life: A flexible, high performance library for the numerical solution of complex finite element problems

Africa, Pasquale Claudio

doi:10.1016/j.softx.2022.101252

Cited by 40 publications

(21 citation statements)

References 41 publications

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“…Preprocessing of the geometry was done using the algorithms presented in Reference [135] as implemented in the software library VMTK. 136 Solvers for the individual core models and for the coupled model were implemented in the C++ library life, [72][73][74] based on the finite element core deal.II. [137][138][139] We run the simulations using 192 parallel processes on the GALILEO100 supercomputer i at the CINECA high-performance computing center (Italy).…”

Section: Numerical Results and Discussionmentioning

confidence: 99%

“…Spatial discretization is achieved by means of the finite element method 70,71 . The proposed computational framework leverages high‐performance computing techniques to enable large‐scale simulations, based on the finite element library life 72–74 …”

Section: Introductionmentioning

confidence: 99%

“…70,71 The proposed computational framework leverages high-performance computing techniques to enable large-scale simulations, based on the finite element library life. [72][73][74] We run a numerical simulation and compare the value of several indicators against normal ranges, obtaining a satisfactory agreement. A qualitative match with physiological behavior is also observed in terms of ventricular pressure and volume traces, as well as three dimensional deformation and flow patterns.…”

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confidence: 99%

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A mathematical model that integrates cardiac electrophysiology, mechanics, and fluid dynamics: Application to the human left heart

Bucelli

Zingaro

Africa

et al. 2023

Numer Methods Biomed Eng

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We propose a mathematical and numerical model for the simulation of the heart function that couples cardiac electrophysiology, active and passive mechanics and hemodynamics, and includes reduced models for cardiac valves and the circulatory system. Our model accounts for the major feedback effects among the different processes that characterize the heart function, including electro‐mechanical and mechano‐electrical feedback as well as force‐strain and force‐velocity relationships. Moreover, it provides a three‐dimensional representation of both the cardiac muscle and the hemodynamics, coupled in a fluid–structure interaction (FSI) model. By leveraging the multiphysics nature of the problem, we discretize it in time with a segregated electrophysiology‐force generation‐FSI approach, allowing for efficiency and flexibility in the numerical solution. We employ a monolithic approach for the numerical discretization of the FSI problem. We use finite elements for the spatial discretization of partial differential equations. We carry out a numerical simulation on a realistic human left heart model, obtaining results that are qualitatively and quantitatively in agreement with physiological ranges and medical images.

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Section: Numerical Results and Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

mentioning

confidence: 99%

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A mathematical model that integrates cardiac electrophysiology, mechanics, and fluid dynamics: Application to the human left heart

Bucelli

Zingaro

Africa

et al. 2023

Numer Methods Biomed Eng

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“…To numerically solve system (1), we used first-order Finite Elements together with fist order semi-implicit discretization in time [54]. The numerical scheme was stabilized by means of a Streamline Upwind Petrov-Galerkin/Pressure-Stabilizing Petrov-Galerkin (SUPG/PSPG) scheme [58] implemented in the multiphysics high performance library li f e x [59] (https://lifex.gitlab.io/) based on the deal.II core [60]. We run the simulations using 384 parallel processes on the GALILEO100 supercomputer (https://www.hpc.cineca.it/hardware/galileo100) at the CINECA high-performance computing center (Italy).…”

Section: Mathematical and Numerical Modelingmentioning

confidence: 99%

Turbulence and blood washout in presence of mitral regurgitation: a computational fluid-dynamics study in the complete left heart

Bennati

Giambruno

Renzi

et al. 2023

Preprint

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In this work we performed a computational image-based study of blood dynamics in the whole left heart, both in a healthy subject and in a patient with mitral valve regurgitation (MVR). We elaborated dynamic cine-MRI images with the aim of reconstructing the geometry and the corresponding motion of left ventricle, left atrium, mitral and aortic valves, and aortic root of the subjects. This allowed us to prescribe such motion to computational blood dynamics simulations where, for the first time, the whole left heart motion of the subject is considered, allowing us to obtain reliable subject-specific information. The final aim is to investigate and compare between the subjects the occurrence of turbulence and the risk of hemolysis and of thrombi formation. In particular, we modeled blood with the Navier-Stokes equations in the Arbitrary Lagrangian-Eulerian framework, with a Large Eddy Simulation model to describe the transition to turbulence and a resistive method to manage the valve dynamics, and we used a Finite Elements discretization implemented in an in-house code for the numerical solution. Our results highlighted that the regurgitant jet in the MVR case gave rise to a large amount of transition to turbulence in the left atrium resulting in a higher risk of formation of hemolysis. Moreover, MVR promoted a more complete washout of stagnant flows in the left atrium during the systolic phase and in the left ventricle apex during diastole.

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“…In this work we introduce life x -fiber, an innovative tool for the generation of myocardial fibers based on life x [8], an open-source, high-performance Finite Element (FE) numerical solver for multi-physics, multi-scale and multi-domain differential problems. It is written in C++ using the most modern programming techniques available in the C++17 standard and is built upon the deal.II 1 [9] FE core.…”

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confidence: 99%

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

et al. 2023

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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 $$\texttt {life}^{\texttt {x}}$$ 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. $$\texttt {life}^{\texttt {x}}$$ life x -fiber is the first publicly released module for cardiac simulations based on $$\texttt {life}^{\texttt {x}}$$ 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 $$\texttt {life}^{\texttt {x}}$$ 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 systems or as open source software.

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life: A flexible, high performance library for the numerical solution of complex finite element problems

Cited by 40 publications

References 41 publications

A mathematical model that integrates cardiac electrophysiology, mechanics, and fluid dynamics: Application to the human left heart

A mathematical model that integrates cardiac electrophysiology, mechanics, and fluid dynamics: Application to the human left heart

Turbulence and blood washout in presence of mitral regurgitation: a computational fluid-dynamics study in the complete left heart

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

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