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benchmarks/Jumps/Project.toml

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@@ -22,7 +22,7 @@ Synapse = "7cc9ea39-daa9-4846-be95-d8a08c9e3c85"
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[compat]
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BenchmarkTools = "1.3.1"
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Catalyst = "12.2"
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Catalyst = "13"
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Conda = "1"
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DataFrames = "1.3.4"
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DifferentialEquations = "7"

benchmarks/Jumps/Spatial_Signaling_Sanft.jmd

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@@ -26,6 +26,7 @@ micromolar_to_invcubicmicrometer(concen) = (6.02214076e2) * concen
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Next we create a well-mixed model with the desired chemistry
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```julia
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rn = @reaction_network begin
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@parameters k₁ ka kd k₄
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k₁, EA --> EA + A
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k₁, EB --> EB + B
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(ka,kd), EA + B <--> EAB
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(ka,kd), EBA + A <--> EBA₂
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k₄, A --> ∅
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k₄, B --> ∅
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end k₁ ka kd k₄
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end
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```
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Let's next make a function to calculate the spatial transport rates, mesh/graph
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that will represent our domain, and initial condition. We use a cubic lattice of

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