"Petr Kuzmic" <pkuzmic at biokin.com> wrote in message
news:3A5E04DA.FE1754B7 at biokin.com...
>>> Herbert M Sauro wrote:
>> > [...] We've got a
> > model at the moment which is full of equilibrium reactions. I'm not sure
how
> > one should go about this sort of modeling in an automatic way because
such
> > systems admit two moiety groups, one group which comes from the slow
> > reactions and the other from the quasi-steady-state group,
>> Pardon my ignorance, what exactly is referred to as a 'moiety' here?
> Does that mean 'species' or 'reactant'?
>> ---
By moiety I mean a conserved species (i.e a group of atoms), it may be a
whole reactant species or it may form part of a reactant species.
Essentially the moiety gets passed around the network without suffering any
net production orconsumption. Examples include things like CoA, NAD, ATP
(the AMP part and the Pi), etc. Granted that over a long period these
species may not be truely conserved but over short enough time scales it is
reasonable to assume they are conserved during the evolution of the system.
I shall check over your reference. I'm sure Petr you know all this but for
those who are not familiar with this topic the way modern simulators work is
that they divide the list of variable species into two groups, a dependent
and an independent set. The idea is that you only integrate the independent
set and compute the dependent set from the independent set. For example for
the simple system (i.e a cycle)
A -> B -> A
there is only one independent species, A (or B but not both). One only
integrates the ODE with respect to A and computes B from the relation, B =
T - A, where T equals the total mass of conserved moiety in the network. For
simple systems it's fairly easy to do this by inspection but for large
systems the task has to be done by computer.
> @book {Smit82,
> author = "W. R. Smith and R. W. Missen",
> title = "Chemical Reaction Equilibrium Analysis",
> publisher = "John Wiley",
> address = "New York",
> year = "1982"}
>
Thanks for the ref.
>> Beware of one potentially serious problem though. Any such mixed system
> of ODEs and algebraic equations (describing rapid equilibria) is a
> "differential-algebraic equation (DAE)" system. The theory of DAEs
> seems to suggest that, usually, one is in trouble with global truncation
> error. Petzold has written extensively on this, see for example the
> first reference on the list below. After I muddled through that article
> some year back, I decided not to pursue a numerical machine of the kind
> you are talking about. But maybe I was too conservative, so take a look
> for yourself.
Agreed. And many thanks for the refs which you added to the end of your
response.
>> - Petr
Herbert Sauro
