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

screenshot showing the automatic rescaling of non-spatial reactions

An example of the automatic rescaling of image depth and reaction rates when importing a non-spatial model