OpenEP: an open-source simulator for electroporation-based tumor treatments

Electroporation (EP), the increase of cell membrane permeability due to the application of electric pulses, is a universal phenomenon with a broad range of applications. In medicine, some of the foremost EP-based tumor treatments are electrochemotherapy (ECT), irreversible electroporation, and gene...

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Autores: Marino, Matias Daniel, Luján, Emmanuel, Mocskos, Esteban Eduardo, Marshall, Guillermo Ricardo
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2021
País:Argentina
Institución:Consejo Nacional de Investigaciones Científicas y Técnicas
Repositorio:CONICET Digital (CONICET)
Idioma:inglés
OAI Identifier:oai:ri.conicet.gov.ar:11336/173166
Acceso en línea:http://hdl.handle.net/11336/173166
Access Level:acceso abierto
Palabra clave:Simulation
Electroporation
Modelling
https://purl.org/becyt/ford/1.2
https://purl.org/becyt/ford/1
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dc.title.none.fl_str_mv OpenEP: an open-source simulator for electroporation-based tumor treatments
title OpenEP: an open-source simulator for electroporation-based tumor treatments
spellingShingle OpenEP: an open-source simulator for electroporation-based tumor treatments
Marino, Matias Daniel
Simulation
Electroporation
Modelling
https://purl.org/becyt/ford/1.2
https://purl.org/becyt/ford/1
title_short OpenEP: an open-source simulator for electroporation-based tumor treatments
title_full OpenEP: an open-source simulator for electroporation-based tumor treatments
title_fullStr OpenEP: an open-source simulator for electroporation-based tumor treatments
title_full_unstemmed OpenEP: an open-source simulator for electroporation-based tumor treatments
title_sort OpenEP: an open-source simulator for electroporation-based tumor treatments
dc.creator.none.fl_str_mv Marino, Matias Daniel
Luján, Emmanuel
Mocskos, Esteban Eduardo
Marshall, Guillermo Ricardo
author Marino, Matias Daniel
author_facet Marino, Matias Daniel
Luján, Emmanuel
Mocskos, Esteban Eduardo
Marshall, Guillermo Ricardo
author_role author
author2 Luján, Emmanuel
Mocskos, Esteban Eduardo
Marshall, Guillermo Ricardo
author2_role author
author
author
dc.subject.none.fl_str_mv Simulation
Electroporation
Modelling
https://purl.org/becyt/ford/1.2
https://purl.org/becyt/ford/1
topic Simulation
Electroporation
Modelling
https://purl.org/becyt/ford/1.2
https://purl.org/becyt/ford/1
description Electroporation (EP), the increase of cell membrane permeability due to the application of electric pulses, is a universal phenomenon with a broad range of applications. In medicine, some of the foremost EP-based tumor treatments are electrochemotherapy (ECT), irreversible electroporation, and gene electrotransfer (GET). The electroporation phenomenon is explained as the formation of cell membrane pores when a transmembrane cell voltage reaches a threshold value. Predicting the outcome of an EP-based tumor treatment consists of finding the electric field distribution with an electric threshold value covering the tumor (electroporated tissue). Threshold and electroporated tissue are also a function of the number of pulses, constituting a complex phenomenon requiring mathematical modeling. We present OpenEP, an open-source specific purpose simulator for EP-based tumor treatments, modeling among other variables, threshold, and electroporated tissue variations in time. Distributed under a free/libre user license, OpenEP allows the customization of tissue type; electrode geometry and material; pulse type, intensity, length, and frequency. OpenEP facilitates the prediction of an optimal EP-based protocol, such as ECT or GET, defined as the critical pulse dosage yielding maximum electroporated tissue with minimal damage. OpenEP displays a highly efficient shared memory implementation by taking advantage of parallel resources; this permits a rapid prediction of optimal EP-based treatment efficiency by pulse number tuning.
publishDate 2021
dc.date.none.fl_str_mv 2021-12
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/11336/173166
Marino, Matias Daniel; Luján, Emmanuel; Mocskos, Esteban Eduardo; Marshall, Guillermo Ricardo; OpenEP: an open-source simulator for electroporation-based tumor treatments; Nature; Scientific Reports; 11; 1; 12-2021; 1-15
2045-2322
CONICET Digital
CONICET
url http://hdl.handle.net/11336/173166
identifier_str_mv Marino, Matias Daniel; Luján, Emmanuel; Mocskos, Esteban Eduardo; Marshall, Guillermo Ricardo; OpenEP: an open-source simulator for electroporation-based tumor treatments; Nature; Scientific Reports; 11; 1; 12-2021; 1-15
2045-2322
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/http://www.nature.com/articles/s41598-020-79858-y
info:eu-repo/semantics/altIdentifier/doi/10.1038/s41598-020-79858-y
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
application/pdf
application/pdf
dc.publisher.none.fl_str_mv Nature
publisher.none.fl_str_mv Nature
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
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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spelling OpenEP: an open-source simulator for electroporation-based tumor treatmentsMarino, Matias DanielLuján, EmmanuelMocskos, Esteban EduardoMarshall, Guillermo RicardoSimulationElectroporationModellinghttps://purl.org/becyt/ford/1.2https://purl.org/becyt/ford/1Electroporation (EP), the increase of cell membrane permeability due to the application of electric pulses, is a universal phenomenon with a broad range of applications. In medicine, some of the foremost EP-based tumor treatments are electrochemotherapy (ECT), irreversible electroporation, and gene electrotransfer (GET). The electroporation phenomenon is explained as the formation of cell membrane pores when a transmembrane cell voltage reaches a threshold value. Predicting the outcome of an EP-based tumor treatment consists of finding the electric field distribution with an electric threshold value covering the tumor (electroporated tissue). Threshold and electroporated tissue are also a function of the number of pulses, constituting a complex phenomenon requiring mathematical modeling. We present OpenEP, an open-source specific purpose simulator for EP-based tumor treatments, modeling among other variables, threshold, and electroporated tissue variations in time. Distributed under a free/libre user license, OpenEP allows the customization of tissue type; electrode geometry and material; pulse type, intensity, length, and frequency. OpenEP facilitates the prediction of an optimal EP-based protocol, such as ECT or GET, defined as the critical pulse dosage yielding maximum electroporated tissue with minimal damage. OpenEP displays a highly efficient shared memory implementation by taking advantage of parallel resources; this permits a rapid prediction of optimal EP-based treatment efficiency by pulse number tuning.Fil: Marino, Matias Daniel. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Computación; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Física del Plasma. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Física del Plasma; ArgentinaFil: Luján, Emmanuel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Física del Plasma. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Física del Plasma; ArgentinaFil: Mocskos, Esteban Eduardo. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Centro de Simulación Computacional para Aplicaciones Tecnológicas; ArgentinaFil: Marshall, Guillermo Ricardo. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Física del Plasma. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Física del Plasma; ArgentinaNature2021-12info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/173166Marino, Matias Daniel; Luján, Emmanuel; Mocskos, Esteban Eduardo; Marshall, Guillermo Ricardo; OpenEP: an open-source simulator for electroporation-based tumor treatments; Nature; Scientific Reports; 11; 1; 12-2021; 1-152045-2322CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/http://www.nature.com/articles/s41598-020-79858-yinfo:eu-repo/semantics/altIdentifier/doi/10.1038/s41598-020-79858-yinfo:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2024-05-08T14:07:47Zoai:ri.conicet.gov.ar:11336/173166instacron: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:34982024-05-08 14:07:47.607CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
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