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mastrof / MicrobeAgents.jl

Agent-based modeling of microbial motile behavior via Agents.jl
MIT License
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Implement steric interactions between microbes #45

Open mastrof opened 1 year ago

mastrof commented 1 year ago

Should be relatively easy to implement a steep soft-core repulsion (e.g. $r^{-12}$) using the CellListMap.PeriodicSystem interface which is already implemented. At least as long as the microbes can be considered spherical.

I will have to think, however, how to combine the current "kinetic" approach with this dynamic component. Also in view of further extensions, I should probably consider whether it's wiser to translate everything into dynamic terms.

Will then need to look into how this can be extended to other shapes but it's something for the future.

mastrof commented 1 year ago

Might be less immediate than I thought. Indeed including a repulsive force term will lead to microbes bouncing off each other, which is not what I want.

mastrof commented 1 year ago

See: Angelani, L., Di Leonardo, R. & Ruocco, G. Self-Starting Micromotors in a Bacterial Bath. Phys. Rev. Lett. 102, 048104 (2009).

mastrof commented 1 year ago

Main issue is that integration of the eqs of motion will need short timesteps and something more accurate than Euler timestepping. Implementation would probably require multiple time-stepping, e.g. keep Euler on large Δt for chemotactic behavior and borrow some method from OrdinaryDiffEq for fast force integration. But seems too big a hassle to implement at the current stage.