Citing HemoCell

When using HemoCell please cite the main HemoCell paper [1]:

@article{Zavodszky:2017,
  author={Závodszky, Gábor and van Rooij, Britt and Azizi, Victor and Hoekstra, Alfons},
  title={Cellular Level In-silico Modeling of Blood Rheology with An Improved Material Model for Red Blood Cells},
  journal={Frontiers in Physiology},
  volume={8},
  pages={563},
  year={2017},
  url={https://www.frontiersin.org/article/10.3389/fphys.2017.00563},
  doi={10.3389/fphys.2017.00563},
  issn={1664-042X},
}

Depending on which features you use, please also consider citing the relevant methodological papers listed below (for example, the optimised red blood cell model [6], cell-binding techniques [5], or the high-performance scaling work [8]).

HemoCell-related publications

[1]

Gábor Závodszky, Britt van Rooij, Victor Azizi, and Alfons Hoekstra. Cellular level in-silico modeling of blood rheology with an improved material model for red blood cells. Frontiers in Physiology, 8:563, 2017. URL: https://www.frontiersin.org/article/10.3389/fphys.2017.00563, doi:10.3389/fphys.2017.00563.

[2]

Gábor Závodszky, Britt van Rooij, Ben Czaja, Victor Azizi, David de Kanter, and Alfons G Hoekstra. Red blood cell and platelet diffusivity and margination in the presence of cross-stream gradients in blood flows. Physics of Fluids, 31(3):031903, 2019.

[3]

B Czaja, G Závodszky, V Azizi Tarksalooyeh, and AG Hoekstra. Cell-resolved blood flow simulations of saccular aneurysms: effects of pulsatility and aspect ratio. Journal of The Royal Society Interface, 15(146):20180485, 2018.

[4]

BJM Van Rooij, G Závodszky, AG Hoekstra, and DN Ku. Haemodynamic flow conditions at the initiation of high-shear platelet aggregation: a combined in vitro and cellular in silico study. Interface Focus, 11(1):20190126, 2021.

[5]

BJM van Rooij, Gábor Závodszky, VW Azizi Tarksalooyeh, and Alfons Georgius Hoekstra. Identifying the start of a platelet aggregate by the shear rate and the cell-depleted layer. Journal of the Royal Society Interface, 16(159):20190148, 2019.

[6]

Victor Azizi Tarksalooyeh, Gábor Závodszky, and Alfons G Hoekstra. Optimizing parallel performance of the cell based blood flow simulation software hemocell. In International Conference on Computational Science, 537–547. Springer, 2019.

[7]

Benjamin Czaja, Mario Gutierrez, Gábor Závodszky, David de Kanter, Alfons Hoekstra, and Omolola Eniola-Adefeso. The influence of red blood cell deformability on hematocrit profiles and platelet margination. PLOS Computational Biology, 16(3):e1007716, 2020.

[8]

S. Alowayyed, G. Závodszky, V. Azizi, and A.G. Hoekstra. Load balancing of parallel cell-based blood flow simulations. Journal of Computational Science, 24:1 – 7, 2018. URL: http://www.sciencedirect.com/science/article/pii/S1877750317302788, doi:https://doi.org/10.1016/j.jocs.2017.11.008.

[9]

Jelle Van Dijk, Gabor Zavodszky, Ana-Lucia Varbanescu, and Andy Pimentel. Embracing load imbalance for energy optimizations: a case-study. In 2025 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW), 405–412. IEEE, 2025.

[10]

Christian J Spieker, Axelle Y Kern, Netanel Korin, Pierre H Mangin, Alfons G Hoekstra, and Gábor Závodszky. Carotid single-and dual-layer stents reduce the wall adhesion of platelets by influencing flow and cellular transport. Computers in Biology and Medicine, 183:109313, 2024.

[11]

Gabor Zavodszky, Christian Spieker, Benjamin Czaja, and Britt van Rooij. Cellular blood flow modeling with hemocell. In High Performance Computing for Drug Discovery and Biomedicine, pages 351–368. Springer, 2023.

[12]

Christian J Spieker, Konstantinos Asteriou, and Gab́or Zav́odszky. Simulating initial steps of platelet aggregate formation in a cellular blood flow environment. In International Conference on Computational Science, 323–336. Springer, 2023.

[13]

Benjamin Czaja, Jonathan de Bouter, Morgan Heisler, Gábor Závodszky, Sonja Karst, Marinko Sarunic, David Maberley, and Alfons Hoekstra. The effect of stiffened diabetic red blood cells on wall shear stress in a reconstructed 3d microaneurysm. Computer Methods in Biomechanics and Biomedical Engineering, 25(15):1691–1709, 2022.

[14]

Jelle van Dijk, Gabor Zavodszky, Ana-Lucia Varbanescu, Andy D Pimentel, and Alfons Hoekstra. Building a fine-grained analytical performance model for complex scientific simulations. In International Conference on Parallel Processing and Applied Mathematics, 183–196. Springer, 2022.

[15]

Christian J Spieker, Gábor Závodszky, Clarisse Mouriaux, Max Van der Kolk, Christian Gachet, Pierre H Mangin, and Alfons G Hoekstra. The effects of micro-vessel curvature induced elongational flows on platelet adhesion. Annals of Biomedical Engineering, 49:3609–3620, 2021.

[16]

Benjamin Czaja, Gábor Závodszky, and Alfons Hoekstra. A heterogeneous multi-scale model for blood flow. In International Conference on Computational Science, 403–409. Springer, 2020.

[17]

Kevin de Vries, Anna Nikishova, Benjamin Czaja, Gábor Závodszky, and Alfons G Hoekstra. Inverse uncertainty quantification of a cell model using a gaussian process metamodel. International Journal for Uncertainty Quantification, 2020.

[18]

Mike Haan, Gábor Závodszky, Victor Azizi, and Alfons Hoekstra. Numerical investigation of the effects of red blood cell cytoplasmic viscosity contrasts on single cell and bulk transport behaviour. Applied Sciences, 8:1616, 09 2018. doi:10.3390/app8091616.