From brunni at netestate.de  Fri Jun 27 09:23:58 2014
From: brunni at netestate.de (Michael Brunnbauer)
Date: Fri Jun 27 09:24:01 2014
Subject: [Compucell3d-users] Explanation for branched structures in
 CompuCell3D angiogenesis example
Message-ID: <20140627162358.GA16790@netestate.de>


hi all

I hope this reaches anyone as it seems to be the first post to this
mailing list since 2010. I also hope this is the right place for my amateur
question.

What is the math behind the forming of branched structures in the angiogenesis
example of the CompuCell3D manual? I am struggling to reproduce the effect
outside CompuCell3D.

I succeded to reproduce the cell-sorting simulation with own python code
following the equations and numbers from the manual. But my blob of endothelial
cells only gets visibly compressed by chemotaxis towards medium and then
stays in shape - roughly ball-like. The VEGF seems to have a stabilizing 
effect but no branched structures develop. And why should they anyway?

I wonder if the branched structures may be only a byproduct of the mode of
simulation in CompuCell3D. It is intriguing that they only seem to form 
diagonally. Or could they be artefacts from the first random developments
and my simulation is stabilizing too fast?

My simulation is 2d but I guess that is not the reason for the missing 
branch structures.

This question can be answered without looking at my code but if you want to
look at it anyway, you can find it here: http://www.brunni.de/ggc/

Regards,

Michael Brunnbauer

-- 
++  Michael Brunnbauer
++  netEstate GmbH
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