Molecular dynamics simulation of small bearing design
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A simulation of the molecular bearing design on page 298 of "Nanosystems" by Eric Drexler. When viewed at 0.15 picoseconds per second of animation, thermal motion of atoms (particularly hydrogens) is visible. At 0.6 picoseconds per second, thermally excited mechanical resonances of the entire structure are seen. At 6 picoseconds per second, the rotation of the shaft (one rotation every 200 psecs) becomes apparent. Simulation was done with NanoEngineer-1 (see http://www.nanoengineer-1.com)... video was created with POV-Ray and ImageMagick.
Canal: Howto & Style
Añadido: November 30, 1999 at 12:00 am
Autor: wware
Duración: 03:02
Puntuación: 4.00
Reproducciones: 6887
Etiquetas: animation dynamics molecular nanotechnology simulation
Comentarios
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wware (November 30, 1999 at 12:00 am)
You're right to doubt that it would have a preferred direction of rotation in the absence of external torque, as it is symmetric in the theta direction. This is not a naturally occurring molecule, it's one Drexler designed that cannot yet be synthesized. It is a mechanical bearing driven by an external torque, see "Bearing (mechanical)" on Wikipedia. In the simulation I drove the bearing with a drive shaft which I did not display in the animation.
freakshow1997 (November 30, 1999 at 12:00 am)
hmmm I still think it's a molecular rotaxane, but that the rotation is in fact not unidirectional, but random. See Stoddart, Nolte and others....
wware (November 30, 1999 at 12:00 am)
OK, I see where I got confused. This isn't a rotaxane and it's not intended to self-assemble. This is a bearing that would be built by some sort of nanofactory, and would be used in some larger piece of machinery (as bearings are used in, say, a lathe or drill press today). Since it's not trying to self-assemble, reversibility isn't much of an issue. It would be pertinent to how much friction the bearing will see.
sjonsigurson (November 30, 1999 at 12:00 am)
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freakshow1997 (November 30, 1999 at 12:00 am)
Well, apparently there is a boundary somewhere, where microreversibility is overruled by energetic "profits". The consensus is that that boundary is in the region of kT. Still and all, there will be a lot of problems making these rotaxanes move unidirectionally. It has already been done, I believe, (Stoddard?) using chiral moieties...
wware (November 30, 1999 at 12:00 am)
Thanks! As I mentioned in another comment, the thermal motion should be about three times as violent, but Dr. Drexler says the bearing will still work correctly. The thermal motion isn't very visible on the slower time scales.I'll have to read up on microreversibility. The machines inside cells (especially ribosomes) work quite reliably, so it seems to me that we should be able to do something similar, but rationally designed instead of naturally evolved.
freakshow1997 (November 30, 1999 at 12:00 am)
POVRAY master... It seems to me that thermal motion is way the heck more than what you've animated. Also, synthesis of such rotaxanes is possible, just the self assembling process is difficult to do. For the working mechanism of such devices, it is fundamentally not possible, because of a condition known as microreversibility. cool though!
frederickfarrell (November 30, 1999 at 12:00 am)
Awesome! I love eric drexlers writings on the nanofactory. this looks like an important development. Well done on the clear animation and descriptions.
wware (November 30, 1999 at 12:00 am)
Thanks for your comments. After doing this animation, I found out the thermal vibrations were too small. It was supposed to be at room temperature but these vibrations correspond to about 70 degrees Kelvin (room temp is 300 K). When time permits I'll redo the simulation and animation. The mechanism would still work at 300 K, it would just bounce around more than you see here. At the slower time scales the thermal vibrations would still just be a blur on the time scale of the shaft rotation.
pacfan999 (November 30, 1999 at 12:00 am)
whao
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