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 (www.espressomd.org).

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.

Immersed objects are represented using the immersed boundary method (IBM), in which the boundary of an object is represented by a triangular mesh containing points on the surface of the object. These points are moving in space under the influence of fluid-object interaction forces, as well as mechanic, elastic and magnetic forces. For each type of immersed object, different forces are applicable.

Interaction between fluid and objects is simulated using the drag force acting on an obstacle moving in the fluid. This principle is well-established and already implemented in ESPResSo.

Short videos showing features of our model are available at Cell-in-Fluid YouTube channel.

Four red blood cells flowing
in an S-shaped channel with obstacles
Red blood cell flowing past obstacles
in microfluidic channel
Relevant articles:


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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