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Evaluation of Reaction Rate

Reaction Rate Dimensions

When calculating species fluxes, SimBiology must determine whether you specified reaction rates in dimensions of amount/time or concentration/time. When all compartments in a model have a capacity of one unit, amount and concentration are numerically equivalent.

For all other models, the numerical results of the simulation depend on which interpretation SimBiology selects. SimBiology determines whether a reaction rate is in dimensions of amount/time or concentration/time via dimensional analysis of ReactionRate expressions. This minimum level of dimensional analysis always occurs, even when DimensionalAnalysis and UnitConversion are off.

The DefaultSpeciesDimension property defines the dimensions of species appearing in a reaction rate. SimBiology infers the dimensions of parameters appearing in a reaction rate from their ValueUnits property. If any parameters appearing in a reaction rate expression do not have units, SimBiology interprets the reaction rate in dimensions of amount/time. Therefore, the only way to specify that a reaction rate has dimensions of concentration/time is to assign appropriate units to all parameters.

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Reactions Spanning Multiple Compartments

Specify reactions that span compartments using the syntax compartment1Name.species1Name –> compartment2Name.species2Name. The reaction rate dimensions must resolve to amount/time when:

• Species span multiple compartments.

• The reaction is reversible mass action and the products are in multiple compartments.

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Examples

Consider a reaction a + b —> c. Using mass action kinetics, the reaction rate is k*a*b, where k is the rate constant of the reaction. If you specify that initial amounts of a and b are 0.01 molarity and 0.005 molarity respectively, then the reaction rate is in concentration/time (and units of molarity/second) if the units of k are 1/(molarity*second). If you specify k with another equivalent unit definition, for example, 1/((moles/liter)*second), SimBiology 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 previous example, you specify that initial amounts of a and b are 0.01 and 0.005 respectively, without specifying units, SimBiology checks whether DefaultSpeciesDimension is substance or concentration. If DefaultSpeciesDimension is concentration, and you set units on the rate constant such that the reaction rate dimensions resolve to concentration/time, SimBiology scales the species amounts for compartment capacity, and returns the species values in concentration.

If you specify initial amounts of a and b as 0.01 molarity and 0.005 mole respectively, include the volume scaling for b in the reaction rate expression. Include volume scaling in the rate constant, and set the units of the rate constant accordingly (1/(mole*second) for concentration/time, or 1/(molarity*second) for amount/time).

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Defining Reaction Rates with Enzyme Kinetics

Using Constant Amount and Boundary Condition for Species

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