# How to represent a network of chemical reactions?

I am trying to figure out a suitable representation for given set of chemical reactions, which happen over an exhaustive set of chemicals.

The chemicals are $A, B, C, D, E$ and the reactions are given below $$A + A \rightarrow B$$ $$B + C \rightarrow D$$ $$B + D \rightarrow E$$ $$C + E \rightarrow D$$ $$E + E \rightarrow A$$

It's only obvious to form a matrix representaion of the reactions. \begin{array}{X} & A & B & C & D & E \\ A & B & * & * & * & * \\ B & - & * & D & E & * \\ C & - & - & * & * & D \\ D & - & - & - & * & * \\ E & - & - & - & - & A \\ \end{array} where $*$ means no product forms

I tried to label elements with unique integer IDs, so that the product (if any) can be treated as the weight of the edge, but I failed to incorporate this new property into a visualisation of the matrix.

Can any one tell me what form of graphs can be used to represent such data, where combinaiton of two nodes gives rise to another?

• Perhaps add a "dummy" state $Z$ and treat $A+A \rightarrow B"$ as an edge from (A, A) to (B, Z)?
– Ian
Apr 1, 2015 at 18:20
• Use the language of Petri nets. Apr 1, 2015 at 18:22
• Here is one way to do this. See also here for the stoichiometric matrix you wrote down. Apr 1, 2015 at 18:25