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

[Andrew F. <af...@ca...>]

Mike

you wrote:

> 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.)
> 

I agree.  But we don't need to get stressed if they screw up the units!

yours
Andrew Finney  

> -----Original Message-----
> From: Michael Hucka [mailto:mh...@ca...] 
> Sent: 11 September 2006 08:26
> To: Andrew Finney
> Cc: 'Rainer Machne'; 'Nicolas Le Novere'; 'SOSlib Development'
> Subject: RE: Request for help with a multicompartment problem
> 
> 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
>