Multigrid block preconditioning for a coupled system of partial differential equations modeling the electrical activity in the heart

The electrical activity of the heart may be modeled with a system of partial differential equations (PDEs) known as the bidomain model. Computer simulations based on these equations may become a helpful tool to understand the relationship between changes in the electrical field and various heart diseases. Because of the rapid variations in the electrical field, sufficiently accurate simulations require a fine-scale discretization of the equations. For realistic geometries this leads to a large number of grid points and consequently large linear systems to be solved for each time step. In this paper, we present a fully coupled discretization of the bidomain model, leading to a block structured linear system. We take advantage of the block structure to construct an efficient preconditioner for the linear system, by combining multigrid with an operator splitting technique.     

An operator splitting method for solving the bidomain equations coupled to a volume conductor model for the torso

In this paper we present a numerical method for the bidomain model, which describes the electrical activity in the heart. The model consists of two partial differential equations (PDEs), which are coupled to systems of ordinary differential equations (ODEs) describing electrochemical reactions in the cardiac cells. Many applications require coupling these equations to a third PDE, describing the electrical fields in the torso surrounding the heart. The resulting system is challenging to solve numerically, because of its complexity and very strict resolution requirements in time and space. We propose a method based on operator splitting and a fully coupled discretization of the three PDEs. Numerical experiments show that for simple simulation cases and fine discretizations, the algorithm is second-order accurate in space and time.     

Solvers for the cardiac bidomain equations

The bidomain equations are widely used for the simulation of electrical activity in cardiac tissue. They are especially important for accurately modeling extracellular stimulation, as evidenced by their prediction of virtual electrode polarization before experimental verification. However, solution of the equations is computationally expensive due to the fine spatial and temporal discretization needed. This limits the size and duration of the problem which can be modeled. Regardless of the specific form into which they are cast, the computational bottleneck becomes the repeated solution of a large, linear system. The purpose of this review is to give an overview of the equations and the methods by which they have been solved. Of particular note are recent developments in multigrid methods, which have proven to be the most efficient.     

Modelling the Effect of Gap Junctions on Tissue-Level Cardiac Electrophysiology

When modelling tissue-level cardiac electrophysiology, a continuum approximation to the discrete cell-level equations, known as the bidomain equations, is often used to maintain computational tractability. Analysing the derivation of the bidomain equations allows us to investigate how microstructure, in particular gap junctions that electrically connect cells, affect tissue-level conductivity properties. Using a one-dimensional cable model, we derive a modified form of the bidomain equations that take gap junctions into account, and compare results of simulations using both the discrete and continuum models, finding that the underlying conduction velocity of the action potential ceases to match up between models when gap junctions are introduced at physiologically realistic coupling levels. We show that this effect is magnified by: (i) modelling gap junctions with reduced conductivity; (ii) increasing the conductance of the fast sodium channel; and (iii) an increase in myocyte length. From this, we conclude that the conduction velocity arising from the bidomain equations may not be an accurate representation of the underlying discrete system. In particular, the bidomain equations are less likely to be valid when modelling certain diseased states whose symptoms include a reduction in gap junction coupling or an increase in myocyte length.     

A linear system of partial differential equations modeling the resting potential of a heart with regional ischemia

Ischemic ST-segment shift has been modeled using scalar stationary approximations of the bidomain model. Here, we propose an alternative simplification of the bidomain equations: a linear system modeling the resting potential, to be used in determining ischemic TP shift. Results of 2D and 3D simulations show that the linear system model is much more accurate than the scalar model. This improved accuracy is important if the model is to be used for solving the inverse problem of determining the size and location of an ischemic region. Furthermore, the model can provide insight into how the resting potential depends on the variations in the extracellular potassium concentration that characterize ischemic regions.     

Wavefront propagation in an activation model of the anisotropic cardiac tissue: asymptotic analysis and numerical simulations

In this paper we present a macroscopic model of the excitation process in the myocardium. The composite and anisotropic structure of the cardiac tissue is represented by a bidomain, i.e. a set of two coupled anisotropic media. The model is characterized by a non linear system of two partial differential equations of parabolic and elliptic type. A singular perturbation analysis is carried out to investigate the cardiac potential field and the structure of the moving excitation wavefront. As a consequence the cardiac current sources are approximated by an oblique dipole layer structure and the motion of the wavefront is described by eikonal equations. Finally numerical simulations are carried out in order to analyze some complex phenomena related to the spreading of the wavefront, like the front-front or front-wall collision. The results yielded by the excitation model and the eikonal equations are compared.     

Efficient solution of ordinary differential equations modeling electrical activity in cardiac cells

The contraction of the heart is preceded and caused by a cellular electro-chemical reaction, causing an electrical field to be generated. Performing realistic computer simulations of this process involves solving a set of partial differential equations, as well as a large number of ordinary differential equations (ODEs) characterizing the reactive behavior of the cardiac tissue. Experiments have shown that the solution of the ODEs contribute significantly to the total work of a simulation, and there is thus a strong need to utilize efficient solution methods for this part of the problem. This paper presents how an efficient implicit Runge-Kutta method may be adapted to solve a complicated cardiac cell model consisting of 31 ODEs, and how this solver may be coupled to a set of PDE solvers to provide complete simulations of the electrical activity.     

Linear algebraic transformations of the bidomain equations: Implications for numerical methods

A mathematical framework is presented for the treatment of the bidomain equations used to model propagation in cardiac tissue. This framework is independent of the model used to represent membrane ionic currents and incorporates boundary conditions and other constraints. By representing the bidomain equations in the operator notation , various algebraic transformations can be expressed as , where P and Q are linear operators. The authors show how previous work fits into this framework and discuss the implications of various transformation for numerical methods of solution. Although such transformations allow many choices of independent variable, these results emphasize the fundamental importance of the transmembrane potential.     

Mathematical modeling of the excitation process in myocardial tissue: influence of fiber rotation on wavefront propagation and potential field

In our macroscopic model the heart tissue is represented as a bidomain coupling the intra- and extracellular media. Owing to the fiber structure of the myocardium, these media are anisotropic, and their conductivity tensors have a principal axis parallel to the local fiber direction. A reaction-diffusion system is derived that governs the distribution and evolution of the extracellular and transmembrane potentials during the depolarization phase of the heart beat. To investigate frontlike solutions, the system is rescaled and transformed into a system dependent on a small parameter. Subsequently a perturbation analysis is carried out that yields zero- and first-order approximations called eikonal equations. The effects of the transmural fiber rotation on wavefront propagation and the corresponding potential field, elicited by point stimulations, are investigated by means of numerical simulations.     

Virtual electrode polarization in the far field: implications for external defibrillation

We recently suggested that failure of implantable defibrillation therapy may be explained by the virtual electrode-induced phase singularity mechanism. The goal of this study was to identify possible mechanisms of vulnerability and defibrillation by externally applied shocks in vitro. We used bidomain simulations of realistic rabbit heart fibrous geometry to predict the passive polarization throughout the heart induced by external shocks. We also used optical mapping to assess anterior epicardium electrical activity during shocks in Langendorff-perfused rabbit hearts (n = 7). Monophasic shocks of either polarity (10-260 V, 8 ms, 150 microF) were applied during the T wave from a pair of mesh electrodes. Postshock epicardial virtual electrode polarization was observed after all 162 applied shocks, with positive polarization facing the cathode and negative polarization facing the anode, as predicted by the bidomain simulations. During arrhythmogenesis, a new wave front was induced at the boundary between the two regions near the apex but not at the base. It spread across the negatively polarized area toward the base of the heart and reentered on the other side while simultaneously spreading into the depth of the wall. Thus a scroll wave with a ribbon-shaped filament was formed during external shock-induced arrhythmia. Fluorescent imaging and passive bidomain simulations demonstrated that virtual electrode polarization-induced scroll waves underlie mechanisms of shock-induced vulnerability and failure of external defibrillation.     

Calculation of optical signal using three-dimensional bidomain/diffusion model reveals distortion of the transmembrane potential

Optical mapping experiments allow investigators to view the effects of electrical currents on the transmembrane potential, V_m, as a shock is applied to the heart. One important consideration is whether the optical signal accurately represents V_m. We have combined the bidomain equations along with the photon diffusion equation to study the excitation and emission of photons during optical mapping of cardiac tissue. Our results show that this bidomain/diffusion model predicts an optical signal that is much smaller than V_m near a stimulating electrode, a result consistent with experimental observations. Yet, this model, which incorporates the effect of lateral averaging, also reveals an optical signal that overestimates V_m at distances >1 mm away from the electrode. Although V_m falls off with distance r from the electrode as exp(−r/λ)/r, the optical signal decays as a simple exponential, exp(−r/λ). Moreover, regions of hyperpolarization adjacent to a cathode are emphasized in the optical signal compared to the region of depolarization under the cathode. Imaging methods utilizing optical mapping techniques will need to account for these distortions to accurately reconstruct V_m.     

Probing field-induced tissue polarization using transillumination fluorescent imaging

Despite major successes of biophysical theories in predicting the effects of electrical shocks within the heart, recent optical mapping studies have revealed two major discrepancies between theory and experiment: 1), the presence of negative bulk polarization recorded during strong shocks; and 2), the unexpectedly small surface polarization under shock electrodes. There is little consensus as to whether these differences result from deficiencies of experimental techniques, artifacts of tissue damage, or deficiencies of existing theories. Here, we take advantage of recently developed near-infrared voltage-sensitive dyes and transillumination optical imaging to perform, for the first time that we know of, noninvasive probing of field effects deep inside the intact ventricular wall. This technique removes some of the limitations encountered in previous experimental studies. We explicitly demonstrate that deep inside intact myocardial tissue preparations, strong electrical shocks do produce considerable negative bulk polarization previously inferred from surface recordings. We also demonstrate that near-threshold diastolic field stimulation produces activation of deep myocardial layers 2-6 mm away from the cathodal surface, contrary to theory. Using bidomain simulations we explore factors that may improve the agreement between theory and experiment. We show that the inclusion of negative asymmetric current can qualitatively explain negative bulk polarization in a discontinuous bidomain model.     

Parallel splitting solvers for the isogeometric analysis of the Cahn-Hilliard equation

Abstract

Modeling tumor growth in biological systems is a challenging problem with important consequences for diagnosis and treatment of various forms of cancer. This growth process requires large simulation complexity due to evolving biological and chemical processes in living tissue and interactions of cellular and vascular constituents in living organisms. Herein, we describe with a phase-field model, namely the Cahn-Hilliard equation the intricate interactions between the tumors and their host tissue. The spatial discretization uses highly-continuous isogeometric elements. For fast simulation of the time-dependent Cahn-Hilliard equation, we employ an alternating directions implicit methodology. Thus, we reduce the original problems to Kronecker products of 1?D matrices that can be factorized in a linear computational cost. The implementation enables parallel multi-core simulations and shows good scalability on shared-memory multi-core machines. Combined with the high accuracy of isogeometric elements, our method shows high efficiency in solving the Cahn-Hilliard equation on tensor-product meshes.     

A numerical solution of the mechanical bidomain model

Introduction: The mechanical bidomain model predicts forces on integrin proteins in the membrane. It has been solved analytically for idealized examples, but a numerical algorithm is needed to address realistic problems. Methods: The bidomain equations are approximated using finite differences. An ischemic region is modeled as a circular area having no active tension, surrounded by normal tissue. Results: The membrane force is large in the ischemic border zone, but is small elsewhere. Strain is distributed widely throughout the ischemic region and surrounding tissue. Conclusion: This calculation provides a testable prediction for the mechanism of mechanotransduction and remodeling in cardiac tissue.     

A second-generation computational modeling of cardiac electrophysiology: response of action potential to ionic concentration changes and metabolic inhibition

Background

Cardiac arrhythmias are becoming one of the major health care problem in the world, causing numerous serious disease conditions including stroke and sudden cardiac death. Furthermore, cardiac arrhythmias are intimately related to the signaling ability of cardiac cells, and are caused by signaling defects. Consequently, modeling the electrical activity of the heart, and the complex signaling models that subtend dangerous arrhythmias such as tachycardia and fibrillation, necessitates a quantitative model of action potential (AP) propagation. Yet, many electrophysiological models, which accurately reproduce dynamical characteristic of the action potential in cells, have been introduced. However, these models are very complex and are very time consuming computationally. Consequently, a large amount of research is consecrated to design models with less computational complexity.

Results

This paper is presenting a new model for analyzing the propagation of ionic concentrations and electrical potential in space and time. In this model, the transport of ions is governed by Nernst-Planck flux equation (NP), and the electrical interaction of the species is described by a new cable equation. These set of equations form a system of coupled partial nonlinear differential equations that is solved numerically. In the first we describe the mathematical model. To realize the numerical simulation of our model, we proceed by a finite element discretization and then we choose an appropriate resolution algorithm.

Conclusions

We give numerical simulations obtained for different input scenarios in the case of suicide substrate reaction which were compared to those obtained in literature. These input scenarios have been chosen so as to provide an intuitive understanding of dynamics of the model. By accessing time and space domains, it is shown that interpreting the electrical potential of cell membrane at steady state is incorrect. This model is general and applies to ions of any charge in space and time domains. The results obtained show a complete agreement with literature findings and also with the physical interpretation of the phenomenon. Furthermore, various numerical experiments are presented to confirm the accuracy, efficiency and stability of the proposed method. In particular, we show that the scheme is second-order accurate in space.

     

Soft Tissue Modelling of Cardiac Fibres for Use in Coupled Mechano-Electric Simulations

The numerical solution of the coupled system of partial differential and ordinary differential equations that model the whole heart in three dimensions is a considerable computational challenge. As a consequence, it is not computationally practical—either in terms of memory or time—to repeat simulations on a finer computational mesh to ensure that convergence of the solution has been attained. In an attempt to avoid this problem while retaining mathematical rigour, we derive a one dimensional model of a cardiac fibre that takes account of elasticity properties in three structurally defined axes within the myocardial tissue. This model of a cardiac fibre is then coupled with an electrophysiological cell model and a model of cellular electromechanics to allow us to simulate the coupling of the electrical and mechanical activity of the heart. We demonstrate that currently used numerical methods for coupling electrical and mechanical activity do not work in this case, and identify appropriate numerical techniques that may be used when solving the governing equations. This allows us to perform a series of simulations that: (i) investigate the effect of some of the assumptions inherent in other models; and (ii) reproduce qualitatively some experimental observations.     

Fitting rhythmic biological data by means of (combinations of) Voltera Integro‐Differential equations

Abstract

A method of analysing rhythmic biological data is presented utilising a curve fitting technique based on solutions of the Volterra Integro‐Differential Equation (VIDE). The technique involves the use of difference equations and the method of moments as the fitting criterion. It is conjectured that combinations of the VIDE can provide a more meaningful fit for such data than does harmonic analysis. The (generating, inhibiting and heredity) parameters of the VIDE may be related to the true biological mechanisms and thus may give the biologist opportunities to understand the underlying processes. A practical example is presented to illustrate the merits and limitations of the method.     

Nonlinear simulations of solid tumor growth using a mixture model: invasion and branching

We develop a thermodynamically consistent mixture model for avascular solid tumor growth which takes into account the effects of cell-to-cell adhesion, and taxis inducing chemical and molecular species. The mixture model is well-posed and the governing equations are of Cahn-Hilliard type. When there are only two phases, our asymptotic analysis shows that earlier single-phase models may be recovered as limiting cases of a two-phase model. To solve the governing equations, we develop a numerical algorithm based on an adaptive Cartesian block-structured mesh refinement scheme. A centered-difference approximation is used for the space discretization so that the scheme is second order accurate in space. An implicit discretization in time is used which results in nonlinear equations at implicit time levels. We further employ a gradient stable discretization scheme so that the nonlinear equations are solvable for very large time steps. To solve those equations we use a nonlinear multilevel/multigrid method which is of an optimal order O(N) where N is the number of grid points. Spherically symmetric and fully two dimensional nonlinear numerical simulations are performed. We investigate tumor evolution in nutrient-rich and nutrient-poor tissues. A number of important results have been uncovered. For example, we demonstrate that the tumor may suffer from taxis-driven fingering instabilities which are most dramatic when cell proliferation is low, as predicted by linear stability theory. This is also observed in experiments. This work shows that taxis may play a role in tumor invasion and that when nutrient plays the role of a chemoattractant, the diffusional instability is exacerbated by nutrient gradients. Accordingly, we believe this model is capable of describing complex invasive patterns observed in experiments.     

Numerical Models for the Simulation of Flexible Artificial Heart Valves: Part I - Computational Methods

Abstract

A numerical model of the coupled motion of a flexing surface in a high Reynolds number flow is presented for the simulation of flexible polyurethane heart valves in the aortic position. This is achieved by matching a Lagrangian dynamic leaflet model with a panel method based flow solver. The two models are coupled via the time-dependent pressure field using the unsteady Bernoulli equation.

Incorporation of sub-cycling in the dynamic model equations and fast pre conditioning techniques in the panel method solver yields efficient convergence and near real-time simulations of valve motion. The generality of dynamic model allows different material properties and/or geometries to be studied easily and interactively. This interactivity is realized by embedding the models within a design environment created using the software IRIS Explorer ^TM.

Two flow domains are developed, an infinite domain and an internal domain using conformal mapping theory. In addition bending stress on the valve is computed using a simple stress model based on spline and circle equation techniques.     

Current injection into a two-dimensional anisotropic bidomain.

A two-dimensional sheet of anisotropic cardiac tissue is represented with the bidomain model, and the finite element method is used to solve the bidomain equations. When the anisotropy ratios of the intracellular and extracellular spaces are not equal, the injection of current into the tissue induces a transmembrane potential that has a complicated spatial dependence, including adjacent regions of depolarized and hyperpolarized tissue. This behavior may have important implications for the electrical stimulation of cardiac tissue and for defibrillation.