DynaFit Scripting Manual

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Mixing delay time

Rationale for a mixing-time constant

The numerical computation of reaction progress curves in DynaFit assumes that at time zero ($t$ = 0) the reactants were just brought into contact, which means that molecular complexes (if any) have not yet been fully formed. For example, in an enzyme reaction following the Michaelis-Menten mechanism,

[mechanism]
   E + S <===> ES  :  k1  k-1
   ES ---> E + P   :  k2
[concentrations]
   E = 0.001
   S = 100.0

the concentrations of chemical species at time zero are exactly equal to the values listed in the [concentration] section of the script file. In particular, the concentration of the enzyme substrate complex ES is strictly zero, and the rate with which the product P is formed is also zero.

Many biochemical kinetic problems solved by DynaFit involve the computation not only of the reaction progress, but also the computation of initial reaction velocities. This creates the necessity of introducing the mixing delay time into the computation. As was explained in the preceding paragraph, the reaction velocity at time zero (defined, in this case, as the rate with which the product P is formed) is by definition zero.

Proper unit of time

The mixing delay time is introduced to account for the fact that in real-world experiments, a certain amount of time (albeit a very short amount in specialized instruments) elapses after the reaction components are mixed and before the first experimental data points is recorded. The duration of this time delay is specified by the keyword delay followed by a numerical value.

ExampleSimulate the reaction progress from time zero to time 300 seconds, with a three-second mixing delay time.

[progress]
   mesh from 0 to 300 step 3
   delay 3
   ...

The mixing delay time must be the same for all progress curves in the given dataset. It cannot be treated as an optimized, adjustable parameter.

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Petr Kuzmic | Jul 12 2005