SimBiology^®

ReactionRate - Reaction rate equation in reaction object

Description

The ReactionRate property defines the reaction rate equation. You can define a ReactionRate with or without the KineticLaw property. KineticLaw defines the type of reaction rate. The addkineticlaw function configures the ReactionRate based on the KineticLaw and the species and parameters specified in the kinetic law object properties SpeciesVariableNames and ParameterVariableNames.

The reaction takes place in the reverse direction if the Reversible property is true. This is reflected in ReactionRate. The ReactionRate includes the forward and reverse rate if reversible

You can specify ReactionRate without KineticLaw. Use the set function to specify the reaction rate equation. SimBiology adds species variables while creating reactionObj using the addreaction method. You must add the parameter variables (to the modelObj in this case). See the example below.

Once you have specified the ReactionRate without KineticLaw, if you later configure the reactionObj to use KineticLaw the ReactionRate is unset until you specify SpeciesVariableNames and ParameterVariableNames.

Characteristics

Applies to	Object: reaction
Data type	`char string`
Data values	Reaction rate string. Default is `''`
Access	Read/Write

Examples

Example 1

Create a model, add a reaction, and assign the expression for the reaction rate equation.

Create a model object, then add a reaction object.

modelObj = sbiomodel('my_model');
reactionObj = addreaction(modelObj, 'a -> c + d');

Create a kinetic law object for the reaction object, of the type 'Henri-Michaelis-Menten'.
```
kineticlawObj = addkineticlaw(reactionObj, 'Henri-Michaelis-Menten');
```
reactionObj KineticLaw property is configured to kineticlawObj.
The 'Henri-Michaelis-Menten' kinetic law has two parameter variables (Vm and Km) and one species variable (S) that you should set. To set these variables, first create the parameter variables as parameter objects (parameterObj1, parameterObj2) with a names Vm_d, Km_d and assign them to kineticlawObj.
```
parameterObj1 = addparameter(kineticlawObj, 'Vm_d');
parameterObj2 = addparameter(kineticlawObj, 'Km_d');
```

Set the variable names for the kinetic law object.

set(kineticlawObj,'ParameterVariableNames', {'Vm_d' 'Km_d'});
set(kineticlawObj,'SpeciesVariableNames', {'a'});

Verify that the reaction rate is expressed correctly in the reaction object ReactionRate property.
```
get (reactionObj, 'ReactionRate')
```
MATLAB^® returns
```
ans =

Vm_d*a/(Km_d + a)
```

Example 2

Create a model, add a reaction, and specify ReactionRate without a kinetic law.