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Evaluation of a Rapid Anisotropic Model for ECG Simulation

Simone Pezzuto, Peter Kal'avský, Mark Potse, Frits W. Prinzen, Angelo Auricchio, Rolf Krause
2017 Frontiers in Physiology  
Both solvers were implemented on graphics processing units and massively parallelized. We studied the numerical convergence and scalability of the approach.  ...  The proposed methods provided a good approximation of activation maps and ECGs computed with a bidomain model, in only a few seconds. Both solvers scaled very well to high-end hardware.  ...  ACKNOWLEDGMENTS The authors sincerely thank Hanspeter Fischer of Biosense Webster for his contribution in data acquisition and for making the data available for offline analysis.  ... 
doi:10.3389/fphys.2017.00265 pmid:28512434 pmcid:PMC5411438 fatcat:axigydifxbgabclyyb5rz4ecsi

A numerical guide to the solution of the bidomain equations of cardiac electrophysiology

Pras Pathmanathan, Miguel O. Bernabeu, Rafel Bordas, Jonathan Cooper, Alan Garny, Joe M. Pitt-Francis, Jonathan P. Whiteley, David J. Gavaghan
2010 Progress in Biophysics and Molecular Biology  
Simulation of cardiac electrical activity using the bidomain equations can be a massively computationally demanding problem. This study provides a comprehensive guide to numerical bidomain modelling.  ...  Each component of bidomain simulationsddiscretisation, ODE-solution, linear system solution, and parallelisationdis discussed, and previously-used methods are reviewed, new methods are proposed, and issues  ...  KUK-C1-013-04, made by King Abdullah University of Science and Technology (KAUST).  ... 
doi:10.1016/j.pbiomolbio.2010.05.006 pmid:20553747 fatcat:gilckmyltvcdzanvo6edi5qmqq

Algebraic Multigrid Solver on Clusters of CPUs and GPUs [chapter]

Aurel Neic, Manfred Liebmann, Gundolf Haase, Gernot Plank
2012 Lecture Notes in Computer Science  
Benchmark results of computations on clusters of CPUs and GPUs will be presented. They will show that a linear equation system with 25 million unknowns can be solved in about 1 second.  ...  We will present a highly parallel CPU and GPU implementation of a conjugate gradient solver with an algebraic multigrid preconditioner in a package called Parallel Toolbox.  ...  The Cardiac Arrhythmias Research Package is a project for the electrophysiological simulation of cardiac tissue which has been developed by Dr. Edward Vigmond and Dr. Gernot Plank [12] .  ... 
doi:10.1007/978-3-642-28145-7_38 fatcat:owkxs4zxxbah5e5ywvh4jvfvma

Models of cardiac tissue electrophysiology: Progress, challenges and open questions

R.H. Clayton, O. Bernus, E.M. Cherry, H. Dierckx, F.H. Fenton, L. Mirabella, A.V. Panfilov, F.B. Sachse, G. Seemann, H. Zhang
2011 Progress in Biophysics and Molecular Biology  
This paper is a critical review of cardiac tissue electrophysiology models, focussing on the micro-structure of cardiac tissue, generic behaviours of action potential propagation, different models of cardiac  ...  Models of cardiac tissue electrophysiology are an important component of the Cardiac Physiome Project, which is an international effort to build biophysically based multi-scale mathematical models of the  ...  Acknowledgements This paper was conceived and drafted during a workshop on the Cardiac Physiome Project held at the Newton Institute for Mathematical Sciences at the University of Cambridge in July 2009  ... 
doi:10.1016/j.pbiomolbio.2010.05.008 pmid:20553746 fatcat:rai5syflw5aonf72ixiv2gss2i

Enabling Detailed, Biophysics-Based Skeletal Muscle Models on HPC Systems

Chris P. Bradley, Nehzat Emamy, Thomas Ertl, Dominik Göddeke, Andreas Hessenthaler, Thomas Klotz, Aaron Krämer, Michael Krone, Benjamin Maier, Miriam Mehl, Tobias Rau, Oliver Röhrle
2018 Frontiers in Physiology  
Parallel Scaling Experiments In the following we conduct parallel scalability experiments to investigate the behavior of the simulation on highly parallel compute clusters.  ...  The error bars indicate estimated standard deviation of runtimes on all involved processes of a single simulation run.  ...  Conflict of Interest Statement: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest  ... 
doi:10.3389/fphys.2018.00816 pmid:30050446 pmcid:PMC6052132 fatcat:bpj6dga43fao3cmfdybtstqqkm

Three-dimensional cardiac computational modelling: methods, features and applications

Alejandro Lopez-Perez, Rafael Sebastian, Jose M Ferrero
2015 BioMedical Engineering OnLine  
Finally, we present examples of several specific applications, mainly related to cardiac EP simulation and model-based image analysis, showing the potential usefulness of 3D cardiac computational modelling  ...  For this reason, three-dimensional (3D) cardiac computational modelling is currently a rising field of research.  ...  Acknowledgements This work was partially supported by the "VI Plan Nacional de Investigación Científica, Desarrollo e Innovación Tecnológica" from the Ministerio de Economía y Competitividad of Spain (  ... 
doi:10.1186/s12938-015-0033-5 pmid:25928297 pmcid:PMC4424572 fatcat:w3t3ewftebdf7hgnbd2fgli6he

Scalable Biophysical Simulations of the Neuromuscular System [article]

Benjamin Maier
2021 arXiv   pre-print
We implemented a comprehensive, state-of-the-art, multi-scale multi-physics model framework that can simulate surface EMG signals and muscle contraction as a result of neuromuscular stimulation.  ...  enables us to simulate muscular surface EMG of the biceps brachii muscle with realistic muscle fiber counts of several hundred thousands.  ...  from small-sized cluster model problems to realistic simulations on HPC clusters" [Röh17] .  ... 
arXiv:2107.07104v1 fatcat:i5simmhifbgjdpcsm6l73vc3pe

Poster Session

2018 Biomedical Engineering  
A precise analysis of pressure progression requires a continuous data transmission from the implant to the reader unit with a data rate of at least 26 Kbit/s.  ...  A bi-directional data transmission between a reader unit and the implant is needed, in order to control the state of the implant.  ...  This procedure is promising an innovative approach which will be screen in a further study.  ... 
doi:10.1515/bmt-2018-6051 fatcat:4yiodooz5jcafnyjzdjq4f3c2m

Numerical Stabilization of the Melt Front for Laser Beam Cutting [chapter]

Torsten Adolph, Willi Schönauer, Markus Niessen, Wolfgang Schulz
2010 Numerical Mathematics and Advanced Applications 2009  
The model is based on Navier-Stokes equations for viscous incompressible flow and convection-diffusion equation describing pollution transport.  ...  We develop a hybrid scheme consisting of a combination of a second order MUSCL scheme and a high order finite difference scheme.  ...  The results show the scalability of the proposed NKS Bidomain solver in terms of both nonlinear and linear iterations, in both cartesian slabs and ellipsoidal cardiac domains.  ... 
doi:10.1007/978-3-642-11795-4_6 fatcat:nx4nvuxaxfbcdjknopny53ck5e

Evaluation of a rapid anisotropic model for ECG simulation

Simone Pezzuto, Peter Kal'avský, Mark Potse, Frits W Prinzen, Angelo Auricchio, Rolf Krause
Both solvers were implemented on graphics processing units and massively parallelized. We studied the numerical convergence and scalability of the approach.  ...  Both solvers were implemented on graphics processing units and massively parallelized. We studied the numerical convergence and scalability of the approach.  ...  ACKNOWLEDGMENTS The authors sincerely thank Hanspeter Fischer of Biosense Webster for his contribution in data acquisition and for making the data available for offline analysis.  ... 
doi:10.5167/uzh-145498 fatcat:rzwjgfnitreuncjyup2jwaauny

VBARMS: A variable block algebraic recursive multilevel solver for sparse linear systems

Bruno Carpentieri, Jia Liao, Masha Sosonkina
2014 Journal of Computational and Applied Mathematics  
In the past decades, the world went through a very exciting phase on computer hardware, passing from single core Central Processing Unit (CPU) to multiple-core CPU, and from CPU to Graphics Processing  ...  energy, three components of the scaled velocity, and the turbulence transport variable) assigned to each node of the computational mesh; a bidomain system in cardiac electrical dynamics couples the intra-and  ...  I would like to thank my colleagues at University of Groningen for providing a positive work environment and pleasant interactions.  ... 
doi:10.1016/ fatcat:f46hhcxkyjcxripop7eb7t3iem

ScopeandObjectives P1 Modelling the neural adjustments in muscle fatigue

Dario, Fulvia Taddei
2009 unpublished
The use of mathematical modeling and Computer simulation for the study and prediction of biological and biomedical processes is growing, covering all aspects of biology, physiology and pathology from the  ...  (Physiome, Virtual Physiological Human, Integrative Biology, etc.) where predictive models describe disparate physiological or pathological sub-processes and are combined to obtain a more systemic understanding  ...  Conclusion We successfully implemented a fully 3-D FE model for the growth of a fusiform aneurysms.  ... 

Parallel-streaming algorithms for solving partial differential equations on unstructured meshes

Zhisong Fu
Fourth, we propose a parallel algorithm for solving the levelset equation on fully unstructured 2D or 3D meshes or manifolds.  ...  processes.  ...  Commodity multimedia processors such as the IBM Cell and graphics processing units (GPUs) are considered forerunners of this trend.  ... 
doi:10.26053/0h-6yar-yyg0 fatcat:iq4j4mbtefbozfb4g24oxxfsfe