Hypothetical Nanofactory Animation

Over at Multipolarity Memes there’s a post about a short (though large), 3D-rendered, animation of a hypothetical nanofactory.

Now, I’ll be the first to admit that I’m no expert at this stuff, but I did take some intermediate chemistry and physics classes in college, so the animation immediately raises a number of questions in my mind; viz.:

• At that size, can they realistically assume that the envisioned structures will be as rigid as they make them out to be?
• What about Brownian motion?
• What about transfer of heat—especially given that there are, presumably, chemical reactions taking place, and these reactions will involve energy transfers?
• What type of bonding is happening at the transfer points? Chemical reactions don't happen magically—and they don't happen without some energy input or energy release—neither of which are being obviously represented in the video.

It's a pretty fantasy, but how realistic is it, really?