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Calculation of non-equilibrium concentrations of species in kinetics

The model definitions and derivations are located in Kinetic_models/.

Calculation of concentrations of species as a function of time in the reaction volume is performed by functions in code/+differential_kinetic_equations/ package. These functions may be used as stand-alone functions to investigate reaction mixture composition separately from fitting sessions.

Example of interface is below:

[concentrations, names] = AB_model(C0_A, C0_B, log10_Ka, k2, time,... model_numeric_solver, model_numeric_options)

where

• C0_A, C0_B, log10_Ka, k2 - the parameters of the model
• time - an array of time points to display integration  results at.
• model_numeric_solver - is either 'analytical' or gives a name of specific ODE solver
• model_numeric_options - solver options
• concentrations - is an array (columns) of computed concentrations of species
• names- their names

Analytical solution is encoded directly into ??_model() function while for a numeric solution we need to create ??_model_numeric() returning a vector of dCdt (left-hand side of the ODE system).

See example of usage is in: test_AB.html (code in tests/Differential_equations/test_AB_one_dataset.m).