### 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