Spatial Jump Simulations

Our introduction to spatial space simulations has already described how to simulate DiscreteSpaceReactionSystems using ODEs. Jump simulations of DiscreteSpaceReactionSystem are carried out using an almost identical approach. Spatial jump simulations in Catalyst are built on top of JumpProcesses.jl's spatial jump simulators, more details on which can be found here.

Below we perform a spatial jump simulation of a simple birth-death process.

using Catalyst, JumpProcesses
bd_model = @reaction_network begin
    (p,d), 0 <--> X
end
diffusion_rx = @transport_reaction D X
space = CartesianGrid((10,10))
dsrs = DiscreteSpaceReactionSystem(bd_model, [diffusion_rx], space)

u0 = [:X => 0]
tspan = (0.0, 200.0)
ps = [:p => 10.0, :d => 1.0, :D => 0.1]
jprob = JumpProblem(dsrs, u0, tspan, ps)
sol = solve(jprob, SSAStepper())

We can now access the values of sol using the interfaces described here, and plot it using the functions described here.

Aggregators can be designated through the aggregator key word argument, By default, NSM() is used. However, DirectCRDirect() is also available and expected to perform better for large networks.