Concentration scale

All concentrations mentioned anywhere in the script file must have the same concentrations scale (unit). It is optimal to choose a ``natural'' concentration scale for the analysis of each experiment, so that the nominal values are as close to unity as possible. This minimizes the truncation and round-off errors in numerical computations.

For example, if all concentrations are in the micromolar range, choose the micromolar unit throughout the script file. If some concentrations are very much different from other concentrations, choose a unit of concentration which is a compromise between the two values.

Example

The concentration of enzyme E was $10^{-9}$ M (kept constant), while the concentration of substrate S was varied between 0.5 and 8 $\times 10^{-3}$ M. The most natural unit of concentrations is therefore $\mu$ M, which also determines the unit for all bimolecular association rate constants and the molar response coefficient (k = 1 means $k = 10^{6}$ M $\phantom{.}^{-1} {\rm sec}^{-1}$ ). Let us assume that the formation of one mole per liter of the reaction product P would cause an increase in the experimental signal (e.g., absorbance) by 1500 units, which means that one micromole per liter (our chosen unit) produces 0.0015 units of the experimental signal.

[mechanism]
   E + S <==> ES : k  ks  |   ES --> E + P :  kr
[constants]
   k = 1, ks = 20, kr = 5
[responses] 
   P = 0.0015
[concentrations]
   E = 0.001
[progress]
   files          f1,  f2,   f3,   f4,   f5,   f6
   vary conc. S = 500, 1000, 2000, 4000, 8000, 16000
[end]

Next: Global and local concentrations Up: Concentrations Previous: Concentrations Index

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Petr Kuzmic | Jul 12 2005