Here’s a frenetic movie made by Richard J. Law, former postdoc in the MacCammon group, that captures very well, the brownian dynamics of molecules in solution.

The nicotonic channel is found in the membrane, and the channel is normally bound to a receptor. When a nicotine molecule binds to the receptor, it opens up the channel, and ions are let through the channel, across the membrane, and into the cell.

This following movie is from a Steered-Moleculer-Dynamics simulation, where an artificial force drags the ion through our nicotonic channel. By dragging an ion through the channel, we can trace the possible paths ions might take in traversing the membrane when the nicotonic channel opens up. The movie’s a bit blurry, but’s only because at the time-scale that it’s been shown, the water molecules and the lipids in the membrane are moving so damn fast. Trust me, it’s easier to watch when the waters and lipids are blurry, plus your bandwidth will thank me:

But how does ion travel through a channel without a dragging force? Mr Law also had a movie on his web-site of the motion of a potassium ion (K+) tunneling through an unspecified channel (I’m guessing the Kcsa channel). This is in excellent resolution, and you can see the individual water molecules forming a really nice ordered shell around K+: