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Re: Conditions in chemical rate equations

From: Michael Kohlhase <m.kohlhase@jacobs-university.de>
Date: Mon, 19 Nov 2007 17:42:07 +0100
Message-ID: <4741BCDF.2060000@jacobs-university.de>
To: Hannah Barjat <Hannah.Barjat@atm.ch.cam.ac.uk>
CC: www-math@w3.org

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Dear Hannah Barjat,

this is a very nice example, I (just my personal preference, there are
other options of course) would probably go for a special conditioned
equality here, represented by a <csymbol>. this equation takes three
arguments: left side, right side and condition.

 So the expression could look something like the following.

<mml:apply>
  <mml:csynbol definitionURL="http://www.iupac-
                   kinetic.ch.cam.ac.uk/mathml/condeq">
    <mml:ci>=</mml:ci>
  </mml:csymbol>
  ... <!-- lhs -->...
  ... <!-- rhs -->...
  ... <!-- condition --> ...
</mml:apply>

where the condition part is the content of your <mml:condition> element
below. The <mml:condition> element in MathML is reserved as a qualifier
in binding expressions (i.e. expressions with bound variables; of which
 there are none around here).

In the upcoming MathML3 (see
http://www.w3.org/TR/2007/WD-MathML3-20071005/Overview.html)  you would
probably write a content dictionary for rate equations, which has symbol
definitions for rate coefficients and (another?) for conditioned
equations. This would also give you the opportunity to associate
notation definitions with these new symbols, and allow you to get the
presentation right.

I hope this helps.

Michael

> 
> Please accept my apologies if this query is too trivial for this email
> list but I have been unable to find a suitable example to follow on the
> Internet. I wish to put a compliation of chemical rate expressions into
> content mathML, the reactions themselves will be expressed in CML. One of
> the simplest examples is where the reaction follows the Arrhenius
> expression
> k=Aexp(-B/T). I have shown an example of this (below), in mathML,
> (ignoring units for the time being) where A=1.9E-12 and B=270 with an
> associated error of plus/minus 500. The equation, in this case, is valid
> where the temperature is between 240 and 340 K. It is this condition
> that I do not know how to write correctly. It does not appear to be
> correct just to place the condition directly after the equation (as
> below). Would I be better to use the domain of application element?
> 
> Thanks for your time, Hannah
> 
> 
> <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"
>                     xmlns:xsi="http://www.w3.org/2001/XMLSchema-
> instance"
>                     xsi:schemaLocation="http://www.w3.
> org/1998/Math/MathML
>                     http://www.w3.org/Math/XMLSchema/mathml2/mathml2.
> xsd">
>    <!--Arrhenius -->
> 
>    <mml:apply>
>        <mml:eq/>
>        <mml:csymbol
>            definitionURL="http://www.iupac-
> kinetic.ch.cam.ac.uk/mathml/ratecoefficient">
>            <mml:ci>k</mml:ci>
>        </mml:csymbol>
>        <mml:apply>
>            <mml:times />
>            <mml:cn type="e-notation"> 1.9 <mml:sep /> -12 </mml:cn>
>            <mml:apply>
>                <mml:exp />
>                <mml:apply>
>                    <mml:divide />
>                    <mml:apply>
>                        <mml:mo>&#177;</mml:mo>
>      <!--According to the mathML spec this should be:
> <mml:csymbol>&PlusMinus;</mml:csymbol> but to get it to render in my
> browser I use the presentation markup - in either case it will not
> render inline using the mathML style sheet-->
>                        <mml:cn> 270 </mml:cn>
>                        <mml:cn> 500 </mml:cn>
>                    </mml:apply>
>                    <mml:csymbol
>   definitionURL="http://www.iupac-kinetic.ch.cam.ac.uk/mathml/temperature">
>                        <mml:ci>T</mml:ci>
>                    </mml:csymbol>
>                </mml:apply>
>            </mml:apply>
>        </mml:apply>
>    </mml:apply>
> 
>    <mml:condition>
> <!-- I'm not sure that I should really tag the condition onto the end of
> the reaction; perhaps I should use <domain of application> directly
> within the equation ? -->
>        <mml:apply>
>            <mml:lt/>
>            <mml:cn> 240 </mml:cn>
>            <mml:csymbol
>               definitionURL="http://www.iupac-kinetic.ch.cam.ac.uk/mathml
>               /temperature"
>                <mml:ci>T</mml:ci>
>            </mml:csymbol>
>            <mml:cn> 340 </mml:cn>
>        </mml:apply>
>    </mml:condition>
> </mml:math>
> 
> 
> 

- --
- ----------------------------------------------------------------------
 Prof. Dr. Michael Kohlhase,       Office: Research 1, Room 62
 Professor of Computer Science     Campus Ring 12,
 School of Engineering & Science   D-28759 Bremen, Germany
 Jacobs University Bremen*         tel/fax: +49 421 200-3140/-493140
 m.kohlhase@jacobs-university.de http://kwarc.info/kohlhase
 skype: m.kohlhase   * International University Bremen until Feb. 2007
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Received on Monday, 19 November 2007 16:41:10 GMT

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