HemoCell development

A high-performance cellular blood flow simulation

HemoCell - 2 mm3 of blood on a cellular level.

HemoCell is a high-performance code aim at solving cellular flow problems with the help of supercomputers. The defining features are high numerical stability at fast flows (i.e., sustained high shear rates), and outstanding computational performance, enabling macroscopic investigations. Good scaling was demonstrated up to 330 000 CPU cores (> 80% efficiency).

In order to achieve this level of performance we build on advanced computational solutions:

  • Time-scale separation of the components
  • Dynamic load-balancing
  • Two-phase optimised communication pattern
  • Fast dynamic octree for node searching

HemoCell, and the surrounding tools have been in development since 2015, involving more than a dozen core contributor.

HemoCell has a series of advanced boundary conditions that enable a broad range of applications:

  • Periodic
  • Continuous cellular inflow
  • Rotating boundary
  • Lees-Edwards

HemoCell has been used in various complex flow scenarios, for instance:

  • Platelet aggregation in complex geometries
  • Platelet margination in healthy and diabetic blood flows
  • Stress on the wall of retinal micro-aneurysms
  • Cellular conditions for high-shear thrombus formation

More information can be found on the website www.hemocell.eu, and in the documentation.

A recent (2023) bookchapter, describing HemoCell is out! Tthe author manuscript is available here: Link.



  1. The influence of red blood cell deformability on hematocrit profiles and platelet margination
    Benjamin Czaja, Mario Gutierrez, Gábor Závodszky, and 3 more authors
    PLoS Computational Biology, 2020


  1. Red blood cell and platelet diffusivity and margination in the presence of cross-stream gradients in blood flows
    Gábor Závodszky, Britt Rooij, Ben Czaja, and 3 more authors
    Physics of Fluids, 2019
  2. Optimizing parallel performance of the cell based blood flow simulation software HemoCell
    Victor Azizi Tarksalooyeh, Gábor Závodszky, and Alfons G Hoekstra
    In Computational Science–ICCS 2019: 19th International Conference, Faro, Portugal, June 12–14, 2019, Proceedings, Part III 19, 2019
  3. Identifying the start of a platelet aggregate by the shear rate and the cell-depleted layer
    BJM Van Rooij, G Závodszky, VW Azizi Tarksalooyeh, and 1 more author
    Journal of the Royal Society Interface, 2019


  1. Inflow and outflow boundary conditions for 2D suspension simulations with the immersed boundary lattice Boltzmann method
    Victor W Azizi Tarksalooyeh, Gábor Závodszky, Britt JM Rooij, and 1 more author
    Computers & fluids, 2018
  2. Numerical investigation of the effects of red blood cell cytoplasmic viscosity contrasts on single cell and bulk transport behaviour
    Mike De Haan, Gabor Zavodszky, Victor Azizi, and 1 more author
    Applied Sciences, 2018
  3. Cell-resolved blood flow simulations of saccular aneurysms: effects of pulsatility and aspect ratio
    B Czaja, G Závodszky, V Azizi Tarksalooyeh, and 1 more author
    Journal of The Royal Society Interface, 2018


  1. Hemocell: a high-performance microscopic cellular library
    Gábor Zavodszky, Britt Rooij, Victor Azizi, and 2 more authors
    Procedia Computer Science, 2017
  2. Cellular level in-silico modeling of blood rheology with an improved material model for red blood cells
    Gábor Závodszky, Britt Van Rooij, Victor Azizi, and 1 more author
    Frontiers in physiology, 2017