How to make simbiology plot concetratin?

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Gary Gorman
Gary Gorman on 9 Sep 2022
Answered: Fulden Buyukozturk on 10 Sep 2022
My species units are millimoles. My compartment units are molarity. But Simbiology does not plot the simulation output in molarity. Simbiology plots the simulation ouput in millimoles. How do I configure Simbiology to plot in units of concentration? Should I change the units of the species to concentration? In general, every time a molecule moves from one compartment to a different compartment the molarity of that molecule should change. But in my two compartment simulation Simbiology will only print out millimoles. In general, molarity changes caused by transfer from one compartment to a different compartment where the different compartments have different volumes should be automatic, I think. But my sims do not work that way. I can only get millimoles, never molarity in the Simbiology plot outputs.

Answers (1)

Fulden Buyukozturk
Fulden Buyukozturk on 10 Sep 2022
SimBiology returns simulation results of quantities (for example, species) in the user specified units. So if a species is in units of millimole, simulation results for that species will be returned in millimole.
If I understand your question correctly, you can plot concentration by first adding a quantity to your model that represents concentration. Let's say you have SpeciesA in millimole inside CompartmentA in milliliter. To monitor concentration you can:
  • add a new species, SpeciesAConc and set its unit to molarity
  • add a repeated assignemnt rule to calculate SpeciesAConc as SpeciesAConc = SpeciesA/CompartmentA
Alternatively, as you point out, if feasible you can choose to represent SpeciesA directly in concentration units in your model instead of amount units.

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