OIF in ESPResSo

We developed an extension of ESPResSo software package that is capable of simulating elastic objects immersed in a fluid. The detailed description of the python implementation of the package can be found in our Python Object-in-fluid User Guide. The initial geometry of each elastic object is defined in two files, the nodes.dat file, where the coordinates of the mesh points are given and triangles.dat file, where the triangular incidences are given. Below, you can find different types of objects, with different mesh densities.

 

motivation.py

 

 Sample script from Python Object-in-fluid User Guide  
spheres.zip The surface of a sphere is triangulated with different numbers of points. The triangulation is two dimensional, that means that it consists of triangles and each edge of the triangle is common exactly to two triangles.  
solid-balls.zip Three dimensional mesh consisting of tetrahedra covering the whole inside of a sphere. Here, an edge can be common to more than two triangles. With this type of a mesh, the elastic parameters kb and kv must not be set.  
rbcs.zip

The surface of a red blood cell is triangulated with different numbers of points. The triangulation is two dimensional, that means that it consists of triangles and each edge of the triangle is common exactly to two triangles.

 
ellipsoids.zip

The surface of an ellipsoid is triangulated with different numbers of points. The triangulation is two dimensional, that means that it consists of triangles and each edge of the triangle is common exactly to two triangles. Two semi-axes of each ellipsoid are the same length and one has different length. The name of each mesh-file includes the ratio of the semi-axes, where "p" represents the decimal point. 

 

Article on Object-in-fluid implementation:

An ESPResSo implementation of elastic objects immersed in a fluid

 

Articles regarding models in Object-in-fluid:

Energy contributions of different elastic moduli in mesh-based modeling of deformable objects

Scalability of forces in mesh-based models of elastic objects

Modelling and simulation of processes in microfluidic devices for biomedical applications

Recent advances in mesh-based modeling of individual cells in biological fluids

 

The ESPResSo scripting interface was changed from Tcl to Python in autumn 2017. We followed this path and we rewrote the Object-in-fluid into python. However, the detailed description of the TCL implementation of the package still can be found in our Tcl Object-in-fluid User Guide

Below, an older version of the scripts (in Tcl) is available)

simulation.tcl

boundaries_part.tcl

boundaries_fluid.tcl

 Sample Tcl scripts from Tcl Object-in-fluid User Guide  

events&news

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
ICNAAM

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 :-)

2010-2017 © Cell-in-fluid, KST ŽUŽ - Všetky práva vyhradené. All right reserved.