Extreme Processing: New Thresholds of Small

Friday, May 21st, 2010 by Robert Cravotta

[Editor's Note: This was originally posted on the Embedded Master]

While the recent stories about the DNA-based Robot and the Synthetic Organism are not techniques that are available to current embedded developers, I think they point out what type of scale future embedded designs may encompass. In short, the stories relate to building machines that designers can program to perform specific tasks at the molecular or cellular level. Before I relate this to this series, let me offer a quick summary about these two announcements.

The synthetic organism is a synthetic cell that the creators at J. Craig Venter Institute claim is completely controlled by man-made genetic instructions. The new bacterium is solely a demonstration project that tests a technique that may be applied to other bacteria to accomplish specific functions, such as developing microbes that help make gasoline. The bacterium’s genetic code began as a digital computer file, with more than one million base pairs of DNA, which was sent to Blue Heron Bio, a DNA sequencing company, where the file was transformed into hundreds of small pieces of chemical DNA. Yeast and other bacteria were used to assemble the DNA strips into the complete genome, which was transplanted into an emptied cell. The tam claims that the cell can reproduce itself.


There are two types of DNA-based robots that were announced recently. Each is a DNA walker, also referred to as a molecular spider that move along a flat surface made out of folded DNA, known as DNA origami, that the walker binds and unbinds with to move around. One of the walkers is able to “follow” a path, and there is a video of the route the walker took to get from one point to another. The other type of walker is controlled by single strands of DNA to collect nano-particles.

These two announcements relate to this series both from a size scale perspective and to our current chapter about energy harvesting. The synthetic organism article does not explicitly discuss how the bacterium obtains energy from the environment, but the molecular robot article hints at how the robots harvest energy from the environment.

“The spider is fueled by the chemical interactions its single-stranded DNA “legs” have with the origami surface. In order to take a “step,” the legs first cleave a DNA strand on the surface, weakening its interaction with that part of the origami surface. This encourages the spider to move forward, pulled towards the intact surface, where its interactions are stronger. When the spider binds to a part of the surface that it is unable to cleave, it stops.”

Based on this description, the “programming” is built into the environment and the actual execution of the program is subject to random variability of the molecular material positioning in the surface. Additionally, the energy to enable the robot to move is also embedded in the surface material. This setup is analogous to designing a set of tubes and ruts for water to follow rather than actually programming the robot to make decisions. When our hypothetical water reaches a gravity minimum, it will stop, in a similar fashion to the robot. Interestingly though, in the video, the robot does not actually stop at the end point, it jumps out of the target circle just before the video ends.

I’m not trying to be too critical here; this is exciting stuff. I will try to get more information about the energy and programming models for these cells and robots. If you would like to participate in a guest post, please contact me at Embedded Insights.

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