From Machine Phase. This is a movie of the atomistic bearing described by Eric Drexler in Nanosystems. Remember to read Drexler's article or watch this video to understand, "the rotation-induced speed of the shaft surface is substantially lower than the (apparent) vibrational speeds of the atoms". The thermal vibrations in the bearing actually take place much faster than the shaft motion. What you see in the video is only maybe 1/1000 of the actual thermal vibration motions. Because these sorts of videos have a limited frame rate, we get a "strobe light effect" where we only selectively see the vibration. If the video were portraying the thermal vibration on a timescale where you could actually see each part of the action, then the actual shaft surface would be moving at a glacial pace. The upshot of all of that is that the friction and heating in this device would not be nearly as high as it appears at a casual glance.
In another post, Tom Moore points out new software by Miron Cuperman which partially automates the process of using csv data from NanoEngineer-1 to render animations in Blender.