DynaFit Scripting Manual

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Optimized parameters

In several sections of the script file certain parameters (rate constants, initial or total concentrations, molar responses, or offsets on the signal axis) can be designated as optimized or adjustable fitting parameters. An adjustable parameter is indicated simply by appending a question mark (?) after the value of the initial estimate. The question mark can either follow immediately after the numerical value, or it can separated by any number of blank spaces.

Example: Optimized rate constants $k_s$ and $k_r$ and initial concentration of substrate $S$.

[mechanism]          
   E + S <==> ES     :     k   ks
   ES --> E + P      :     kr
[rate constants]
   k  = 1, ks = 10?, kr = 1 ?
[concentrations]
   S = 2.34 ?

Optionally the programs performs a confidence interval estimation for selected rate constants (but not for other kinds of parameters, such as concentrations or molar responses). These rate constants or equilibrium constants are identified by appending to their initial estimate two question marks (without any blank spaces between them).

In the example below, both rate constants $k_s$ and $k_r$ are treated as optimized parameter, but dissociation rate constant $k_s$ is given special attention. The program determines not only its best-fit value and the formal standard error, but also an approximate confidence interval.

Example: Confidence interval for rate constant $k_r$.

[rate constants]
   k  = 1, ks = 10 ?, kr = 1 ??
[concentrations]
   S = 2.34 ?

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Petr Kuzmic | Jul 12 2005