MICROCARD

MICROCARD Publications

preprints

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. (accepted), 2023. (preprint) [pdf] [link] [bibtex] [arxiv]

@article{huynh:BDDC,
 author = {Huynh, Ngoc Mai Monica and Chegini, Fatemeh and Pavarino, Luca Franco and Weiser, Martin and Scacchi, Simone},
 journal = {SIAM J. Sci. Comp.},
 pdf = {https://arxiv.org/pdf/2212.12295v2.pdf},
 title = {Convergence analysis of {BDDC} preconditioners for
composite {DG} discretizations of the cardiac
cell-by-cell model},
 url = {https://arxiv.org/abs/2212.12295v2},
 volume = {(accepted)},
 year = {2023}
}

Giacomo Rosilho de Souza, Rolf Krause, and Simone Pezzuto. Boundary Integral Formulation of the Cell-by-Cell Model of Cardiac Electrophysiology.
(submitted), 2023. (preprint) [pdf] [link] [bibtex] [arxiv]

@article{rosilhoBEM,
 author = {Rosilho de Souza, Giacomo and Krause, Rolf and Pezzuto, Simone},
 journal = {(submitted)},
 pdf = {https://arxiv.org/pdf/2302.05281.pdf},
 title = {Boundary Integral Formulation of the Cell-by-Cell Model of
Cardiac Electrophysiology},
 url = {https://arxiv.org/abs/2302.05281},
 year = {2023}
}

journal articles

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, 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},
 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, 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},
 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, 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},
 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, 5 2022. [link] [bibtex]

@article{Sanchez-2022-908069,
 author = {Sánchez, Jorge and Loewe, Axel},
 doi = {10.3389/fphys.2022.908069},
 journal = {Frontiers in Physiology},
 month = {5},
 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, 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},
 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, 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},
 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, 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},
 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, 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},
 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

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, 2023. [bibtex] [abstract]
```
@inproceedings{chehade:fvca2023,
 author = {Chehade, Zeina and Coudière, Yves},
 booktitle = {Tenth International Symposium on Finite Volumes for Complex Applications},
 publisher = {Springer},
 title = {The Two-Point Finite Volume scheme for the Microscopic Bidomain Model of Electrocardiology},
 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.
Euro-Par 2023: Parallel Processing, pp. 549–563, Springer Nature Switzerland, Cham, 2023. [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 = {Euro-Par 2023: Parallel Processing},
 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},
 pages = {549--563},
 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.

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, 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},
 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, 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},
 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, 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},
 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, 2023. [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},
 pages = {68-80},
 publisher = {Association for Computing Machinery},
 series = {CGO 2023},
 title = {Lifting Code Generation of Cardiac Physiology Simulation to Novel Compiler Technology},
 url = {https://doi.org/10.1145/3579990.3580008},
 year = {2023}
}

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, 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},
 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, 2022. [link] [bibtex]

@inproceedings{WeiserChegini2022,
 author = {Weiser, Martin and Chegini, Fatemeh},
 booktitle = {7th International Conference on Computational and
Mathematical Biomedical Engineering (CMBE22)},
 pages = {528--531},
 title = {Adaptive multirate integration of cardiac electrophysiology with spectral deferred correction methods},
 url = {https://www.compbiomed.net/2021/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, 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)},
 pages = {535--538},
 title = {Parallel-in-time multirate explicit stabilized method
for the monodomain model in cardiac electrophysiology},
 url = {https://www.compbiomed.net/2021/cmbe-proceedings.htm},
 volume = {2},
 year = {2022}
}

conference abstracts

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, 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},
 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, 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},
 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}
}

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}
}

invited lectures

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. [bibtex]

@lecture{rosilho:eccomas23,
 address = {Porto, Portugal},
 author = {Rosilho de Souza, Giacomo and Pezzuto, Simone and Krause, Rolf},
 booktitle = {VII ECCOMAS Young Investigators Conference},
 month = {June},
 title = {Boundary integral formulation and numerical experiments on the Cell-by-Cell model for electrophysiology},
 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}
}

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}
}

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. [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},
 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 3 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 = {3},
 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}
}

Martin Weiser. Exploiting the Flexibility of Spectral Deferred Correction Methods.
TU Hamburg, 14 11 2022. [bibtex]

@lecture{weiserTUHH2022,
 address = {TU Hamburg},
 author = {Weiser, Martin},
 month = {11},
 title = {Exploiting the Flexibility of Spectral Deferred Correction Methods},
 year = {2022}
}

Martin Weiser and Fatemeh Chegini. Adaptive multirate integration of cardiac electrophysiology with spectral deferred correction methods.
International Multigrid Conference, Lugano, CH, 25 8 2022. [bibtex]

@lecture{weiserIMG2022,
 address = {Lugano, CH},
 author = {Weiser, Martin and Chegini, Fatemeh},
 booktitle = {International Multigrid Conference},
 month = {8},
 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, I, 28 6 2022. [bibtex]

@lecture{weiserCMBE2022,
 address = {Milan, I},
 author = {Weiser, Martin and Chegini, Fatemeh},
 booktitle = {Computational and Mathematical Biomedical Engineering},
 month = {6},
 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}
}

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

@lecture{potse22hipeac,
 address = {Budapest},
 author = {Potse, Mark},
 booktitle = {HiPEAC 2022},
 month = {June},
 title = {Modeling the heart, cell by cell},
 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}
}

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]

@lecture{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. 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}
}

M. Weiser and T. Steinke. Numerik auf Höchstleistungsrechnern.
Kolloquium GI Regionalgruppe Berlin-Brandenburg, online, 25 11 2021. [bibtex]

@lecture{weiserSteinkeGI2021,
 address = {online},
 author = {Weiser, M. and Steinke, T.},
 booktitle = {Kolloquium GI Regionalgruppe Berlin-Brandenburg},
 month = {11},
 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

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

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, 2021. (our record on the EU's CORDIS system) [link] [bibtex]

@website{microcard-cordis,
 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

journal articles

conference articles

conference abstracts

invited lectures

news about us

miscellaneous

Latest news

13 September: Interview with Fatemeh Chegini

Euro-par conference 2023 in Limassol, Cyprus

ICIAM 2023 in Tokyo

MICROCARD workshop on 4 and 5 July

Agenda

1-4 October

Wednesday 4 October

Thursday 12 October

Friday 20 October