Explicit stabilized multirate methods for the monodomain model in cardiac electrophysiology DOI
Giacomo Rosilho de Souza, Marcus J. Grote, Simone Pezzuto

et al.

ESAIM. Mathematical modelling and numerical analysis, Journal Year: 2024, Volume and Issue: unknown

Published: April 23, 2024

Fully explicit stabilized multirate (mRKC) methods are well-suited for the numerical solution of large multiscale systems stiff ordinary differential equations thanks to their improved stability properties. To demonstrate efficiency stiff, multiscale, nonlinear parabolic PDE's, we apply mRKC monodomain equation from cardiac electrophysiology. In doing so, propose an version, specifically tailored model, which leads exponential (emRKC) method. Several experiments conducted evaluate both and emRKC, while taking into account different finite element meshes (structured unstructured) realistic ionic models. The new emRKC method typically outperforms a standard implicit-explicit baseline Code profiling strong scalability results further that is faster inherently parallel without sacrificing accuracy.

Language: Английский

Modeling Excitable Cells with the EMI Equations: Spectral Analysis and Iterative Solution Strategy DOI Creative Commons
Pietro Benedusi, Paola Ferrari, Marie E. Rognes

et al.

Journal of Scientific Computing, Journal Year: 2024, Volume and Issue: 98(3)

Published: Feb. 4, 2024

Abstract In this work, we are interested in solving large linear systems stemming from the extra–membrane–intra model, which is employed for simulating excitable tissues at a cellular scale. After setting related of partial differential equations equipped with proper boundary conditions, provide its finite element discretization and focus on resulting systems. We first give relatively complete spectral analysis using tools theory Generalized Locally Toeplitz matrix sequences. The obtained information used designing appropriate preconditioned Krylov solvers. Through numerical experiments, show that presented solution strategy robust w.r.t. problem parameters, efficient scalable.

Language: Английский

Citations

10
A Splitting, Discontinuous Galerkin Solver for the Cell-by-Cell Electroneutral Nernst–Planck Framework DOI
Ada J. Ellingsrud, Pietro Benedusi, Miroslav Kuchta

et al.

SIAM Journal on Scientific Computing, Journal Year: 2025, Volume and Issue: 47(2), P. B477 - B504

Published: April 1, 2025

Language: Английский

Citations

1
Evaluating computational efforts and physiological resolution of mathematical models of cardiac tissue DOI Creative Commons
Karoline Horgmo Jæger, James Trotter, Xing Cai

et al.

Scientific Reports, Journal Year: 2024, Volume and Issue: 14(1)

Published: July 23, 2024

Computational techniques have significantly advanced our understanding of cardiac electrophysiology, yet they predominantly concentrated on averaged models that do not represent the intricate dynamics near individual cardiomyocytes. Recently, accurate representing cells gained popularity, enabling analysis electrophysiology at micrometer level. Here, we evaluate five mathematical to determine their computational efficiency and physiological fidelity. Our findings reveal cell-based introduced in recent literature offer both precision for simulating small tissue samples (comprising thousands cardiomyocytes). Conversely, traditional bidomain model its simplified counterpart, monodomain model, are more appropriate larger masses (encompassing millions billions For simulations requiring detailed parameter variations along cell membranes, EMI emerges as only viable choice. This distinctively accounts extracellular (E), membrane (M), intracellular (I) spaces, providing a comprehensive framework studies. Nonetheless, model's applicability large-scale tissues is limited by substantial demands subcellular resolution.

Language: Английский

Citations

7
Algebraic Multigrid Methods for Metric-Perturbed Coupled Problems DOI

Ana Budiša,

Xiaozhe Hu, Miroslav Kuchta

et al.

SIAM Journal on Scientific Computing, Journal Year: 2024, Volume and Issue: 46(3), P. A1461 - A1486

Published: May 2, 2024

.We develop multilevel methods for interface-driven multiphysics problems that can be coupled across dimensions and where complexity strength of the interface coupling deteriorates performance standard methods. We focus on aggregation-based algebraic multigrid with custom smoothers preserve information each coarse level. prove that, proper choice subspace splitting, we obtain uniform convergence in discretization physical parameters two-level setting. Additionally, show parameter robustness scalability regard to number degrees freedom system several numerical examples related biophysical processes brain, namely, electric signaling excitable tissue modeled by bidomain, extracellular-membrane-intracellular (EMI) model, reduced EMI equations.Reproducibility computational results.This paper has been awarded "SIAM Reproducibility Badge: Code data available" as a recognition authors have followed reproducibility principles valued SISC scientific computing community. allow readers reproduce results this are available at https://github.com/anabudisa/metric-amg-examples supplementary materials (metric-amg-examples-master.zip [30KB]).Keywordsalgebraic methodpreconditioningiterative methodcoupled problemsgraph LaplacianMSC codes65F0865N5565S05

Language: Английский

Citations

6
Scalable Approximation and Solvers for Ionic Electrodiffusion in Cellular Geometries DOI
Pietro Benedusi, Ada J. Ellingsrud, Halvor Herlyng

et al.

SIAM Journal on Scientific Computing, Journal Year: 2024, Volume and Issue: 46(5), P. B725 - B751

Published: Oct. 16, 2024

Language: Английский

Citations

4
Determining properties of human‐induced pluripotent stem cell‐derived cardiomyocytes using spatially resolved electromechanical metrics DOI Creative Commons
Karoline Horgmo Jæger, Verena Charwat, Kevin E. Healy

et al.

The Journal of Physiology, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 17, 2025

Abstract Human‐induced pluripotent stem cell‐derived cardiomyocytes (hiPSC‐CMs) are increasingly important in preclinical drug assessments, particularly for identifying potential cardiotoxicity. In this study, we utilize data from microphysiological systems of hiPSC‐CMs to evaluate cellular characteristics, such as action duration, beat rate, conduction velocity and mechanical displacement. Based on these data, high‐fidelity mathematical models facilitate precise assessments critical biophysical parameters the cells, including membrane ion channel conductances, cross‐bridge cycle transition rates cell‐to‐cell conductance. We emphasize distinction between synchronized transients travelling waves, highlighting their implications deducing properties hiPSC‐CMs. analyse effects compounds flecainide, quinidine, nifedipine, verapamil, blebbistatin omecamtiv. Our findings show that drug‐induced changes describing currents contractile machinery close ranges reported literature, computed biomarkers align well with measured biomarkers. This study is first apply spatially resolved, cell‐based identify through measurements transmembrane displacement, marking a significant step forward using computational evaluating safety offering new approach early identification adverse reactions. image Key points Optical human‐induced present opportunities advance understanding how human heart cells function interact. Although direct optical yield valuable biomarkers, they fall short revealing underlying properties, example, novel perturb channels. Drug best understood capture cell dynamics based physical laws. Traditionally, have been averaged over all collections, thus overlooking spatiotemporal waves. Here, use recently developed models, representing spatial electrical coupling, determine collections

Language: Английский

Citations

0
Parallel Algebraic Multigrid Solvers for Composite Discontinuous Galerkin Discretization of the Cardiac EMI Model in Heterogeneous Media DOI Creative Commons
Edoardo Centofanti, Ngoc Mai Monica Huynh, Luca F. Pavarino

et al.

Computer Methods in Applied Mechanics and Engineering, Journal Year: 2025, Volume and Issue: 442, P. 118001 - 118001

Published: April 24, 2025

Language: Английский

Citations

0
The simplified Kirchhoff network model (SKNM): a cell-based reaction–diffusion model of excitable tissue DOI Creative Commons
Karoline Horgmo Jæger, Aslak Tveito

Scientific Reports, Journal Year: 2023, Volume and Issue: 13(1)

Published: Sept. 30, 2023

Abstract Cell-based models of excitable tissues offer the advantage cell-level precision, which cannot be achieved using traditional homogenized electrophysiological models. However, this enhanced accuracy comes at cost increased computational demands, necessitating development efficient cell-based The widely-accepted bidomain model serves as standard in cardiac electrophysiology, and under certain anisotropy ratio conditions, it is well known that can reduced to simpler monodomain model. Recently, Kirchhoff Network Model (KNM) was developed a counterpart In paper, we aim demonstrate KNM simplified same steps employed derive from We present Simplified (SKNM), produces results closely aligned with those while requiring significantly less resources.

Language: Английский

Citations

8
An explicit local space-time adaptive framework for monodomain models in cardiac electrophysiology DOI Creative Commons
Dennis Ogiermann, Daniel Balzani, Luigi E. Perotti

et al.

Computer Methods in Applied Mechanics and Engineering, Journal Year: 2024, Volume and Issue: 422, P. 116806 - 116806

Published: Feb. 7, 2024

We present a new explicit local space–time adaptive framework to decrease the time required for monodomain simulations cardiac electrophysiology. Based on localized structure of steep activation wavefront in solutions problems, proposed adopts small steps and tree-based mesh refinement scheme only regions necessary resolve these structures. The step adaptation selection process is fully controlled by combination error indicators. main contributions this work consist introduction primal symmetric interior penalty formulation model an efficient algorithmic strategy manage stepping its temporal discretization. In first serial implementation framework, we report that our between 50% 95% faster (in wall clock time) compared optimized commonly used numerical without significant loss solution accuracy, showing promising candidate accelerate Preliminary studies parallel version alongside novel load balancing are found appendix show that, although scaling limited, remains than classic operator splitting scheme.

Language: Английский

Citations

1
GDSW preconditioners for composite Discontinuous Galerkin discretizations of multicompartment reaction–diffusion problems DOI Creative Commons
Ngoc Mai Monica Huynh, Luca F. Pavarino, Simone Scacchi

et al.

Computer Methods in Applied Mechanics and Engineering, Journal Year: 2024, Volume and Issue: 433, P. 117501 - 117501

Published: Nov. 4, 2024

Language: Английский

Citations

1