.. The Queens University of Belfast; Irlanda
Materia
Nanopartículas
Simulaciones
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/100244
Acceder
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network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Using Intrinsic Surfaces to Calculate the Free-Energy Change When Nanoparticles Adsorb on MembranesKlug, JoaquínTriguero, Carlesdel Popolo, Mario GabrielTribello, Gareth A.NanopartículasSimulacioneshttps://purl.org/becyt/ford/1.4https://purl.org/becyt/ford/1A reaction coordinate that can be used when investigating binding to dynamical surfaces with molecular dynamics is introduced. This coordinate measures the distance between the adsorbate and an isocontour in a density field. Furthermore, the coordinate is continuous so simulation biases that are a function of this coordinate can be added to the Hamiltonian to increase the rate of adsorption/desorption. The efficacy of this new coordinates is demonstrated by performing metadynamics simulations to measure the strength with which a hydrophilic nanoparticle binds to a lipid bilayer. An investigation of the binding mechanism that is performed using the coordinate demonstrates that the lipid bilayer undergoes a series of concerted changes in structure as the nanoparticle binds.Fil: Klug, Joaquín. The Queens University of Belfast; Irlanda. Universidad Nacional de Cuyo. Facultad de Ciencias Exactas y Naturales; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza; ArgentinaFil: Triguero, Carles. The Queens University of Belfast; IrlandaFil: del Popolo, Mario Gabriel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza; Argentina. Universidad Nacional de Cuyo. Facultad de Ciencias Exactas y Naturales; Argentina. The Queens University of Belfast; IrlandaFil: Tribello, Gareth A.. The Queens University of Belfast; IrlandaAmerican Chemical Society2018-06info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/100244Klug, Joaquín; Triguero, Carles; del Popolo, Mario Gabriel; Tribello, Gareth A.; Using Intrinsic Surfaces to Calculate the Free-Energy Change When Nanoparticles Adsorb on Membranes; American Chemical Society; Journal of Physical Chemistry B; 122; 24; 6-2018; 6417-64221520-6106CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.1021/acs.jpcb.8b03661info:eu-repo/semantics/altIdentifier/url/https://pubs.acs.org/doi/10.1021/acs.jpcb.8b03661info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T09:34:43Zoai:ri.conicet.gov.ar:11336/100244instacron: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:34982025-09-29 09:34:43.838CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Using Intrinsic Surfaces to Calculate the Free-Energy Change When Nanoparticles Adsorb on Membranes
title Using Intrinsic Surfaces to Calculate the Free-Energy Change When Nanoparticles Adsorb on Membranes
spellingShingle Using Intrinsic Surfaces to Calculate the Free-Energy Change When Nanoparticles Adsorb on Membranes
Klug, Joaquín
Nanopartículas
Simulaciones
title_short Using Intrinsic Surfaces to Calculate the Free-Energy Change When Nanoparticles Adsorb on Membranes
title_full Using Intrinsic Surfaces to Calculate the Free-Energy Change When Nanoparticles Adsorb on Membranes
title_fullStr Using Intrinsic Surfaces to Calculate the Free-Energy Change When Nanoparticles Adsorb on Membranes
title_full_unstemmed Using Intrinsic Surfaces to Calculate the Free-Energy Change When Nanoparticles Adsorb on Membranes
title_sort Using Intrinsic Surfaces to Calculate the Free-Energy Change When Nanoparticles Adsorb on Membranes
dc.creator.none.fl_str_mv Klug, Joaquín
Triguero, Carles
del Popolo, Mario Gabriel
Tribello, Gareth A.
author Klug, Joaquín
author_facet Klug, Joaquín
Triguero, Carles
del Popolo, Mario Gabriel
Tribello, Gareth A.
author_role author
author2 Triguero, Carles
del Popolo, Mario Gabriel
Tribello, Gareth A.
author2_role author
author
author
dc.subject.none.fl_str_mv Nanopartículas
Simulaciones
topic Nanopartículas
Simulaciones
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.4
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv A reaction coordinate that can be used when investigating binding to dynamical surfaces with molecular dynamics is introduced. This coordinate measures the distance between the adsorbate and an isocontour in a density field. Furthermore, the coordinate is continuous so simulation biases that are a function of this coordinate can be added to the Hamiltonian to increase the rate of adsorption/desorption. The efficacy of this new coordinates is demonstrated by performing metadynamics simulations to measure the strength with which a hydrophilic nanoparticle binds to a lipid bilayer. An investigation of the binding mechanism that is performed using the coordinate demonstrates that the lipid bilayer undergoes a series of concerted changes in structure as the nanoparticle binds.
Fil: Klug, Joaquín. The Queens University of Belfast; Irlanda. Universidad Nacional de Cuyo. Facultad de Ciencias Exactas y Naturales; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza; Argentina
Fil: Triguero, Carles. The Queens University of Belfast; Irlanda
Fil: del Popolo, Mario Gabriel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza; Argentina. Universidad Nacional de Cuyo. Facultad de Ciencias Exactas y Naturales; Argentina. The Queens University of Belfast; Irlanda
Fil: Tribello, Gareth A.. The Queens University of Belfast; Irlanda
description A reaction coordinate that can be used when investigating binding to dynamical surfaces with molecular dynamics is introduced. This coordinate measures the distance between the adsorbate and an isocontour in a density field. Furthermore, the coordinate is continuous so simulation biases that are a function of this coordinate can be added to the Hamiltonian to increase the rate of adsorption/desorption. The efficacy of this new coordinates is demonstrated by performing metadynamics simulations to measure the strength with which a hydrophilic nanoparticle binds to a lipid bilayer. An investigation of the binding mechanism that is performed using the coordinate demonstrates that the lipid bilayer undergoes a series of concerted changes in structure as the nanoparticle binds.
publishDate 2018
dc.date.none.fl_str_mv 2018-06
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/11336/100244
Klug, Joaquín; Triguero, Carles; del Popolo, Mario Gabriel; Tribello, Gareth A.; Using Intrinsic Surfaces to Calculate the Free-Energy Change When Nanoparticles Adsorb on Membranes; American Chemical Society; Journal of Physical Chemistry B; 122; 24; 6-2018; 6417-6422
1520-6106
CONICET Digital
CONICET
url http://hdl.handle.net/11336/100244
identifier_str_mv Klug, Joaquín; Triguero, Carles; del Popolo, Mario Gabriel; Tribello, Gareth A.; Using Intrinsic Surfaces to Calculate the Free-Energy Change When Nanoparticles Adsorb on Membranes; American Chemical Society; Journal of Physical Chemistry B; 122; 24; 6-2018; 6417-6422
1520-6106
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/doi/10.1021/acs.jpcb.8b03661
info:eu-repo/semantics/altIdentifier/url/https://pubs.acs.org/doi/10.1021/acs.jpcb.8b03661
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv American Chemical Society
publisher.none.fl_str_mv American Chemical Society
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
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score 13.070432

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