RE: Multiple kineticLaw Sections Per Reaction
10 Mar '06 04:15
On Fri, 10 Mar 2006, Nicolas Le Novere wrote:
> Ouch! The reversible flag has a very clear meaning, and is essential
> for various treatments (graphical output, treatment of fast reactions
> where one ignore kineticLaws etc).
I'm sorry if I seemed harsh in my previous message.
Part of why I wanted to have multiple kineticLaws was that I want the
graphical output to look better. You bring up a good point about fast
reactions, and I think that if multiple kineticLaws are accepted then the
fast attribute should be optional for kineticLaws as well as reactions.
> I am probably misunderstanding the issue here, but you can just define
> two reactions as Herbert says BUT set the reversible flag to
> "false". It is true by default.
I can do that, but as you said above that breaks the graphical
> Remind-me why can't you use a reversible reaction with a kineticLaw of
> the form
> kon * react - koff * prod
I do stochastic reactions where the probability of each reaction is
tracked. In many cases, a reversible reaction is the one where I'm most
interested in the exact number of individual species created, and if I
have a single kinetic law to specify what is essentially the net movement
of molecules from the reactant side to the product side then I miss some
of the detail of the gross movement.
A more concrete example is
A <-> B
B -> C
where perhaps the A -> B reaction is slow but the B -> A and B -> C
reactions are fast. If I just do the kinetic law as you stated above,
essentially no B will ever be created because it does not have a
high probability of being created. Because of this, no C will be created,
and if that's my species of interest my stochastic simulation will not
capture the behavior that I'm looking for.
"Fools ignore complexity. Pragmatists suffer it. Some can avoid it.
Geniuses remove it."
-- Alan Perlis