One stretching cell

The example in examples/stretchCell presents a validation example for the material models used in HemoCell. A single cell is initialised in a periodic domain, i.e. all external surfaces are subjected to periodic boundary conditions.

The setup mimics the optical-tweezer stretching measurement. A pair of external forces are applied on the outer points of the cell pointing in opposite directions. These forces stretch the cell, where its deformation can be validated with respect to experimental data.

After compilation, the example can be run using single core as:

# run the simulation from the `examples/stretchCell/`
mpirun -n 1 ./stretchCell config.xml

# generate Paraview compatible output files
../../scripts/batchPostProcess.sh

Note

The stretching cell examples should be run with just a single processor, so either mpirun -n 1 ./stretchCell config.xml as above, or directly ./stretchCell config.xml, as the helper function used to specify the stretching forces on the cell only supports sequential operation.

The outcome files are generated in tmp/, where the flow field and particle fields can be visualised separately by viewing the tmp/Fluid.*.xmf and tmp/RBC.*.xmf files in Paraview.

A deformed red blood cell after being subjected to opposing forces at either side of the RBC, where the arrows visualise the applied forcing.

Note

The stretchCell executable also collects the axial and transverse dimensions of the cell for each iteration for the used stretch force $f. These are collection in ./stretch-$f.log and can be used for validation purposes.

Configuration

There is one parameter that can be modified in this example, i.e. the applied stretching force in pico Newton:

• <parameters><stretchForce>: the applied stretching force in pico Newton.

Validation

The script validation.sh helps to perform basic validation of the cell stretch model as originally presented in [1]. The script runs through various evaluations of stretchCell with different values for the considered stretch force stretchFoce (Configuration). The resulting log files stretch-*log contain the axial and transverse dimensions of the RBC for the different stretch forces. From here, Figure 4 ([1]) can be recreated. If gnuplot is available on the system, the figure is automatically generated under stretchCell/validation/validation.png.

After compilation stretchCell the validation can be evaluated through:

./validation.sh
open validation/validation.png

Note

In validation/ a number of reference values are provided that correspond to the curves presented in [1] which provide a clear reference point when investigating cell stretch models.