Physics 434, 2016: Project 2

From Ilya Nemenman: Theoretical Biophysics @ Emory
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Microbial Behavior

Updated: 09:47, 17 November 2016 (EST) Updated: 13:30, 21 November 2016 (EST)

The Riedel-Kruse lab at Stanford has developed a remote, online experimentation platform (see [1]), where one can shine light onto light-sensitive microorganisms in real time, remotely. The microbes escape the lab, and the trajectories of the microbes are reported to the external experimenter. Do these remote experiments using the interface here and find equations describing how the microbe moves. Is the motion described by second order equations or the first? (for the, see if the microbes follow the light immediately, or with delay/memory, signifying a higher order process). To distinguish possible models, try different temporal profiles for the light dynamics. Once you have a good guess for the behavior dynamics, verify your model by predicting response to a new light pattern and testing whether you predicted correctly. We discussed in class how different diagrams explaining the dynamics of the response conditional on the stimulus would result in different response dynamics. I expect you to analyze a few different putative diagrams of how the signal feeds into the behavior, make semi-quantitative predictions that would disambiguate these different designs, and then test and see what really happens in the lab.

Instructions for doing experiments can be found here: Euglena Lab instructions. Additionally, Ingmar Riedel-Kruse notes that "the responses may not be optimal [at this time]. But if you press “Live” on “Eug15” – that one has good responses." So work with this preparation.

Matlab modules (ignore the one that says Farmsahre) can be found here:

Finally, also read instructions for these Matlab modules.

Also read this paper for samples of work with the related system: