fix ID rate/saturate N species-ID half volscale react1-ID react2-ID ...
fix mine rate/saturate 1 NFkB-nuc 100 c1 u1 u3
Adjust one or more reaction rates based on the current concentration of a chosen species. This is a way to have a time-dependent rate for a reaction that goes to zero as the concentration of one of its reactants increases, so that the amount of product produced effectively saturates rather than increases forever. For example, it can be used to model gene transcription resulting in mRNA production.
Here is how the fix operates. Every N timesteps, the rates for the listed reactions are scaled to new values in the following way:
r_new = r_initial * half / (half + [species-ID])
R_new(t) is the new scaled reaction rate. R_initial is the rate set for this reaction initially in the input script. Half is the concentration value set by this command. [Species-ID] is the current concentration of the selected species.
For continuum ODE simulations this concentration is stored directly by ChemCell and is correct for whatever compartment the species may be in. Thus the volscale parameter is ignored. For stochastic models, the concentration is computed by the molecule count divided by the volume. It is then scaled by the specified volscale parameter. This should be set to 1.0 if the system volume is the one in which species-ID is present. If the concentration is for a species in a smaller volume (e.g. the nucleus), then volscale should be set to the ratio of the system volume to the smaller volume, e.g. 10.0 if the cell is 10x larger than the nucleus.
Note that the half parameter is the concentration of species-ID at which the effective rate will be cut in half. Note that the scale factor half / (half + [species-ID]) is unitless.
This fix can only be used with non-spatial simulations.
Related commands: none