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Re: From reactions to differential equations

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  • Subject: [mg93358] Re: From reactions to differential equations
  • From: dh <dh at>
  • Date: Wed, 5 Nov 2008 04:51:58 -0500 (EST)
  • References: <gepb55$skd$>

Hi Istvan,

the reaction kinetic equations only tell you what is changed into what. 

But they do not give you the speed (rate constants). But the diff. 

equation are actually about speeds and you need the rate constants to 

write them.

Further, Subscripts are only optical sugar, but they make programming 

hard. Therefore do not use it, or at least only for input/output.

hope this helps, Daniel

zac wrote:

> Dear All,


> from some time now I=E1m working with more and more complex differential

> equations.

> Is there a package to transform a set of reaction-kinetic equations

> such as:


> {

> Subscript[a, i] + Subscript[b, j] -> Subscript[c, i, j],

>  Subscript[a, i] + Subscript[c, i, j] -> 2 Subscript[a, i] +

> Subscript[b, j],

>  Subscript[b, i] + Subscript[c, j, i] -> 2 Subscript[b, i] +

> Subscript[c, j]

> }


> to differential equations expressing the growth of a_i, b_i and c_i,j,

> regarding

> that I leave the parameters i and j undefined?

> I am fully aware of software packages like COPASI and Systems Biology

> that are available, but I think they are far more complex than what is

> needed here, and furthermore I would like to understand the method how

> these reactions are actually converted to diff.equations. Which I

> completely miss if I'm to rely on a concealed algorithm.

> I've already started to write a parser in Mathematica, but it became

> too cumbersome after a point to deal with indexed variables (without

> indices it is fairly simple), and I really don't want to invent

> something that (perhaps) already exists on the field.

> Any ideas?


> Istvan Zachar



Daniel Huber

Metrohm Ltd.

Oberdorfstr. 68

CH-9100 Herisau

Tel. +41 71 353 8585, Fax +41 71 353 8907

E-Mail:<mailto:dh at>


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