Fig. 3

Reaction network (left) and stoichiometric matrix \(\mathbf {S}\) (top right) showing reactions \(r_1\)-\(r_4\), Eq. (26), in gray and the isomerization reactions \(r_5\)-\(r_7\), Eq. (27) in light red. For the basic system (gray) we have \(\dim \ker \mathbf {S}^\top =3\). The three MCLs are shown below \(\mathbf {S}\). In the full system, \(r_1\)-\(r_7\), we have \(\dim \ker \mathbf {S}^\top =1\) with the unique MCL shown at the bottom right. In the full system U, V, and W form obligatory isomers of the monomer D. Similarly, X and Y are also obligatory isomers composed of two D units, while Z is a trimer of D units. The vector \(\mathbf {v}=(-1,0,1,0,0,1,0)\) is represented by the composite reaction \({\mathrm{X + (U + W) + V} \rightarrow \mathrm{(U + V) + Y + W}}\) and specifies the net isometrization reaction \({ \mathrm X \rightarrow \mathrm Y }\)