title: Simulations of complex and microscopic models of cardiac electrophysiology powered by multi-GPU platforms.
abstract: Key aspects of cardiac electrophysiology, such as slow conduction, conduction block, and saltatory effects have been the research topic of many studies since they are strongly related to cardiac arrhythmia, reentry, fibrillation, or defibrillation. However, to reproduce these phenomena the numerical models need to use subcellular discretization for the solution of the PDEs and nonuniform, heterogeneous tissue electric conductivity. Due to the high computational costs of simulations that reproduce the fine microstructure of cardiac tissue, previous studies have considered tissue experiments of small or moderate sizes and used simple cardiac cell models. In this paper, we develop a cardiac electrophysiology model that captures the microstructure of cardiac tissue by using a very fine spatial discretization (8 μm) and uses a very modern and complex cell model based on Markov chains for the characterization of ion channel's structure and dynamics. To cope with the computational challenges, the model was parallelized using a hybrid approach: cluster computing and GPGPUs (general-purpose computing on graphics processing units). Our parallel implementation of this model using a multi-GPU platform was able to reduce the execution times of the simulations from more than 6 days (on a single processor) to 21 minutes (on a small 8-node cluster equipped with 16 GPUs, i.e., 2 GPUs per node).
authors.affiliation: Computational Modeling, Federal University of Juiz de Fora, 36036-900 Juiz de Fora, MG, Brazil.
authors.forename: Bruno
authors.initials: B
authors.lastname: Gouvêa de Barros
authors.forename: Rafael
authors.initials: R
authors.lastname: Sachetto Oliveira
authors.forename: Wagner
authors.initials: W
authors.lastname: Meira
authors.forename: Marcelo
authors.initials: M
authors.lastname: Lobosco
authors.forename: Rodrigo
authors.initials: R
authors.lastname: Weber dos Santos
mesh_terms: D000465:Algorithms; D054849:Cardiac Electrophysiology / Q000379:methods*; D003196:Computer Graphics; D003198:Computer Simulation; D004553:Electric Conductivity; D020342:Finite Element Analysis; D017629:Gap Junctions / Q000502:physiology; D006321:Heart / Q000502:physiology; D006801:Humans; D008390:Markov Chains; D008955:Models, Cardiovascular; D008962:Models, Theoretical; D009206:Myocardium / Q000378:metabolism; D012984:Software; D013997:Time Factors