BioControl:Week2: Difference between revisions
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** Actuators: I guess the big one in cells is somehow affecting the transcription or translation process. | ** Actuators: I guess the big one in cells is somehow affecting the transcription or translation process. | ||
*NWP: Thought experiments to ponder for Friday and while reading paper - | *NWP: Thought experiments to ponder for Friday and while reading paper - | ||
**If you were engineering chemotaxis where would you apply gain to the existing system to improve performance? | **If you were engineering chemotaxis where would you apply gain to the existing system to improve performance? | ||
**Simple sounding task, How would you engineer a cell to move away from a chemoattranctant instead of towards? | **Simple sounding task, How would you engineer a cell to move away from a chemoattranctant instead of towards? | ||
**How does time delay affect the stability of the feedback system and the choice of gain placement in this system? | **How does time delay affect the stability of the feedback system and the choice of gain placement in this system? | ||
**If we made an analogy to PID controllers, are there combinations we can rule out and why? | **If we made an analogy to PID controllers, are there combinations we can rule out and why? | ||
**High robustness comes with a heavy price, i.e. fragility somewhere in the system… How does biased stochasticity create dynamic instability in this system? Or put another way, how does the cell use fragility to its advantage? Fragility to robustness conversion, eh? | **High robustness comes with a heavy price, i.e. fragility somewhere in the system… How does biased stochasticity create dynamic instability in this system? Or put another way, how does the cell use fragility to its advantage? Fragility to robustness conversion, eh? | ||
**What are the equilibrium points for this system? Or put another way, does the system show any stable states which if the cell comes close to, it stays close? And do these equilibrium points depend on any of the system parameters? | **What are the equilibrium points for this system? Or put another way, does the system show any stable states which if the cell comes close to, it stays close? And do these equilibrium points depend on any of the system parameters? | ||
**Can anyone think of engineering systems that use this type of control? | **Can anyone think of engineering systems that use this type of control? | ||
*[[Josh Michener|Josh]]: Some comments: | |||
**Sensing (particularly gradient sensing in chemotaxis) is more complicated than it might seem. Prokaryotes, for instance, are too small to sense spatial gradients, so they have to sense temporal gradients instead. | |||
**Actuation can happen much faster by affecting protein function directly (allostery) - think kinase/phosphatases. | |||
**Chemorepellents: | |||
***Eukaryotic - make the probability of lamellipod extension decrease for increasing chemorepellent. | |||
***Prokaryotic - make the tumble probability increase for increasing chemorepellent. | |||
**Gain: Noise should quickly become a problem - both stochastics (the paper seems to have simulated ~3 lamellipodia per cell at any given time) and environmental fluctuations (need to damp out fast fluctuations, or else you just spin around in place). | |||
**Robustness: I'd say you trade off robustness and performance, rather than fragility (not sure what exactly you mean by fragility, incidentally). If the cell picked one direction and went that way as fast as it could, it'd get there faster, but some times it would head in the wrong direction. It's interesting that both prokaryotic and eukaryotic chemotaxis convergently evolved to a similar biased random walk. Suggests to me that this is pretty close to an optimal solution to the physical problem. | |||
== Discussion == | == Discussion == | ||
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Latest revision as of 16:23, 15 November 2006
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What are the biological analogues of Sensors and Actuators?
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