title: Parallel acceleration for modeling of calcium dynamics in cardiac myocytes.
abstract: Spatial-temporal calcium dynamics due to calcium release, buffering, and re-uptaking plays a central role in studying excitation-contraction (E-C) coupling in both healthy and defected cardiac myocytes. In our previous work, partial differential equations (PDEs) had been used to simulate calcium dynamics with realistic geometries extracted from electron microscopic imaging data. However, the computational costs of such simulations are very high on a single processor. To alleviate this problem, we have accelerated the numerical simulations of calcium dynamics by using graphics processing units (GPUs). Computational performance and simulation accuracy are compared with those based on a single CPU and another popular parallel computing technique, OpenMP.
authors.affiliation: Department of Computer Science, University of Wisconsin-Milwaukee, WI, USA.
authors.forename: Ke
authors.initials: K
authors.lastname: Liu
authors.forename: Guangming
authors.initials: G
authors.lastname: Yao
authors.forename: Zeyun
authors.initials: Z
authors.lastname: Yu
mesh_terms: D000054:Acceleration; D000465:Algorithms; D002118:Calcium / Q000378:metabolism*; D019295:Computational Biology; D003196:Computer Graphics; D003198:Computer Simulation; D006801:Humans; D008854:Microscopy, Electron; D008955:Models, Cardiovascular; D032383:Myocytes, Cardiac / Q000502:physiology*; D015203:Reproducibility of Results; D012984:Software; D013997:Time Factors
chemical_list: D002118:Calcium
keywords: CUDA; GPU; OpenMP; PDEs; calcium dynamics; parallel