translate KINETIC block to DERIVATIVE block
Posted: Mon Jun 24, 2019 5:15 am
Hi,
I am trying to compare two mod files but one is written using the KINETIC block and the other the DERIVATIVE block. Since I would like to solve the ODEs using the same method and not (SOLVE kin METHOD sparse) or (SOLVE deriv METHOD cnexp), I am thinking to rewrite the KINETIC block as the DERIVATIVE block, but I don't know how to write the conservation law.
In the KINETIC block it is simply CONSERVE A + B + C = 1; is there any way to impose the conservation law when the DERIVATIVE block is used instead of the KINETIC one? Can I do like this?
For example if I have:
KINETIC kin {
rates(v)
A <-> B (v1,v2)
B <-> C (v3,v4)
CONSERVE A + B + C = 1
}
can I 'translate' this block in the following way:
DERIVATIVE deriv {
rates(v)
A' = v2*B - v1*A
B' = v1*A - v4*C - (v2+v3)*B
C = 1 - (A + B)
}
So instead of writing C'= v3*B - v4*C, in order to include the conservation law, can I write C=1-(A+B)?
I also wonder how can I set the initial conditions. In the KINETIC block it is simply:
INITIAL {
SOLVE kin
STEADYSTATE sparse
},
what is the equivalent in the DERIVATIVE block?
Thank you for your help,
Ilaria
I am trying to compare two mod files but one is written using the KINETIC block and the other the DERIVATIVE block. Since I would like to solve the ODEs using the same method and not (SOLVE kin METHOD sparse) or (SOLVE deriv METHOD cnexp), I am thinking to rewrite the KINETIC block as the DERIVATIVE block, but I don't know how to write the conservation law.
In the KINETIC block it is simply CONSERVE A + B + C = 1; is there any way to impose the conservation law when the DERIVATIVE block is used instead of the KINETIC one? Can I do like this?
For example if I have:
KINETIC kin {
rates(v)
A <-> B (v1,v2)
B <-> C (v3,v4)
CONSERVE A + B + C = 1
}
can I 'translate' this block in the following way:
DERIVATIVE deriv {
rates(v)
A' = v2*B - v1*A
B' = v1*A - v4*C - (v2+v3)*B
C = 1 - (A + B)
}
So instead of writing C'= v3*B - v4*C, in order to include the conservation law, can I write C=1-(A+B)?
I also wonder how can I set the initial conditions. In the KINETIC block it is simply:
INITIAL {
SOLVE kin
STEADYSTATE sparse
},
what is the equivalent in the DERIVATIVE block?
Thank you for your help,
Ilaria