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lifex-ep: a robust and efficient software for cardiac electrophysiology simulations

BACKGROUND: Simulating the cardiac function requires the numerical solution of multi-physics and multi-scale mathematical models. This underscores the need for streamlined, accurate, and high-performance computational tools. Despite the dedicated endeavors of various research teams, comprehensive an...

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Autores principales: Africa, Pasquale Claudio, Piersanti, Roberto, Regazzoni, Francesco, Bucelli, Michele, Salvador, Matteo, Fedele, Marco, Pagani, Stefano, Dede’, Luca, Quarteroni, Alfio
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10571323/
https://www.ncbi.nlm.nih.gov/pubmed/37828428
http://dx.doi.org/10.1186/s12859-023-05513-8
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author Africa, Pasquale Claudio
Piersanti, Roberto
Regazzoni, Francesco
Bucelli, Michele
Salvador, Matteo
Fedele, Marco
Pagani, Stefano
Dede’, Luca
Quarteroni, Alfio
author_facet Africa, Pasquale Claudio
Piersanti, Roberto
Regazzoni, Francesco
Bucelli, Michele
Salvador, Matteo
Fedele, Marco
Pagani, Stefano
Dede’, Luca
Quarteroni, Alfio
author_sort Africa, Pasquale Claudio
collection PubMed
description BACKGROUND: Simulating the cardiac function requires the numerical solution of multi-physics and multi-scale mathematical models. This underscores the need for streamlined, accurate, and high-performance computational tools. Despite the dedicated endeavors of various research teams, comprehensive and user-friendly software programs for cardiac simulations, capable of accurately replicating both normal and pathological conditions, are still in the process of achieving full maturity within the scientific community. RESULTS: This work introduces [Formula: see text] -ep, a publicly available software for numerical simulations of the electrophysiology activity of the cardiac muscle, under both normal and pathological conditions. [Formula: see text] -ep employs the monodomain equation to model the heart’s electrical activity. It incorporates both phenomenological and second-generation ionic models. These models are discretized using the Finite Element method on tetrahedral or hexahedral meshes. Additionally, [Formula: see text] -ep integrates the generation of myocardial fibers based on Laplace–Dirichlet Rule-Based Methods, previously released in Africa et al., 2023, within [Formula: see text] -fiber. As an alternative, users can also choose to import myofibers from a file. This paper provides a concise overview of the mathematical models and numerical methods underlying [Formula: see text] -ep, along with comprehensive implementation details and instructions for users. [Formula: see text] -ep features exceptional parallel speedup, scaling efficiently when using up to thousands of cores, and its implementation has been verified against an established benchmark problem for computational electrophysiology. We showcase the key features of [Formula: see text] -ep through various idealized and realistic simulations conducted in both normal and pathological scenarios. Furthermore, the software offers a user-friendly and flexible interface, simplifying the setup of simulations using self-documenting parameter files. CONCLUSIONS: [Formula: see text] -ep provides easy access to cardiac electrophysiology simulations for a wide user community. It offers a computational tool that integrates models and accurate methods for simulating cardiac electrophysiology within a high-performance framework, while maintaining a user-friendly interface. [Formula: see text] -ep represents a valuable tool for conducting in silico patient-specific simulations.
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spelling pubmed-105713232023-10-14 lifex-ep: a robust and efficient software for cardiac electrophysiology simulations Africa, Pasquale Claudio Piersanti, Roberto Regazzoni, Francesco Bucelli, Michele Salvador, Matteo Fedele, Marco Pagani, Stefano Dede’, Luca Quarteroni, Alfio BMC Bioinformatics Software BACKGROUND: Simulating the cardiac function requires the numerical solution of multi-physics and multi-scale mathematical models. This underscores the need for streamlined, accurate, and high-performance computational tools. Despite the dedicated endeavors of various research teams, comprehensive and user-friendly software programs for cardiac simulations, capable of accurately replicating both normal and pathological conditions, are still in the process of achieving full maturity within the scientific community. RESULTS: This work introduces [Formula: see text] -ep, a publicly available software for numerical simulations of the electrophysiology activity of the cardiac muscle, under both normal and pathological conditions. [Formula: see text] -ep employs the monodomain equation to model the heart’s electrical activity. It incorporates both phenomenological and second-generation ionic models. These models are discretized using the Finite Element method on tetrahedral or hexahedral meshes. Additionally, [Formula: see text] -ep integrates the generation of myocardial fibers based on Laplace–Dirichlet Rule-Based Methods, previously released in Africa et al., 2023, within [Formula: see text] -fiber. As an alternative, users can also choose to import myofibers from a file. This paper provides a concise overview of the mathematical models and numerical methods underlying [Formula: see text] -ep, along with comprehensive implementation details and instructions for users. [Formula: see text] -ep features exceptional parallel speedup, scaling efficiently when using up to thousands of cores, and its implementation has been verified against an established benchmark problem for computational electrophysiology. We showcase the key features of [Formula: see text] -ep through various idealized and realistic simulations conducted in both normal and pathological scenarios. Furthermore, the software offers a user-friendly and flexible interface, simplifying the setup of simulations using self-documenting parameter files. CONCLUSIONS: [Formula: see text] -ep provides easy access to cardiac electrophysiology simulations for a wide user community. It offers a computational tool that integrates models and accurate methods for simulating cardiac electrophysiology within a high-performance framework, while maintaining a user-friendly interface. [Formula: see text] -ep represents a valuable tool for conducting in silico patient-specific simulations. BioMed Central 2023-10-13 /pmc/articles/PMC10571323/ /pubmed/37828428 http://dx.doi.org/10.1186/s12859-023-05513-8 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Software
Africa, Pasquale Claudio
Piersanti, Roberto
Regazzoni, Francesco
Bucelli, Michele
Salvador, Matteo
Fedele, Marco
Pagani, Stefano
Dede’, Luca
Quarteroni, Alfio
lifex-ep: a robust and efficient software for cardiac electrophysiology simulations
title lifex-ep: a robust and efficient software for cardiac electrophysiology simulations
title_full lifex-ep: a robust and efficient software for cardiac electrophysiology simulations
title_fullStr lifex-ep: a robust and efficient software for cardiac electrophysiology simulations
title_full_unstemmed lifex-ep: a robust and efficient software for cardiac electrophysiology simulations
title_short lifex-ep: a robust and efficient software for cardiac electrophysiology simulations
title_sort lifex-ep: a robust and efficient software for cardiac electrophysiology simulations
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10571323/
https://www.ncbi.nlm.nih.gov/pubmed/37828428
http://dx.doi.org/10.1186/s12859-023-05513-8
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