Problems with the 'null' variable in Simbiology

Hello,

I have the following mass-action reactions in simbiology:

null -> T

T+V -> Tstar

V -> null

T -> null

Tstar -> null

Unfortunately, V and T have different units (both concentration though). So, when I try to 'verify' or 'run' this model, I get the following error:

"Error using localReactionsToCode (line 897) Reaction null -> T has reactants in multiple compartments or the reactant is null. The reaction rate must be defined in units of amount per unit time not concentration per unit time."

I can change the first equation to foo -> T, but that creates the 'foo' variable. This isn't a problem, since the creation of T is first order and "independent" of 'foo'. But, it seems like something is wrong and I shouldn't have to define the variable foo.

best, David

Answer 1

[Arthur Goldsipe]

Hi David,

The problem is with the units on the rate constant for the reaction null -> T. Let's say you have the reaction rate set to a parameter K. Then K must have dimensions of amount/time, for example, mole/second. If your parameter K currently has dimensions of concentration/time, then you probably just need a new parameter whose value is K*C, where C is (the volume of) the compartment that contains species T.

-Arthur