Thursday, December 07, 2006

Molecular dynamics simulation of small bearing design

This video was created using the simulation facilities of NanoEngineer-1 (see, together with open-source animation tools like Pov-RAY, ImageMagick, and mpeg2encode. This is 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.
Update: On more careful analysis we discovered that the temperature is incorrectly represented in this video. The atoms should shake more violently to represent an ambient temperature of 300 Kelvin (ordinary room temperature). The vibrations you see in the video correspond to about 70 Kelving (very chilly). In spite of the more violent thermal vibrations, the structure remains chemically stable and mechanically workable at room temperature.

1 comment:

itcon said...

I have a possibility to simulate Molecular dynamics (MD). I want to find someone who need it. I propose to simulate ab initio quantum mechanical molecular dynamics (MD) using pseudopotentials and a plane wave basis set. The interaction between ions and electrons is described using ultrasoft Vanderbilt pseudopotentials (US-PP) or the projector augmented wave method (PAW).