Multiple concentration

[Harry Wilson]

Hello,

I am new to Copasi and I want to estimate the rate constants for a multistep reaction that proceeds in this way:

A + B -> I + E

I + 3A -> J + 3E

2J -> C + D

Here, A and B are the starting materials, I & J are the intermediates and C, D and E are products. To get more idea into the mechanism I have performed multiple kinetics experiments with varying concentrations of A and B resulting in varying rates of formation of C and E. Therefore, I have different set of initial concentrations of A and B and accordingly a bunch of values for E and C. Is there a way in copasi where I can put in all these data to get a rate constant that matches all different initial concentrations of A and B.  Thank you for your attention to this matter.

Thanking you,

Harry

[Frank Bergmann]

Hello Harry, 

to do this, you would add the different initial concentrations for A and B to your experimental data file. There at the initial time (usually t = 0), you would add a column for A and a column for B. Then when mapping the data for those two columns, in the mapping from column to model element, you would choose 'independent' to signify that it is a starting condition that you change. In the window that pops up you select the initial concentrations for the respective species. 

Let me know if you need help with that, feel free to send me your setup and I can help you with it on your concrete case. 

best

Frank

[Harry Wilson]

Dear Frank,

Thank you for your reply. Until now I have been trying to run different experiments corresponding to each different initial concentration.

I will be attaching an experiment data with two set of experiments. These are the queries that I have:

1.) The way in which I determined the concentration of E and C are different and this can be seen from different times at which I got these values. How should I account for this for the copasi to take this into account.

2.) As you said in the previous email, I have added a column for different initial concentrations (In the data I have shown only one set in which I am varying the initial concentration of A and B).  Is it a problem if I dont have the concentration of C in all the cases?

Could you check the file and kindly let me know.

Thanking you,

Harry 

[Frank Bergmann]

Hello Harry, 

1) it is fine to have missing values for where you dont have data. But i would not map C for the last experiment where you have no dependent data for C at all. 

2) the column for the initial concentrations look fine, though you only need them at the initial time. (but it wont hurt to have them there for the remaining values)

let us know if you encounter any issues along the way

best

Frank

[Harry Wilson]

Dear Frank,

That helped me a lot to run the experiment in copasi.

Like I said, the initial concentrations that I have taken in the 3 experiments are not the same and can you please confirm that in the following experiment that I ran in copasi takes into account these different initial values and not the same value I submitted in the compartment. (Because in the model>biochemical>species section, I have to input initial concentrations of A and B. But this value is only for 1 experiment whereas for the other 2, its different initial values for A and B.) I hope you understand my doubt. I will be attaching copasi file and exp data for your reference.

Thanking you,

Harry