lifex-fiber: an open tool for myofibers generation in cardiac computational models

Background Modeling the whole cardiac function involves the solution of several complex multi-physics and multi-scale models that are highly computationally demanding, which call for simpler yet accurate, high-performance computational tools. Despite the efforts made by several research groups, no s...

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Vydáno v:BMC bioinformatics Ročník 24; číslo 1; s. 143 - 32
Hlavní autoři: Africa, Pasquale Claudio, Piersanti, Roberto, Fedele, Marco, Dede’, Luca, Quarteroni, Alfio
Médium: Journal Article
Jazyk:angličtina
Vydáno: London BioMed Central 12.04.2023
BioMed Central Ltd
Springer Nature B.V
BMC
Témata:
Algorithms
Analysis
Binary systems
Bioengineering
Bioinformatics
Biomedical and Life Sciences
Cardiac fibers
Cardiac function
Cardiology
Cardiomyocytes
Circulatory system
Computational Biology/Bioinformatics
Computational cardiology
Computer Appl. in Life Sciences
Computer applications
Computer Simulation
Computer-generated environments
Dirichlet problem
Fibers
Finite element methods
Geometry
Health aspects
Heart
High-performance computing
Life Sciences
Mathematical modeling
Mathematical models
Mechanical properties
Medicine
Methods
Microarrays
Modules
Myocytes, Cardiac
Open source software
Physics
Physiology
Public software
Pulmonary arteries
Scale models
Simulation
Software
Solvers
Switzerland
Primary 68-04, 68N30
Cardiac fibers
High-performance computing
Mathematical modeling
Finite element methods
Secondary 35-04, 65-04, 65M60, 65N30, 65Y05, 65Y20, 92-04, 92C50
Computational cardiology
ISSN:1471-2105, 1471-2105
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Popis
Shrnutí:Background Modeling the whole cardiac function involves the solution of several complex multi-physics and multi-scale models that are highly computationally demanding, which call for simpler yet accurate, high-performance computational tools. Despite the efforts made by several research groups, no software for whole-heart fully-coupled cardiac simulations in the scientific community has reached full maturity yet. Results In this work we present life x -fiber, an innovative tool for the generation of myocardial fibers based on Laplace-Dirichlet Rule-Based Methods, which are the essential building blocks for modeling the electrophysiological, mechanical and electromechanical cardiac function, from single-chamber to whole-heart simulations. life x -fiber is the first publicly released module for cardiac simulations based on life x , an open-source, high-performance Finite Element solver for multi-physics, multi-scale and multi-domain problems developed in the framework of the iHEART project, which aims at making in silico experiments easily reproducible and accessible to a wide community of users, including those with a background in medicine or bio-engineering. Conclusions The tool presented in this document is intended to provide the scientific community with a computational tool that incorporates general state of the art models and solvers for simulating the cardiac function within a high-performance framework that exposes a user- and developer-friendly interface. This report comes with an extensive technical and mathematical documentation to welcome new users to the core structure of life x -fiber and to provide them with a possible approach to include the generated cardiac fibers into more sophisticated computational pipelines. In the near future, more modules will be successively published either as pre-compiled binaries for x86-64 Linux systems or as open source software.
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ISSN:1471-2105
1471-2105
DOI:10.1186/s12859-023-05260-w