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Dimensional analysis fail for reaction on simbiology

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Chi Chun Jacky Yeung
Chi Chun Jacky Yeung on 26 Jun 2020
When I run the programm, it shows the Dimensinal analysis failed for the reaction, I'm a beginner of simbiology, so I would like to ask what is the probelm of my model and how can I slolve it? I attached the file below, and the data of this model is based on this articel :https://link.springer.com/article/10.1007/s13361-012-0533-5

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Answers (1)

Sietse Braakman
Sietse Braakman on 26 Jun 2020
Hi Chi Chun,
The dimensional analysis ensures that the units in your model are consistent. However, this requires you to specify units for every compenent of your model (species, compartments, parameters), and for them to be consistent. See the screenshot (attached), you are missing the unit for the cells and the unit for kon is inconsistent. You can use the reaction rate to determine which units you should use. E.g. your reaction is P+L <-> PL. The reaction rate is P*L*kon-PL*koff. The unit of a reaction should be in amount or concentration per unit time. So each term in the reaction rate should have those units. Given that you defined P, L and PL in micromole (amount), the unit for kon needs to be 1/micromole/picomole. Once you have added/changed the units, you can verify the model to make sure that the unit conversion works and the units are consistent.
On another note, it looks like one of your reactants (Streptavidin) is quadrivalent. Looking at the reactions defined in the model, there are different reaction rates depending on how many binding sites are occupied. To model that, I suggest having species for P, L, PL1, PL2, PL3, PL4. So far you have implemented the reaction between P, L and PL1. From there you can create a network of reactions to model the complete binding of P to L, as described in the model. You'll also need to define koff and kon rates for each reaction.

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Chi Chun Jacky Yeung
Chi Chun Jacky Yeung on 2 Jul 2020
Thank you so much, I would like to ask, if I want to simulate the affinity binding curve, is there any functino I can use in simbiology?

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