The qORAC framework
qORAC stands for Specific Flux (q) Optimisation by Robust Adaptive Control. It is a method in which a metabolic pathway may be controlled dynamically by prescribing enzyme synthesis functions. These functions are chosen in such a way that, when coupled to the dynamics of the pathway in which these enzymes play a role, guarantee that a steady state of the system achieves maximal flux per unit expended enzyme in the pathway (called specific flux).
The following files are used to illustrate qORAC in the paper Maintaining maximal metabolic flux using gene expression control, PLoS Comp Biol (2018).
The Matlab files may be run to generate the images in that paper. Read the README before running the files.
- README
- Running Newton's method. Required for some of the scripts below. multinewton.m
- Printing figures to disk print_fig.m
- Figure 2B: sensor_optimum_enz_CN_newton.m
- Figure 2C: daes_CN.m
- Figure 3A: daes_extra_param.m
- Figure 3B: daes_extra_param_wrong.m
- Figure S1: daes_double_branched_sym.m
- Figure S2: daes_CN_minimal_ICs.m
- Figure S3: daes_linearchain_reversal.m