Fundamental Units

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.

Derived Units

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
  • 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