Volume change in simbiology
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Ardeshir Goliaei on 21 Aug 2019
I have a question about how Simbiology handles volume changes during a simulation. I understand that by assigning ConstantCapacity to false we can allow the capacity of a compartment to change according to some rule; as an example, a tumor compartment that responds to drug treatment. But how does Simbiology handle the concentration of species that reside in this compartment? If tumor is shrinking, the concentration of species within it will increase, which is an artefact.
Any comment would be greatly appreciate.
Arthur Goldsipe on 22 Aug 2019
As described here, SimBiology conserves amounts when changing compartment volumes. If I were building the model, I would not use SimBiology's compartment volume to track the tumor volume. Instead, I would track tumor volume in a "non-constant SimBiology parameter" and set me SimBiology compartment volume to some standard reference volume (e.g., 1 milliliter).
I already logged an enhancement request in our database to allow conservation of concentrations instead of amounts. I'll make sure to add this use case to the request.