Nanomachines: How the Videos Lie to Scientists

Sound physical inference from an illusory premise

Don’t let this animation
fool you about the physics!

By now, many scientists have seen videos of molecular-scale mechanical devices like the one shown here, and I have no way to know how many have concluded that the devices are a lot of rubbish (and have perhaps formulated an unfortunate corollary regarding your author). The reasons for this conclusion would seem clear and compelling to someone new to the topic, but because I was too close to it, I saw no problem. Familiarity with the actual dynamics of these devices kept me from recognizing that what the videos seem to show is, in one crucial respect, utterly unlike reality.

If only all these videos could be recalled and upgraded in the way shown below…

Glacially slow at 1 Gigahertz

Video showing a shaft rotating at 1 GHz
at a frame rate fast enough to track thermal motion.
Video courtesy of J. Storrs Hall.
Software by Nanorex.

First, I should note that the standard videos have considerable merit. They show the output of realistic molecular dynamics simulations based on conventional molecular mechanics force fields. Further, the behavior of most of the mechanical devices shown is remarkably insensitive to perturbing forces, and hence is insensitive to force-field inaccuracies. The simulations can be used to assess engineering parameters such as coupling stiffnesses, static friction, and dynamic drag. They also show the amplitude of thermal motion correctly — but then comes the break between appearance and reality.

The small, jittery animation at the top shows a shaft rotating in a sleeve. The friction in this device would in reality be quite low, enabling the device serve as good bearing. But compare the motion of the shaft and the (apparent) vibrational motions of the atoms: Although the rotation-induced speed of the shaft surface is substantially lower than the (apparent) vibrational speeds of the atoms, the two speeds are (apparently) comparable.

It’s easy to see that thermal motions and shaft motions would be strongly coupled, if this were true. The motion of the shaft would be fast enough to pump in vibrational energy, and this vibrational energy would quickly dissipate as heat. Relative to the (apparent) thermal speeds, the shaft surface speed is much too high, far outside the operating limits for a sensible system design. (For perspective, the implied rotational frequency would be on the rough order of 100 GHz; dissipation scales as the square of the speed, which might typically be 1/1000 of this.)

In short, the videos seem to show devices in which the drag of sliding friction would be enormous, and the rate of heating would be astronomical. This would preclude nanosystems with reasonably efficient molecular machinery, manufacturing, etc.

So what’s wrong with this conclusion? Well, one hint is that all the atomic vibrations are at the same frequency — the frame rate of the video. What the video shows isn’t vibrational motion, or the blur that one would see at this speed, but instead a stroboscopic sample of atomic positions at what are, in the relevant sense, very long intervals. If the frame rate were fast enough to follow the thermal vibrations, the shaft rotation would be almost imperceptible. And if one wanted to show realistic motion blur, well, sorry, but there’s no software that will do the required rendering and image combination automatically, starting with a molecular dynamics trajectory file, and so it doesn’t get done. (Would someone fix this, please?)

To the best of my knowledge, only one video in existence shows all this, and (with thanks to Will Ware for a lot of work), here it is:

(Erratum: the simulated temperature is somewhat too low; at 300 K, motion amplitudes would be about 20% larger than shown.)

J. Storrs Hall has prepared a video that shows thermal motion properly and directly, but this makes a shaft rotating at 1 GHz appear glacially slow, which is why videos showing machines haven’t ordinarily been done this way. If you watch, you’ll eventually see that the rotation is clockwise.

Please note that the ability to make molecular structures of the sort shown here is far down the likely roadmap. Previous posts have said more about where we are today and directions forward.

  

Tagged as: friction, nanomachines, Nanotechnology, thermal fluctuations, Videos