Subject: Re: CCL:gear iterators

From: Kenneth Geisshirt <[email-masked]>
Date: 16 Apr 2002 06:45:39 +0200

On Mon, 2002-04-15 at 21:44, H. Martin Gillis wrote:

> If anyone knows where I can obtain software of GEAR Iterators (prefereably freeware) it will be most appreciated.

GNU Scientific Library implements a number of ODE solvers. Check out
http://sources.redhat.com/gsl/

-- 
Kenneth Geisshirt, M.Sc., Ph.D.         http://kenneth.geisshirt.dk
Grøndals Parkvej 2A, 3. sal                    [email-masked]
DK-2720 Vanløse                                     +45 38 87 78 38

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From: Bruce Allan Palfey <[email-masked]>
Date: Tue, 16 Apr 2002 00:50:24 -0400 (EDT)

Marcelo

There are anumber of programs (including free programs) that will simulate
chemical kinetics.  Look under "software" at
http://www.med.umich.edu/biochem/enzresources/

KINSIM and its various ports uses the Gear algorithm, which is useful for
"stiff" systems; that may not be necessary for your kinetic system.
Berkeley Madonna is a very versatile package that includes the Gear
algorithm, but it is not free (though the demo is almost fully
functional).  Rather than solve differential equations, CKS (free from
IBM) uses a stochastic approach to simulate reactions, avoiding the
pitfalls of stiff systems.  There are many others; hope this helps.

ciao,
Bruce Palfey
University of Michigan
Department of Biological Chemistry
Ann Arbor, MI 48109-0606

On Mon, 15 Apr 2002, H. Martin Gillis wrote:

> I want to model reaction rate constants where all four compunds A,B,C
> and D are interconvertble and where an equilibrium is eventually
> established.
>
> I have searched the literature and found that the use of an algorythm
> known as GEAR iteration will do the job provided that the concentrations
> of all 4 components versus time are known.
>
> If anyone knows where I can obtain software of GEAR Iterators
> (prefereably freeware) it will be most appreciated.
>
> Marcelo Sales
> Dept of Chemistry
> University of Saskatchewan
> [email-masked]
>
>
>