IUBio

On direct simulation

Herbert M Sauro HSauro at fssc.demon.co.uk
Mon Feb 10 18:09:00 EST 1997


In article <287cd$13b15.8b at enzyme.demon.co.uk>, Pedro Mendes
<pedro at enzyme.demon.co.uk> writes
>In article <wmGcAGAUZ6+yEwEK at fssc.demon.co.uk>, HSauro at fssc.demon.co.uk says...
>>[...]
>>Interestingly, both Henirk and Jim Burns did quite a bit of simulation
>>early on in the development of MCA and in fact the summation theorem was
>>'discovered' through a computer simulation. They reasoned that if there
>
>Herbert,
>This is actually one of the most powerful arguments in favour of simulation. In 
>the field of nonlinear dynamics this usage of simulation is called 
>"experimental mathematics". The following review (dedicated to the memory of 
>Stanilaw Ulam, of soliton fame) rehearses the the arguments:
Very true, I've nothing against simulation for such a purpose, what I'm
not too happy with is the blind use of simulation without any reference
to theory. That's essentially what happenned to Garfinkel's work,
massive simulations, very impressive, but no hope of understanding what
was going on. His work has pretty much sunk without trace, except of
course he inspired may of us to work in this area.

Higgins also did a lot of simulation but he also combined it with theory
and probably for this reason his work still gets quoted.

>On a different note, the only thing that bothers me about steady state
>analyses is that steady states are mostly inexistent in the wild. I know that 
Also probably true, but we've got to start somewhere, so best start with
the simplest things and move to more complex cases, oops you've said it
in the line below - didn't see it.
>the steady state is used as it is easier to deal with. Maybe it is time we 
>depart from this to the more complicated (but more interesting) analysis of 
>non-steady states. The late 1980's work you did with Acerenza and Kacser was a
>good starting point, more recently Hans Westerhoff's group has developed MCA 
I like to think so, there is a lot of untapped potential in that work
which sadly nobody took up, but who was the bastard who refused to fund
further work? Towards the end of that work a start was made on modifying
SCAMP to deal computing the time-dependent coefficients, we'd worked out
algorithms to do it. We realised that to go further we needed to do more
simlulations to get more information and help with the development of
the theory. 
>for oscillating states but we still have a lot to do in this area. Maybe the 
And Acerenza.
>use of simulation will be a great help to let us explore behaviours and find 
>regularities (and ultimatly some laws)
>
Definitely agree with you. It seems we share the same approach (which I
always thought anyway)!

Herbert
-- 
Herbert M Sauro
email:     HSauro at fssc.demon.co.uk
Telephone: 01974 282428
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