Anton, a special-purpose machine for molecular dynamics simulation
Proceedings of the 34th annual international symposium on Computer architecture
Computing and Visualization in Science
GPU-Based Parallelization for Computer Simulation of Electrocardiogram
CIT '09 Proceedings of the 2009 Ninth IEEE International Conference on Computer and Information Technology - Volume 02
Real-Time and Realistic Simulation for Cardiac Intervention with GPU
ICCMS '10 Proceedings of the 2010 Second International Conference on Computer Modeling and Simulation - Volume 03
Real-Time and Realistic Simulation for Cardiac Intervention with GPU
ICCMS '10 Proceedings of the 2010 Second International Conference on Computer Modeling and Simulation - Volume 03
Computer Methods and Programs in Biomedicine
A Multi-Scale Heart Simulation on Massively Parallel Computers
Proceedings of the 2010 ACM/IEEE International Conference for High Performance Computing, Networking, Storage and Analysis
Source-to-source optimization of CUDA C for GPU accelerated cardiac cell modeling
EuroPar'10 Proceedings of the 16th international Euro-Par conference on Parallel processing: Part I
CUDA by Example: An Introduction to General-Purpose GPU Programming
CUDA by Example: An Introduction to General-Purpose GPU Programming
Accelerating cardiac excitation spread simulations using graphics processing units
Concurrency and Computation: Practice & Experience
Efficient simulation of cardiac electrical propagation using high order finite elements
Journal of Computational Physics
Approximate bisimulations for sodium channel dynamics
CMSB'12 Proceedings of the 10th international conference on Computational Methods in Systems Biology
Towards real-time computation of cardiac electrophysiology for training simulator
STACOM'12 Proceedings of the third international conference on Statistical Atlases and Computational Models of the Heart: imaging and modelling challenges
Curvature Analysis of Cardiac Excitation Wavefronts
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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We show that through careful and model-specific optimizations of their GPU implementations, simulations of realistic, detailed cardiac-cell models now can be performed in 2D and 3D in times that are close to real time using a desktop computer. Previously, large-scale simulations of detailed mathematical models of cardiac cells were possible only using supercomputers. In our study, we consider five different models of cardiac electrophysiology that span a broad range of computational complexity: the two-variable Karma model, the four-variable Bueno-Orovio-Cherry-Fenton model, the eight-variable Beeler-Reuter model, the 19-variable Ten Tusscher-Panfilov model, and the 67-variable Iyer-Mazhari-Winslow model. For each of these models, we treat both their single- and double-precision versions and demonstrate linear or even sub-linear growth in simulation times with an increase in the size of the grid used to model cardiac tissue. We also show that our GPU implementations of these models can increase simulation speeds to near real-time for simulations of complex spatial patterns indicative of cardiac arrhythmic disorders, including spiral waves and spiral wave breakup. The achievement of real-time applications without the need for supercomputers may, in the near term, facilitate the adoption of modeling-based clinical diagnostics and treatment planning, including patient-specific electrophysiological studies.