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Simulation of cardiac electrical activity using the bi-domain equations can be a massively computationally demanding problem. This study provides a comprehensive guide to numerical bi-domain modelling. Each component of bi-domain simulations--discretization, ODE-solution, linear system solution, and parallelization--is discussed, and previously-used methods are reviewed, new methods are proposed, and issues which cause particular difficulty are highlighted. Particular attention is paid to the choice of stimulus currents, compatibility conditions for the equations, the solution of singular linear systems, and convergence of the numerical scheme.
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http://dx.doi.org/10.1016/j.pbiomolbio.2010.05.006 | DOI Listing |
Math Biosci
September 2023
Department of Mathematics, University of Toronto, Toronto, ON, M5S 2E4, Canada. Electronic address:
We present a detailed physiological model of the (human) retina that includes the biochemistry and electrophysiology of phototransduction, neuronal electrical coupling, and the spherical geometry of the eye. The model is a parabolic-elliptic system of partial differential equations based on the mathematical framework of the bi-domain equations, which we have generalized to account for multiple cell-types. We discretize in space with non-uniform finite differences and step through time with a custom adaptive time-stepper that employs a backward differentiation formula and an inexact Newton method.
View Article and Find Full Text PDFJ Neurosci Methods
October 2017
Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India. Electronic address:
Background: Computational modeling of biological cells usually ignores their extracellular fields, assuming them to be inconsequential. Though such an assumption might be justified in certain cases, it is debatable for networks of tightly packed cells, such as in the central nervous system and the syncytial tissues of cardiac and smooth muscle.
New Method: In the present work, we demonstrate a technique to couple the extracellular fields of individual cells within the NEURON simulation environment.
Phys Med Biol
May 2012
LMAC, GI, University of Technology of Compiègne (UTC), Royallieu, BP 20529, 60205 Compiègne, France. INRIA Paris-Rocquencourt, BP 105, 78153 Le Chesnay, France.
This paper addresses a complex multi-physical phenomenon involving cardiac electrophysiology and hemodynamics. The purpose is to model and simulate a phenomenon that has been observed in magnetic resonance imaging machines: in the presence of a strong magnetic field, the T-wave of the electrocardiogram (ECG) gets bigger, which may perturb ECG-gated imaging. This is due to a magnetohydrodynamic (MHD) effect occurring in the aorta.
View Article and Find Full Text PDFProg Biophys Mol Biol
September 2010
Oxford University Computing Laboratory, Wolfson Building, Parks Road, Oxford OX13QD, UK.
Simulation of cardiac electrical activity using the bi-domain equations can be a massively computationally demanding problem. This study provides a comprehensive guide to numerical bi-domain modelling. Each component of bi-domain simulations--discretization, ODE-solution, linear system solution, and parallelization--is discussed, and previously-used methods are reviewed, new methods are proposed, and issues which cause particular difficulty are highlighted.
View Article and Find Full Text PDFBiophys J
April 2006
Oxford University Computing Laboratory, Oxford, United Kingdom.
Fluorescent photon scattering is known to distort optical recordings of cardiac transmembrane potentials; however, this process is not well quantified, hampering interpretation of experimental data. This study presents a novel model, which accurately synthesizes fluorescent recordings over the irregular geometry of the rabbit ventricles. Using the model, the study aims to provide quantification of fluorescent signal distortion for different optical characteristics of the preparation and of the surrounding medium.
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