Codes used for the my master's thesis in biological and medical engineering.

Contains code used for the simulation of the response curves for the three different activity functions tested in the thesis:

• First function corresponds to a thermodynamic ensemble model.
• Second function corresponds to a Hill-response model.
• Third function corresponds to a simplfied Hill-type function obtained from elementary reactions. Figures from chapter 5.1 were generated using this code

Contains the code used for the numerical integration of the ODE system. Figures from chapter 5.2 and 5.3 were generated using this code.

Contains the Julia code used for the bifurcation analysis of the ODE system and for the calculation of the steady states. Figures from chapter 5.4 were generated using this code.

Contains the code used for the simulation of the square grid of cells for the RDIM system. Figures from chapter 6 onward were generated using this code.

Contains the code used for the CellModeller simulations of the RDIM system. Figures from chapter 6.4 were generated using this code.

Contains the code used for processing the output data from the RDIM_MODEL_SIMULATIONS. Necessary for obtaining the final figures of each simulation, where the concentrations of the reporter proteins are converted to 8 bit values.

Contains the code for calculating the magnetization of a given RDIM lattice. Figures from chapter 8 were generated using this code.

Contains the code for the generation of the phase diagram in chapter 9.

Contains the matlab code used for the MLE fits to the powerlaw. Data used for chapter 7 were generated using this code.

Contains the code used for generating the powerlaw graphs from the data obtained in POWERLAW_FITS.m. Figures from chapter 7 were generated using this code.