Help with Copasi

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Angelo Pisciotta

Jan 22, 2024, 7:32:40 PMJan 22
to COPASI User Forum
Hello everyone, I'm a student preparing for an exam on the COPASI model of Fenton degradation on malachite green. I've already opened a forum, but I noticed that the file I uploaded doesn't open. I hope this one opens because I could use some help. I don't know why, but I'm not getting the diagram to see if degradation is occurring, only the table with the values. Is there a way to view the graph? Because from what I can tell, the model is working, but I'm unsure if it fits with the article.

Thanks to everyone who responds. I'm attaching the article and the COPASI file.
FENTON (vedere se è da correggere).cps
reazioni fenton.pdf
FENTON (vedere se è da correggere).txt

Angelo Pisciotta

Jan 22, 2024, 7:47:56 PMJan 22
to COPASI User Forum
I now I managed to see the graph, and the model doesn't fit with what is reported in the article. Could someone help me?

Matthias König

Jan 23, 2024, 4:14:15 AMJan 23
Hi Angelo,
here my minor comments.

- model looks pretty straight forward and I assume they just put in irreversible mass action kinetics for all the reactions listed in Tab1.
- initial conditions are not given consistently: I would assume everything is 0. Then you set for the different experiments the initial concentrations given in Tab2.
- make sure the units are correct on your model and make sure you set the right units for your species. I.e. you can see the rate constants given in [1/(M*s)] = [L/mole/s]. So your time units should be seconds and your species units mole/L. So you have to set initial conditions e.g. for Fe2+ as 28.8E-6 M (28.8 µM).
- the rate units provided in the table are [1/(M*s) * M * M) = M/s; but should be mole/s; So either the provided units in Tab1 for k are wrong, or you have to make sure to get the units right by scaling with the volume: J0: Fe2 + H2O2 -> ...;    J0 = k0*V * [Fe2] * [H2O2]   [1/(M*s) * L * M * M] = [mole/s]
- I am pretty sure they messed up handling the volumes/units/amounts/concentrations correctly, so will be difficult to get the model to reproduce. You should request access to the ODE system in the programming language they have and work from the code instead from the provided information in the manuscript (which is patchy and not completely clear.

Best M

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Angelo Pisciotta

Jan 25, 2024, 5:49:36 AMJan 25

I managed to get the model running, and fortunately, the K values are correct. Now I would like to ask if it is possible to create the model for mineralization [TOC], and if the reaction described is MGCB + OrH -> Products, where 'Products' represent mineralization

Angelo Pisciotta

Jan 25, 2024, 6:47:03 AMJan 25
I want to know how i insert a scaravenger species in the model, because in the article there is TBA (scaravenger), but don't give the k
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