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
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
The stretching cell examples should be run with just a single processor, so
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/RBC.*.xmf files in Paraview.
The stretchCell executable also collects the axial and transverse
dimensions of the cell for each iteration for the used stretch force
These are collection in ./stretch-$f.log and can be used for validation
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.sh helps to perform basic validation of the cell
stretch model as originally presented in . The script runs
through various evaluations of
stretchCell with different values for the
considered stretch force
stretchFoce (Configuration). The resulting
stretch-*log contain the axial and transverse dimensions of the
RBC for the different stretch forces. From here, Figure 4
() can be recreated. If gnuplot is available on the
system, the figure is automatically generated under
stretchCell the validation can be
./validation.sh open validation/validation.png
validation/ a number of reference values are provided that correspond
to the curves presented in  which provide a clear
reference point when investigating cell stretch models.