“…The stoichiometric coefficients for the k reactants and l products are given by the sparse vectors A = col{ α 1 , …, α k , 0 n − k } and B = col{0 k , β 1 , …, β l , 0 n − k − l }, respectively. This thermodynamically consistent reaction rate has the following structure where T is the temperature, R is the ideal gas constant, D r is a reaction diffusion coefficient, ε 0 ∈ [0, 1] is a constant related to the point where the transition state occurs in the mesoscopic reaction path (for further detail, see), and are the direct and reverse affinities, and and are the standard direct and reverse affinities that do not depend on the extend of the reaction. Here is the chemical potential of species i = 1,2,…, n , and a i is the activity.…”