ADGenKinetics contains an implementation of a specific set
of reaction kinetics, namely, generalized simplified kinetic
formats. It follows many of the guidelines recommended by the
Biochem library. The underlying simplified kinetics formats are
represented by generalized structured kinetics formulas suitable
for arbitrary biochemical reactions with arbitrary number of
substrates, products, inhibitors and activators. In this way,
matabolic reaction networks can be easily assembled using a few
number of reaction kinetics.
ADGenKinetics is the first algorithmically differentiated Modelica library. Constructed models can also be used for computing parameter sensitivities with little modifications to the used interfaces and by initializing the input Jacobian, i.e. the parameters w.r.t. derivatives are sought.
Structure of the
Library
The following packages are available:
Further two subpackages within NodeElements and Reactions exist corresponding to two ways of declaration of connectors within components:
The main differences of both ways and their advantages and
disadvantages are emphasized in this section along with the given
examples.
Common interfaces and abstract classes are located above these packages.
That is concentration of a substance is the potential variable
while the flow rate of materials (i.e. the chemical transformation
process) represents the flow variables when connecting nodes and
reactions together, cf. ADGenKinetics.Interfaces.ChemicalPort.
Further subtypes of connectors exist:
Further interfaces and abstract classes are used within implemented
reactions for simplifying their implementations and emphasizing
their classification. The most important of which are:
ADGenKinetics.Interfaces.Reversible.ReactionReversibility: for determining the reversibility of reactions. The extended interfaces OneWay, TwoWay are used for irreversible, reversible reactions, respectively:
Typically, the component ADGenKinetics.NodeElements.dynamic.Node
or ADGenKinetics.NodeElements.static.Node
is the basic one needed for constructing biochemical reaction
networks. Further types can be also imported from available
implementation of the Biochem library.
Reaction kinetics are available in the packages ADGenKinetics.Reactions.convenience.{dynamic.static}.
For instance, ADGenKinetics.Reactions.convenience.dynamic.IrrKinetic
is used for irreversible reactions with arbitrary number of
substrates and products, while ADGenKinetics.Reactions.convenience.dynamic.InhRevKinetic
for reversible inhibited reactions with arbitrary number of
substrates, products and inhibitors.
Static packages provide reaction kinetics with fixed reaction
structure. For instance ADGenKinetics.Reactions.convenience.static.IrrKinetic2S1P1I.
Examples of constructing biochemical networks are given in
ADGenKinetics.Examples.Spirallusdyn
and ADGenKinetics.Examples.Spirallustatic.
Given a biochemical reaction network model, the same model can be
used for computing parameter sensitivities by additional slight
modification in the declaration part:
For instance compare the model given in ADGenKinetics.Examples.Spirallusdyn with ADGenKinetics.Derivatives.Examples.SpirallusdynAll