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Calculation of equilibrium concentrations of species

Equilibrium concentrations of species are computed before signals from equilibrium experiments can be calculated.

The model definitions and derivations were performed in Equilibrium_thermodynamic_models/

The functions to perform this task are placed in code/+equilibrium_thermodynamic_equations/. These functions may be used as stand-alone functions to investigate reaction mixture composition separately from fitting sessions.

Example of functional interface is:

[concentrations, species_names] = U_model(Rtotal, LRratio, K_A,... model_numeric_solver, model_numeric_options)

where

• Rtotal is total concentration of the R species
• LRratio is molar ratio of total ligand and receptor quantities =Ltotal/Rtotal
• K_A and so on are equilibrium constants
• Two last parameters set the numeric solver and its options.
• r - is an array of concentration of all R-containing species
• g - an array of concentration of all other species
• r_names and g_names are the cell arrays with name labels for species

The solution of equilibrium thermodynamic equations is either analytical or numeric. A switch between the two is through model_numeric_solver='analytical' or ='ode45' (as an example). Some models wouldn't have analytical solution.

You can display progression of a titration using plot_populations.m (see Tutorial 6 for examples).

For numeric solutions the function to solve is provided separately (for example, see U_R_model_numeric.m)