Open RobertGregg opened 2 years ago
I just wanted to bump this issue with an update. I've been building up a Cellular Potts Modeling package and want to incorporate spatial diffusion with JumpProcesses.jl. Given that these types of models already discretize biological cells onto a grid, I think it makes a lot of sense to use a discrete model for simulating chemical reaction networks within the model.
Basically my question becomes: Does using the hopping_constants
in a callback to match the cell's moving boundary the right approach? Or is there a better way to approach this problem?
Sorry in advance if this isn't the best place to have this discussion. I just didn't want this issue to become an xy problem
Looks like a great package! Sorry we haven't made progress on this yet -- unfortunately this semester got busy and I haven't had time yet to get to it. I'm hoping I can make progress on it in a couple weeks once winter break starts.
No worries! I just thought of it the other day and wanted to follow up. No rush.
The main issue is that the cells containing the chemical reactions move in these models so I have to figure out how to deal with that.
This is in response to a discourse question:
https://discourse.julialang.org/t/jumpproblem-hopping-constants-callback/86045?u=robertgregg
Essentially, it would be nice to be able to modify
hopping_constants
in a callback to simulate a moving boundary separates two regions with different diffusion rates. It sounds likereset_aggregated_jumps!
would have to be modified to allow this functionality.