A massively parallel computational electrophysiology model of the heart

This paper presents a patient-sensitive simulation strategy capable of using the most efficient way the high-performance computational resources. The proposed strategy directly involves three different players: Computational Mechanics Scientists (CMS), Image Processing Scientists and Cardiologists, each one mastering its own expertise area within the project. This paper describes the general integrative scheme but focusing on the CMS side presents a massively parallel implementation of computational electrophysiology applied to cardiac tissue simulation. The paper covers different angles of the computational problem: equations, numerical issues, the algorithm and parallel implementation. The proposed methodology is illustrated with numerical simulations testing all the different possibilities, ranging from small domains up to very large ones. A key issue is the almost ideal scalability not only for large and complex problems but also for medium-size meshes. The explicit formulation is particularly well suited for solving this highly transient problems, with very short time-scale. Copyright © 2011 John Wiley & Sons, Ltd.

[1]  Guillaume Houzeaux,et al.  A massively parallel fractional step solver for incompressible flows , 2009, J. Comput. Phys..

[2]  Andrew D McCulloch,et al.  Integrative biological modelling in silico. , 2002, Novartis Foundation symposium.

[3]  Denis Noble,et al.  Integrative models of the heart: achievements and limitations , 2001, Philosophical Transactions of the Royal Society of London. Series A: Mathematical, Physical and Engineering Sciences.

[4]  C. Henriquez,et al.  Modeling impulse propagation and extracellular potential distributions in anisotropic cardiac tissue using a finite volume element discretization , 2002 .

[5]  Ramon Codina,et al.  Shock capturing viscosities for the general fluid mechanics algorithm , 1998 .

[6]  R. FitzHugh.  Impulses and Physiological States in Theoretical Models of Nerve Membrane. , 1961, Biophysical journal.

[7]  L. Younes,et al.  Ex vivo 3D diffusion tensor imaging and quantification of cardiac laminar structure , 2005, Magnetic resonance in medicine.

[8]  R. Lux,et al.  Effect of Myocardial Fiber Direction on Epicardial Potentials , 1994, Circulation.

[9]  Andrew D. McCulloch,et al.  Computational Methods for Cardiac Electrophysiology , 2004 .

[10]  M. Vazquez,et al.  NUMERICAL SCHEMES FOR THE SIMULATION OF THREE-DIMENSIONAL CARDIAC ELECTRICAL PROPAGATION IN PATIENT-SPECIFIC VENTRICULAR GEOMETRIES , 2006 .

[11]  Takumi Washio,et al.  A Multi-Scale Heart Simulation on Massively Parallel Computers , 2010, 2010 ACM/IEEE International Conference for High Performance Computing, Networking, Storage and Analysis.

[12]  Claes Johnson,et al.  Computational Differential Equations , 1996 .

[13]  Frank B. Sachse,et al.  Computational Cardiology , 2004, Lecture Notes in Computer Science.

[14]  P. Hunter,et al.  Bioinformatics, multiscale modeling and the IUPS Physiome Project , 2008, Briefings Bioinform..

[15]  Masashi Komeda,et al.  Towards new understanding of the heart structure and function. , 2005, European journal of cardio-thoracic surgery : official journal of the European Association for Cardio-thoracic Surgery.

[16]  Giorgio Fotia,et al.  Simulation of cardiac electrophysiology on next-generation high-performance computers , 2009, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences.

[17]  Guillaume Houzeaux,et al.  Extension of fractional step techniques for incompressible flows: The preconditioned Orthomin(1) for the pressure Schur complement , 2011 .

[18]  Alan Garny,et al.  A numerical guide to the solution of the bi-domain equations of cardiac electrophysiology. , 2010, Progress in biophysics and molecular biology.

[19]  Miguel O. Bernabeu,et al.  Shock-induced arrhythmogenesis in the human heart: A computational modelling study , 2010, 2010 Annual International Conference of the IEEE Engineering in Medicine and Biology.

[20]  Dd. Streeter,et al.  Gross morphology and fiber geometry of the heart , 1979 .

[21]  Nicholas Ayache.  Computational Models for the Human Body , 2004 .

[22]  P. Hunter,et al.  New developments in a strongly coupled cardiac electromechanical model. , 2005, Europace : European pacing, arrhythmias, and cardiac electrophysiology : journal of the working groups on cardiac pacing, arrhythmias, and cardiac cellular electrophysiology of the European Society of Cardiology.

[23]  Guillaume Houzeaux,et al.  A HIGH PERFORMANCE COMPUTATIONAL ELECTROPHYSIOLOGY MODEL , 2007 .

[24]  Francesc Carreras,et al.  Base-to-apex ventricular activation: Fourier studies in 29 normal individuals , 2005, European Journal of Nuclear Medicine and Molecular Imaging.

[25]  Rainald Löhner,et al.  Deflated preconditioned conjugate gradient solvers for the Pressure-Poisson equation , 2008, J. Comput. Phys..

[26]  Ramon Codina,et al.  A discontinuity-capturing crosswind-dissipation for the finite element solution of the convection-diffusion equation , 1993 .

[27]  Saleh Saleh,et al.  Structure/function interface with sequential shortening of basal and apical components of the myocardial band. , 2006, European journal of cardio-thoracic surgery : official journal of the European Association for Cardio-thoracic Surgery.

[28]  R. Winslow,et al.  Electrophysiological modeling of cardiac ventricular function: from cell to organ. , 2000, Annual review of biomedical engineering.

[29]  I. Legrice,et al.  The architecture of the heart: a data–based model , 2001, Philosophical Transactions of the Royal Society of London. Series A: Mathematical, Physical and Engineering Sciences.

[30]  F. Fenton,et al.  Vortex dynamics in three-dimensional continuous myocardium with fiber rotation: Filament instability and fibrillation. , 1998, Chaos.

[31]  Olivier Blanc.  A computer model of human atrial arrhythmia , 2002 .

[32]  Guillaume Houzeaux,et al.  Hybrid MPI-OpenMP performance in massively parallel computational fluid dynamics , 2010 .

[33]  Peter Brucker,et al.  Scheduling Algorithms , 1995 .

[34]  D. Le Bihan,et al.  Diffusion tensor imaging: Concepts and applications , 2001, Journal of magnetic resonance imaging : JMRI.

[35]  Xiao-Chuan Cai,et al.  A fully implicit parallel algorithm for simulating the non‐linear electrical activity of the heart , 2004, Numer. Linear Algebra Appl..

[36]  F. Fenton,et al.  Modeling wave propagation in realistic heart geometries using the phase-field method. , 2005, Chaos.

[37]  Gerald D Buckberg,et al.  'The electrical spiral of the heart': its role in the helical continuum. The hypothesis of the anisotropic conducting matrix. , 2006, European journal of cardio-thoracic surgery : official journal of the European Association for Cardio-thoracic Surgery.

[38]  Jukka Nenonen,et al.  Simulation of Anisotropic Propagation in the Myocardium with a Hybrid Bidomain Model , 2001, FIMH.