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Create a Rate Rule for the Rate of Change That Is Determined by Another Species

This example shows how to create a rate rule where a species from one reaction can determine the rate of another reaction if it is in the second reaction rate equation. Similarly, a species from a reaction can determine the rate of another species if it is in the rate rule that defines that other species. Suppose you have a SimBiology model with three species (a, b, and c), one reaction (a -> b), and two parameters (k1 and k2). The rate equation is defined as , and rate rule is . The solution for the species in the reaction are:

, .

Since the rate rule is dependent on the reaction, . The solution is:

Enter the following commands to set up a SimBiology model accordingly and simulate it.

m = sbiomodel('m');
c = addcompartment(m,'comp');
s1 = addspecies(m,'a','InitialAmount',10,'InitialAmountUnits','mole');
s2 = addspecies(m,'b','InitialAmount',0,'InitialAmountUnits','mole');
s3 = addspecies(m,'c','InitialAmount',5,'InitialAmountUnits','mole');
rxn = addreaction(m,'a -> b');
kl = addkineticlaw(rxn,'MassAction');
p1 = addparameter(kl,'k1','Value',1,'ValueUnits','1/second');
rule = addrule(m,'c = k2 * a','RuleType','rate');
kl.ParameterVariableNames = 'k1';
p2 = addparameter(m,'k2','Value',1,'ValueUnits','1/second');
[t,sd,species] = sbiosimulate(m);
plot(t,sd);
legend(species);
xlabel('Time');
ylabel('Species Amount');

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