Arbitrary system of equations

[Siarhei Hladyshau]

Hello, everyone,

Is it possible to specify an arbitrary system of  RD equations to solve with Ready?

Best,

Siarhei

[Dan Wills]

Hi Siarhei,

I think the answer is yes, you can either stick with formula-mode (for cases where you always want the laplacian for all reagents) and edit the formula, or switch to 'Full Kernel' mode in which you are free to write the entire kernel yourself.

In either case you get to completely define how the reagents behave (~react and diffuse), or (in the Full Kernel case) any other neighborhood-function you'd like to write.

Maybe it would be easier to help if you gave a bit more background on what it is that you are trying to do?

Best of luck,

Dan

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[Siarhei Hladyshau]

Thank you, Dan!

I am very new in using Ready, so probably my question is obvious.

But here is my objective: I am interested in applying modifications of wave pinning model (https://www.ncbi.nlm.nih.gov/pubmed/18212014). It will involve more than two reacting components, and I want to solve it in a 2D domain with no-flux boundary conditions (ideally domain may have any shape).

My question is about the functionality of Ready, whether it allows implementing any system of RD equations and different types of boundary conditions.

Siarhei

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[Dan Wills]

No worries Siarhei! :)

I *think*, but I can't be sure because I'm not 100% clear on wave pinning yet, that what you are talking about should in theory be doable as a regular 'Formula-mode' formula in Ready, as long as it can work with 'diffusion'-style reagent-transport. It would also be possible to implement other types of transport by using a fully custom 'Full Kernel' setup, but at that point you're perhaps not far ahead of other OpenCL/Kernel frameworks as you're basically implementing the whole thing yourself anyway.

In terms of boundary conditions, I would expect that as long as you're clear on how to implement the maths based on some voxel/raster-based representation of the boundary, then that should be able to be worked out too, perhaps by using an extra reagent to represent the shape of the boundary, be that in a kind of 'density' form or some kind of '(perhaps-signed)-distance-to-surface' field.

I guess this probably isn't any more helpful than my previous post in that i'm still basically saying "it sounds possible in theory" but perhaps in order to be able to give any better assistance we might need a bit more detail about the specific algorithm that you are trying to implement? :)

I hope it works out, it sounds really interesting! I'd love to read more about wave-pinning if you have any other links :D

Have a choice one,

Dan

Siarhei

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