dear BioDynaMo team,
I have a few questions regarding how NeuriteElements work and whether their use could be further extended towards simulating tubular structures (vessels, etc).
- It is not entirely clear to me how force is transmitted along NeuriteElements from a NeuronSoma agent. I run a toy simulation containing a soma with a single branch of neurite elements, and several other agents: motile cells. The behaviour of the neurites (displacement) was rather oscillatory unless I set the “adhesion” parameter a very high value (i.e., 10e+3).
- Following up from the above, Agent (cells) – NeuriteElement mechanical interaction is not clear also to me.
- Is it possible to search for a NeuriteElement without necessarily iterating over all GetDaughters’s instead? Similarly, is it feasible to search for a NeuriteElement that is a branch / bifurcation?
- The concept of NeuriteElement currently permits branching of an existing sprout, or the bifurcation. However, I was wondering if it could support the notion of anastomosis, i.e. a tip NeuriteElement intersects an existing NeuriteElement sprout to create a new branch. If not currently supported, is it possible BioDynaMo feature it?
- Would it be possible also for BioDynaMo permit in the near future the creation of NeuriteElements without necessarily initializing them from a NeuronSoma? It would be particularly useful modelling prospectively blood-vessel dynamics (outgrowth, remodelling, etc.).
- Last but not least, I was also wondering if the naming of some classes could generalize, as it’s been adopted for Cell → Agent already So, could I propose having in the next major update a NeuronElement be renamed into something like Vessel?
Look very much for your comments, and apologies for the very long-winded message.