Local concentrations

Initial concentrations of reactants that are applicable to all progress curves listed in the given script are given in the [concentration] section of the script file (Chapter 5). In addition, the [progress] curve section can contain concentrations that are specifically linked to particular data. The concentration values related to a particular progress curve file are indicated by the keyword concentration, which can be abbreviated as conc.

Example 1The concentration of enzyme E is 0.001 $\mu$ M in datasets F1, F2, and F3. The concentration of substrate S is 10, 20, and 30 $\mu$ M, respectively.

[concentrations]
   E = 0.001
[progress]
   file f1
   concentration S = 10
   file f2
   concentration S = 20
   file f3
   concentration S = 30

The concentration of a certain species can appear both in the [concentration] section (globally) and in the [progress] section (locally). In this case the local concentration overrides the global concentration.

Example 2The concentration of enzyme E is 0.001 $\mu$ M in datasets F1, F2, and F3. The concentration of substrate S is 10 $\mu$ M in data sets F1 and F3 but 30 $\mu$ M in data set F3.

[concentrations]
   E = 0.001, S = 10
[progress]
   file f1
   file f2
   file f3
   concentration S = 30

Locally optimized concentrations

It is often advantageous to treat certain concentrations as locally optimized parameters, to account for the fact that in delivering reaction volumes the experimenters necessarily make random errors (pipetting errors). Some or all local concentrations can be made adjustable by appending the question mark after their numerical values.

ExampleThe concentration of enzyme E is held constant at 0.001 $\mu$ M in datasets F1, F2, and F3. The concentration of substrate S is held constant at 10 $\mu$ M in data set F1, while the concentrations 20 and 30 $\mu$ M, respectively, in data sets F2 and F3 are treated as locally optimized parameters.

[concentrations]
   E = 0.001
[progress]
   file f1
   concentration S = 10
   file f2
   concentration S = 20 ?
   file f3
   concentration S = 30 ?

Multiple local concentrations

The keyword concentration or conc can be followed by any number of species names and associated concentrations, separated by commas. Some or all concentrations listed in this manner can be treated as locally adjustable parameters.

ExampleThe concentration of enzyme E is held constant at 0.001 $\mu$ M in the dataset F1. The same value is treated as a locally adjustable parameter for data sets F2 and F3. The concentration of substrate S is held constant at 10 $\mu$ M in data set F1, while the concentrations 20 and 30 $\mu$ M, respectively, in data sets F2 and F3 are treated as locally optimized parameters. Here we used the abbreviated form of the keyword concentration and the shorthand ``|'' for line break.

[concentrations]
   ; empty
[progress]
   file f1 | conc E = 0.001  , S = 10
   file f2 | conc E = 0.001 ?, S = 20 ?
   file f3 | conc E = 0.001 ?, S = 30 ?

Next: Local response coefficients Up: Progress Curves Previous: Offset Index

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Petr Kuzmic | Jul 12 2005