MICROCARD

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MICROCARD Publications

preprints

Fritz Göbel, Ngoc Mai Monica Huynh, Fatemeh Chegini, Luca Franco Pavarino, Martin Weiser, Simone Scacchi, and Hartwig Anzt. A BDDC Preconditioner for the Cardiac EMI Model in Three Dimensions.
SIAM SISC, arXiv:2502.07722, 2025. (preprint) [pdf] [link] [bibtex] [arxiv]

@inproceedings{goebel:sisc25,
 author = {G{\"o}bel, Fritz and Huynh, Ngoc Mai Monica and Chegini, Fatemeh and Pavarino, Luca Franco and Weiser, Martin and Scacchi, Simone and Anzt, Hartwig},
 booktitle = {SIAM SISC},
 pdf = {https://arxiv.org/pdf/2502.07722.pdf},
 title = {A {BDDC} Preconditioner for the Cardiac {EMI} Model
in Three Dimensions},
 url = {https://arxiv.org/abs/2502.07722},
 year = {2025}
}

Giacomo Rosilho de Souza, Simone Pezzuto, and Rolf Krause. High-order parallel-in-time method for the monodomain equation in cardiac electrophysiology.
arXiv:2405.19994, May 2024. (preprint) [pdf] [link] [bibtex] [arxiv]

@article{rosilho_pint,
 author = {Rosilho de Souza, Giacomo and Pezzuto, Simone and Krause, Rolf},
 month = {May},
 pdf = {https://arxiv.org/pdf/2405.19994.pdf},
 title = {High-order parallel-in-time method for the monodomain equation in cardiac electrophysiology},
 url = {https://arxiv.org/abs/2405.19994},
 year = {2024}
}

book chapters

Marie Houillon, Jochen Klar, Tomas Stary, and Axel Loewe. Automated Software Metadata Conversion and Publication Based on CodeMeta.
E-Science-Tage 2023: Empower Your Research – Preserve Your Data, pp. 228–234, heiBOOKS, November 2023. [link] [bibtex]

@inbook{Houillon_Klar_Stary_Loewe_2023,
 author = {Houillon, Marie and Klar, Jochen and Stary, Tomas and Loewe, Axel},
 booktitle = {E-Science-Tage 2023: Empower Your Research – Preserve Your Data},
 doi = {10.11588/heibooks.1288.c18081},
 editor = {Heuveline, Vincent and Bisheh, Nina and Kling, Philipp},
 month = {November},
 pages = {228–234},
 publisher = {heiBOOKS},
 title = {Automated Software Metadata Conversion and Publication Based on {CodeMeta}},
 url = {https://dx.doi.org/10.11588/heibooks.1288.c18081},
 year = {2023}
}

journal articles

Edoardo Centofanti, Ngoc Mai Monica Huynh, and Luca F. Pavarino. Parallel Algebraic Multigrid Solvers for Composite Discontinuous Galerkin Discretization of the Cardiac EMI Model in Heterogeneous Media.
Comp. Meth. Appl. Mech. Engnrng., vol. 442, article nr. 118001, 2025. [link] [bibtex]

@article{centofanti25,
 article_number = {118001},
 author = {Centofanti, Edoardo and Huynh, Ngoc Mai Monica and Pavarino, Luca F.},
 doi = {10.1016/j.cma.2025.118001},
 journal = {Comp. Meth. Appl. Mech. Engnrng.},
 pages = {118001},
 title = {Parallel Algebraic Multigrid Solvers for Composite
Discontinuous {Galerkin} Discretization of the
Cardiac {EMI} Model in Heterogeneous Media},
 url = {https://dx.doi.org/10.1016/j.cma.2025.118001},
 volume = {442},
 year = {2025}
}

Axel Loewe, Peter J. Hunter, and Peter Kohl. Computational modelling of biological systems now and then: revisiting tools and visions from the beginning of the century.
Philosophical Transactions A of the Royal Society, vol. 383, no. 2296, pp. 20230384, May 2025. [link] [bibtex]

@article{Millenium,
 author = {Loewe, Axel and Hunter, Peter J. and Kohl, Peter},
 doi = {10.1098/rsta.2023.0384},
 journal = {Philosophical Transactions A of the Royal Society},
 month = {May},
 number = {2296},
 pages = {20230384},
 title = {Computational modelling of biological systems now and then: revisiting tools and visions from the beginning of the century},
 url = {https://dx.doi.org/10.1098/rsta.2023.0384},
 volume = {383},
 year = {2025}
}

Moritz Linder, Tomas Stary, Gergő Bitay, Norbert Nagy, and Axel Loewe. Sympathetic Stimulation Can Compensate for Hypocalcaemia-Induced Bradycardia in Human and Rabbit Sinoatrial Node Cells.
The Journal of Physiology, 2025. (epub ahead) [link] [bibtex]

@article{Linder2024.08.30.610432,
 author = {Linder, Moritz and Stary, Tomas and Bitay, Gerg{\H o} and Nagy, Norbert and Loewe, Axel},
 doi = {10.1113/JP287557},
 journal = {The Journal of Physiology},
 title = {Sympathetic Stimulation Can Compensate for Hypocalcaemia-Induced Bradycardia in Human and Rabbit Sinoatrial Node Cells},
 url = {https://doi.org/10.1113/JP287557},
 year = {2025}
}

C. Barrios Espinosa, J. Sánchez, S. Appel, S. Becker, J. Krauß, P. Martínez Díaz, L. Unger, Marie Houillon, and Axel Loewe. A Cyclical Fast Iterative Method for Simulating Reentries in Cardiac Electrophysiology Using an Eikonal-Based Model.
Engineering with Computers, arXiv:2406.18619, June 2025. (epub ahead) [link] [bibtex] [arxiv]

@article{espinosa2024cyclicalfastiterativemethod,
 author = {C. Barrios Espinosa and J. Sánchez and S. Appel and S. Becker and J. Krauß and P. Martínez Díaz and L. Unger and Marie Houillon and Axel Loewe},
 doi = {10.1007/s00366-024-02094-9},
 journal = {Engineering with Computers},
 month = {June},
 primaryclass = {physics.med-ph},
 title = {A Cyclical Fast Iterative Method for Simulating Reentries in Cardiac Electrophysiology Using an Eikonal-Based Model},
 url = {https://doi.org/10.1007/s00366-024-02094-9},
 year = {2025}
}

Vincent Alba, Olivier Aumage, Denis Barthou, Marie-Christine Counilh, and Amina Guermouche. Performance portability of generated cardiac simulation kernels through automatic dimensioning and load balancing on heterogeneous nodes.
Journal of Supercomputing, vol. 81, article nr. 1047, 2025. (extended conference paper) [link] [bibtex]

@article{alba25,
 article_number = {1047},
 author = {Alba, Vincent and Aumage, Olivier and Barthou, Denis and Counilh, Marie-Christine and Guermouche, Amina},
 doi = {10.1007/s11227-025-07510-5},
 journal = {Journal of Supercomputing},
 title = {Performance portability of generated cardiac
simulation kernels through automatic dimensioning
and load balancing on heterogeneous nodes},
 url = {https://dx.doi.org/10.1007/s11227-025-07510-5},
 volume = {81},
 year = {2025}
}

Nicolás A Barnafi, Ngoc Mai Monica Huynh, Luca F Pavarino, and Simone Scacchi. Robust parallel nonlinear solvers for implicit time discretizations of the Bidomain equations with staggered ionic models.
Computers & Mathematics with Applications, vol. 167, pp. 134–149, 2024. [pdf] [link] [bibtex]

@article{barnafi2022robust,
 author = {Barnafi, Nicol{\'a}s A and Huynh, Ngoc Mai Monica and Pavarino, Luca F and Scacchi, Simone},
 doi = {10.1016/j.camwa.2024.04.014},
 journal = {Computers & Mathematics with Applications},
 pages = {134-149},
 pdf = {https://arxiv.org/pdf/2209.05193},
 title = {Robust parallel nonlinear solvers for implicit time
discretizations of the Bidomain equations with
staggered ionic models},
 url = {https://dx.doi.org/10.1016/j.camwa.2024.04.014},
 volume = {167},
 year = {2024}
}

Karoline Jæger, James Trotter, Xing Cai, Hermenegild Arevalo, and Aslak Tveito. Evaluating computational efforts and physiological resolution of mathematical models of cardiac tissue.
Scientific Reports, vol. 13, pp. 16954, July 2024. [link] [bibtex]

@article{Jæger24_scirep,
 author = {Jæger, Karoline and Trotter, James and Cai, Xing and Arevalo, Hermenegild and Tveito, Aslak},
 doi = {10.1038/s41598-024-67431-w},
 journal = {Scientific Reports},
 month = {July},
 pages = {16954},
 title = {Evaluating computational efforts and physiological
resolution of mathematical models of cardiac tissue},
 url = {https://dx.doi.org/10.1038/s41598-024-67431-w},
 volume = {13},
 year = {2024}
}

Arun Thangamani, Vincent Loechner, and Stéphane Genaud. A Survey of General-purpose Polyhedral Compilers.
ACM Trans. Archit. Code Optim., Association for Computing Machinery, New York, NY, USA, June 2024. (Just Accepted) [link] [bibtex] [abstract]
```
@article{10.1145/3674735,
 address = {New York, NY, USA},
 author = {Thangamani, Arun and Loechner, Vincent and Genaud, St\'{e}phane},
 doi = {10.1145/3674735},
 journal = {ACM Trans. Archit. Code Optim.},
 month = {June},
 publisher = {Association for Computing Machinery},
 title = {A Survey of General-purpose Polyhedral Compilers},
 url = {https://doi.org/10.1145/3674735},
 year = {2024}
}
```
abstract: Since the 1990’s many implementations of polyhedral compilers have been written and distributed, either as source-to-source translating compilers or integrated into wider purpose compilers. This paper provides a survey on those various available implementations as of today, 2024. We list and describe most commonly available polyhedral schedulers and compiler implementations. Then, we compare the general-purpose polyhedral compilers using two main criteria, robustness and performance, on the PolyBench/C set of benchmarks.
Edoardo Centofanti and Simone Scacchi. A comparison of Algebraic Multigrid Bidomain solvers on hybrid CPU–GPU architectures.
Computer Methods in Applied Mechanics and Engineering, vol. 423, pp. 116875, 2024. [link] [bibtex] [abstract]
```
@article{CENTOFANTI2024116875,
 author = {Edoardo Centofanti and Simone Scacchi},
 doi = {https://doi.org/10.1016/j.cma.2024.116875},
 journal = {Computer Methods in Applied Mechanics and Engineering},
 pages = {116875},
 title = {A comparison of Algebraic Multigrid Bidomain solvers on hybrid CPU–GPU architectures},
 url = {https://www.sciencedirect.com/science/article/pii/S0045782524001312},
 volume = {423},
 year = {2024}
}
```
abstract: The numerical simulation of cardiac electrophysiology is a highly challenging problem in scientific computing. The Bidomain system is the most complete mathematical model of cardiac bioelectrical activity. It consists of an elliptic and a parabolic partial differential equation (PDE), of reaction–diffusion type, describing the spread of electrical excitation in the cardiac tissue. The two PDEs are coupled with a stiff system of ordinary differential equations (ODEs), representing ionic currents through the cardiac membrane. Developing efficient and scalable preconditioners for the linear systems arising from the discretization of such computationally challenging model is crucial in order to reduce the computational costs required by the numerical simulations of cardiac electrophysiology. In this work, focusing on the Bidomain system as a model problem, we have benchmarked two popular implementations of the Algebraic Multigrid (AMG) preconditioner embedded in the PETSc library and we have studied the performance on the calibration of specific parameters. We have conducted our analysis on modern HPC architectures, performing scalability tests on multi-core and multi-GPUs settings. The results have shown that, for our problem, although scalability is verified on CPUs, GPUs are the optimal choice, since they yield the best performance in terms of solution time.

Giacomo Rosilho de Souza, Marcus Grote, Simone Pezzuto, and Rolf Krause. Explicit stabilized multirate methods for the monodomain model in cardiac electrophysiology.
ESAIM: Mathematical Modelling and Numerical Analysis, arXiv:2401.01745, April 2024. (to appear) [link] [bibtex] [arxiv]

@article{rosilho_emRKC,
 author = {Rosilho de Souza, Giacomo and Grote, Marcus and Pezzuto, Simone and Krause, Rolf},
 doi = {10.1051/m2an/2024030},
 journal = {ESAIM: Mathematical Modelling and Numerical Analysis},
 month = {April},
 title = {Explicit stabilized multirate methods for the monodomain model in cardiac electrophysiology},
 url = {https://doi.org/10.1051/m2an/2024030},
 year = {2024}
}

Giacomo Rosilho de Souza, Rolf Krause, and Simone Pezzuto. Boundary Integral Formulation of the Cell-by-Cell Model of Cardiac Electrophysiology.
Engineering Analysis with Boundary Elements, vol. 158, pp. 239–251, January 2024. [link] [bibtex] [arxiv]

@article{rosilhoBEM,
 author = {Rosilho de Souza, Giacomo and Krause, Rolf and Pezzuto, Simone},
 doi = {10.1016/j.enganabound.2023.10.021},
 journal = {Engineering Analysis with Boundary Elements},
 month = {January},
 pages = {239-251},
 title = {Boundary Integral Formulation of the Cell-by-Cell Model of
Cardiac Electrophysiology},
 url = {https://www.sciencedirect.com/science/article/pii/S0955799723005131},
 volume = {158},
 year = {2024}
}

Edoardo Centofanti and Simone Scacchi. A comparison of Algebraic Multigrid Bidomain solvers on hybrid CPU–GPU architectures.
Computer Methods in Applied Mechanics and Engineering, vol. 423, pp. 116875, Elsevier, 2024. [link] [bibtex]

@article{centofanti2024comparison,
 author = {Centofanti, Edoardo and Scacchi, Simone},
 doi = {10.1016/j.cma.2024.116875},
 journal = {Computer Methods in Applied Mechanics and Engineering},
 pages = {116875},
 publisher = {Elsevier},
 title = {A comparison of Algebraic Multigrid Bidomain solvers on hybrid {CPU--GPU} architectures},
 url = {https://dx.doi.org/10.1016/j.cma.2024.116875},
 volume = {423},
 year = {2024}
}

Simone Scacchi, Piero Colli Franzone, Luca F Pavarino, Vincenzo Gionti, and Cesare Storti. Epicardial Dispersion of Repolarization Promotes the Onset of Reentry in Brugada Syndrome: A Numerical Simulation Study.
Bulletin of Mathematical Biology, vol. 85, no. 3, pp. 22, Springer, 2023. [link] [bibtex]

@article{scacchi2023epicardial,
 author = {Scacchi, Simone and Colli Franzone, Piero and Pavarino, Luca F and Gionti, Vincenzo and Storti, Cesare},
 doi = {10.1007/s11538-023-01124-9},
 journal = {Bulletin of Mathematical Biology},
 number = {3},
 pages = {22},
 publisher = {Springer},
 title = {Epicardial Dispersion of Repolarization Promotes the Onset of Reentry in {Brugada} Syndrome: A Numerical Simulation Study},
 url = {https://dx.doi.org/10.1007/s11538-023-01124-9},
 volume = {85},
 year = {2023}
}

Ngoc Mai Monica Huynh, Fatemeh Chegini, Luca Franco Pavarino, Martin Weiser, and Simone Scacchi. Convergence analysis of BDDC preconditioners for composite DG discretizations of the cardiac cell-by-cell model.
SIAM J. Sci. Comp., vol. 45 (6), pp. A2836 – A2857, 2023. [pdf] [link] [bibtex]

@article{huynh:BDDC,
 author = {Huynh, Ngoc Mai Monica and Chegini, Fatemeh and Pavarino, Luca Franco and Weiser, Martin and Scacchi, Simone},
 doi = {10.1137/22M1542532},
 journal = {SIAM J. Sci. Comp.},
 pages = {A2836 - A2857},
 pdf = {https://arxiv.org/pdf/2212.12295},
 title = {Convergence analysis of {BDDC} preconditioners for
composite {DG} discretizations of the cardiac
cell-by-cell model},
 url = {https://dx.doi.org/10.1137/22M1542532},
 volume = {45 (6)},
 year = {2023}
}

Joshua Steyer, Thomas Lilienkamp, Stefan Luther, and Ulrich Parlitz. The role of pulse timing in cardiac defibrillation.
Frontiers in Network Physiology, vol. 2, pp. 1007585, January 2023. [link] [bibtex]

@article{steyer2023_frontiers,
 author = {Steyer, Joshua and Lilienkamp, Thomas and Luther, Stefan and Parlitz, Ulrich},
 doi = {10.3389/fnetp.2022.1007585},
 journal = {Frontiers in Network Physiology},
 month = {January},
 pages = {1007585},
 title = {The role of pulse timing in cardiac defibrillation},
 url = {https://dx.doi.org/10.3389/fnetp.2022.1007585},
 volume = {2},
 year = {2023}
}

Emmanuelle Saillard and Mark Potse. À quoi servent les ordinateurs les plus puissants au monde ? Un exemple en cardiologie.
The Conversation, December 2022. [link] [bibtex]

@article{saillard:super,
 author = {Saillard, Emmanuelle and Potse, Mark},
 journal = {The Conversation},
 month = {December},
 title = {À quoi servent les ordinateurs les plus puissants au monde ? Un exemple en cardiologie},
 url = {https://theconversation.com/a-quoi-servent-les-ordinateurs-les-plus-puissants-au-monde-un-exemple-en-cardiologie-195266},
 year = {2022}
}

Nicolas Alejandro Barnafi, Ngoc Monica Mai Huynh, Luca Franco Pavarino, and Simone Scacchi. Parallel nonlinear solvers in computational cardiac electrophysiology.
IFAC-PapersOnLine, vol. 55, no. 20, pp. 187–192, September 2022. [link] [bibtex]

@article{barnafi_IFAC-Papers_2022,
 author = {Barnafi, Nicolas Alejandro and Huynh, Ngoc Monica Mai and Pavarino, Luca Franco and Scacchi, Simone},
 doi = {10.1016/j.ifacol.2022.09.093},
 journal = {IFAC-PapersOnLine},
 month = {September},
 number = {20},
 pages = {187-192},
 title = {Parallel nonlinear solvers in computational cardiac electrophysiology},
 url = {https://dx.doi.org/10.1016/j.ifacol.2022.09.093},
 volume = {55},
 year = {2022}
}

Ngoc Monica Mai Huynh, Luca Franco Pavarino, and Simone Scacchi. Scalable and Robust Dual-Primal Newton–Krylov Deluxe Solvers for Cardiac Electrophysiology with Biophysical Ionic Models.
Vietnam Journal of Mathematics, vol. 50, pp. 1029–1052, September 2022. [link] [bibtex]

@article{Huynh_VJOM_2022,
 author = {Huynh, Ngoc Monica Mai and Pavarino, Luca Franco and Scacchi, Simone},
 doi = {10.1007/s10013-022-00576-1},
 journal = {Vietnam Journal of Mathematics},
 month = {September},
 pages = {1029–1052},
 title = {Scalable and Robust Dual-Primal {N}ewton–{K}rylov Deluxe
Solvers for Cardiac Electrophysiology with Biophysical Ionic Models},
 url = {https://dx.doi.org/10.1007/s10013-022-00576-1},
 volume = {50},
 year = {2022}
}

Antoine Amsaleg, Jorge Sánchez, Ralf Mikut, and Axel Loewe. Characterization of the Pace-and-Drive Capacity of the Human Sinoatrial Node: a 3D in silico Study.
Biophysical Journal, vol. 121, no. 22, pp. 4247–4259, October 2022. [link] [bibtex]

@article{Amsaleg-unknown-ID17996,
 author = {Amsaleg, Antoine and Sánchez, Jorge and Mikut, Ralf and Loewe, Axel},
 doi = {10.1016/j.bpj.2022.10.020},
 journal = {Biophysical Journal},
 month = {October},
 number = {22},
 pages = {4247-4259},
 title = {Characterization of the Pace-and-Drive Capacity of the Human
Sinoatrial Node: a {3D} in silico Study},
 url = {https://dx.doi.org/10.1016/j.bpj.2022.10.020},
 volume = {121},
 year = {2022}
}

Jorge Sánchez and Axel Loewe. A Review of Healthy and Fibrotic Myocardium Microstructure Modeling and Corresponding Intracardiac Electrograms.
Frontiers in Physiology, vol. 13, May 2022. [link] [bibtex]

@article{Sanchez-2022-908069,
 author = {Sánchez, Jorge and Loewe, Axel},
 doi = {10.3389/fphys.2022.908069},
 journal = {Frontiers in Physiology},
 month = {May},
 title = {A Review of Healthy and Fibrotic Myocardium Microstructure
Modeling and Corresponding Intracardiac Electrograms},
 url = {https://dx.doi.org/10.3389/fphys.2022.908069},
 volume = {13},
 year = {2022}
}

Kristian Gregorius Hustad and Xing Cai. Resource-Efficient Use of Modern Processor Architectures For Numerically Solving Cardiac Ionic Cell Models.
Frontiers in Physiology, vol. 13, article nr. 904648, June 2022. [link] [bibtex]

@article{Hustad2022_frontiers,
 article_number = {904648},
 author = {Hustad, Kristian Gregorius and Cai, Xing},
 doi = {10.3389/fphys.2022.904648},
 journal = {Frontiers in Physiology},
 month = {June},
 pages = {904648},
 title = {Resource-Efficient Use of Modern Processor Architectures
For Numerically Solving Cardiac Ionic Cell Models},
 url = {https://dx.doi.org/10.3389/fphys.2022.904648},
 volume = {13},
 year = {2022}
}

Omer Berenfeld, Valentina Corino, Axel Loewe, Juan Pablo Martínez, and Jose F Rodriguez Matas. Editorial: Atrial Fibrillation - Technology for Diagnosis, Monitoring, and Treatment.
Frontiers in Physiology, vol. 13, article nr. 848096, February 2022. [link] [bibtex]

@article{EditorialAF_Frontiers,
 article_number = {848096},
 author = {Omer Berenfeld and Valentina Corino and Axel Loewe and Juan Pablo Martínez and Jose F Rodriguez Matas},
 doi = {10.3389/fphys.2022.848096},
 journal = {Frontiers in Physiology},
 month = {February},
 pages = {848096},
 title = {Editorial: {A}trial Fibrillation - Technology for Diagnosis, Monitoring, and Treatment},
 url = {https://dx.doi.org/10.3389/fphys.2022.848096},
 volume = {13},
 year = {2022}
}

Felix Bach, Jochen Klar, Axel Loewe, Jorge Sánchez, Gunnar Seemann, Yung-Lin Huang, and Robert Ulrich. The openCARP CDE – Concept for and implementation of a sustainable collaborative development environment for research software.
Bausteine Forschungsdatenmanagement, vol. 2022, no. 1, March 2022. [link] [bibtex]

@article{cde-fdm,
 author = {Bach, Felix and Klar, Jochen and Loewe, Axel and Sánchez, Jorge and Seemann, Gunnar and Huang, Yung-Lin and Ulrich, Robert},
 doi = {10.17192/bfdm.2022.1.8368},
 journal = {Bausteine Forschungsdatenmanagement},
 month = {March},
 number = {1},
 title = {The {openCARP CDE} -- Concept for and implementation of a sustainable collaborative development environment for research software},
 url = {https://dx.doi.org/10.17192/bfdm.2022.1.8368},
 volume = {2022},
 year = {2022}
}

Jorge Sánchez, Beatriz Trenor, Javier Saiz, Olaf Dössel, and Axel Loewe. Fibrotic Remodeling during Persistent Atrial Fibrillation: In Silico Investigation of the Role of Calcium for Human Atrial Myofibroblast Electrophysiology.
Cells, vol. 10, pp. 2852, October 2021. [link] [bibtex]

@article{sanchez-myofib,
 author = {Sánchez, Jorge and Trenor, Beatriz and Saiz, Javier and Dössel, Olaf and Loewe, Axel},
 doi = {10.3390/cells10112852},
 journal = {Cells},
 month = {October},
 pages = {2852},
 title = {Fibrotic Remodeling during Persistent Atrial Fibrillation:
In Silico Investigation of the Role of Calcium for
Human Atrial Myofibroblast Electrophysiology},
 url = {https://dx.doi.org/10.3390/cells10112852},
 volume = {10},
 year = {2021}
}

conference articles

Marie Houillon, Jorge Sánchez, Matthias AF Gsell, Aurel Neic, Anton J Prassl, Gunnar Seemann, Gernot Plank, Edward J Vigmond, and Axel Loewe. Facilitating Reproducible in silico Experiments with openCARP: a Step Toward FAIR and Open Science in Cardiac Electrophysiology.
Computing in Cardiology, vol. 51, Karlsruhe, Germany, September 2024. [link] [bibtex]

@inproceedings{HouillonCinC2024,
 address = {Karlsruhe, Germany},
 author = {Houillon, Marie and Sánchez, Jorge and Gsell, Matthias AF and Neic, Aurel and Prassl, Anton J and Seemann, Gunnar and Plank, Gernot and Vigmond, Edward J and Loewe, Axel},
 booktitle = {Computing in Cardiology},
 month = {September},
 title = {Facilitating Reproducible in silico Experiments with openCARP: a Step Toward FAIR and Open Science in Cardiac Electrophysiology},
 url = {https://cinc.org/2024/Program/accepted/232.html},
 volume = {51},
 year = {2024}
}

Joshua Steyer, Fatemeh Chegini, Mark Potse, Tomáş Starý, Axel Loewe, and Martin Weiser. The Role of Computational Methods in Understanding Cardiac Electrogram Genesis on a Cell-by-Cell Scale.
9th European Congress on Computational Methods in Applied Sciences and Engineering, 2024. [pdf] [link] [bibtex]

@inproceedings{Joshua-ECCOMAS-2024,
 author = {Steyer, Joshua and Chegini, Fatemeh and Potse, Mark and Star{\'y}, Tom{\'a}{\c{s}} and Loewe, Axel and Weiser, Martin},
 booktitle = {9th European Congress on Computational Methods in Applied Sciences and Engineering},
 hal_id = {hal-04838204v1},
 pdf = {https://hal.archives-ouvertes.fr/hal-04838204v1/document},
 title = {The Role of Computational Methods in Understanding Cardiac Electrogram Genesis on a Cell-by-Cell Scale},
 url = {https://eccomas2024.org/event/contribution/41682ea2-96a0-11ee-8a2d-000c29ddfc0c},
 year = {2024}
}

Vincent Alba, Olivier Aumage, Denis Barthou, Raphaël Colin, Marie-Christine Counilh, Stéphane Genaud, Amina Guermouche, Vincent Loechner, and Arun Thangamani. Performance Portability of Generated Cardiac Simulation Kernels Through Automatic Dimensioning and Load Balancing on Heterogeneous Nodes.
PDSEC workshop, 2024 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW), pp. 1006–1015, 31 May 2024. [link] [bibtex]

@inproceedings{alba:ipdps24,
 author = {Alba, Vincent and Aumage, Olivier and Barthou, Denis and Colin, Raphaël and Counilh, Marie-Christine and Genaud, Stéphane and Guermouche, Amina and Loechner, Vincent and Thangamani, Arun},
 booktitle = {PDSEC workshop, 2024 IEEE International Parallel and
Distributed Processing Symposium Workshops (IPDPSW)},
 doi = {10.1109/IPDPSW63119.2024.00171},
 hal_id = {hal-04606388},
 month = {May},
 pages = {1006-1015},
 title = {Performance Portability of Generated Cardiac Simulation Kernels Through
Automatic Dimensioning and Load Balancing on Heterogeneous Nodes},
 url = {https://dx.doi.org/10.1109/IPDPSW63119.2024.00171},
 year = {2024}
}

Joshua Steyer, Fatemeh Chegini, Tomas Stary, Mark Potse, Martin Weiser, and Axel Loewe. Electrograms in a Cardiac Cell-by-Cell Model.
Workshop Biosignals, Göttingen, Germany, February 2024. [link] [bibtex]

@inproceedings{SteyerBiosig,
 address = {Göttingen, Germany},
 author = {Steyer, Joshua and Chegini, Fatemeh and Stary, Tomas and Potse, Mark and Weiser, Martin and Loewe, Axel},
 booktitle = {Workshop Biosignals},
 doi = {10.47952/gro-publ-194},
 month = {February},
 title = {Electrograms in a Cardiac Cell-by-Cell Model},
 url = {https://dx.doi.org/10.47952/gro-publ-194},
 year = {2024}
}

Tomas Stary, Moritz Linder, and Axel Loewe. Sinoatrial Node Cell Response to Isoprenaline Stimulation and Hypocalcemia.
Computing in Cardiology, vol. 50, Atlanta, Georgia, USA, October 2023. [link] [bibtex]

@inproceedings{TomasCinC_2023,
 address = {Atlanta, Georgia, USA},
 author = {Stary, Tomas and Linder, Moritz and Loewe, Axel},
 booktitle = {Computing in Cardiology},
 doi = {10.22489/CinC.2023.114},
 month = {October},
 title = {Sinoatrial Node Cell Response to Isoprenaline Stimulation and Hypocalcemia},
 url = {https://dx.doi.org/10.22489/CinC.2023.114},
 volume = {50},
 year = {2023}
}

Joshua Steyer, Fatemeh Chegini, Mark Potse, Axel Loewe, and Martin Weiser. Continuity of Microscopic Cardiac Conduction in a Computational Cell-by-Cell Model.
Computing in Cardiology, vol. 50, Atlanta, Georgia, USA, October 2023. [link] [bibtex]

@inproceedings{JoshuaCinC_2023,
 address = {Atlanta, Georgia, USA},
 author = {Steyer, Joshua and Chegini, Fatemeh and Potse, Mark and Loewe, Axel and Weiser, Martin},
 booktitle = {Computing in Cardiology},
 doi = {10.22489/CinC.2023.385},
 month = {October},
 title = {Continuity of Microscopic Cardiac Conduction in a
Computational Cell-by-Cell Model},
 url = {https://dx.doi.org/10.22489/CinC.2023.385},
 volume = {50},
 year = {2023}
}

Zeina Chehade and Yves Coudière. The Two-Point Finite Volume scheme for the Microscopic Bidomain Model of Electrocardiology.
Tenth International Symposium on Finite Volumes for Complex Applications, Springer, October 2023. [link] [bibtex] [abstract]
```
@inproceedings{chehade:fvca2023,
 author = {Chehade, Zeina and Coudière, Yves},
 booktitle = {Tenth International Symposium on Finite Volumes for Complex Applications},
 doi = {10.1007/978-3-031-40864-9},
 month = {October},
 publisher = {Springer},
 title = {The Two-Point Finite Volume scheme for the Microscopic Bidomain Model of Electrocardiology},
 url = {https://dx.doi.org/10.1007/978-3-031-40864-9},
 year = {2023}
}
```
abstract: We are interested in the approximation of a cardiac microscopic model. It is a set of Laplace equations with non-standard, time-dependent, transmission conditions, for which finite volume methods are of real interest. The transmission conditions state as ordinary differential equations on the jump of the potential, namely the transmembrane voltage, so that we keep this voltage as an unknown in our scheme. Here we extend the two-point flux approximation to the discretization of this model, show that it converges, and compute error estimates.
Tiago Trevisan Jost, Arun Thangamani, Raphaël Colin, Vincent Loechner, Stéphane Genaud, and Bérenger Bramas. GPU Code Generation of Cardiac Electrophysiology Simulation with MLIR.
29th International European Conference on Parallel and Distributed Computing (Euro-Par), pp. 549–563, Springer Nature Switzerland, Cham, August 2023. [pdf] [link] [bibtex] [abstract]
```
@inproceedings{trevisanjost:EP23,
 address = {Cham},
 author = {Trevisan Jost, Tiago and Thangamani, Arun and Colin, Rapha{\"e}l and Loechner, Vincent and Genaud, St{\'e}phane and Bramas, B{\'e}renger},
 booktitle = {29th International European Conference on Parallel and Distributed Computing (Euro-Par)},
 doi = {10.1007/978-3-031-39698-4_37},
 editor = {Cano, Jos{\'e}
and Dikaiakos, Marios D.
and Papadopoulos, George A.
and Peric{\`a}s, Miquel
and Sakellariou, Rizos},
 month = {August},
 pages = {549-563},
 pdf = {https://inria.hal.science/hal-04206195v1/document},
 publisher = {Springer Nature Switzerland},
 title = {{GPU} Code Generation of Cardiac Electrophysiology Simulation with {MLIR}},
 url = {https://dx.doi.org/10.1007/978-3-031-39698-4_37},
 year = {2023}
}
```
abstract: We show the benefits of the novel MLIR compiler technology to the generation of code from a DSL, namely EasyML used in openCARP, a widely used simulator in the cardiac electrophysiology community. Building on an existing work that deeply modified openCARP's native DSL code generator to enable efficient vectorized CPU code, we extend the code generation for GPUs (Nvidia CUDA and AMD ROCm). Generating optimized code for different accelerators requires specific optimizations and we review how MLIR has been used to enable multi-target code generation from an integrated generator. Experiments conducted on the 48 ionic models provided by openCARP show that the GPU code executes 3.17 times faster and delivers more than 7 times more FLOPS per watt than the vectorized CPU code, on an Nvidia A100 GPU versus a 36-cores AVX-512 Intel CPU.

Sofia Botti, Chiara Bartolucci, Rolf Krause, Luca F Pavarino, and Stefano Severi. An in silico Study of Cardiac hiPSC Electronic Maturation by Dynamic Clamp.
International Conference on Functional Imaging and Modeling of the Heart, pp. 175–183, 2023. [link] [bibtex]

@inproceedings{botti2023silico,
 author = {Botti, Sofia and Bartolucci, Chiara and Krause, Rolf and Pavarino, Luca F and Severi, Stefano},
 booktitle = {International Conference on Functional Imaging and Modeling of the Heart},
 organization = {Springer},
 pages = {175--183},
 title = {An in silico Study of Cardiac {hiPSC} Electronic Maturation by Dynamic Clamp},
 url = {https://www.researchgate.net/publication/371621623},
 year = {2023}
}

Fatemeh Chegini, Algiane Froehly, Ngoc Mai Monica Huynh, Luca Pavarino, Mark Potse, Simone Scacchi, and Martin Weiser. Efficient numerical methods for simulating cardiac electrophysiology with cellular resolution.
Int. Conf. Comp. Meth. Coupled Problems Sci. Eng. 2023, Chania, Greece, June 2023. [link] [bibtex]

@inproceedings{WeiserEtAl2023,
 address = {Chania, Greece},
 author = {Chegini, Fatemeh and Froehly, Algiane and Huynh, Ngoc Mai Monica and Pavarino, Luca and Potse, Mark and Scacchi, Simone and Weiser, Martin},
 booktitle = {Int. Conf. Comp. Meth. Coupled Problems Sci. Eng. 2023},
 doi = {10.23967/c.coupled.2023.004},
 month = {June},
 title = {Efficient numerical methods for simulating cardiac
electrophysiology with cellular resolution},
 url = {https://www.scipedia.com/public/_2023f},
 year = {2023}
}

Lia Gander, Rolf Krause, Martin Weiser, Francisco Sahli Costabal, and Simone Pezzuto. On the Accuracy of Eikonal Approximations in Cardiac Electrophysiology in the Presence of Fibrosis.
Functional Imaging and Modeling of the Heart, vol. 13958 in Lecture Notes in Computer Science, pp. 137–146, Springer, Cham, June 2023. [link] [bibtex]

@inproceedings{GanderEikoDiff23,
 address = {Cham},
 author = {Gander, Lia and Krause, Rolf and Weiser, Martin and Sahli Costabal, Francisco and Pezzuto, Simone},
 booktitle = {Functional Imaging and Modeling of the Heart},
 doi = {10.1007/978-3-031-35302-4_14},
 editor = {Bernard, Olivier and
Clarysse, Patrick and
Duchateau, Nicolas and
Ohayon, Jacques and
Viallon, Magalie},
 month = {June},
 pages = {137-146},
 publisher = {Springer},
 series = {Lecture Notes in Computer Science},
 title = {On the Accuracy of Eikonal Approximations in Cardiac Electrophysiology
in the Presence of Fibrosis},
 url = {https://dx.doi.org/10.1007/978-3-031-35302-4_14},
 volume = {13958},
 year = {2023}
}

Giacomo Rosilho de Souza, Simone Pezzuto, and Rolf Krause. Effect of Gap Junction Distribution, Size, and Shape on the Conduction Velocity in a Cell-by-Cell Model for Electrophysiology.
Functional Imaging and Modeling of the Heart, vol. 13958 in Lecture Notes in Computer Science, pp. 117–126, Springer, Cham, June 2023. [link] [bibtex]

@inproceedings{deSouzaGaps23,
 address = {Cham},
 author = {Rosilho de Souza, Giacomo and Pezzuto, Simone and Krause, Rolf},
 booktitle = {Functional Imaging and Modeling of the Heart},
 doi = {10.1007/978-3-031-35302-4_12},
 editor = {Bernard, Olivier and
Clarysse, Patrick and
Duchateau, Nicolas and
Ohayon, Jacques and
Viallon, Magalie},
 month = {June},
 pages = {117-126},
 publisher = {Springer},
 series = {Lecture Notes in Computer Science},
 title = {Effect of Gap Junction Distribution, Size, and Shape
on the Conduction Velocity in a Cell-by-Cell Model for Electrophysiology},
 url = {https://dx.doi.org/10.1007/978-3-031-35302-4_12},
 volume = {13958},
 year = {2023}
}

Joshua Steyer, Lourdes Patricia Martínez Diaz, Laura Anna Unger, and Axel Loewe. Simulated Excitation Patterns in the Atria and Their Corresponding Electrograms.
Functional Imaging and Modeling of the Heart, pp. 204–212, Springer Nature Switzerland, Cham, June 2023. [link] [bibtex]

@inproceedings{steyer:fimh23,
 address = {Cham},
 author = {Steyer, Joshua and Diaz, Lourdes Patricia Mart{\'i}nez and Unger, Laura Anna and Loewe, Axel},
 booktitle = {Functional Imaging and Modeling of the Heart},
 doi = {10.1007/978-3-031-35302-4_21},
 editor = {Bernard, Olivier
and Clarysse, Patrick
and Duchateau, Nicolas
and Ohayon, Jacques
and Viallon, Magalie},
 month = {June},
 pages = {204--212},
 publisher = {Springer Nature Switzerland},
 title = {Simulated Excitation Patterns in the Atria and Their Corresponding Electrograms},
 url = {https://dx.doi.org/10.1007/978-3-031-35302-4_21},
 year = {2023}
}

Arun Thangamani, Tiago Trevisan Jost, Vincent Loechner, Stéphane Genaud, and Bérenger Bramas. Lifting Code Generation of Cardiac Physiology Simulation to Novel Compiler Technology.
Proceedings of the 21st ACM/IEEE International Symposium on Code Generation and Optimization in CGO 2023, pp. 68–80, Association for Computing Machinery, New York, NY, USA, February 2023. [pdf] [link] [bibtex]

@inproceedings{10.1145/3579990.3580008,
 address = {New York, NY, USA},
 author = {Thangamani, Arun and Jost, Tiago Trevisan and Loechner, Vincent and Genaud, St{\'e}phane and Bramas, B{\'e}renger},
 booktitle = {Proceedings of the 21st ACM/IEEE International Symposium on Code Generation and Optimization},
 doi = {10.1145/3579990.3580008},
 month = {February},
 pages = {68-80},
 pdf = {https://hal.science/hal-03977688v1},
 publisher = {Association for Computing Machinery},
 series = {CGO 2023},
 title = {Lifting Code Generation of Cardiac Physiology Simulation to Novel Compiler Technology},
 url = {https://dx.doi.org/10.1145/3579990.3580008},
 year = {2023}
}

Sofia Botti, Chiara Bartolucci, Claudia Altomare, Lucio Barile, Rolf Krause, Luca F Pavarino, and Stefano Severi. Numerical Simulations Indicate IK1 Dynamic Clamp Can Unveil the Phenotype of Cardiomyocytes Derived from Induced Pluripotent Stem Cells.
2022 Computing in Cardiology (CinC), vol. 498, pp. 1–4, 2022. [link] [bibtex]

@inproceedings{botti2022numerical,
 author = {Botti, Sofia and Bartolucci, Chiara and Altomare, Claudia and Barile, Lucio and Krause, Rolf and Pavarino, Luca F and Severi, Stefano},
 booktitle = {2022 Computing in Cardiology (CinC)},
 pages = {1--4},
 title = {Numerical Simulations Indicate {IK1} Dynamic Clamp Can Unveil the Phenotype of Cardiomyocytes Derived from Induced Pluripotent Stem Cells},
 url = {https://www.cinc.org/archives/2022/pdf/CinC2022-101.pdf},
 volume = {498},
 year = {2022}
}

Amina Guermouche. Combining Uncore Frequency and Dynamic Power Capping to Improve Power Savings.
IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW), pp. 1028–1037, May 2022. [link] [bibtex]

@inproceedings{guermouche:ipdpsw22,
 author = {Guermouche, Amina},
 booktitle = {IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW)},
 doi = {10.1109/IPDPSW55747.2022.00164},
 month = {May},
 pages = {1028-1037},
 title = {Combining Uncore Frequency and Dynamic Power Capping to Improve Power Savings},
 url = {https://dx.doi.org/10.1109/IPDPSW55747.2022.00164},
 year = {2022}
}

Jorge Sánchez and Axel Loewe. Mechanical Consequences of Electrical Remodeling due to Persistent Atrial Fibrillation: a Cellular Level Sensitivity Analysis.
Computing in Cardiology, vol. 49, Tampere, Finland, September 2022. [link] [bibtex]

@inproceedings{JorgeCinC_2022,
 address = {Tampere, Finland},
 author = {Sánchez, Jorge and Loewe, Axel},
 booktitle = {Computing in Cardiology},
 month = {September},
 title = {Mechanical Consequences of Electrical Remodeling due to Persistent
Atrial Fibrillation: a Cellular Level Sensitivity Analysis },
 url = {https://cinc.org/2022/Program/accepted/37_Preprint.pdf},
 volume = {49},
 year = {2022}
}

Mark Potse, Luca Cirrottola, and Algiane Froehly. A practical algorithm to build geometric models of cardiac muscle structure.
8th European Congress on Computational Methods in Applied Sciences and Engineering (ECCOMAS), Oslo, Norway, June 2022. [link] [bibtex]

@inproceedings{potse-eccomas22,
 address = {Oslo, Norway},
 author = {Potse, Mark and Cirrottola, Luca and Froehly, Algiane},
 booktitle = {8th European Congress on Computational Methods in
Applied Sciences and Engineering (ECCOMAS)},
 doi = {10.23967/eccomas.2022.027},
 month = {June},
 title = {A practical algorithm to build geometric models of
cardiac muscle structure},
 url = {https://dx.doi.org/10.23967/eccomas.2022.027},
 year = {2022}
}

Martin Weiser and Fatemeh Chegini. Adaptive multirate integration of cardiac electrophysiology with spectral deferred correction methods.
7th International Conference on Computational and Mathematical Biomedical Engineering (CMBE22), vol. 2, pp. 528–531, June 2022. [link] [bibtex]

@inproceedings{WeiserChegini2022,
 author = {Weiser, Martin and Chegini, Fatemeh},
 booktitle = {7th International Conference on Computational and
Mathematical Biomedical Engineering (CMBE22)},
 month = {June},
 pages = {528--531},
 title = {Adaptive multirate integration of cardiac electrophysiology with spectral deferred correction methods},
 url = {https://www.compbiomed.net/2022/cmbe-proceedings.htm},
 volume = {2},
 year = {2022}
}

Giacomo Rosilho de Souza, Simone Pezzuto, and Rolf Krause. Parallel-in-time multirate explicit stabilized method for the monodomain model in cardiac electrophysiology.
7th International Conference on Computational and Mathematical Biomedical Engineering (CMBE22), vol. 2, pp. 535–538, June 2022. [link] [bibtex]

@inproceedings{rosilhodesouza-cmbe22,
 author = {Rosilho de Souza, Giacomo and Pezzuto, Simone and Krause, Rolf},
 booktitle = {7th International Conference on Computational and
Mathematical Biomedical Engineering (CMBE22)},
 month = {June},
 pages = {535--538},
 title = {Parallel-in-time multirate explicit stabilized method
for the monodomain model in cardiac electrophysiology},
 url = {https://www.compbiomed.net/2022/cmbe-proceedings.htm},
 volume = {2},
 year = {2022}
}

conference abstracts

Vincent Loechner. A Survey of General-purpose Polyhedral Compilers.
HiPEAC 2025 Conference, Barcelona, Spain, January 2025. [link] [bibtex]

@abstract{loechner-hipeac25,
 address = {Barcelona, Spain},
 author = {Loechner, Vincent},
 booktitle = {HiPEAC 2025 Conference},
 month = {January},
 organization = {},
 title = {A Survey of General-purpose Polyhedral Compilers},
 url = {https://www.hipeac.net/2025/barcelona/#/program/sessions/8226/},
 year = {2025}
}

Mark Potse. The MICROCARD project; Modeling the heart cell by cell on exascale supercomputers.
EuroHPC Summit: To exascale and beyond, Antwerp, Belgium, March 2024. (poster presentation) [pdf] [link] [bibtex]

@abstract{potse24eurohpc,
 address = {Antwerp, Belgium},
 author = {Potse, Mark},
 booktitle = {EuroHPC Summit: To exascale and beyond},
 hal_id = {hal-04713117},
 month = {March},
 organization = {EuroHPC},
 pdf = {https://hal.archives-ouvertes.fr/hal-04713117/document},
 title = {The {MICROCARD} project; Modeling the heart cell by cell on exascale supercomputers},
 url = {https://inria.hal.science/hal-04713117},
 year = {2024}
}

Xing Cai and James Trotter. Enabling Cell-Based Simulations of Cardiac Electrophysiology with High-Performance Computing.
2024 SIAM Conference on Parallel Processing for Scientific Computing, Baltimore, MD, March 2024. [link] [bibtex]

@abstract{trotter24_siam,
 address = {Baltimore, MD},
 author = {Cai, Xing and Trotter, James},
 booktitle = {2024 SIAM Conference on Parallel Processing for Scientific Computing},
 month = {March},
 title = {Enabling Cell-Based Simulations of Cardiac
Electrophysiology with High-Performance Computing},
 url = {https://meetings.siam.org/sess/dsp_talk.cfm?p=132650},
 year = {2024}
}

James Trotter. Distributed memory parallel simulator of the EMI model.
Cardiac Physiome 2024, Freiburg, Germany, September 2024. [link] [bibtex]

@abstract{trotter24_cardphys,
 address = {Freiburg, Germany},
 author = {Trotter, James},
 booktitle = {Cardiac Physiome 2024},
 month = {September},
 title = {Distributed memory parallel simulator of the {EMI} model},
 url = {https://www.uniklinik-freiburg.de/fileadmin/mediapool/09_zentren/herzzentrum/bilder/kardiovaskulaere-medizin/CardiacPhysiome/eBooklet_CardiacPhysiome2024.pdf},
 year = {2024}
}

Karoline Jæger, James Trotter, Xing Cai, Hermenegild Arevalo, and Aslak Tveito. Modeling Ion Channel Reorganisation Due to Ischemia in Cell-Based Models of the Myocyte.
Cardiac Physiome 2024, Freiburg, Germany, September 2024. [link] [bibtex]

@abstract{arevalo24_cardphys,
 address = {Freiburg, Germany},
 author = {Jæger, Karoline and Trotter, James and Cai, Xing and Arevalo, Hermenegild and Tveito, Aslak},
 booktitle = {Cardiac Physiome 2024},
 month = {September},
 title = {Modeling Ion Channel Reorganisation Due to Ischemia in Cell-Based Models of the Myocyte},
 url = {https://www.uniklinik-freiburg.de/fileadmin/mediapool/09_zentren/herzzentrum/bilder/kardiovaskulaere-medizin/CardiacPhysiome/eBooklet_CardiacPhysiome2024.pdf},
 year = {2024}
}

Alessandro Gatti, James Trotter, Tor Skeie, Hermenegild Arevalo, and Xing Cai. A Resource-Efficient Open-Source Solver for Monodomain Equations in Cardiac Electrophysiology.
Cardiac Physiome 2024, Freiburg, Germany, September 2024. [link] [bibtex]

@abstract{gatti24_cardphys,
 address = {Freiburg, Germany},
 author = {Gatti, Alessandro and Trotter, James and Skeie, Tor and Arevalo, Hermenegild and Cai, Xing},
 booktitle = {Cardiac Physiome 2024},
 month = {September},
 title = {A Resource-Efficient Open-Source Solver for Monodomain Equations in Cardiac Electrophysiology},
 url = {https://www.uniklinik-freiburg.de/fileadmin/mediapool/09_zentren/herzzentrum/bilder/kardiovaskulaere-medizin/CardiacPhysiome/eBooklet_CardiacPhysiome2024.pdf},
 year = {2024}
}

Alessandro Gatti, James Trotter, Tor Skeie, Hermenegild Arevalo, and Xing Cai. A Resource-Efficient Open-Source Solver for Monodomain Equations in Cardiac Electrophysiology.
Computing in Cardiology 2024, Karlsruhe, Germany, September 2024. [link] [bibtex]

@abstract{gatti24_cinc,
 address = {Karlsruhe, Germany},
 author = {Gatti, Alessandro and Trotter, James and Skeie, Tor and Arevalo, Hermenegild and Cai, Xing},
 booktitle = {Computing in Cardiology 2024},
 month = {September},
 title = {A Resource-Efficient Open-Source Solver for Monodomain Equations in Cardiac Electrophysiology},
 url = {https://cinc.org/2024/Program/accepted/319.html},
 year = {2024}
}

T. Stary, M. Houillon, M. Linder, G. Seemann, and A. Loewe. Jupyter-based Notebooks for Cardiac Simulations.
Cardiac Physiome meeting, Freiburg, Germany, September 2024. [link] [bibtex]

@abstract{stary24cp,
 address = {Freiburg, Germany},
 author = {Stary, T. and Houillon, M. and Linder, M. and Seemann, G. and Loewe, A.},
 booktitle = {Cardiac Physiome meeting},
 month = {September},
 title = {Jupyter-based Notebooks for Cardiac Simulations},
 url = {https://www.uniklinik-freiburg.de/experimental-cardiovascular-medicine/cardiac-physiome-2024/programme.html},
 year = {2024}
}

J. Steyer, F. Chegini, M. Potse, T. Starý, M. Houillon, M. Weiser, and A. Loewe. The Impact of Explicitly Represented Electrodes in a Cell-by-Cell Model on Its Recorded Electrograms.
Cardiac Physiome meeting, Freiburg, Germany, September 2024. [pdf] [link] [bibtex]

@abstract{steyer24cp,
 address = {Freiburg, Germany},
 author = {Steyer, J. and Chegini, F. and Potse, M. and Star{\'y}, T. and Houillon, M. and Weiser, M. and Loewe, A.},
 booktitle = {Cardiac Physiome meeting},
 hal_id = {hal-04838077v1},
 month = {September},
 pdf = {https://hal.archives-ouvertes.fr/hal-04838077v1/document},
 title = {The Impact of Explicitly Represented Electrodes in a
Cell-by-Cell Model on Its Recorded Electrograms},
 url = {https://www.uniklinik-freiburg.de/experimental-cardiovascular-medicine/cardiac-physiome-2024/programme.html},
 year = {2024}
}

L. Mottet, C. Prigent, A. Froehly, and M. Potse. Challenges in meshing tissue at the micro-scale for cardiac modeling.
Cardiac Physiome meeting, Freiburg, Germany, September 2024. [link] [bibtex]

@abstract{mottet24cp,
 address = {Freiburg, Germany},
 author = {Mottet, L. and Prigent, C. and Froehly, A. and Potse, M.},
 booktitle = {Cardiac Physiome meeting},
 month = {September},
 title = {Challenges in meshing tissue at the micro-scale for cardiac modeling},
 url = {https://www.uniklinik-freiburg.de/experimental-cardiovascular-medicine/cardiac-physiome-2024/programme.html},
 year = {2024}
}

Mark Potse. Modeling the heart cell by cell: the MICROCARD project.
Cardiac Physiome meeting, Freiburg, Germany, September 2024. [pdf] [link] [bibtex]

@abstract{potse24cp,
 address = {Freiburg, Germany},
 author = {Potse, Mark},
 booktitle = {Cardiac Physiome meeting},
 hal_id = {hal-04713134v1},
 month = {September},
 pdf = {https://hal.archives-ouvertes.fr/hal-04713134v1/document},
 title = {Modeling the heart cell by cell: the {MICROCARD} project},
 url = {https://inria.hal.science/hal-04713134},
 year = {2024}
}

Giacomo Rosilho de Souza, Simone Pezzuto, and Rolf Krause. Parallel-in-time methods for the monodomain model in cardiac electrophysiology.
PinT 2024: 13th Workshop on Parallel-in-Time Integration, Bruges, Belgium, July 2024. [link] [bibtex]

@abstract{rosilho:pint24,
 address = {Bruges, Belgium},
 author = {Rosilho de Souza, Giacomo and Pezzuto, Simone and Krause, Rolf},
 booktitle = {PinT 2024: 13th Workshop on Parallel-in-Time Integration},
 month = {July},
 title = {Parallel-in-time methods for the monodomain model in cardiac electrophysiology},
 url = {https://time-x.eu/pint-2024/#:~:text=The%2013th%20Workshop%20on%20Parallel,of%20charge%20to%20all%20researchers.},
 year = {2024}
}

Simone Pezzuto. Reconstruction of the local contractility of the cardiac muscle from deficient apparent kinematics.
Cardiac Physiome, Freiburg, Germany, September 2024. [link] [bibtex]

@abstract{pezzutoPhysiome24,
 address = {Freiburg, Germany},
 author = {Pezzuto, Simone},
 booktitle = {Cardiac Physiome},
 month = {September},
 title = {Reconstruction of the local contractility of the cardiac muscle
from deficient apparent kinematics},
 url = {https://www.uniklinik-freiburg.de/experimental-cardiovascular-medicine/cardiac-physiome-2024/programme.html},
 year = {2024}
}

Fritz Göbel, Terry Cojean, and Hartwig Anzt. BDDC preconditioning on GPUs for Cardiac Simulations.
29th International European Conference on Parallel and Distributed Computing (Euro-Par), arXiv:2410.14786, Limassol, Cyprus, August 2023. [link] [bibtex] [arxiv]

@abstract{europar-poster,
 address = {Limassol, Cyprus},
 author = {Göbel, Fritz and Cojean, Terry and Anzt, Hartwig},
 booktitle = {29th International European Conference on Parallel and Distributed Computing (Euro-Par)},
 doi = {10.1007/978-3-031-48803-0_30},
 month = {August},
 title = {{BDDC} preconditioning on {GPU}s for Cardiac Simulations},
 url = {https://dx.doi.org/10.1007/978-3-031-48803-0_30},
 year = {2023}
}

Giacomo Rosilho de Souza, Simone Pezzuto, and Rolf Krause. Boundary integral formulation and numerical experiments on the Cell-by-Cell model for electrophysiology.
VII ECCOMAS Young Investigators Conference, Porto, Portugal, June 2023. [link] [bibtex]

@abstract{rosilho:eccomas23,
 address = {Porto, Portugal},
 author = {Rosilho de Souza, Giacomo and Pezzuto, Simone and Krause, Rolf},
 booktitle = {VII ECCOMAS Young Investigators Conference},
 doi = {10.5281/zenodo.8393047},
 month = {June},
 title = {Boundary integral formulation and numerical experiments on the Cell-by-Cell model for electrophysiology},
 url = {https://dx.doi.org/10.5281/zenodo.8393047},
 year = {2023}
}

Tomas Stary, Marie Houillon, Jochen Klar, and Axel Loewe. Pipelines for Software Metadata Conversion and Publication.
deRSE23 - Conference for Research Software Engineering in Germany, Potsdam, February 2023. [pdf] [conference] [bibtex] [abstract]
```
@abstract{deRSE-CI,
 address = {Potsdam},
 author = {Stary, Tomas and Houillon, Marie and Klar, Jochen and Loewe, Axel},
 booktitle = {deRSE23 - Conference for Research Software Engineering in Germany},
 conference_url = {https://de-rse23.sciencesconf.org/program},
 month = {February},
 pdf = {docs/deRSE2023.pdf},
 title = {Pipelines for Software Metadata Conversion and Publication},
 year = {2023}
}
```
abstract: Reproducible research requires publication of software and datasets together with ap- propriate metadata. We present continuous integration pipelines to automatically generate such metadata for software (www.openCARP.org/CI). They are successfully used in the openCARP project and can be readily integrated into other projects. The user maintains only a CodeMeta file. which is a popular metadata standard tailored to research software. From there, further citation files are generated and can serve their purpose during specific phases of the software lifecycle: DataCite for software archiving, BagIt and BagPack for creation of tagged releases, deposition of releases in the RADAR data repository, and synchronisation of documentation files with the project’s webpage.
Marie Houillon, Jochen Klar, Tomas Stary, and Axel Loewe. Automated Software Metadata Conversion and Publication Based on CodeMeta.
E-Science-Tage 2023: Data to Knowledge, Heidelberg, March 2023. [pdf] [conference] [poster] [bibtex] [abstract]
```
@abstract{eScience23-CI,
 address = {Heidelberg},
 author = {Houillon, Marie and Klar, Jochen and Stary, Tomas and Loewe, Axel},
 booktitle = {E-Science-Tage 2023: Data to Knowledge},
 conference_url = {https://e-science-tage.de/index.php/en/agenda23},
 month = {March},
 pdf = {docs/2023_manuscript_poster_e_science_tage_1109-2.pdf},
 poster_url = {https://archiv.ub.uni-heidelberg.de/volltextserver/33137/},
 title = {Automated Software Metadata Conversion and Publication Based on CodeMeta},
 year = {2023}
}
```
abstract: Different metadata standards exist for different steps in the research software publication process. The Citation File Format (CFF) became very popular to provide information on how users are supposed to cite the software. For software archiving, DataCite is one of the established standards. The CodeMeta standard is an extension of schema.org specifically tailored to research software. All of these standards serve a purpose and are required for specific phases of the software lifecycle. However, research software developers should ideally not be burdened with maintaining a whole set of metadata files in different formats and largely overlapping content. This poses a risk both to data consistency and to adoption of good software publication practices in the first place. Therefore, we developed Python pipelines that put the developers in a position to only maintain a CodeMeta file. CFF and DataCite files are automatically generated based on the CodeMeta file. The open source pipelines (https://www.openCARP.org/CI) can easily be integrated in continuous integration and deployment environments and are being successfully used for the openCARP project (https://www.openCARP.org). Further aspects of the software lifecycle that are covered by the set of continuous integration scripts are creation of tagged releases including the update of the metadata files, creation of BagIt and BagPack files, deposition of releases in the RADAR research data repository, and the synchronization of documentation files in the repository to the project's webpage. We believe the automated metadata conversion based on CodeMeta can be a useful tool for many research software developers and can facilitate the adoption of good software publication practices by reducing the effort for developers.

Giacomo Rosilho de Souza, Simone Pezzuto, and Rolf Krause. Boundary Element Method for the Cell-by-Cell Model in Cardiac Electrophysiology.
15th World Congress on Computational Mechanics, Yokohama, Japan (Virtual), August 2022. [bibtex]

@abstract{rosilho:wccm22,
 address = {Yokohama, Japan (Virtual)},
 author = {Rosilho de Souza, Giacomo and Pezzuto, Simone and Krause, Rolf},
 booktitle = {15th World Congress on Computational Mechanics},
 month = {August},
 title = {Boundary Element Method for the Cell-by-Cell Model in Cardiac Electrophysiology},
 year = {2022}
}

Giacomo Rosilho de Souza, Simone Pezzuto, and Rolf Krause. Parallel-in-Time Multirate Explicit Stabilized method for the Monodomain model in Cardiac Electrophysiology.
PinT 2022: 11th Workshop on Parallel-in-Time Integration, Marseille, France, July 2022. [link] [bibtex]

@abstract{rosilho:pint22,
 address = {Marseille, France},
 author = {Rosilho de Souza, Giacomo and Pezzuto, Simone and Krause, Rolf},
 booktitle = {PinT 2022: 11th Workshop on Parallel-in-Time Integration},
 month = {July},
 title = {Parallel-in-Time Multirate Explicit Stabilized method for the Monodomain model in Cardiac Electrophysiology},
 url = {https://www.cirm-math.fr/RepOrga/2642/Abstracts/RozillodeSuza.pdf},
 year = {2022}
}

Simone Pezzuto, Giacomo Rosilho de Souza, and Rolf Krause. Boundary integral discretization of the cell-to-cell bidomain model of cardiac electrophysiology.
8th European Congress on Computational Methods in Applied Sciences and Engineering (ECCOMAS), Oslo, Norway, June 2022. [link] [bibtex]

@abstract{pezzuto-eccomas22,
 address = {Oslo, Norway},
 author = {Pezzuto, Simone and Rosilho de Souza, Giacomo and Krause, Rolf},
 booktitle = {8th European Congress on Computational Methods in
Applied Sciences and Engineering (ECCOMAS)},
 month = {June},
 title = {Boundary integral discretization of the cell-to-cell
bidomain model of cardiac electrophysiology},
 url = {https://www.eccomas2022.org/admin/files/fileabstract/a692.pdf},
 year = {2022}
}

Mark Potse. Microscale cardiac electrophysiology on exascale supercomputers.
SIAM Conference on Parallel Processing for Scientific Computing (PP22), Seattle, WA, USA, February 2022. [link] [bibtex]

@abstract{potse-pp22,
 address = {Seattle, WA, USA},
 author = {Potse, Mark},
 booktitle = {SIAM Conference on Parallel Processing for Scientific Computing (PP22)},
 month = {February},
 organization = {SIAM},
 title = {Microscale cardiac electrophysiology on exascale supercomputers},
 url = {https://www.siam.org/Portals/0/Conferences/PP22/PP22_ABSTRACTS.pdf},
 year = {2022}
}

theses

Zeina Chehade. Finite volume methods on unstructured meshes for the microscopic bidomain model in cardiac electrophysiology.
PhD thesis, Université de Bordeaux, 30 June 2025. [bibtex]

@phdthesis{chehade:thesis,
 author = {Zeina Chehade},
 month = {June},
 school = {Université de Bordeaux},
 title = {Finite volume methods on unstructured meshes for the
microscopic bidomain model in cardiac
electrophysiology},
 year = {2025}
}

Arun Thangamani. Optimized Code Generation for Parallel and Polyhedral Loop Nests using MLIR.
PhD thesis, Université de Strasbourg, September 2024. [pdf] [link] [bibtex]

@phdthesis{thangamani:thesis,
 author = {Thangamani, Arun},
 hal_id = {tel-04718259},
 month = {September},
 pdf = {https://inria.hal.science/tel-04718259v1/file/PhD_Thesis_Arun.pdf},
 school = {{}Université de Strasbourg},
 title = {{Optimized Code Generation for Parallel and Polyhedral Loop Nests using MLIR}},
 url = {https://inria.hal.science/tel-04718259},
 year = {2024}
}

Edoardo Centofanti. Efficient Solvers and Machine Learning Approaches in Cardiac Electrophysiology on High-Performance Computing Architectures.
PhD thesis, Università degli studi di Pavia, December 2024. [bibtex]

@phdthesis{centofantiThesis,
 author = {Centofanti, Edoardo},
 month = {December},
 school = {Universit{\`a} degli studi di Pavia},
 title = {Efficient Solvers and Machine Learning Approaches in Cardiac Electrophysiology
on High-Performance Computing Architectures},
 year = {2024}
}

Ngoc Mai Monica Huynh. Newton-Krylov Dual-Primal Methods for Implicit Time Discretizations in Cardiac Electrophysiology.
PhD thesis, Università degli studi di Pavia, December 2021. [bibtex]

@phdthesis{huynh2021newton,
 author = {Huynh, Ngoc Mai Monica},
 month = {December},
 school = {Universit{\`a} degli studi di Pavia},
 title = {Newton-Krylov Dual-Primal Methods for Implicit Time Discretizations in Cardiac Electrophysiology},
 year = {2021}
}

invited lectures

Vincent Loechner. Code Generation of Electrophysiology Kernels using MLIR.
GDR SOC2 Colloquium, CNRS, Lorient, France, July 2025. [link] [bibtex]

@lecture{loechner25SOC2,
 address = {Lorient, France},
 author = {Vincent Loechner},
 booktitle = {GDR SOC2 Colloquium, CNRS},
 month = {July},
 title = {Code Generation of Electrophysiology Kernels using MLIR},
 url = {https://gdr-soc2-2025.sciencesconf.org/},
 year = {2025}
}

Luca F. Pavarino. Parallel Newton-Krylov and Quasi-Newton Solvers for Nonlinear Cardiac Models.
WCCM2024 (World Congress in Computational Mechanics 2024), Vancouver, Canada, 24 July 2024. [link] [bibtex]

@lecture{pavarinoWCCM24,
 address = {Vancouver, Canada},
 author = {Pavarino, Luca F.},
 booktitle = {WCCM2024 (World Congress in Computational Mechanics 2024)},
 month = {July},
 title = {Parallel Newton-Krylov and Quasi-Newton Solvers for Nonlinear Cardiac Models},
 url = {https://www.wccm2024.org/},
 year = {2024}
}

Scacchi Pavarino, Luca F.. Organizer of INdAM Workshop on Mathematical and Numerical Modeling of the Cardiovascular System.
INdAM Workshop on Mathematical and Numerical Modeling of the Cardiovascular System, Rome, Italy, April 2024. [link] [bibtex]

@lecture{pavarinoDD22,
 address = {Rome, Italy},
 author = {Pavarino, Luca F., Scacchi, Simone, Vergara, Christian, Rozza, Gianluigi},
 booktitle = {INdAM Workshop on Mathematical and Numerical Modeling of the Cardiovascular System},
 month = {April},
 title = {Organizer of INdAM Workshop on Mathematical and Numerical Modeling of the Cardiovascular System},
 url = {http://www.mat.unimi.it/users/scacchi/wcardio24/},
 year = {2024}
}

Pratik Nayak. Scalable distributed preconditioners in Ginkgo.
International Conference On Preconditioning Techniques For Scientific and Industrial Applications, Atlanta, GA, USA, 12 June 2024. [link] [bibtex] [abstract]
```
@lecture{nayak:precond24,
 address = {Atlanta, GA, USA},
 author = {Nayak, Pratik},
 booktitle = {International Conference On Preconditioning Techniques
For Scientific and Industrial Applications},
 month = {June},
 title = {Scalable distributed preconditioners in Ginkgo},
 url = {https://www.math.emory.edu/~yxi26/Precond24/program.html#Bookmark22},
 year = {2024}
}
```
abstract: Efficient preconditioners are critical in scientific applications to accelerate the solution of linear systems. The latest exascale machines, being heterogenous and GPU-centric, require implementations that ensure efficient utilization of fine-grained parallelism of the GPUs, while distributing them over multiple of these heterogeneous nodes. In this talk, we will present our approach to performance-portable distributed preconditioners in Ginkgo. We will talk about our approach to distributed multigrid, which separates the coarsening methods from the multigrid level hierarchy enabling users to compose different smoothers, coarsening methods, coarse solvers and precisions in a very efficient manner. We will also briefly talk about domain decomposition preconditioners in Ginkgo such as Schwarz and balanced domain decomposition by constraints (BDDC). Finally, we will show performance results for these preconditioners and some examples from applications which use them.

Ngoc Mai Monica Huynh. Cardiac electrophysiology at microscopic level: scalable preconditioners and parallel solvers.
ECCOMAS, Lisbon, Portugal, June 2024. [link] [bibtex]

@lecture{huynhECCOMAS2024,
 address = {Lisbon, Portugal},
 author = {Huynh, Ngoc Mai Monica},
 booktitle = {ECCOMAS},
 month = {June},
 title = {Cardiac electrophysiology at microscopic level: scalable preconditioners and parallel solvers},
 url = {https://eccomas2024.org/event/contribution/5a1865a7-8e14-11ee-a683-000c29ddfc0c},
 year = {2024}
}

Fatemeh Chegini, Thomas Steinke, and Martin Weiser. Compressed communication and algebraic adaptivity for efficient BDDC preconditioners in cardiac simulation.
ECCOMAS, Lisbon, Portugal, June 2024. [link] [bibtex]

@lecture{WeiserECCOMAS2024,
 address = {Lisbon, Portugal},
 author = {Chegini, Fatemeh and Steinke, Thomas and Weiser, Martin},
 booktitle = {ECCOMAS},
 month = {June},
 title = {Compressed communication and algebraic adaptivity for
efficient {BDDC} preconditioners in cardiac
simulation},
 url = {https://eccomas2024.org/event/contribution/139090b2-95ab-11ee-8178-000c29ddfc0c},
 year = {2024}
}

Axel Loewe. Computational models of the human heart: linking information across species and scales.
5th Translational Workshop of the German Cardiac Society, Hamburg, Germany, September 2024. [bibtex]

@lecture{LoeweDGKtrans,
 address = {Hamburg, Germany},
 author = {Loewe, Axel},
 booktitle = {5th Translational Workshop of the German Cardiac Society},
 month = {September},
 title = {Computational models of the human heart: linking information across species and scales},
 year = {2024}
}

Ngoc Mai Monica Huynh. Preconditioned solvers for composite DG discretizations of cardiac cell-by-cell models.
16th World Congress on Computational Mechanics and 4th Pan American Congress on Computational Mechanics, Vancouver, Canada, July 2024. [bibtex]

@lecture{huynhWCCMC2024,
 address = {Vancouver, Canada},
 author = {Huynh, Ngoc Mai Monica},
 booktitle = {16th World Congress on Computational Mechanics and
4th Pan American Congress on Computational Mechanics},
 month = {July},
 title = {Preconditioned solvers for composite DG discretizations of cardiac cell-by-cell models},
 year = {2024}
}

Fatemeh Chegini, Thomas Steinke, and Martin Weiser. Efficiency and Accuracy in Large-Scale Cardiac Simulations with Compressed Communication and Algebraic Adaptivity in BDDC Preconditioners.
16th World Congress on Computational Mechanics and 4th Pan American Congress on Computational Mechanics, Vancouver, Canada, July 2024. [bibtex]

@lecture{cheginiWCCMC2024,
 address = {Vancouver, Canada},
 author = {Chegini, Fatemeh and Steinke, Thomas and Weiser, Martin},
 booktitle = {16th World Congress on Computational Mechanics and
4th Pan American Congress on Computational Mechanics},
 month = {July},
 title = {Efficiency and Accuracy in Large-Scale Cardiac Simulations with Compressed
Communication and Algebraic Adaptivity in BDDC Preconditioners},
 year = {2024}
}

Mark Potse. Modeling the heart, cell by cell.
INdAM Workshop: Mathematical and Numerical Modeling of the Cardiovascular System, Rome, Italy, April 2024. [pdf] [link] [bibtex]

@lecture{potse24_indam,
 address = {Rome, Italy},
 author = {Potse, Mark},
 booktitle = {INdAM Workshop: Mathematical and Numerical Modeling of the Cardiovascular System},
 hal_id = {hal-04838121v1},
 month = {April},
 pdf = {https://hal.archives-ouvertes.fr/hal-04838121v1/document},
 title = {Modeling the heart, cell by cell},
 url = {http://www.mat.unimi.it/users/scacchi/wcardio24/index.html},
 year = {2024}
}

Aslak Tveito. Numerical simulation of the electrophysiology of stem cell-derived cardiomyocytes in microphysiological systems.
INdAM Workshop: Mathematical and Numerical Modeling of the Cardiovascular System, Rome, Italy, April 2024. [link] [bibtex]

@lecture{tveito24_indam,
 address = {Rome, Italy},
 author = {Tveito, Aslak},
 booktitle = {INdAM Workshop: Mathematical and Numerical Modeling of the Cardiovascular System},
 month = {April},
 title = {Numerical simulation of the electrophysiology of
stem cell-derived cardiomyocytes in
microphysiological systems },
 url = {http://www.mat.unimi.it/users/scacchi/wcardio24/index.html},
 year = {2024}
}

Ngoc Mai Monica Huynh. Tailoring preconditioners for enhanced efficiency in cardiac modeling: insights from Domain Decomposition.
INdAM Workshop: Mathematical and Numerical Modeling of the Cardiovascular System, Rome, Italy, April 2024. [link] [bibtex]

@lecture{huynh_indam,
 address = {Rome, Italy},
 author = {Huynh, Ngoc Mai Monica},
 booktitle = {INdAM Workshop: Mathematical and Numerical Modeling of the Cardiovascular System},
 month = {April},
 title = {Tailoring preconditioners for enhanced efficiency in cardiac modeling: insights from Domain Decomposition},
 url = {http://www.mat.unimi.it/users/scacchi/wcardio24/index.html},
 year = {2024}
}

Fatemeh Chegini, Thomas Steinke, and Martin Weiser. Efficient simulation of cardiac electrophysiology with algebraic adaptivity.
INdAM Workshop: Mathematical and Numerical Modeling of the Cardiovascular System, Rome, Italy, April 2024. [link] [bibtex]

@lecture{chegini_indam,
 address = {Rome, Italy},
 author = {Chegini, Fatemeh and Steinke, Thomas and Weiser, Martin},
 booktitle = {INdAM Workshop: Mathematical and Numerical Modeling of the Cardiovascular System},
 month = {April},
 title = {Efficient simulation of cardiac electrophysiology with algebraic adaptivity},
 url = {http://www.mat.unimi.it/users/scacchi/wcardio24/index.html},
 year = {2024}
}

Hermenegild Arevalo. Understanding and Treating Cardiac Disease Using Personalized Heart Models.
Simula Seminar Series: Personalised medicine and the digital transition in healthcare, Oslo, Norway, April 2024. [bibtex]

@lecture{arevalo24_simsem,
 address = {Oslo, Norway},
 author = {Arevalo, Hermenegild},
 month = {April},
 publisher = {Simula Seminar Series: Personalised medicine and the digital transition in healthcare},
 title = {Understanding and Treating Cardiac Disease Using Personalized Heart Models},
 year = {2024}
}

Mark Potse. Modeling the heart cell by cell.
Computing in Cardiology 2024, Karlsruhe, September 2024. [pdf] [link] [bibtex]

@lecture{potse24cinc,
 address = {Karlsruhe},
 author = {Potse, Mark},
 booktitle = {Computing in Cardiology 2024},
 hal_id = {hal-04838217v1},
 month = {September},
 pdf = {https://hal.archives-ouvertes.fr/hal-04838217v1/document},
 title = {Modeling the heart cell by cell},
 url = {https://cinc2024.org/program/sunday-symposium},
 year = {2024}
}

Edoardo Centofanti. Parallel Performance of Robust and Scalable Multilevel Preconditioners for the Cell-by-Cell Model.
9th European Congress on Computational Methods in Applied Sciences and Engineering, Lisbon, Portugal, June 2024. [link] [bibtex]

@lecture{eccomas_centofanti,
 address = {Lisbon, Portugal},
 author = {Centofanti, Edoardo},
 booktitle = {9th European Congress on Computational Methods in Applied Sciences and Engineering},
 month = {June},
 title = {Parallel Performance of Robust and Scalable Multilevel Preconditioners for the Cell-by-Cell Model},
 url = {https://eccomas2024.org/event/sessions_search?search=MS199},
 year = {2024}
}

Fatemeh Chegini, Thomas Steinke, and Martin Weiser. Efficient Simulation of Cardiac Electrophysiology with Algebraic Adaptivity.
9th European Congress on Computational Methods in Applied Sciences and Engineering, Lisbon, Portugal, June 2024. [bibtex]

@lecture{eccomas_chegini,
 address = {Lisbon, Portugal},
 author = {Chegini, Fatemeh and Steinke, Thomas and Weiser, Martin},
 booktitle = {9th European Congress on Computational Methods in Applied Sciences and Engineering},
 month = {June},
 title = {Efficient Simulation of Cardiac Electrophysiology with Algebraic Adaptivity},
 year = {2024}
}

Vincent Loechner. Optimized Code Generation of Electrophysiology Kernels using MLIR.
Workshop on Compiler-assisted Correctness Checking and Performance Optimization for HPC (C3PO), Hamburg, Germany, May 2024. [link] [bibtex]

@lecture{LoechnerC3PO,
 address = {Hamburg, Germany},
 author = {Loechner, Vincent},
 booktitle = {Workshop on Compiler-assisted Correctness Checking and
Performance Optimization for {HPC} {(C3PO)}},
 month = {May},
 title = {Optimized Code Generation of Electrophysiology Kernels using {MLIR}},
 url = {https://c3po-workshop.github.io/2024/program},
 year = {2024}
}

Axel Loewe. Digital chimeras of the human atria to enable in silico trials at scale.
Fickle Heart: The intersection of UQ, AI and Digital Twins, Isaac Newton Institute, Cambridge, UK, June 2024. [bibtex]

@lecture{LoeweFickle,
 address = {Isaac Newton Institute, Cambridge, UK},
 author = {Loewe, Axel},
 booktitle = {Fickle Heart: The intersection of UQ, AI and Digital Twins},
 month = {June},
 title = {Digital chimeras of the human atria to enable in silico trials at scale},
 year = {2024}
}

Mark Potse. Modeling the heart at the micrometer scale.
49th International Congress on Electrocardiology, Lund, Sweden, June 2024. [pdf] [link] [bibtex]

@lecture{potse:ICE24,
 address = {Lund, Sweden},
 author = {Potse, Mark},
 booktitle = {49th International Congress on Electrocardiology},
 hal_id = {hal-04838191v1},
 month = {June},
 pdf = {https://hal.archives-ouvertes.fr/hal-04838191v1/document},
 title = {Modeling the heart at the micrometer scale},
 url = {https://www.mkon.nu/ice2024/Scientificprogram},
 year = {2024}
}

Axel Loewe. Computational modeling and simulation of the ECG as an enabling technology for machine learning.
49th International Congress on Electrocardiology, Lund, Sweden, June 2024. [link] [bibtex]

@lecture{LoeweICE,
 address = {Lund, Sweden},
 author = {Loewe, Axel},
 booktitle = {49th International Congress on Electrocardiology},
 month = {June},
 title = {Computational modeling and simulation of the {ECG} as an
enabling technology for machine learning},
 url = {https://www.mkon.nu/ice2024/Scientificprogram},
 year = {2024}
}

Axel Loewe. Real-world and synthetic ECG data for prediction models: synergistic combination of mechanistic and data-driven models.
Atrial Signals, Maastricht, The Netherlands, June 2024. [bibtex]

@lecture{LoeweAS,
 address = {Maastricht, The Netherlands},
 author = {Loewe, Axel},
 booktitle = {Atrial Signals},
 month = {June},
 title = {Real-world and synthetic {ECG} data for prediction models:
synergistic combination of mechanistic and data-driven models},
 year = {2024}
}

Martin Weiser. Advanced Computing for Medicine @ ZIB - An Overview.
ICAM Workshop, Lugano, Switzerland, 2024. [bibtex]

@lecture{Weiser-ICAM2024,
 address = {Lugano, Switzerland},
 author = {Weiser, Martin},
 booktitle = {ICAM Workshop},
 title = {Advanced Computing for Medicine @ {ZIB} - An Overview},
 year = {2024}
}

Axel Loewe. Modeling & simulation of cardiac function: combining mechanistic models and artificial intelligence.
Medical Informatics Seminar, Augsburg, Germany, May 2024. [bibtex]

@lecture{LoeweAugsburg,
 address = {Augsburg, Germany},
 author = {Loewe, Axel},
 booktitle = {Medical Informatics Seminar},
 month = {May},
 title = {Modeling \& simulation of cardiac function:
combining mechanistic models and artificial intelligence},
 year = {2024}
}

Fritz Göbel, Terry Cojean, Hartwig Anzt, and Marcel Koch. Implementing a GPU-resident BDDC preconditioner for cardiac simulations on sub-cellular resolution.
SIAM Conference on Parallel Processing for Scientific Computing, Baltimore, Maryland, USA, March 2024. [bibtex]

@lecture{siampp,
 address = {Baltimore, Maryland, USA},
 author = {Göbel, Fritz and Cojean, Terry and Anzt, Hartwig and Koch, Marcel},
 booktitle = {SIAM Conference on Parallel Processing for Scientific Computing},
 month = {March},
 title = {Implementing a {GPU}-resident {BDDC} preconditioner for cardiac
simulations on sub-cellular resolution},
 year = {2024}
}

Edoardo Centofanti. Parallel Performance of Scalable Multilevel Preconditioners for the Cardiac Cell-by-Cell Model.
28th International Conference on Domain Decomposition Methods (DD28), KAUST, Saudi Arabia, January 2024. [link] [bibtex]

@lecture{DD28_centofanti,
 address = {KAUST, Saudi Arabia},
 author = {Centofanti, Edoardo},
 booktitle = {28th International Conference on Domain Decomposition Methods (DD28)},
 month = {January},
 title = {Parallel Performance of Scalable Multilevel Preconditioners for the Cardiac Cell-by-Cell Model},
 url = {https://dd28.kaust.edu.sa/program/},
 year = {2024}
}

Fatemeh Chegini and Martin Weiser. Efficient Domain Decomposition Reconditioners For Time Stepping In EMI Models.
Seventh Chilean Workshop on Numerical Analysis of Partial Differential Equations (WONAPDE), Concepción, Chile, January 2024. [bibtex]

@lecture{WONAPDE_chegini,
 address = {Concepción, Chile},
 author = {Chegini, Fatemeh and Weiser, Martin},
 booktitle = {Seventh Chilean Workshop on Numerical Analysis of Partial Differential Equations (WONAPDE)},
 month = {January},
 title = {Efficient Domain Decomposition Reconditioners For Time Stepping In {EMI} Models},
 year = {2024}
}

Martin Weiser. Adaptive multirate integration of cardiac electrophysiology in the EMI model.
RICAM Special Semester on Mathematical Methods in Medicine: Cardiovascular Modeling and simulation, Linz, Austria, November 2024. [bibtex]

@lecture{weiser-RICAM2023,
 address = {Linz, Austria},
 author = {Weiser, Martin},
 booktitle = {RICAM Special Semester on Mathematical Methods in Medicine: Cardiovascular Modeling and simulation},
 month = {November},
 title = {Adaptive multirate integration of cardiac electrophysiology in the {EMI} model},
 year = {2024}
}

Simone Pezzuto. Closing the gaps between virtual and physical models.
NumeriCor Workshop, Graz, Austria, September 2024. [bibtex]

@lecture{pezzutoGraz24,
 address = {Graz, Austria},
 author = {Pezzuto, Simone},
 booktitle = {NumeriCor Workshop},
 month = {September},
 title = {Closing the gaps between virtual and physical models},
 year = {2024}
}

Simone Pezzuto. La matematica del cuore: Come costruire il gemello digitale del motore della vita.
CISMED, Trento, Italy, May 2024. [link] [bibtex]

@lecture{pezzutoCISMED24,
 address = {Trento, Italy},
 author = {Pezzuto, Simone},
 booktitle = {CISMED},
 month = {May},
 title = {La matematica del cuore:
Come costruire il gemello digitale del motore della vita},
 url = {https://webmagazine.unitn.it/evento/cismed/119972/modelli-matematici-del-cuore-e-della-stimolazione-cardiaca},
 year = {2024}
}

Simone Pezzuto. Probabilistic learning of the cardiac activation from the ECG.
INdAM Workshop "Modeling of the Cardiovascular System", Rome, Italy, April 2024. [link] [bibtex]

@lecture{pezzutoRome24,
 address = {Rome, Italy},
 author = {Pezzuto, Simone},
 booktitle = {INdAM Workshop "Modeling of the Cardiovascular System"},
 month = {April},
 title = {Probabilistic learning of the cardiac activation from the {ECG}},
 url = {http://www.mat.unimi.it/users/scacchi/wcardio24/program.pdf},
 year = {2024}
}

Simone Pezzuto. Laboratory of Mathematics for Biology and Medicine.
ICAM Workshop, Lugano, Switzerland, May 2024. [link] [bibtex]

@lecture{pezzutoICAM24,
 address = {Lugano, Switzerland},
 author = {Pezzuto, Simone},
 booktitle = {ICAM Workshop},
 month = {May},
 title = {Laboratory of Mathematics for Biology and Medicine},
 url = {https://icam.unipv.it/news/icam-workshop-2024/},
 year = {2024}
}

Simone Pezzuto. Scientific Machine Learning for Precision Cardiology.
Algoritmy 2024, High Tatra Mountains, Slovakia, March 2024. [link] [bibtex]

@lecture{pezzutoTatra24,
 address = {High Tatra Mountains, Slovakia},
 author = {Pezzuto, Simone},
 booktitle = {Algoritmy 2024},
 month = {March},
 title = {Scientific Machine Learning for Precision Cardiology},
 url = {https://www.math.sk/alg2024/minisymposia-abstracts/#machine_learning},
 year = {2024}
}

Simone Pezzuto. Sex-specific computational electrophysiological models of AF to guide therapies.
DGK 2024, Mannheim, Germany, April 2024. [link] [bibtex]

@lecture{pezzutoDGK24,
 address = {Mannheim, Germany},
 author = {Pezzuto, Simone},
 booktitle = {DGK 2024},
 month = {April},
 title = {Sex-specific computational electrophysiological models
of AF to guide therapies},
 url = {https://herzmedizin.de/fuer-aerzte-und-fachpersonal/kongresse/dgk-jahrestagung-2024/programm/sex_differences_in_atrial_fibrillation__from_epidemiology_and_me.html},
 year = {2024}
}

Simone Pezzuto. Physics-informed Machine Learning for Precision Cardiology.
Computational Biology Seminar, Oxford, virtual, March 2024. [bibtex]

@lecture{pezzutoOxford24,
 address = {virtual},
 author = {Pezzuto, Simone},
 booktitle = {Computational Biology Seminar, Oxford},
 month = {March},
 title = {Physics-informed Machine Learning for Precision Cardiology},
 year = {2024}
}

Luca F. Pavarino. Review and roadmap of MICROCARD WP5 Tasks.
Microcard WP3-5 workshop, ZIB, Berlin, Germany, 17 March 2023. [link] [bibtex]

@lecture{pavarinoZIB23,
 address = {ZIB, Berlin, Germany},
 author = {Pavarino, Luca F.},
 booktitle = {Microcard WP3-5 workshop},
 month = {March},
 title = {Review and roadmap of MICROCARD WP5 Tasks},
 url = {https://www.zib.de/de},
 year = {2023}
}

Luca F. Pavarino. Role of infarct scar dimensions, border zone repolarization properties and anisotropy in the origin and maintenance of cardiac reentry.
DynamicsDays Europe, Napoli, Italy, 4 September 2023. [link] [bibtex]

@lecture{pavarinoDynamicDays23,
 address = {Napoli, Italy},
 author = {Pavarino, Luca F.},
 booktitle = {DynamicsDays Europe},
 month = {September},
 title = {Role of infarct scar dimensions, border zone repolarization properties and anisotropy in the origin and maintenance of cardiac reentry},
 url = {https://sites.google.com/view/dynamicsdayseurope2023},
 year = {2023}
}

Luca F. Pavarino. Scalable parallel solvers for cardiac reaction-diffusion cell-by-cell models.
RICAM Workshop2 on Cardiovascular Modeling and simulation, Linz, Austria, 13 November 2023. [link] [bibtex]

@lecture{pavarinoRICAM23,
 address = {Linz, Austria},
 author = {Pavarino, Luca F.},
 booktitle = {RICAM Workshop2 on Cardiovascular Modeling and simulation},
 month = {November},
 title = {Scalable parallel solvers for cardiac reaction-diffusion cell-by-cell models},
 url = {https://www.ricam.oeaw.ac.at/specsem/specsem2023/workshop2/},
 year = {2023}
}

Luca Pavarino, Ngoc Mai Monica Huynh, Simone Scacchi, Fatemeh Chegini, and Martin Weiser. Scalable domain decomposition solvers for cardiac reaction-diffusion cell-by-cell models.
10th International Congress on Industrial and Applied Mathematics (ICIAM), Tokyo, Japan, 22 August 2023. [link] [bibtex] [abstract]
```
@lecture{pavarinoICIAM23,
 address = {Tokyo, Japan},
 author = {Pavarino, Luca and Huynh, Ngoc Mai Monica and Scacchi, Simone and Chegini, Fatemeh and Weiser, Martin},
 booktitle = {10th International Congress on Industrial and Applied Mathematics (ICIAM)},
 month = {August},
 title = {Scalable domain decomposition solvers for cardiac
reaction-diffusion cell-by-cell models},
 url = {https://iciam2023.org/registered_data?id=00911#04144},
 year = {2023}
}
```
abstract: Scalable preconditioners are constructed and analyzed for the iterative solution of composite Discontinuous Galerkin discretizations of reaction-diffusion systems of ordinary and partial differential equations arising in cardiac cell-by-cell models. These models lead to large-scale ill-conditioned discrete systems which have discontinuous global solutions across cells (subdomains) boundaries. A scalable convergence rate bound is proved for dual-primal cell-by-cell preconditioned operators. Numerical tests validate this bound and investigate its dependence on the discretization parameters.
Ngoc Mai Monica Huynh. Scalable multilevel preconditioners for hybrid-DG discretizations of nonlinear cell-by-cell cardiac models.
10th International Congress on Industrial and Applied Mathematics (ICIAM), Tokyo, Japan, 21 August 2023. [link] [bibtex] [abstract]
```
@lecture{huynhICIAM23,
 address = {Tokyo, Japan},
 author = {Huynh, Ngoc Mai Monica},
 booktitle = {10th International Congress on Industrial and Applied Mathematics (ICIAM)},
 month = {August},
 title = {Scalable multilevel preconditioners for hybrid-DG discretizations of nonlinear
cell-by-cell cardiac models},
 url = {https://iciam2023.org/registered_data?id=00749#01460},
 year = {2023}
}
```
abstract: We present theoretical and numerical results for a scalable and quasi-optimal BDDC preconditioner for Discontinuous Galerkin discretizations of cardiac cell-by-cell models in order to approximate the discontinuous nature of cellular networks. The resulting discrete cell-by-cell models have discontinuous global solutions across the cell boundaries, hence the proposed BDDC preconditioner is based on appropriate dual and primal spaces with additional constraints which transfer information between cells/subdomains without influencing the overall discontinuity of the global solution.

Aslak Tveito. Bidomain/Monodomain=KNM/SKNM.
EMIx Workshop, Oslo, Norway, August 2023. [bibtex]

@lecture{tveito23_emix,
 address = {Oslo, Norway},
 author = {Tveito, Aslak},
 booktitle = {EMIx Workshop},
 month = {August},
 title = {Bidomain/Monodomain={KNM/SKNM}},
 year = {2023}
}

Hermenegild Arevalo. Numerical modeling of cardiac electrophysiology at the cellular scale (MICROCARD EuroHPC project).
EMIx Workshop, Oslo, Norway, August 2023. [bibtex]

@lecture{arevalo23_emix,
 address = {Oslo, Norway},
 author = {Arevalo, Hermenegild},
 month = {August},
 publisher = {EMIx Workshop},
 title = {Numerical modeling of cardiac electrophysiology at
the cellular scale ({MICROCARD EuroHPC} project)},
 year = {2023}
}

Axel Loewe. Digital chimeras to enable in silico clinical trials of ablation strategies to terminate atrial fibrillation and prevent recurrence.
RICAM Special Semester on Mathematical Methods in Medicine, Linz, Austria, 30 November 2023. [bibtex]

@lecture{loewe-RICAM,
 address = {Linz, Austria},
 author = {Axel Loewe},
 month = {November},
 publisher = {RICAM Special Semester on Mathematical Methods in Medicine},
 title = {Digital chimeras to enable in silico clinical trials of
ablation strategies to terminate atrial fibrillation
and prevent recurrence},
 year = {2023}
}

Mark Potse. Numerical modeling of cardiac electrophysiology at the cellular scale.
Symposium ``Where computation meets cardiology'', Maastricht, The Netherlands, November 2023. [bibtex]

@lecture{potse-mumc23,
 address = {Maastricht, The Netherlands},
 author = {Potse, Mark},
 booktitle = {Symposium ``Where computation meets cardiology''},
 month = {November},
 title = {Numerical modeling of cardiac electrophysiology at the cellular scale},
 year = {2023}
}

Edoardo Centofanti. Parallel Performance of Robust and Scalable Multilevel Preconditioners in Cardiac Electrophysiology.
10th International Congress on Industrial and Applied Mathematics (ICIAM), Tokyo, Japan, August 2023. [link] [bibtex]

@lecture{iciam_centofanti,
 address = {Tokyo, Japan},
 author = {Centofanti, Edoardo},
 booktitle = {10th International Congress on Industrial and Applied Mathematics (ICIAM)},
 month = {August},
 title = {Parallel Performance of Robust and Scalable Multilevel Preconditioners in Cardiac Electrophysiology},
 url = {https://iciam2023.org/registered_data?id=00708},
 year = {2023}
}

Fritz Göbel, Hartwig Anzt, Terry Cojean, and Marcel Koch. Implementing Platform Portable Solvers and Preconditioners for Cardiac Simulations in the MICROCARD Project.
10th International Congress on Industrial and Applied Mathematics (ICIAM), Tokyo, Japan, August 2023. [bibtex]

@lecture{iciam,
 address = {Tokyo, Japan},
 author = {Göbel, Fritz and Anzt, Hartwig and Cojean, Terry and Koch, Marcel},
 booktitle = {10th International Congress on Industrial and Applied Mathematics (ICIAM)},
 month = {August},
 title = {Implementing Platform Portable Solvers and Preconditioners
for Cardiac Simulations in the {MICROCARD} Project},
 year = {2023}
}

Lea Strubberg. To couple models for cardiac electrophysiology with transparent interface conditions.
International Conference on Operations Research 2023, Hamburg, Germany, August 2023. [bibtex]

@lecture{strubberg:OR23,
 address = {Hamburg, Germany},
 author = {Strubberg, Lea},
 booktitle = {International Conference on Operations Research 2023},
 month = {August},
 title = {To couple models for cardiac electrophysiology with transparent interface conditions},
 year = {2023}
}

Fatemeh Chegini. Higher order time Integration for EMI Cardiac Electrophysiology Simulations with Nested Subset Selection and BDDC Preconditioning.
10th International Congress on Industrial and Applied Mathematics (ICIAM), Tokyo, Japan, August 2023. [bibtex]

@lecture{chegini:iciam23,
 address = {Tokyo, Japan},
 author = {Chegini, Fatemeh},
 booktitle = {10th International Congress on Industrial and Applied Mathematics (ICIAM)},
 month = {August},
 title = {Higher order time Integration for {EMI} Cardiac
Electrophysiology Simulations with Nested Subset
Selection and {BDDC} Preconditioning},
 year = {2023}
}

Fritz Göbel, Hartwig Anzt, Terry Cojean, and Marcel Koch. Distributed Preconditioning for Cardiac Simulations on modern GPUs with BDDC.
21st Copper Mountain Conference On Multigrid Methods, Copper Mountain, Colorado, USA, April 2023. [bibtex]

@lecture{multigrid-conference,
 address = {Copper Mountain, Colorado, USA},
 author = {Göbel, Fritz and Anzt, Hartwig and Cojean, Terry and Koch, Marcel},
 booktitle = {21st Copper Mountain Conference On Multigrid Methods},
 month = {April},
 title = {Distributed Preconditioning for Cardiac Simulations on modern {GPUs} with {BDDC}},
 year = {2023}
}

Mark Potse. Large Numerical modeling of cardiac electrophysiology at the cellular scale.
EuroHPC Summit: European Supercomputing Excellence in the Exascale Era, Göteborg, Sweden, March 2023. [link] [bibtex]

@lecture{potse23eurohpc,
 address = {G{\"o}teborg, Sweden},
 author = {Potse, Mark},
 booktitle = {EuroHPC Summit: European Supercomputing Excellence
in the Exascale Era},
 month = {March},
 organization = {EuroHPC},
 title = {Large Numerical modeling of cardiac electrophysiology at the cellular scale},
 url = {https://www.eurohpcsummit.eu/#monday},
 year = {2023}
}

Ngoc Mai Monica Huynh. Scalable BDDC preconditioners for hybrid DG discretizations of cardiac microscopic models.
VII ECCOMAS Young Investigators Conference, Oporto, Portugal, June 2023. [bibtex]

@lecture{huynhECCOMAS23,
 address = {Oporto, Portugal},
 author = {Huynh, Ngoc Mai Monica},
 booktitle = {VII ECCOMAS Young Investigators Conference},
 month = {June},
 title = {Scalable {BDDC} preconditioners for hybrid {DG} discretizations of cardiac microscopic models},
 year = {2023}
}

Ngoc Mai Monica Huynh. Robust preconditioned solvers for cardiac electrical models at microscales.
Math2Product 2023, Taormina, Italy, June 2023. [bibtex]

@lecture{huynhM2P2023,
 address = {Taormina, Italy},
 author = {Huynh, Ngoc Mai Monica},
 booktitle = {Math2Product 2023},
 month = {June},
 title = {Robust preconditioned solvers for cardiac electrical models at microscales},
 year = {2023}
}

Fatemeh Chegini. Implementing the µCARP simulator.
openCARP User Workshop, Karlsruhe, Germany, May 2023. [bibtex]

@lecture{chegini:openCARP23,
 address = {Karlsruhe, Germany},
 author = {Chegini, Fatemeh},
 booktitle = {openCARP User Workshop},
 month = {May},
 title = {Implementing the {µCARP} simulator},
 year = {2023}
}

Martin Weiser. The EMI model and some implications on discretization and solution.
openCARP User Workshop, Karlsruhe, Germany, May 2023. [bibtex]

@lecture{weiser:openCARP23,
 address = {Karlsruhe, Germany},
 author = {Weiser, Martin},
 booktitle = {openCARP User Workshop},
 month = {May},
 title = {The {EMI} model and some implications on discretization and solution},
 year = {2023}
}

Ngoc Mai Monica Huynh. Dual-primal domain decomposition preconditioners for composite discontinuous Galerkin discretizations in cardiac electrophysiology.
Simula Research Laboratory, Norway, May 2023. [bibtex]

@lecture{huynhEMIx23,
 address = {Simula Research Laboratory, Norway},
 author = {Huynh, Ngoc Mai Monica},
 month = {May},
 title = {Dual-primal domain decomposition preconditioners for composite discontinuous 
Galerkin discretizations in cardiac electrophysiology},
 year = {2023}
}

Ngoc Mai Monica Huynh. BDDC preconditioners for hybrid discontinuous Galerkin discretizations in cardiac electrophysiology.
SIAM Conference on Computational Science and Engineering, Amsterdam, NL, 1 March 2023. [bibtex]

@lecture{huynhSIAMCSE2023,
 address = {Amsterdam, NL},
 author = {Huynh, Ngoc Mai Monica},
 booktitle = {SIAM Conference on Computational Science and Engineering},
 month = {March},
 title = {{BDDC} preconditioners for hybrid discontinuous {Galerkin} discretizations in cardiac electrophysiology},
 year = {2023}
}

Simone Pezzuto. Scientific Machine Learning for Cardiac Electrophysiology Applications.
CCMC Workshop, Maastricht, The Netherlands, November 2023. [bibtex]

@lecture{pezzutoMaastricht23,
 address = {Maastricht, The Netherlands},
 author = {Pezzuto, Simone},
 booktitle = {CCMC Workshop},
 month = {November},
 title = {Scientific Machine Learning for Cardiac Electrophysiology Applications},
 year = {2023}
}

Simone Pezzuto. Scientific Machine Learning for Cardiac Electrophysiology Applications.
Special Semester on Mathematical Methods in Medicine, Linz, Austria, November 2023. [link] [bibtex]

@lecture{pezzutoRICAM23,
 address = {Linz, Austria},
 author = {Pezzuto, Simone},
 booktitle = {Special Semester on Mathematical Methods in Medicine},
 month = {November},
 title = {Scientific Machine Learning for Cardiac Electrophysiology Applications},
 url = {https://www.ricam.oeaw.ac.at/specsem/specsem2023/workshop2/},
 year = {2023}
}

Simone Pezzuto. La matematica del cuore: come costruire il gemello digitale del motore della vita.
Scuola Estiva di Orientamento, Rovereto, Italy, 31 August 2023. [bibtex]

@lecture{Pezzuto2023Orienta,
 address = {Rovereto, Italy},
 author = {Pezzuto, Simone},
 booktitle = {Scuola Estiva di Orientamento},
 month = {August},
 title = {La matematica del cuore: come costruire il gemello digitale del
motore della vita},
 year = {2023}
}

Simone Pezzuto, Lia Gander, and Rolf Krause. An anisotropic eikonal model for cardiac repolarization and arrhythmias.
10th International Congress on Industrial and Applied Mathematics (ICIAM), Tokyo, Japan, 27 June 2023. [link] [bibtex]

@lecture{Pezzuto2023ICIAM,
 address = {Tokyo, Japan},
 author = {Pezzuto, Simone and Gander, Lia and Krause, Rolf},
 booktitle = {10th International Congress on Industrial and Applied Mathematics (ICIAM)},
 month = {June},
 title = {An anisotropic eikonal model for cardiac repolarization and arrhythmias},
 url = {https://iciam2023.org/registered_data?id=00708#03521},
 year = {2023}
}

Giacomo Rosilho de Souza, Rolf Krause, and Simone Pezzuto. Boundary Integral Formulation of the Cell-by-Cell Model of Cardiac Electrophysiology.
Simula Research Laboratory, Norway, June 2023. [bibtex]

@lecture{pezzutoEMIx23,
 address = {Simula Research Laboratory, Norway},
 author = {Rosilho de Souza, Giacomo and Krause, Rolf and Pezzuto, Simone},
 month = {June},
 title = {Boundary Integral Formulation of the Cell-by-Cell Model of
Cardiac Electrophysiology},
 year = {2023}
}

Giacomo Rosilho de Souza, Rolf Krause, and Simone Pezzuto. Boundary Integral Formulation of the Cell-by-Cell Model of Cardiac Electrophysiology.
SIAM Conference on Computational Science and Engineering, Amsterdam, The Netherlands, February 2023. [link] [bibtex]

@lecture{pezzutoSIAM23,
 address = {Amsterdam, The Netherlands},
 author = {Rosilho de Souza, Giacomo and Krause, Rolf and Pezzuto, Simone},
 booktitle = {SIAM Conference on Computational Science and Engineering},
 month = {February},
 title = {Boundary Integral Formulation of the Cell-by-Cell Model of
Cardiac Electrophysiology},
 url = {https://meetings.siam.org/sess/dsp_talk.cfm?p=125540},
 year = {2023}
}

Martin Weiser, Fatemeh Chegini, and Thomas Steinke. Adaptive multirate integration of cardiac electrophysiology with spectral deferred correction methods.
SIAM Conference on Computational Science and Engineering, Amsterdam, NL, 3 March 2023. [bibtex]

@lecture{weiserSIAMCSE2023,
 address = {Amsterdam, NL},
 author = {Weiser, Martin and Chegini, Fatemeh and Steinke, Thomas},
 booktitle = {SIAM Conference on Computational Science and Engineering},
 month = {March},
 title = {Adaptive multirate integration of cardiac electrophysiology with spectral deferred correction methods},
 year = {2023}
}

Edward Vigmond. Challenges and opportunities for cardiac simulation at exascale.
HiPEAC 2023, Toulouse, January 2023. (HeLP-DC Workshop on Heterogeneous and Low-Power Data Center technologies) [bibtex]

@lecture{vigmond23hipeac,
 address = {Toulouse},
 author = {Vigmond, Edward},
 booktitle = {HiPEAC 2023},
 month = {January},
 title = {Challenges and opportunities for cardiac simulation at exascale},
 year = {2023}
}

Luca F. Pavarino. Scalable multilevel preconditioners for cardiac electro-mechanics.
IMG2022 (International Multigrid Conference 2022), USI, Lugano, Switzerland, 24 August 2022. [link] [bibtex]

@lecture{pavarinoUSI2022,
 address = {USI, Lugano, Switzerland},
 author = {Pavarino, Luca F.},
 booktitle = {IMG2022 (International Multigrid Conference 2022)},
 month = {August},
 title = {Scalable multilevel preconditioners for cardiac electro-mechanics},
 url = {https://www.img2022.usi.ch/},
 year = {2022}
}

Martin Weiser. Exploiting the Flexibility of Spectral Deferred Correction Methods.
TU Hamburg, 14 November 2022. [bibtex]

@lecture{weiserTUHH2022,
 address = {TU Hamburg},
 author = {Weiser, Martin},
 month = {November},
 title = {Exploiting the Flexibility of Spectral Deferred Correction Methods},
 year = {2022}
}

Fatemeh Chegini and Martin Weiser. Higher order time integration with algebraic adaptivity in a cell by cell discretization of cardiac excitation.
WCCMC 2022, Yokohama, Japan, August 2022. [bibtex]

@lecture{cheginiWCCMC22,
 address = {Yokohama, Japan},
 author = {Chegini, Fatemeh and Weiser, Martin},
 booktitle = {WCCMC 2022},
 month = {August},
 title = {Higher order time integration with algebraic adaptivity in a cell by cell discretization of cardiac excitation},
 year = {2022}
}

Edoardo Centofanti. Parallel Performance of Multigrid Preconditioners for the Cardiac Bidomain Model Using HPC Architectures.
International Multigrid Conference, Lugano, CH, August 2022. [link] [bibtex]

@lecture{centofantiIMG2022,
 address = {Lugano, CH},
 author = {Centofanti, Edoardo},
 booktitle = {International Multigrid Conference},
 month = {August},
 title = {Parallel Performance of Multigrid Preconditioners for the
Cardiac Bidomain Model Using {HPC} Architectures},
 url = {https://www.img2022.usi.ch/index.php?option=com_content&view=article&id=38&Itemid=305},
 year = {2022}
}

Martin Weiser and Fatemeh Chegini. Adaptive multirate integration of cardiac electrophysiology with spectral deferred correction methods.
International Multigrid Conference, Lugano, CH, 25 August 2022. [bibtex]

@lecture{weiserIMG2022,
 address = {Lugano, CH},
 author = {Weiser, Martin and Chegini, Fatemeh},
 booktitle = {International Multigrid Conference},
 month = {August},
 title = {Adaptive multirate integration of cardiac electrophysiology with spectral deferred correction methods},
 year = {2022}
}

Martin Weiser and Fatemeh Chegini. Adaptive multirate integration of cardiac electrophysiology with spectral deferred correction methods.
Computational and Mathematical Biomedical Engineering, Milan, Italy, 28 June 2022. [bibtex]

@lecture{weiserCMBE2022,
 address = {Milan, Italy},
 author = {Weiser, Martin and Chegini, Fatemeh},
 booktitle = {Computational and Mathematical Biomedical Engineering},
 month = {June},
 title = {Adaptive multirate integration of cardiac electrophysiology with spectral deferred correction methods},
 year = {2022}
}

Mark Potse. The MICROCARD project and gender.
#RESET your project with gender, 15 November 2022. (webinar) [link] [bibtex]

@lecture{potse-RESET3,
 author = {Potse, Mark},
 booktitle = {\#RESET your project with gender},
 month = {November},
 title = {The {MICROCARD} project and gender},
 url = {https://wereset.eu/newsroom/news/webinar-reset-your-research-project-with-gender/},
 year = {2022}
}

Yves Coudière and Zeina Chehade. Towards finite volume methods for the cardiac micromodel.
Workshop on Discrete Duality Finite Volume Method and Applications, Marseille, France, October 2022. [bibtex]

@lecture{coudiere22cirm,
 address = {Marseille, France},
 author = {Coudi\`ere, Yves and Chehade, Zeina},
 booktitle = {Workshop on Discrete Duality Finite Volume Method and Applications},
 month = {October},
 title = {Towards finite volume methods for the cardiac micromodel},
 year = {2022}
}

Martin Weiser. Theoretically optimal inexact spectral deferred correction methods.
U Pavia, Italy, June 2022. [bibtex]

@lecture{weiser22Pavia,
 address = {U Pavia, Italy},
 author = {Weiser, Martin},
 month = {June},
 title = {Theoretically optimal inexact spectral deferred correction methods},
 year = {2022}
}

Mark Potse. Modeling the heart, cell by cell.
HiPEAC 2022, Budapest, June 2022. (HeLP-DC Workshop on Heterogeneous and Low-Power Data Center technologies) [link] [bibtex]

@lecture{potse22hipeac,
 address = {Budapest},
 author = {Potse, Mark},
 booktitle = {HiPEAC 2022},
 month = {June},
 title = {Modeling the heart, cell by cell},
 url = {https://www.hipeac.net/2022},
 year = {2022}
}

Mark Potse. MICROCARD: modeling the heart cell by cell.
TERATEC Forum, Paris, June 2022. (workshop HPC Technologies and Health) [link] [bibtex]

@lecture{potse22teratec,
 address = {Paris},
 author = {Potse, Mark},
 booktitle = {TERATEC Forum},
 month = {June},
 title = {{MICROCARD}: modeling the heart cell by cell},
 url = {https://teratec.eu/gb/forum/atelier_2.html},
 year = {2022}
}

Terry Cojean, Fritz Göbel, and Marie Houillon. Porting the openCARP cardiac electrophysiology simulation framework to GPU architectures.
Fifth ISC Workshop on HPC Applications in Precision Medecine, Hamburg, Germany, 2 June 2022. [bibtex]

@lecture{2022_OpenCARP_Ginkgo_HAPM_Workshop,
 address = {Hamburg, Germany},
 author = {Cojean, Terry and Göbel, Fritz and Houillon, Marie},
 month = {June},
 publisher = {Fifth ISC Workshop on HPC Applications in Precision Medecine},
 title = {Porting the {openCARP} cardiac electrophysiology simulation framework to {GPU} architectures},
 year = {2022}
}

Axel Loewe. Computational Cardiac Modeling – Synergies with Machine Learning.
Annual Meeting of the German Cardiac Society, Mannheim, Germany, 22 April 2022. [bibtex]

@lecture{loewe-DGK22,
 address = {Mannheim, Germany},
 author = {Axel Loewe},
 month = {April},
 publisher = {Annual Meeting of the German Cardiac Society},
 title = {Computational Cardiac Modeling -- Synergies with Machine Learning},
 year = {2022}
}

Mark Potse. MICROCARD: Numerical modeling of cardiac electrophysiology at the cellular scale.
openCARP Contributor Meeting, online, 14 March 2022. [bibtex]

@lecture{potse-openCarpCM22,
 address = {online},
 author = {Mark Potse},
 month = {March},
 publisher = {openCARP Contributor Meeting},
 title = {{MICROCARD}: Numerical modeling of cardiac electrophysiology at the cellular scale},
 year = {2022}
}

Vincent Loechner. Modern Compiler Technology to Optimize Code From Ionic Models.
Colloquium of the ITI IRMIA++, Université de Strasbourg, France, 17 March 2022. [bibtex]

@lecture{loechner-IRMIA22,
 address = {Université de Strasbourg, France},
 author = {Vincent Loechner},
 month = {March},
 publisher = {Colloquium of the ITI IRMIA++},
 title = {Modern Compiler Technology to Optimize Code From Ionic Models},
 year = {2022}
}

Luca F. Pavarino. Numerical Modeling of Cardiac Reentry in the Presence of Infarct Scars and Border Zones.
SIMAI 2021 National Congress, Parma, Italy, 1 September 2021. [link] [bibtex]

@lecture{pavarinoSIMAI2021,
 address = {Parma, Italy},
 author = {Pavarino, Luca F.},
 booktitle = {SIMAI 2021 National Congress},
 month = {September},
 title = {Numerical
Modeling of Cardiac Reentry in the Presence of Infarct Scars and Border Zones},
 url = {https://www.simai.eu/congresso-nazionale-simai2020/},
 year = {2021}
}

M. Weiser and T. Steinke. Numerik auf Höchstleistungsrechnern.
Kolloquium GI Regionalgruppe Berlin-Brandenburg, online, 25 November 2021. [bibtex]

@lecture{weiserSteinkeGI2021,
 address = {online},
 author = {Weiser, M. and Steinke, T.},
 booktitle = {Kolloquium GI Regionalgruppe Berlin-Brandenburg},
 month = {November},
 title = {Numerik auf {H\"{o}chstleistungsrechnern}},
 year = {2021}
}

Mark Potse. The MICROCARD Project.
IHU Liryc, Université de Bordeaux, France, 22 February 2021. [bibtex]

@lecture{potse-Liryc21,
 address = {Université de Bordeaux, France},
 author = {Mark Potse},
 month = {February},
 publisher = {IHU Liryc},
 title = {The {MICROCARD} Project},
 year = {2021}
}

news about us

Digitale Zwillinge – Mit hoch skalierbaren Algorithmen simulieren Supercomputer Patientenherzen.
c't Magazin für Computertechnik, March 2025. [link] [bibtex]

@news{ct,
 month = {March},
 publisher = {c't Magazin für Computertechnik},
 title = {Digitale Zwillinge -- Mit hoch skalierbaren Algorithmen simulieren Supercomputer Patientenherzen},
 url = {https://www.heise.de/select/ct/2025/7/2504311301389077742},
 year = {2025}
}

Axel Loewe, Aurel Neic, Gunnar Seemann, Edward Vigmond, and Gernot Plank. openCARP: Personalized Computational Model of the Heart Examines Cardiac Rhythm.
Society for Industrial and Applied Mathematics (SIAM), March 2025. [link] [bibtex]

@news{SIAMnewsOC,
 author = {Loewe, Axel and Neic, Aurel and Seemann, Gunnar and Vigmond, Edward and Plank, Gernot},
 month = {March},
 publisher = {Society for Industrial and Applied Mathematics (SIAM)},
 title = {{openCARP}: Personalized Computational Model of the Heart Examines Cardiac Rhythm},
 url = {https://www.siam.org/publications/siam-news/articles/opencarp-personalized-computational-model-of-the-heart-examines-cardiac-rhythm/},
 year = {2025}
}

EuroHPC JU launches two new projects to advance medicine: MICROCARD-2 and dealii-X.
EuroHPC, 24 November 2024. (press release) [link] [bibtex]

@news{eurohpc-11-2024,
 month = {November},
 publisher = {EuroHPC},
 title = {EuroHPC JU launches two new projects to advance medicine: {MICROCARD-2} and {dealii-X}},
 url = {https://eurohpc-ju.europa.eu/eurohpc-ju-launches-two-new-projects-advance-medicine-microcard-2-and-dealii-x-2024-11-27_en},
 year = {2024}
}

How supercomputers can help defuse ‘cardiac time bombs’.
CORDIS (European Commission), July 2024. [link] [bibtex]

@news{cordis-result24,
 month = {July},
 publisher = {CORDIS (European Commission)},
 title = {How supercomputers can help defuse ‘cardiac time bombs’},
 url = {https://cordis.europa.eu/article/id/452279?WT.mc_id=exp},
 year = {2024}
}

Leading the way in European Supercomputing; A projects info pack by CORDIS.
European Commission, April 2022. [link] [bibtex]

@news{cordis-leading22,
 month = {April},
 publisher = {European Commission},
 title = {Leading the way in {European} Supercomputing; A projects info pack by {CORDIS}},
 url = {https://eurohpc-ju.europa.eu/sites/default/files/2022-04/ED-7309_CORDIS%20LotB_PIP%20European%20Supercomputing_Brochure_EN_LR%20acc.pdf},
 year = {2022}
}

Digitalisierung: Simulationsplattform für Herzrhythmusstörungen.
Karlsruher Institut für Technologie, May 2021. (KIT press release MICROCARD kickoff) [link] [bibtex]

@news{KIT-kickoff-2021,
 month = {May},
 publisher = {Karlsruher Institut für Technologie},
 title = {{Digitalisierung: Simulationsplattform für Herzrhythmusstörungen}},
 url = {https://www.kit.edu/kit/29027.php},
 year = {2021}
}

European High-Performance Computing Projects Handbook.
European Technology Platform for High Performance Computing, August 2021. [link] [bibtex]

@news{etp4hpc-handbook-2021,
 month = {August},
 publisher = {European Technology Platform for High Performance Computing},
 title = {European High-Performance Computing Projects Handbook},
 url = {https://www.etp4hpc.eu/pujades/files/European%20HPC%20Handbook%202021%20final.pdf},
 year = {2021}
}

Calcul haute performance : Inria impliqué dans huit projets européens.
Inria, 26 May 2021. [link] [bibtex]

@news{inria-8-exascale-projects,
 month = {May},
 publisher = {Inria},
 title = {Calcul haute performance : Inria impliqué dans huit projets européens},
 url = {https://www.inria.fr/fr/calcul-haute-performance-euro-hpc-partenariats-europe},
 year = {2021}
}

Liryc - 3 scientific projects selected by Horizon 2020 in support of medical treatment challenges.
International newsletter of Université de Bordeaux, Université de Bordeaux, February 2021. (to appear in June 2021)

@news{UBx-newsletter-2021-06,
 journal = {International newsletter of Université de Bordeaux},
 month = {February},
 publisher = {Université de Bordeaux},
 title = {Liryc - 3 scientific projects selected by Horizon 2020 in
support of medical treatment challenges},
 year = {2021}
}

Moisson de projets européens de recherche pour l’université.
Université de Bordeaux, February 2021. [link] [bibtex]

@news{UBx-moisson-2020,
 month = {February},
 publisher = {Université de Bordeaux},
 title = {Moisson de projets européens de recherche pour l’université},
 url = {https://www.u-bordeaux.fr/Actualites/De-la-recherche/Moisson-de-projets-europeens-de-recherche-pour-l-universite},
 year = {2021}
}

Strong success for European research projects.
Université de Bordeaux, February 2021. [link] [bibtex]

@news{UBx-harvest-2020,
 month = {February},
 publisher = {Université de Bordeaux},
 title = {Strong success for {European} research projects},
 url = {https://www.u-bordeaux.com/News/Strong-success-for-European-research-projects},
 year = {2021}
}

Kick-off of the European project MICROCARD.
IHU Liryc, 19 April 2021. [link] [bibtex]

@news{Liryc-start-en,
 month = {April},
 publisher = {IHU Liryc},
 title = {Kick-off of the {European} project {MICROCARD}},
 url = {https://ihu-liryc.fr/en/actualites/b/lancement-du-projet-europeen-microcard},
 year = {2021}
}

Lancement du Projet Européen MICROCARD.
IHU Liryc, 19 April 2021. [link] [bibtex]

@news{Liryc-start-fr,
 month = {April},
 publisher = {IHU Liryc},
 title = {Lancement du Projet Européen MICROCARD},
 url = {https://ihu-liryc.fr/fr/actualites/b/lancement-du-projet-europeen-microcard},
 year = {2021}
}

The European High Performance Computing Joint Undertaking launched thirteen R&I projects in April.
EuroHPC, April 2021. [link] [bibtex]

@news{EuroHPC-start,
 month = {April},
 publisher = {EuroHPC},
 title = {The {European} High Performance Computing Joint Undertaking launched thirteen {R\&I} projects in April},
 url = {https://eurohpc-ju.europa.eu/news/european-high-performance-computing-joint-undertaking-launched-thirteen-ri-projects-april},
 year = {2021}
}

Al via progetto europeo ``MICROCARD''.
Università degli Studi di Pavia, May 2021. [link] [bibtex]

@news{unipv56848,
 month = {May},
 publisher = {Università degli Studi di Pavia},
 title = {Al via progetto europeo ``{MICROCARD}''},
 url = {http://news.unipv.it/?p=56848},
 year = {2021}
}

miscellaneous

Movie provided for the EuroHPC stand at the ISC High Performance meeting.
Hamburg, April 2024. [bibtex]

@misc{movie:ISC24,
 address = {Hamburg},
 month = {April},
 title = {Movie provided for the {EuroHPC} stand at the {ISC High Performance} meeting},
 year = {2024}
}

Numerical modeling of cardiac electrophysiology at the cellular scale.
website, European Commission, November 2024. (The MICROCARD-2 record on the EU's CORDIS system) [link] [bibtex]

@website{microcard2-cordis,
 month = {November},
 publisher = {European Commission},
 title = {Numerical modeling of cardiac electrophysiology at the cellular scale},
 url = {https://cordis.europa.eu/project/id/101172576},
 year = {2024}
}

Simone Pezzuto and Martin Weiser. Minisymposium on Multilevel methods for cardiac simulations.
International Multigrid Conference, Lugano, CH, 25 August 2022. [link] [bibtex]

@workshop{pezzutoWeiserIMG22,
 address = {Lugano, CH},
 author = {Pezzuto, Simone and Weiser, Martin},
 booktitle = {International Multigrid Conference},
 month = {August},
 title = {Minisymposium on Multilevel methods for cardiac simulations},
 url = {https://www.img2022.usi.ch/index.php?option=com_content&view=article&id=6&Itemid=295},
 year = {2022}
}

European Researchers Night.
exhibition, The MICROCARD consortium, Bordeaux, France, September 2022. (MICROCARD was present with a movie and flyers) [link] [bibtex]

@exhibition{ERN22-Bordeaux,
 address = {Bordeaux, France},
 month = {September},
 publisher = {The MICROCARD consortium},
 title = {European Researchers Night},
 url = {https://www.u-bordeaux.fr/en/research/science-and-society/european-researchers-night},
 year = {2022}
}

MICROCARD est un projet européen qui cherche à combattre les maladies cardiovasculaires ... en codant !.
flyer, The MICROCARD consortium, September 2022. [link] [bibtex]

@flyer{flyer-MICROCARD-ERN22-fr,
 month = {September},
 publisher = {The MICROCARD consortium},
 title = {{MICROCARD} est un projet européen qui cherche à combattre
les maladies cardiovasculaires ... en codant !},
 url = {https://microcard.eu/docs/flyer1.pdf},
 year = {2022}
}

Numerical modeling of cardiac electrophysiology at the cellular scale.
website, European Commission, April 2021. (The MICROCARD record on the EU's CORDIS system) [link] [bibtex]

@website{microcard-cordis,
 month = {April},
 publisher = {European Commission},
 title = {Numerical modeling of cardiac electrophysiology at the cellular scale},
 url = {https://cordis.europa.eu/project/id/955495},
 year = {2021}
}

MICROCARD Publications

preprints

book chapters

journal articles

conference articles

conference abstracts

theses

invited lectures

news about us

miscellaneous

Latest news

30 June 2025: defense Zeina Chehade

Kick-off meeting agenda online

23-24 June: MICROCARD Summer Workshop in Oslo

Agenda

24-27 June

Friday 27 June

Monday 30 June

Wednesday 2 July

Thursday 3 July

Friday 4 July

Friday 11 July