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MICROCARD Publications

journal articles

1. 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] 
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   @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}
   }
2. 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] 
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   @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}
   }
3. 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] 
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   @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}
   }
4. 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] 
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   @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}
   }
5. 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] 
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   @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}
   }
6. 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] 
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   @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}
   }
7. 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] 
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   @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}
   }
8. 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] 
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   @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}
   }
9. 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] 
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   @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

1. 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] 
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   @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}
   }
2. 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. [bibtex] 
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   @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 },
    volume = {49},
    year = {2022}
   }
3. Nicolas Alejandro Barnafi, Ngoc Monica Mai Huynh, Luca Franco Pavarino, and Simone Scacchi. Parallel nonlinear solvers in computational cardiac electrophysiology..
   IFAC-PapersOnLine, Vienna, Austria, July 2022. [bibtex] 
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   @inproceedings{huynh_2022,
    address = {Vienna, Austria},
    author = {Barnafi, Nicolas Alejandro  and Huynh, Ngoc Monica Mai and Pavarino, Luca Franco and Scacchi, Simone},
    booktitle = {IFAC-PapersOnLine},
    month = {July},
    title = {Parallel nonlinear solvers in computational cardiac electrophysiology.},
    year = {2022}
   }
4. 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] 
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   @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}
   }
5. 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] 
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   @inproceedings{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}
   }
6. 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), pp. 528–531, 2022. [bibtex] 
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   @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},
    year = {2022}
   }
7. 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), Milan, Italy, June 2022. [bibtex] 
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   @inproceedings{rosilhodesouza-cmbe22,
    address = {Milan, Italy},
    author = {Rosilho de Souza, Giacomo and Pezzuto, Simone and Krause, Rolf},
    booktitle = {7th International Conference on Computational and
   Mathematical Biomedical Engineering (CMBE22)},
    month = {June},
    organization = {CMBE},
    title = {Parallel-in-time multirate explicit stabilized method
   for the monodomain model in cardiac electrophysiology},
    year = {2022}
   }
8. Mark Potse. Microscale cardiac electrophysiology on exascale supercomputers.
   SIAM Conference on Parallel Processing for Scientific Computing (PP22), Seattle, WA, USA, February 2022. [bibtex] 
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   @inproceedings{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},
    year = {2022}
   }

invited lectures

1. 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] 
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   @lecture{vigmond22hipeac,
    address = {Toulouse},
    author = {Vigmond, Edward},
    booktitle = {HiPEAC 2023},
    month = {January},
    title = {Challenges and opportunities for cardiac simulation at exascale},
    year = {2023}
   }
2. Mark Potse. The MICROCARD project and gender.
   #RESET your project with gender, 15 November 2022. (webinar)  [link]  [bibtex] 
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   @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}
   }
3. 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] 
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   @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}
   }
4. 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] 
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   @lecture{potse22hipeac,
    address = {Budapest},
    author = {Potse, Mark},
    booktitle = {HiPEAC 2022},
    month = {June},
    title = {Modeling the heart, cell by cell},
    year = {2022}
   }
5. Mark Potse. MICROCARD: modeling the heart cell by cell.
   TERATEC Forum, Paris, June 2022. (workshop HPC Technologies and Health)  [link]  [bibtex] 
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   @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}
   }
6. 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] 
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   @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}
   }
7. Axel Loewe. Computational Cardiac Modeling – Synergies with Machine Learning.
   Annual Meeting of the German Cardiac Society, Mannheim, Germany, 22 April 2022. [bibtex] 
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   @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}
   }
8. Mark Potse. MICROCARD: Numerical modeling of cardiac electrophysiology at the cellular scale.
   OpenCARP Contributor Meeting, online, 14 March 2022. [bibtex] 
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   @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}
   }
9. Vincent Loechner. Modern Compiler Technology to Optimize Code From Ionic Models.
   Colloquium of the ITI IRMIA++, Université de Strasbourg, France, 17 March 2022. [bibtex] 
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   @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}
   }
10. Mark Potse. The MICROCARD Project.
    IHU Liryc, Université de Bordeaux, France, 22 February 2021. [bibtex] 
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    @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

1. Leading the way in European Supercomputing; A projects info pack by CORDIS.
   European Commission, April 2022. [link]  [bibtex] 
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   @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}
   }
2. Digitalisierung: Simulationsplattform für Herzrhythmusstörungen.
   Karlsruher Institut für Technologie, May 2021. (KIT press release MICROCARD kickoff)  [link]  [bibtex] 
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   @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}
   }
3. European High-Performance Computing Projects Handbook.
   European Technology Platform for High Performance Computing, August 2021. [link]  [bibtex] 
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   @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}
   }
4. Calcul haute performance : Inria impliqué dans huit projets européens.
   Inria, 26 May 2021. [link]  [bibtex] 
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   @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}
   }
5. 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)  [bibtex] 
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   @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}
   }
6. Moisson de projets européens de recherche pour l’université.
   Université de Bordeaux, February 2021. [link]  [bibtex] 
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   @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}
   }
7. Strong success for European research projects.
   Université de Bordeaux, February 2021. [link]  [bibtex] 
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   @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}
   }
8. Kick-off of the European project MICROCARD.
   IHU Liryc, 19 April 2021. [link]  [bibtex] 
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   @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}
   }
9. Lancement du Projet Européen MICROCARD.
   IHU Liryc, 19 April 2021. [link]  [bibtex] 
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   @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}
   }
10. The European High Performance Computing Joint Undertaking launched thirteen R&I projects in April.
    EuroHPC, April 2021. [link]  [bibtex] 
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    @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}
    }
11. Al via progetto europeo “MICROCARD”.
    Università degli Studi di Pavia, May 2021. [link]  [bibtex] 
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    @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

1. European Researchers Night.
   , September 2022. (MICROCARD was present with a movie and flyers)  [bibtex] 
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   @exhibition{ERN22-Bordeaux,
    month = {September},
    title = {European Researchers Night},
    year = {2022}
   }
2. MICROCARD est un projet européen qui cherche à combattre les maladies cardiovasculaires ... en codant !.
   , September 2022. [bibtex] 
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   @flyer{flyer-MICROCARD-ERN22-fr,
    month = {September},
    title = {MICROCARD est un projet européen qui cherche à combattre
   les maladies cardiovasculaires ... en codant !},
    year = {2022}
   }
3. Numerical modeling of cardiac electrophysiology at the cellular scale.
   European Commission, 2021. (our record on the EU's CORDIS system)  [link]  [bibtex] 
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   @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}
   }