Re: [SOSlib-devel] Request for help with a multicompartment problem

[Michael H. <mh...@ca...>]

Hi Andrew,

  afinney> describes a phenomena that only really works in a
  afinney> single compartment.  i.e. when two species are in
  afinney> the same compartment and therefore can freely
  afinney> react with each other the rate of reaction is
  afinney> proportional to the concentrations of the
  afinney> species.

I suspect Nicolas will say something about it too, but I
want to mention I got an email from Bob Phair on the same
question, and he entirely contradicted the claim that this
is an unusual situation.  In his words, "The situation you
describe actually occurs frequently. I don't see anything
weird here", and goes on to give an example of extracellular
signal molecule binding to membrane receptors where you have
to deal with separate volumes.

(His solution to the problem was change the rate constant.
I'll ask if I can forward his reply around.)

What may be a bit confusing is the rate law I used,
mass-action, has assumptions about molecular interactions.
If you remove that, perhaps it won't require thinking that
the reactants have to be in the same space.

More generally, I think you would agree that modelers should
be able to express a compound rate expression that involves
whatever compartmental organization they feel is appropriate
for their problem.  (And indeed, Nicolas will attest to the
fact that models in the wild do this.)

MH