Different dilution effect on the kinetics of a time course

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Luis B. Walter 2024-6-14

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评论： Luis B. Walter 2024-6-17

Pregunta 14_06_2024 para el Simbiology community.pdf

Hi to everyone!

To simplify the explanation and the problem, I simulated the kinetics of an irreversible first-order reaction, A -> B. I implemented it in two independent compartments, R and P. I simulated the effect of a dilution in R by doubling at t= 0,1 the R volume. I programmed in P that, at t = 0.1, the instantaneous concentration of A and B would be reduced by half. I am sending an attach with the implementation of these simulations in the Simbiology interface.

When the simulations of the two compartments are plotted, it can be seen that the responses are not equal. That is, from t = 0.1 s, the reaction follow an exponential function in R with half of the initial amplitude and half of the initial value of k1. That is, the relaxation time is doubled. Meanwhile, in P, from t = 0.1, the reaction follows exponential kinetics with half the amplitude value but maintaining the initial value of k = 10. Without a doubt, the correct simulation is the latter (compartment P) where only the effect is observed in the amplitude and not in the relaxation time. Could you tell me what the error is that makes these kinetics that should be equal not be?

Thank you in advance!

Luis B.

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Umar 2024-6-15

To address the issue and ensure consistent simulation results between compartments R and P, you need to review the code that handles the dilution and concentration reduction processes. Check for any inconsistencies or errors in how these processes are applied to each compartment.

Luis B. Walter 2024-6-17

Thanks, Umar.

I didn't write any code on my part. I just implemented three Events (as can be see in the attachment) in the Simbiology interface for this elemental reaction:

time >= 0.1, R = 2*R
time >= 0.1, P.A = P.A/2
time >= 0.1, P.B = P.B/2

Luis B.

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Answer 1

Arthur Goldsipe 2024-6-17

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编辑：Arthur Goldsipe 2024-6-17

Hi Luis,

Because you don't use units in your model, SimBiology interprets the reaction rates to have dimensions of amount/time. (This is documented here.) The easiest way to fix this is to add units of 1/second to your rate constants. Then, the two appoaches for dilution behave identically.

One debugging tip mentioned on the above page is to view the differential equations for your model. You can find more details on how to do that in the SimBiology Model Builder app here.

-Arthur