Autologous chemotaxis at high cell density

Here you will find all scripts and simulation files used to generate the code in (...)

Figure Drawing files

fig1.m -> generates figure 1 in the manuscript using chi_calc.m as the function script and bluewhitered.m as the colormap
fig2b.m -> generates figure 2b in the manuscript, this uses a .xlsx file to read out the data generated by the COMSOL simulation
fig4.m -> generates figure 4 in the manuscript

Simulation files

generaterandomspheres.m -> creates a list of 1x3 vectors which are coordinates to plot a sphere of radius 10 with non-overlapping/non-clipping rules enforced
theta_phi_at_surface_with_flow3.m -> measures the anisotropy from COMSOL file using the technique described in the manuscript 1cell.mph -> this is the COMSOL simulation file, in order to use it:

1. feed the coordinates created from the .csv file (cellcoordinates.csv) generated by generaterandomspheres.m into Add Spheres 1 (this automatically places a sphere in the middle and creates the box and meshes everything, however one may play with the meshing after loading if they so wish...)
2. all of the walls and boundaries are properly given their conditions for the Brinkman and AC equations, however one must check to see all the constants are correct (absorbing and binding have different fluxes, for example)
3. click compute
4. once data has finished running and the concentration plots look correct, export them
5. in matlab, run theta_phi_at_sruface_with_flow3.m to generate the anisotropy (the anistropy value to be recorded coincides with newA_com)