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 and...

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Bibliographic Details
Published in:BMC bioinformatics Vol. 24; no. 1; pp. 1 - 38
Main Authors: Africa, Pasquale Claudio, Piersanti, Roberto, Regazzoni, Francesco, Bucelli, Michele, Salvador, Matteo, Fedele, Marco, Pagani, Stefano, Dede’, Luca, Quarteroni, Alfio
Format: Journal Article
Language:English
Published: London BioMed Central 13.10.2023
BioMed Central Ltd
Springer Nature B.V
BMC
Subjects:
Algorithms
Arrhythmia
Bioinformatics
Biomedical and Life Sciences
Cardiac arrhythmia
Cardiac electrophysiology
Cardiac function
Cardiac muscle
Cardiology
Cardiomyocytes
Care and treatment
Computational Biology/Bioinformatics
Computational cardiology
Computer Appl. in Life Sciences
Computer applications
Computer simulation
Diagnosis
Dirichlet problem
Electrocardiography
Electrophysiology
Fibers
Finite element method
Heart
High-performance computing
Life Sciences
Mathematical modeling
Mathematical models
Microarrays
Numerical analysis
Numerical methods
Ordinary differential equations
Partial differential equations
Propagation
Robustness (mathematics)
Simulation
Simulation methods
Software
Africa
Finite element method
Primary 92-04
secondary 35-04
High-performance computing
Mathematical modeling
68N30
65M60
65Y05
Cardiac electrophysiology
Computational cardiology
92C50
ISSN:1471-2105, 1471-2105
Online Access:Get full text
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Summary: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 life x -ep , a publicly available software for numerical simulations of the electrophysiology activity of the cardiac muscle, under both normal and pathological conditions. life x -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, life x -ep integrates the generation of myocardial fibers based on Laplace–Dirichlet Rule-Based Methods, previously released in Africa et al., 2023, within life x -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 life x -ep , along with comprehensive implementation details and instructions for users. life x -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 life x -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 life x -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. life x -ep represents a valuable tool for conducting in silico patient-specific simulations.
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ISSN:1471-2105
1471-2105
DOI:10.1186/s12859-023-05513-8