This repository provides the toolkit for finding strong buffering structures and simulation for the paper on Hirono Y†, Moon S, Hong H, Kim JK†, “Topological Criterion for Robust Perfect Adaptation of Reaction Fluxes in Biological Networks" (2024).
examples-flux-rpa.nb: Mathematica code for finding strong buffering structures in the example reaction networks in the paper. This Mathematica code requires a package file called "RPAFinder.wl" in another repository of one of the authors: /~https://github.com/yhirono/RPAFinder.
EColi.ipynb: Julia Jupyter notebook code for conducting simulation in the example of E. Coli.
Pyrimidine-metabolism.ipynb: Julia Jupyter notebook code for conducting simulation in the example of pyrimidine metabolism
Schematic_Mass-action.ipynb: Julia Jupyter notebook code for conducting simulation in the schematic example with the mass-action kinetics.
Schematic_MM.ipynb: Julia Jupyter notebook code for conducting simulation in the schematic example with the Michalis-Menten kinetics.
Schematic_PowerLaw.ipynb: Julia Jupyter notebook code for conducting simulation in the schematic example with the power-law kinetics.