Rescale Reactions
A non-spatial ODE model contains reaction rates that specify a rate of change of species total amount in a given compartment.
In a PDE model, we have
compartment reactions: rate of change of species concentration
membrane reactions: rate of species amount crossing unit area of the membrane
The last step in importing a non-spatial model is to rescale the reactions appropriately, by clicking on “rescale reactions” in the bottom right of the window.
This opens a guided workflow that automatically rescales the image depth and the reaction rate expressions, with the goal of constructing a valid PDE model that initially reproduces the behaviour of the imported ODE model, in the following limit of the spatial model:
no initial spatial dependence of species concentrations
infinitely fast diffusion
consistent compartment volumes between ODE model and PDE model geometry
An example of the automatic rescaling of image depth and reaction rates when importing a non-spatial model