Friday, December 29, 2006

More fabrication techniques

In the late 1990s, Tom Knight at MIT worked on something he called microbial engineering, the intentional redesign of simple (prokaryotic) bacteria, which has resulted in MIT's Biological Parts Project. The idea is to identify re-usable components that can be included in rationally designed microorganisms to perform various functions.

This idea is not without precedent: in 1978, Genentech re-engineered E. coli bacteria to produce inexpensive human insulin, vital to the survival of diabetes patients. Previously insulin had been extracted from ground-up organs of farm animals at considerably greater expense. The 1978 work did not have access to a catalog of biological parts or many of the techniques and other knowledge infrastructure that will grow up around the MIT work.

In an earlier posting I described some very interesting work being done by Christian Schafmeister, who is assembling monomer chains to create structures with specific, controllable, and reasonably rigid shapes. He is developing a collection of 15 or 20 monomers, and perhaps that number will grow over time, which can be strung together using synthetic chemistry techniques. Schafmeister has an article in this month's Scientific American.

DNA origami exploits the very selective self-stickiness of DNA. It is likely that DNA (which can be created in any desired sequence) will become a very flexible framework on which to position molecules. Proteins can also be engineered, provided we can predict how they will fold, and this should be a solvable problem if we restrict ourselves to a subset of well-understood proteins. Many proteins like to cling to DNA at very specific locations. A combined approach using a DNA scaffolding, with attached proteins to provide local functionality, could yield very interesting results.

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.