Solving the Coupled System Improves Computational Efficiency of the Bidomain Equations

Handle URI:
http://hdl.handle.net/10754/599673
Title:
Solving the Coupled System Improves Computational Efficiency of the Bidomain Equations
Authors:
Southern, J.A.; Plank, G.; Vigmond, E.J.; Whiteley, J.P.
Abstract:
The bidomain equations are frequently used to model the propagation of cardiac action potentials across cardiac tissue. At the whole organ level, the size of the computational mesh required makes their solution a significant computational challenge. As the accuracy of the numerical solution cannot be compromised, efficiency of the solution technique is important to ensure that the results of the simulation can be obtained in a reasonable time while still encapsulating the complexities of the system. In an attempt to increase efficiency of the solver, the bidomain equations are often decoupled into one parabolic equation that is computationally very cheap to solve and an elliptic equation that is much more expensive to solve. In this study, the performance of this uncoupled solution method is compared with an alternative strategy in which the bidomain equations are solved as a coupled system. This seems counterintuitive as the alternative method requires the solution of a much larger linear system at each time step. However, in tests on two 3-D rabbit ventricle benchmarks, it is shown that the coupled method is up to 80% faster than the conventional uncoupled method-and that parallel performance is better for the larger coupled problem.
Citation:
Southern JA, Plank G, Vigmond EJ, Whiteley JP (2009) Solving the Coupled System Improves Computational Efficiency of the Bidomain Equations. IEEE Trans Biomed Eng 56: 2404–2412. Available: http://dx.doi.org/10.1109/TBME.2009.2022548.
Publisher:
Institute of Electrical and Electronics Engineers (IEEE)
Journal:
IEEE Transactions on Biomedical Engineering
KAUST Grant Number:
KUK-C1-013-04
Issue Date:
Oct-2009
DOI:
10.1109/TBME.2009.2022548
PubMed ID:
19457741
Type:
Article
ISSN:
0018-9294; 1558-2531
Sponsors:
This workwas supported by the King Abdullah University of Science and Technology(KAUST) under Award KUK-C1-013-04.
Appears in Collections:
Publications Acknowledging KAUST Support

Full metadata record

DC FieldValue Language
dc.contributor.authorSouthern, J.A.en
dc.contributor.authorPlank, G.en
dc.contributor.authorVigmond, E.J.en
dc.contributor.authorWhiteley, J.P.en
dc.date.accessioned2016-02-28T06:07:14Zen
dc.date.available2016-02-28T06:07:14Zen
dc.date.issued2009-10en
dc.identifier.citationSouthern JA, Plank G, Vigmond EJ, Whiteley JP (2009) Solving the Coupled System Improves Computational Efficiency of the Bidomain Equations. IEEE Trans Biomed Eng 56: 2404–2412. Available: http://dx.doi.org/10.1109/TBME.2009.2022548.en
dc.identifier.issn0018-9294en
dc.identifier.issn1558-2531en
dc.identifier.pmid19457741en
dc.identifier.doi10.1109/TBME.2009.2022548en
dc.identifier.urihttp://hdl.handle.net/10754/599673en
dc.description.abstractThe bidomain equations are frequently used to model the propagation of cardiac action potentials across cardiac tissue. At the whole organ level, the size of the computational mesh required makes their solution a significant computational challenge. As the accuracy of the numerical solution cannot be compromised, efficiency of the solution technique is important to ensure that the results of the simulation can be obtained in a reasonable time while still encapsulating the complexities of the system. In an attempt to increase efficiency of the solver, the bidomain equations are often decoupled into one parabolic equation that is computationally very cheap to solve and an elliptic equation that is much more expensive to solve. In this study, the performance of this uncoupled solution method is compared with an alternative strategy in which the bidomain equations are solved as a coupled system. This seems counterintuitive as the alternative method requires the solution of a much larger linear system at each time step. However, in tests on two 3-D rabbit ventricle benchmarks, it is shown that the coupled method is up to 80% faster than the conventional uncoupled method-and that parallel performance is better for the larger coupled problem.en
dc.description.sponsorshipThis workwas supported by the King Abdullah University of Science and Technology(KAUST) under Award KUK-C1-013-04.en
dc.publisherInstitute of Electrical and Electronics Engineers (IEEE)en
dc.titleSolving the Coupled System Improves Computational Efficiency of the Bidomain Equationsen
dc.typeArticleen
dc.identifier.journalIEEE Transactions on Biomedical Engineeringen
dc.contributor.institutionFujitsu Laboratories of Europe Ltd., Hayes UB4 8FE, U.K.en
dc.contributor.institutionComputing Laboratory, University of Oxford, Oxford OX1 3QD, U.K.en
dc.contributor.institutionInstitute of Physiology, Medical University of Graz, Graz 8010, Austriaen
dc.contributor.institutionDepartment of Electrical and Computer Engineering, University of Calgary, Calgary, AB T2N 1N4, Canadaen
kaust.grant.numberKUK-C1-013-04en

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