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lines changed Original file line number Diff line number Diff line change @@ -22,7 +22,7 @@ Synapse = "7cc9ea39-daa9-4846-be95-d8a08c9e3c85"
2222
2323[compat ]
2424BenchmarkTools = " 1.3.1"
25- Catalyst = " 12.2 "
25+ Catalyst = " 13 "
2626Conda = " 1"
2727DataFrames = " 1.3.4"
2828DifferentialEquations = " 7"
Original file line number Diff line number Diff line change @@ -26,6 +26,7 @@ micromolar_to_invcubicmicrometer(concen) = (6.02214076e2) * concen
2626Next we create a well-mixed model with the desired chemistry
2727```julia
2828rn = @reaction_network begin
29+ @parameters k₁ ka kd k₄
2930 k₁, EA --> EA + A
3031 k₁, EB --> EB + B
3132 (ka,kd), EA + B <--> EAB
@@ -34,7 +35,7 @@ rn = @reaction_network begin
3435 (ka,kd), EBA + A <--> EBA₂
3536 k₄, A --> ∅
3637 k₄, B --> ∅
37- end k₁ ka kd k₄
38+ end
3839```
3940Let's next make a function to calculate the spatial transport rates, mesh/graph
4041that will represent our domain, and initial condition. We use a cubic lattice of
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