SimBiology®

DefaultSpeciesDimension - Species dimension

Description

The DefaultSpeciesDimension property specifies whether the species dimensions are substance or concentration. If however, you specify the species units in the InitialAmountUnits property, these units define the species dimension regardless of the value in DefaultSpeciesDimension. Thus, if DefaultSpeciesDimension is concentration and you specify species units as molecule, the species dimensions are evaluated as substance.

You can find DefaultSpeciesDimension in the CompileOptions property.

When DefaultSpeciesDimension is set to substance, species quantities ignore compartment capacity, unless capacity is explicitly defined in an expression (reaction rate, rule, or event expression).

When DefaultSpeciesDimension is set to concentration, species quantities are scaled for compartment capacity in reaction rate, rule, or event expressions. CompartmentCapacity has a default value of 1, thus when capacity and capacity unit are not defined, species amount is equivalent to concentration.

For example, consider a reaction a + b —> c. Using mass action kinetics, the reaction rate is defined as a*b*k, where k is the rate constant of the reaction. If you specify that initial amounts of a and b are 0.01M and 0.005M respectively, then units of k are 1/(M*second). If you specify k with another equivalent unit definition, for example, 1/[(moles/liter)*second], DimensionalAnalysis checks whether the physical quantities match. If the physical quantities do not match, you see an error and the model is not simulated.

If in the above example, you define initial amounts of a and b are 0.01 and 0.005 respectively, without specifying units, the compile options check whether DefaultSpeciesDimension is substance or concentration. If the DefaultSpeciesDimension is concentration, and the reaction rate dimensions resolve to concentration/time the model is simulated with species amounts scaled for compartment capacity, and the solver returns the species values in concentration.

Valid physical quantities for reaction rates are amount/time, mass/time, or concentration/time.

Characteristics

See Also

CompileOptions, DimensionalAnalysis, get, getconfigset, sbiosimulate, set

DataNames

DimensionalAnalysis