title: Computational techniques for solving the bidomain equations in three dimensions.
abstract: The bidomain equations are the most complete description of cardiac electrical activity. Their numerical solution is, however, computationally demanding, especially in three dimensions, because of the fine temporal and spatial sampling required. This paper methodically examines computational performance when solving the bidomain equations. Several techniques to speed up this computation are examined in this paper. The first step was to recast the equations into a parabolic part and an elliptic part. The parabolic part was solved by either the finite-element method (FEM) or the interconnected cable model model (ICCM). The elliptic equation was solved by FEM on a coarser grid than the parabolic problem and at a reduced frequency. The performance of iterative and direct linear equation system solvers was analyzed as well as the scalability and parallelizability of each method. Results indicate that the ICCM was twice as fast as the FEM for solving the parabolic problem, but when the total problem was considered, this resulted in only a 20% decrease in computation time. The elliptic problem could be solved on a coarser grid at one-quarter of the frequency at which the parabolic problem was solved and still maintain reasonable accuracy. Direct methods were faster than iterative methods by at least 50% when a good estimate of the extracellular potential was required. Parallelization over four processors was efficient only when the model comprised at least 500,000 nodes. Thus, it was possible to speed up solution of the bidomain equations by an order of magnitude with a slight decrease in accuracy.
authors.affiliation: Department of Electrical and Computer Engineering, University of Calgary, 2500 University Dr. NW, Calgary, AB T2N 1N4, Canada. vigmond@ucalgary.ca
authors.forename: Edward J
authors.initials: EJ
authors.lastname: Vigmond
authors.forename: Felipe
authors.initials: F
authors.lastname: Aguel
authors.forename: Natalia A
authors.initials: NA
authors.lastname: Trayanova
mesh_terms: D000465:Algorithms; D016880:Anisotropy; D003205:Computing Methodologies; D004553:Electric Conductivity; D004594:Electrophysiology / Q000379:methods*; D020342:Finite Element Analysis; D006321:Heart / Q000502:physiology*; D006329:Heart Conduction System / Q000502:physiology; D006801:Humans; D008564:Membrane Potentials / Q000502:physiology; D008955:Models, Cardiovascular; D009206:Myocardium; D009716:Numerical Analysis, Computer-Assisted; D011786:Quality Control; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity