To describe a spatial model we need to define the following fundamental units:
amount(e.g. Mole)length(e.g. metre)time(e.g. second)
Volume is not a fundamental unit. However, for user convenience we treat volume as a fundamental unit
volume(e.g. litre)
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
amount/volume
- have units of
- reactions inside a compartment
- describe the rate of change of the concentration of species
- have units of concentration / time, i.e.
amount/volume/time
- 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.
amount/length/length/time
- diffusion constants
- have units of area / time, i.e.
length*length/time
- have units of area / time, i.e.
For more information see units.pdf <units.pdf>