A Single Source Of Truth

DiffEqRxn has a model definition file that is written in a plaintext format with an extension of rxn.

The model file is one chemical reaction per line.

Defining a forwards chemical reaction.

A chemical reaction is defined as follows:

A + B ==> C + B {f_1}

This is probably the simplest definition possible. It states that A + B creates the species C + B at a rate of \(f_1\).

Defining a reversible chemical reaction.

A more reversible reaction looks like so:

A + B <==> C + B {f_1, r_1}

The above definition takes the is exactly the same as the one above, but it also includes a reverse reaction at a rate of \(r_1\).

Note

The above reaction is shorthand for:

A + B ==> C + B {f_1}
A + B <== C + B {r_1}

The whole point of this program is to make writing down chemical equations simpler, so similar “syntactic sugar” is commonly used.

Note

Chemicals can be re-used across multiple reactions, so there’s never a reason to cram everything into one big chemical expression

Moving forwards.

We now have all the tools we need to specify linear systems of mass action kinetics; however, the next chapters will cover common useful topics such as holes in the model and non-linearity (such as Hill Kinetics).