To describe a spatial model we need to define the following fundamental units:
Volume is not a fundamental unit. However, for user convenience we treat volume as a fundamental unit
This allows the use of units such as cm for length and mMol/mL for concentration, instead of the equivalent but less common mMol/cm^3.
All quantities in the model have units that can be written as some combination of these fundamental units:
- species concentrations
have units of
- reactions inside a compartment
describe the rate of change of the concentration of species
have units of concentration / time, i.e.
- reactions between two compartments
describe that rate at which a unit amount of species crosses a unit area of the membrane
where the membrane is the area where the two compartments touch each other
have units of amount / membrane-area / time, i.e.
- diffusion constants
have units of area / time, i.e.