DynaFit Scripting Manual

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Constant rates in open reaction systems

DynaFit can be used for simulation and fitting of biochemical reactions occuring in open systems, where certain species are being continuously supplied at a constant rate, for example via a metabolic pathway. The same or other species may be continously removed at a constant rate, for example due to a deactivation on the surface of the reaction vessel, or via a metabolic pathway.

Constant-rate steps are denoted in DynaFit by an arrow which does not have a species on either the left- or the right-hand side. For example if the substrate of an enzyme reaction is supplied to the system at a constant rate, $v_{in}$, and if the product is continuously removed at a constant rate, $v_{out}$, we may write

[mechanism]
    ---> S    :    v(in)
  P --->      :    v(out)
    etc.

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Petr Kuzmic | Jul 12 2005