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Tumbles of finite duration #77

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mastrof opened this issue Mar 22, 2024 · 0 comments · Fixed by #82
Closed

Tumbles of finite duration #77

mastrof opened this issue Mar 22, 2024 · 0 comments · Fixed by #82
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breaking Breaking change enhancement New feature or request

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@mastrof
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mastrof commented Mar 22, 2024

Tumbles should be considered as a different step from runs.
This would allow the user to define e.g. a run_time and a tumble_time, and the microbe would be switching between the running state and the tumbling state with transition rates defined by these timescales.

More generally, this could go hand in hand with a full rewrite of the Motility implementation (#78).

The advantage is that setting a tumble_time=0 (or anything below the model.timestep) would reduce to the current implementation of instantaneous tumbles, but the new approach would allow the implementation of more refined models of chemotaxis and the reformulation of the run-tumble switching in terms of CCW bias, which is a more modern approach than just considering the tumbling rate.

@mastrof mastrof added enhancement New feature or request breaking Breaking change labels Mar 22, 2024
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