redefine mass action kinetics

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George A. 2017-12-15

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评论： Arthur Goldsipe 2017-12-16

Hi All.

I am looking for a general way to redefine the mass-action kinetics. The way they are implemented in Matlab is that for a reaction of type 2A->B with reaction constant k, the rate of the reaction is given by k*A^2.

I would like to change the reaction rate to k*A*(A-1).

I know how to do it for a specific type of reactions using the sbioaddtolibrary function. But this solution doesn't take care of a reaction of type 2A+2B->C.

Thank you for your help.

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Answer 1

Arthur Goldsipe 2017-12-16

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It's not currently possible to create a custom kinetic law that depends on the reaction's stoichiometry. You will need to manually write each reaction rate.

Based on the form of your reaction rate, I suspect you're trying to model a system containing a small numbers of reacting molecules. Have you considered using one of SimBiology's stochastic solvers? That would likely be a better model of your system than using deterministic solver with the reaction rates you describe.

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George A. 2017-12-16

Thanks for the reply. Is choosing a stochastic solver going to change the form of mass-action kinetics?

Arthur Goldsipe 2017-12-16

Yes, the stochastic solvers model mass action kinetics differently. They take into account the discrete number of molecules. For example, if your reaction is 2 A -> B, and you only have 1 molecule of A, then B would never form. I'm guessing this is the sort of effect you want to model when you say you want to use a rate of the form k*A*(A-1).

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