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I came up with the following electro-mechanical model of a voltage-gated ion channel, resp. of its voltage sensor as described here and here. The voltage sensor is a bistable system with two local energy minima $E_1(V)$, $E_2(V)$, the first one indicating "closed", the second one "open":

enter image description here

From Bezanilla, The Voltage Sensor in Voltage-Dependent Ion Channels, p. 567.
You can interactively explore a voltage-dependent energy surface here (schematically).

I created a spring model with Algodoo which looks like this (green: the voltage sensor (= a peptide subunit), white springs: keep it in place, blue: favours the closed state, red: simulates voltage, opens the gate):

enter image description here

(You can download the model here and explore it interactively with Algodoo.)

To behave stochastically - i.e. the probability of being open $p(V) \sim e^{-\Delta Q(V)/kT}$ which presupposes a thermal equilibrium - there must be fluctuations that can lift the system above the energy barrier between the two energy minima.

My question concerns the source of these fluctuations in the real ion channel: are these thermal (mechanical) fluctuations (e.g. other molecules hitting or tearing the sensor) or are these fluctuations of the membrane potential?

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    $\begingroup$ And I'll note that this isn't something special with ion channels, it's true of many other types of proteins as well as non-biological molecules. $\endgroup$
    – Bryan Krause
    Jan 5, 2018 at 16:59
  • $\begingroup$ My model definitely does have (two distinct) energy minima, as can be seen by just watching it (above) or trying it out (at Algodoo) or by checking the Geogebra link which reflects the Algodoo model. It's not about one spring, but about a system of springs that definitely may have different and distinct energy minima. $\endgroup$ Jan 5, 2018 at 17:40
  • $\begingroup$ I don't understand your second comment. $\endgroup$ Jan 5, 2018 at 17:46
  • $\begingroup$ Ah I'm sorry I missed the structure of your model entirely. You can disregard. My second comment was just to state that this isn't unique to ion channels; lots and lots of other molecules or proteins have the same sort of behavior where they switch between distinct states. $\endgroup$
    – Bryan Krause
    Jan 5, 2018 at 19:46
  • $\begingroup$ @BryanKrause: Do you have any idea concerning my original question: Do the random fluctuations stem more from the immediate molecular (mechanical) environment of the voltage sensor or from the membrane potential (which in turn stems from dendritic input/PSPs). $\endgroup$ Jan 5, 2018 at 21:35

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The fluctuations arise form thermal energy and can be described by the Eyring equation

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