Getting started with Copasi

Author Name : T.K.Subazini

Mail ID : subavijay_at_au-kbc.org

We will see a simple example of Reaction Diffusion System Model

- The famous Brusselator model in which chemical species X catalyzes its own formation.

The reactions are

R1:       A -> X

R2:       2*X+Y -> 3*X

R3:       X + B -> Y + D

R4:       X-> E

We are going to do Time Course analysis for these set of reactions with initial concentration of [X] =3, [Y]=3,[A] = 0.5, [B] = 3 , [D] = 0, [E] =0

Step1:

Click Model

In the right pane near in the text box near model name give a new name for model,

Specify Time unit as S. It indicates S as Second

Volume unit as ml. ml indicates Millilitre

Quantity unit as mmol. mmol indicates millimoles

Click Commit

Step2:

Click + near Model

Sub-branches become visible

Click + near Biochemical

Click on reactions

Below name type R1 (Name of the reaction)

Below Equation type A -> X

Click commit

Similarly do the same for rest of the reactions

If you want to do any changes in the reaction R1

Click on sub-branch R1

Select Rate law as Mass action [irreversible]

Set Parameter value for K1 as 1

Then click commit

Step3:

The Species involved in the reactions will automatically added

You can click on species name and alter the initial concentration of the species

Then click commit

Step 4:

Now click  + symbol near output

Click on plots

Below name type name of the plot eg plot1

Step5:

Double click plot1

Click new curve

A small popup with 2 panes of x and y axis appear

Click + symbol near time and select Model Time below X axis

Click + symbol below speces and select Transient Concentration below Y axis

Click Ok

Click commit

Step5:

Now click on + symbol near Tasks

Click on Time course

Click Run

You will get a graph as shown below

 The graph show X increases with time upto 0.225s and then decreases while Y decreases with time upto 0.225s and then increases while the rest of species A,B,D and E remains constant.