Numerical modeling of cardiac electrophysiology at the cellular scale

Project Information

MICROCARD

Grant agreement ID: 955495

DOI 10.3030/955495

Project closed

EC signature date 18 December 2020

Start date 1 April 2021

End date 30 September 2024

Funded under

• INDUSTRIAL LEADERSHIP - Leadership in enabling and industrial technologies - Information and Communication Technologies (ICT)

Total cost € 5 858 546,25

EU contribution € 2 777 053,32

Coordinated by

UNIVERSITE DE BORDEAUX
France

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Deliverables

Documents, reports (9)

Report on task-based parallelization

Publication of a report on task-based parallelization.

Report on MPI communication optimization

Publication of a report on optimization of MPI communication in the code.

Report on the sustainable roadmap for MICROCARD platform and software

Publication of a report on the sustainable roadmap for the MICROCARD platform and software.

A Software Management Plan for the HPC simulation platform μ CARP

Creation of a Software Management Plan for the HPC simulation platform CARP

Results of the surveys conducted in M18 and M36 on ease of use of the cloud-based web platform

Publication of a report on the results of the surveys conducted in M18 and M36 on ease of use of the cloud-based web platform

Linear solver development and performance assessment report

Publication of a report on the development of linear solvers and an assessment of their performance

Report on High-Performance Data Output

Publication of a report on High-Performance Data Output

Report on automatic checkpoint placement strategy

Publication of a report on automatic checkpoint placement strategy in the code

Report on the implemented DevOps toolchain as a best-practice example

Demonstrators, pilots, prototypes (2)

Linear solver application integration proof

Demonstration of the application of the newly integrated linear solver(s).

Resilient parallelization support

Prototype of the code with task-based parallellization that is resilient to hardware failures.

Open Research Data Pilot (1)

Online publication of the use cases

Posts on the use cases intended for a large audience, on the project website.

Publications

Peer reviewed articles (18)

A comparison of Algebraic Multigrid Bidomain solvers on hybrid CPU–GPU architectures

Author(s): Edoardo Centofanti, Simone Scacchi
Published in: Computer Methods in Applied Mechanics and Engineering, Issue 423, 2024, Page(s) 116875, ISSN 0045-7825
Publisher: Elsevier BV
DOI: 10.1016/j.cma.2024.116875

Explicit stabilized multirate methods for the monodomain model in cardiac electrophysiology

Author(s): Giacomo Rosilho de Souza, Marcus Grote, Simone Pezzuto, Rolf Krause
Published in: ESAIM: Mathematical Modelling and Numerical Analysis, 2024, ISSN 2822-7840
Publisher: edpsciences
DOI: 10.1051/m2an/2024030

A Review of Healthy and Fibrotic Myocardium Microstructure Modeling and Corresponding Intracardiac Electrograms

Author(s): Sánchez, J.; Loewe, A.
Published in: Frontiers in Physiology, 2022, ISSN 1664-042X
Publisher: Frontiers Research Foundation
DOI: 10.3389/fphys.2022.908069

Scalable and Robust Dual-Primal Newton–Krylov Deluxe Solvers for Cardiac Electrophysiology with Biophysical Ionic Models

Author(s): Ngoc Mai Monica Huynh; Luca F. Pavarino; Simone Scacchi
Published in: Vietnam Journal of Mathematics, Issue 50, 2022, ISSN 2305-221X
Publisher: Springer Science + Business Media
DOI: 10.1007/s10013-022-00576-1

Boundary integral formulation of the cell-by-cell model of cardiac electrophysiology

Author(s): Giacomo Rosilho de Souza, Rolf Krause, Simone Pezzuto
Published in: Engineering Analysis with Boundary Elements, Issue 158, 2023, Page(s) 239-251, ISSN 0955-7997
Publisher: Pergamon Press Ltd.
DOI: 10.1016/j.enganabound.2023.10.021

Characterization of the pace-and-drive capacity of the human sinoatrial node: A 3D in silico study

Author(s): Antoine Amsaleg; Jorge Sánchez; Ralf Mikut; Axel Loewe
Published in: Biophysical Journal, Issue 121, 2022, Page(s) 4247–4259, ISSN 0006-3495
Publisher: Biophysical Society
DOI: 10.1016/j.bpj.2022.10.020

Unexpected impairment of INa underpins reentrant arrhythmias in a knock-in swine model of Timothy syndrome

Author(s): Andreu Porta-Sánchez, Andrea Mazzanti, Carmen Tarifa, Deni Kukavica, Alessandro Trancuccio, Muhammad Mohsin, Elisa Zanfrini, Andrea Perota, Roberto Duchi, Kevin Hernandez-Lopez, Miguel Eduardo Jáuregui-Abularach, Valerio Pergola, Eugenio Fernandez, Rossana Bongianino, Elisa Tavazzani, Patrick Gambelli, Mirella Memmi, Simone Scacchi, Luca F. Pavarino, Piero Colli Franzone, Giovanni Lentini, David
Published in: Nature Cardiovascular Research, Issue 2, 2023, Page(s) 1291-1309, ISSN 2731-0590
Publisher: Springer Nature
DOI: 10.1038/s44161-023-00393-w

A Survey of General-purpose Polyhedral Compilers

Author(s): Arun Thangamani, Vincent Loechner, Stéphane Genaud
Published in: ACM Transactions on Architecture and Code Optimization, 2024, ISSN 1544-3566
Publisher: Association for Computing Machinary, Inc.
DOI: 10.1145/3674735

Epicardial Dispersion of Repolarization Promotes the Onset of Reentry in Brugada Syndrome: A Numerical Simulation Study

Author(s): Simone Scacchi, Piero Colli Franzone, Luca F. Pavarino, Vincenzo Gionti, Cesare Storti
Published in: Bulletin of Mathematical Biology, Issue 85, 2023, ISSN 0092-8240
Publisher: Academic Press
DOI: 10.1007/s11538-023-01124-9

The openCARP CDEConcept for and implementation of a sustainable collaborativedevelopment environment for research software

Author(s): Felix Bach, Jochen Klar, Axel Loewe, Jorge Sánchez, Gunnar Seemann, Yung-Lin Huang, Robert Ulrich
Published in: Bausteine Forschungsdatenmanagement, Issue Nr.1, 2022, ISSN 2626-7489
Publisher: Marburg: Philipps-Universität
DOI: 10.17192/bfdm.2022.1.8368

À quoi servent les ordinateurs les plus puissants au monde ? Un exemple en cardiologie.

Author(s): Emmanuelle Saillard; Mark Potse
Published in: The Conversation, 2022, ISSN 2431-2134
Publisher: The Conversation Media Group

The role of pulse timing in cardiac defibrillation

Author(s): Joshua Steyer, Thomas Lilienkamp, Stefan Luther, Ulrich Parlitz
Published in: Frontiers in Network Physiology, Issue 2, 2023, ISSN 2674-0109
Publisher: Frontiers
DOI: 10.3389/fnetp.2022.1007585

Attractor selection in nonlinear oscillators by temporary dual-frequency driving

Author(s): Péter Krähling, Joshua Steyer, Ulrich Parlitz, Ferenc Hegedűs
Published in: Nonlinear Dynamics, Issue 111, 2024, Page(s) 19209-19224, ISSN 0924-090X
Publisher: Kluwer Academic Publishers
DOI: 10.1007/s11071-023-08855-3

Evaluating computational efforts and physiological resolution of mathematical models of cardiac tissue

Author(s): Karoline Horgmo Jæger, James D. Trotter, Xing Cai, Hermenegild Arevalo, Aslak Tveito
Published in: Scientific Reports, Issue 14, 2024, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-024-67431-w

Editorial: Atrial Fibrillation: Technology for Diagnosis, Monitoring, and Treatment

Author(s): Omer Berenfeld, Valentina D. A. Corino, Axel Loewe, Juan Pablo Martínez and Jose F. Rodriguez Matas
Published in: Frontiers in Physiology, 2022, ISSN 1664-042X
Publisher: Frontiers Research Foundation
DOI: 10.3389/fphys.2022.848096

Resource-Efficient Use of Modern Processor Architectures For Numerically Solving Cardiac Ionic Cell Models

Author(s): Kristian Gregorius Hustad; Xing Cai
Published in: Frontiers in Physiology, 2022, ISSN 1664-042X
Publisher: Frontiers Research Foundation
DOI: 10.3389/fphys.2022.904648

Convergence Analysis of BDDC Preconditioners for Composite DG Discretizations of the Cardiac Cell-By-Cell Model

Author(s): Ngoc Mai Monica Huynh, Fatemeh Chegini, Luca Franco Pavarino, Martin Weiser, Simone Scacchi
Published in: SIAM Journal on Scientific Computing, Issue 45, 2023, Page(s) A2836-A2857, ISSN 1064-8275
Publisher: Society for Industrial and Applied Mathematics
DOI: 10.1137/22m1542532

Fibrotic Remodeling during Persistent Atrial Fibrillation: In Silico Investigation of the Role of Calcium for Human Atrial Myofibroblast Electrophysiology

Author(s): Jorge Sánchez , Beatriz Trenor, Javier Saiz, Olaf Dössel and Axel Loewe
Published in: Cells, Issue 10, 2021, ISSN 2073-4409
Publisher: MDPI
DOI: 10.3390/cells10112852

Conference proceedings (2)

Parallel nonlinear solvers in computational cardiac electrophysiology

Author(s): Nicolas Alejandro BARNAFI; Ngoc Mai Monica HUYNH; Luca Franco PAVARINO; Simone SCACCHI
Published in: IFAC-PapersOnLine, 2022
Publisher: Elsevier
DOI: 10.1016/j.ifacol.2022.09.093

Combining Uncore Frequency and Dynamic Power Capping to Improve Power Savings

Author(s): Amina Guermouche
Published in: 2022 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW), 2022, ISBN 978-1-6654-9748-0
Publisher: IEEE
DOI: 10.1109/ipdpsw55747.2022.00164