ic regulation matrix (nr x nm)
   ind_ext   - indices of external metabolites
   c0        - Vector of chemical equilibrium concentrations (optional)
   c         - Vector of concentrations
   u         - Vector of enzyme levels
   J         - Flux vector
   Keq       - Vector of equilibrium constants
   mu        - Vector of chemical potentials
   K         - Kernel matrix 
   Kma       - Vector of mass-action ratios
   zeta      - zeta vector computed from reaction affinities
   A         - Vector of reac