title: Parallel Optimization of 3D Cardiac Electrophysiological Model Using GPU.
abstract: Large-scale 3D virtual heart model simulations are highly demanding in computational resources. This imposes a big challenge to the traditional computation resources based on CPU environment, which already cannot meet the requirement of the whole computation demands or are not easily available due to expensive costs. GPU as a parallel computing environment therefore provides an alternative to solve the large-scale computational problems of whole heart modeling. In this study, using a 3D sheep atrial model as a test bed, we developed a GPU-based simulation algorithm to simulate the conduction of electrical excitation waves in the 3D atria. In the GPU algorithm, a multicellular tissue model was split into two components: one is the single cell model (ordinary differential equation) and the other is the diffusion term of the monodomain model (partial differential equation). Such a decoupling enabled realization of the GPU parallel algorithm. Furthermore, several optimization strategies were proposed based on the features of the virtual heart model, which enabled a 200-fold speedup as compared to a CPU implementation. In conclusion, an optimized GPU algorithm has been developed that provides an economic and powerful platform for 3D whole heart simulations.
authors.affiliation: School of Computer Science and Technology, Harbin Institute of Technology, Harbin 150001, China.
authors.forename: Yong
authors.initials: Y
authors.lastname: Xia
authors.affiliation: School of Computer Science and Technology, Harbin Institute of Technology, Harbin 150001, China.
authors.forename: Kuanquan
authors.initials: K
authors.lastname: Wang
authors.affiliation: School of Computer Science and Technology, Harbin Institute of Technology, Harbin 150001, China ; Biological Physics Group, School of Physics & Astronomy, University of Manchester, Manchester M13 9PL, UK.
authors.forename: Henggui
authors.initials: H
authors.lastname: Zhang
mesh_terms: D000465:Algorithms; D000818:Animals; D016275:Atrial Function; D054849:Cardiac Electrophysiology / Q000379:methods / Q000706:statistics & numerical data; D019295:Computational Biology; D003196:Computer Graphics; D003198:Computer Simulation; D055724:Electrophysiological Phenomena; D006801:Humans; D021621:Imaging, Three-Dimensional; D008955:Models, Cardiovascular; D034561:Sheep, Domestic; D014584:User-Computer Interface