The research areas of the group involve modelling and simulations in computational tool Object-in-fluid. 

Current research grants

  • Slovak Research and Development Agency,  grant number APVV-15-0751
  • Ministry of Education, Science, Research and Sport of the Slovak Republic,  grant number VEGA 1/0643/17.
  • Faculty of Management Science nad Informatics, University of Zilina, grant FVG.
  • Aktion Oesterreich-Slowakei, grant number 2016-05-15-002


Simulation package

We work on the simulation framework that makes the simulation of flow with immersed objects easy to use. In the well-established software ESPResSo we implemented the so called OIF (name comes from object-in-fluid) framework. In its current state it is possible to create 3D objects that can be directly put into a flow of a fluid. For the geometry only coordinate file and incidence file is needed. More details can be found in the user guide of ESPResSo software.


About model

Our research group is interested in modelling of elastic objects in fluid flow in solid channels (microfluidic devices). We have developed Object-in-fluid framework as a part of extensible open source package ESPResSo (

The dynamics of the fluid is modeled by the lattice-Boltzmann method (LBM). The LBM is fast and easy parallelizable, which is necessary for simulations that contain large number of immersed objects.

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Elastic object, elastic behavior

Model of elastic object is based on a triangular spring mesh on the object's surface. In our model we consider the mesh points to be connected with springs that exert forces according to their prolongation.

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The biological concepts of adhesion rely on creating receptor-ligand (R-L) complexes between the receptor patches located on the surface of the cell and ligands distributed on the functionalized surfaces.

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Magnetic particles in flow

In biomedical applications the interaction of biological fluids with magnetic fields offers great opportunities. Magnetic properties can be used to separate certain cells, either directly by cells magnetization or by attaching magnetic beads to cells.

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Finished research grants

  • Marie-Curie CIG grant BiomedMicrofluidics grant No. PCIG10-GA-2011-303580, 2012-2016
  • Aktion Oesterreich-Slowakei, grant number 2012-03-15-0003, 2012
  • Slovak Research and Development Agency,  grant No. APVV-0441-11, 2012-2016



04.04. 2017
New PhD positions

In our research group we open two PhD positions starting from September 2017. More information are available at dedicated page.

10.01. 2017
Invitation to a Workshop

Cell-in-fluid Research Group organizes the 2nd Workshop on Modelling of Biological Cells, Fluid Flow and Microfluidics - February 5-9, 2017. More information here.

10.05. 2016
New article published

The members of our group published an article in Journal of Computational Science (2015 Impact Factor 1.231). The title of the article is Simulation study of rare cell trajectories and capture rate in periodic obstacle arrays. Congratulate Martin, Iva, Renáta and Ivan.

08.04. 2016
New article published

Recently, new article has been published in Computer Methods in Biomechanics and Biomedical Engineering,  (Impact Factor 1.770). The title of the article is Collision rates for rare cell capture in periodic obstacle arrays strongly depend on density of cell suspension. The article is available at journal website or at our publication section

08.01. 2016
New article published

Recently, new article has been published in International Journal for Numerical Methods in Biomedical Engineering (Impact Factor 2.052). The title of the article is Non-uniform force allocation for area preservation in spring network models. The article is available at journal website or at our publication section. Congratulate Iveta and Ivan.

04.09. 2015
Welcome new colleagues

Starting in September, two doctoral students joined the group: Martin Slavik and Marek Kotus. Welcome!

26.08. 2015
PhD degree obtained

We congratulate Iveta on obtaining the PhD degree. Good luck (not only) in your further scientific research.

02.08. 2015
Conference in Edinburg

In July, Iveta and Martin B. attended the Discrete Simulation of Fluid Dynamics (DSFD2015) conference. They presented our preliminary results on analysis of periodic obstacle arrays.

15.10. 2014

Our group participated at ICNAAM 2014 conference. I.Cimrák organized a symposium at the conference with title Modelling of Biological Cells, Fluid Flow and Microfluidics. 

05.09. 2014
New members in the group

Two new PhD students have joined our research group: Jana Kadlecová and Martina Bušík. Welcome :-)

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