Computational tools for modeling electrical activity in cardiac tissue

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Abstract

Computer models offer many attractive benefits. However, the modeling of cardiac tissue is computationally expensive due to several physical constraints which result in fine spatiotemporal discretization over large spatiotemporal regions. Our laboratory has been actively trying to develop new techniques to make large scale cardiac simulations tractable over the past 15 years. This paper describes the latest modeling software that our group has developed, called Carp (Cardiac arrhythmias research package). It is designed to run in both shared memory and clustered computing environments. Carp aims to be modular and flexible by following a plug-in framework. This allows the latest models and most efficient solvers to be incorporated as well as enabling run-time selection of techniques. Performance results are given for a large-scale simulation which utilized a comprehensive membrane ionic current description.

Section snippets

Electric current flow in the anisotropic myocardium

The complex functional electrical properties of the heart are, in fact, inextricably linked to its ultrastructure and fiber architecture (9). Careful modeling of electrical activity in cardiac tissue requires modeling current flow in three distinct domains: 1) within and between cells, 2) in the extracellular medium, and (3) across the cell membrane. The myocardium is composed of myocytes which are rod-like cells approximately 20 μm in diameter and 100 μm long. Each cell is bounded by a

The software (Carp)

There were 2 key design factors in the development of the Cardiac Arrhythmias Research Package (Carp): accuracy (both numerical and physical), and speed. A third and somewhat less important factor was flexibility. Carp is shown schematically in Figure 1. The program consists of three main components: a parabolic solver, an ionic current component, and an elliptic solver. Each of these components has a set of sockets in which to plug the components which do the bulk of the work. The parabolic

Performance

Sample performance is given for a simple three dimensional problem comprising 425,000 nodes running on a 2.4 MHz Pentium Machine in Table 1. The ionic model employed was the Courtemanche human atrial model. Both bidomain and monodomain simulations were performed. From the much longer times for bidomain simulations, it is evident that the solution of the elliptic problem dominates the computation. The conjugate gradient (CG) iterative solver with ILU preconditioning takes about three times

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This work was supported by MITACS, the National Science and Engineering Research Council of Canada, and The Heart and Stroke Foundation of Alberta.

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