A monolithic algorithm for the simulation of cardiac electromechanics in the human left ventricle

Antonello Gerbi, Alfio Quarteroni
AMER INST MATHEMATICAL SCIENCES-AIMS, 2018
Journal paper

Abstract

In this paper, we propose a monolithic algorithm for the numerical solution of the electromechanics model of the left ventricle in the human heart. Our coupled model integrates the monodomain equation with the Bueno-Orovio minimal model for electrophysiology and the Holzapfel-Ogden constitutive law for the passive mechanics of the myocardium; a distinguishing feature of our electromechanics model is the use of the active strain formulation for muscle contraction, which we exploit - for the first time in this context - by means of a transmurally variable active strain formulation. We use the Finite Element method for space discretization and Backward Differentiation Formulas for time discretization, which we consider for both implicit and semi-implicit schemes. We compare and discuss the two schemes in terms of computational efficiency as the semi-implicit scheme poses significant restrictions on the timestep size due to stability considerations, while the implicit scheme yields instead a nonlinear problem, which we solve by means of the Newton method. Emphasis is laid on preconditioning strategy of the linear solver, which we perform by factorizing a block Gauss-Seidel preconditioner in combination with combination with parallel preconditioners for each of the single core models composing the integrated electromechanics model. We carry out several numerical simulations in the High Performance Computing framework for both idealized and patient-specific left ventricle geometries and meshes, which we obtain by segmenting medical MRI images. We produce personalized pressure-volume loops by means of the computational procedure, which we use to synthetically interpret and analyze the outputs of the electromechanics model.

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https://infoscience.epfl.ch/record/272355?ln=en

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Antonello Gerbi, Alfio Quarteroni
AMER INST MATHEMATICAL SCIENCES-AIMS, 2018
Journal paper

Abstract

Official source

https://infoscience.epfl.ch/record/272355?ln=en

About this result

Related concepts (17)

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This work concerns the mathematical and numerical modeling of the heart. The aim is to enhance the understanding of the cardiac function in both physiological and pathological conditions. Along this road, a challenge arises from the multi-scale and multi-physics nature of the mathematical problem at hand. In this paper, we propose an electromechanical model that, in bi-ventricle geometries, combines the monodomain equation, the Bueno-Orovio minimal ionic model, and the Holzapfel-Ogden strain energy function for the passive myocardial tissue modelling together with the active strain approach combined with a model for the transmurally heterogeneous thickening of the myocardium. Since the distribution of the electric signal is dependent on the fibres orientation of the ventricles, we use a Laplace-Dirichlet Rule-Based algorithm to determine the myocardial fibres and sheets configuration in the whole bi-ventricle. In this paper, we study the influence of different fibre directions and incompressibility constraint and penalization on the compressibility of the material (bulk modulus) on the pressure-volume relation simulating a full heart beat. The coupled electromechanical problem is addressed by means of a fully segregated scheme. The numerical discretization is based on the Finite Element Method for the spatial discretization and on Backward Differentiation Formulas for the time discretization. The arising non-linear algebraic system coming from application of the implicit scheme is solved through the Newton method. Numerical simulations are carried out in a patient-specific bi-ventricle geometry to highlight the most relevant results of both electrophysiology and mechanics and to compare them with physiological data and measurements. We show how various fibre configurations and bulk modulus modify relevant clinical quantities such as stroke volume, ejection fraction and ventricle contractility.

2020

Parallel Algorithms for the Solution of Large-Scale Fluid-Structure Interaction Problems in Hemodynamics

Davide Forti

This thesis addresses the development and implementation of efficient and parallel algorithms for the numerical simulation of Fluid-Structure Interaction (FSI) problems in hemodynamics. Indeed, hemodynamic conditions in large arteries are significantly affected by the interaction of the pulsatile blood flow with the arterial wall. The simulation of fluid-structure interaction problems requires the approximation of a coupled system of Partial Differential Equations (PDEs) and the set up of efficient numerical solution strategies. Blood is modeled as an incompressible Newtonian fluid whose dynamics is governed by the Navier-Stokes equations. Different constituive models are used to describe the mechanical response of the arterial wall; specifically, we rely on hyperelastic isotropic and anistotropic material laws. The finite element method is used for the space discretization of both the fluid and structure problems. In particular, for the Navier-Stokes equations we consider a semi-discrete formulation based on the Variational Multiscale (VMS) method. Among a wide range of possible solution strategies for the FSI problem, here we focus on strongly coupled monolithic approaches wherein the nonlinearities are treated in a fully implicit mode. To cope with the high computational complexity of the three dimensional FSI problem, a parallel solution framework is often mandatory. To this end, we develop a new block parallel preconditioner for the coupled linearized FSI system obtained after space and time discretization. The proposed preconditioner, named FaCSI, exploits the factorized form of the FSI Jacobian matrix, the use of static condensation to formally eliminate the interface degrees of freedom of the fluid equations, and the use of a SIMPLE preconditioner for unsteady Navier-Stokes equations. In FSI problems, the different resolution requirements in the fluid and structure physical domains, as well as the presence of complex interface geometries make the use of matching fluid and structure meshes problematic. In such situations, it is much simpler to deal with discretizations that are nonconforming at the interface, provided however that the matching conditions at the interface are properly fulfilled. In this thesis we develop a novel interpolation-based method, named INTERNODES, for numerically solving partial differential equations by Galerkin methods on computational domains that are split into two (or several) subdomains featuring nonconforming interfaces. By this we mean that either a priori independent grids and/or local polynomial degrees are used to discretize each subdomain. INTERNODES can be regarded as an alternative to the mortar element method: it combines the accuracy of the latter with the easiness of implementation in a numerical code. The aforementioned techniques have been applied for the numerical simulation of large-scale fluid-structure interaction problems in the context of biomechanics. The parallel algorithms developed showed scalability up to thousands of cores utilized on high performance computing machines.

EPFL2016

Mathematical and numerical aspects of viscoelastic flows are investigated here. Two simplified mathematical models are considered. They are motivated by a splitting algorithm for solving viscoelastic flows with free surfaces. The first model is a simplified Oldroyd-B model. Existence on a fixed time interval is proved in several Banach spaces provided the data are small enough. Short time existence is also proved for arbitrarily large data in Hölder spaces for the time variable. These results are based on the maximal regularity property of the Stokes operator and on the analycity behavior of the corresponding semi-group. A finite element discretization in space is then proposed. Existence of the numerical solution is proved for small data, as well as a priori error estimates, using an implicit function theorem framework. Then, the extension of these results to a stochastic simplified Hookean dumbbells model is discussed. Because of the presence of the Brownian motion, existence in a fixed time interval, provided the data are small enough, is proved only in some of the Banach spaces considered previously. The dumbbells' elongation is split in two parts, one satisfying a standart stochastic differential equation, the other satisfying a partial differential equation with a stochastic source term. A finite element discretization in space is also proposed. Existence of the numerical solution is proved for small data, as well as a priori error estimates. A numerical algorithm for solving viscoelastic flows with free surfaces is also described. This algorithm is based on a splitting method in time and two different meshes are used for the space discretization. Convergence of the numerical model is checked for the pure extensional flow and the filling of a pipe. Then, numerical results are reported for the stretching of a filament and for jet buckling.

EPFL2006

Parallel Algorithms for the Solution of Large-Scale Fluid-Structure Interaction Problems in Hemodynamics

Davide Forti

EPFL2016