FrogHeart

I’m on a metaphor kick these days so here goes, origami (Japanese paper folding), and shapeshifting are metaphors used to describe a certain biological process that nanoscientists from fields not necessarily associated with biology find fascinating, protein folding.

Origami

Take for example a research team at the California Institute of Technology (Caltech) working to exploit the electronic properties of carbon nanotubes (mentioned in a Nov. 9, 2010 news item on Nanowerk). One of the big issues is that since all of the tubes in a sample are made of carbon getting one tube to react on its own without activating the others is quite challenging when you’re trying to create nanoelectronic circuits. The research team decided to use a technique developed in a bioengineering lab (from the news item),

DNA origami is a type of self-assembled structure made from DNA that can be programmed to form nearly limitless shapes and patterns (such as smiley faces or maps of the Western Hemisphere or even electrical diagrams). Exploiting the sequence-recognition properties of DNA base paring, DNA origami are created from a long single strand of viral DNA and a mixture of different short synthetic DNA strands that bind to and “staple” the viral DNA into the desired shape, typically about 100 nanometers (nm) on a side.

Single-wall carbon nanotubes are molecular tubes composed of rolled-up hexagonal mesh of carbon atoms. With diameters measuring less than 2 nm and yet with lengths of many microns, they have a reputation as some of the strongest, most heat-conductive, and most electronically interesting materials that are known. For years, researchers have been trying to harness their unique properties in nanoscale devices, but precisely arranging them into desirable geometric patterns has been a major stumbling block.

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… To integrate the carbon nanotubes into this system, the scientists colored some of those pixels anti-red, and others anti-blue, effectively marking the positions where they wanted the color-matched nanotubes to stick. They then designed the origami so that the red-labeled nanotubes would cross perpendicular to the blue nanotubes, making what is known as a field-effect transistor (FET), one of the most basic devices for building semiconductor circuits.

Although their process is conceptually simple, the researchers had to work out many kinks, such as separating the bundles of carbon nanotubes into individual molecules and attaching the single-stranded DNA; finding the right protection for these DNA strands so they remained able to recognize their partners on the origami; and finding the right chemical conditions for self-assembly.

After about a year, the team had successfully placed crossed nanotubes on the origami; they were able to see the crossing via atomic force microscopy. These systems were removed from solution and placed on a surface, after which leads were attached to measure the device’s electrical properties. When the team’s simple device was wired up to electrodes, it indeed behaved like a field-effect transistor

Shapeshifting

For another more recent example (from an August 5, 2010 article on physorg.com by Larry Hardesty,  Shape-shifting robots),

By combining origami and electrical engineering, researchers at MIT and Harvard are working to develop the ultimate reconfigurable robot — one that can turn into absolutely anything. The researchers have developed algorithms that, given a three-dimensional shape, can determine how to reproduce it by folding a sheet of semi-rigid material with a distinctive pattern of flexible creases. To test out their theories, they built a prototype that can automatically assume the shape of either an origami boat or a paper airplane when it receives different electrical signals. The researchers reported their results in the July 13 issue of the Proceedings of the National Academy of Sciences.

As director of the Distributed Robotics Laboratory at the Computer Science and Artificial Intelligence Laboratory (CSAIL), Professor Daniela Rus researches systems of robots that can work together to tackle complicated tasks. One of the big research areas in distributed robotics is what’s called “programmable matter,” the idea that small, uniform robots could snap together like intelligent Legos to create larger, more versatile robots.

Here’s a video from this site at MIT (Massachusetts Institute of Technology) describing the process,

Folding and over 50, 000 authors

With all this I’ve been leading up to a fascinating project, a game called Foldit, that a team from the University of Washington has published results from in the journal Nature (Predicting protein structures with a multiplayer online game), Aug. 5, 2010.

With over 50,000 authors, this study is a really good example of citizen science (discussed in my May 14, 2010 posting and elsewhere here) and how to use games to solve science problems while exploiting a fascination with folding and origami. From the Aug. 5, 2010 news item on Nanowerk,

The game, Foldit, turns one of the hardest problems in molecular biology into a game a bit reminiscent of Tetris. Thousands of people have now played a game that asks them to fold a protein rather than stack colored blocks or rescue a princess.

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Scientists know the pieces that make up a protein but cannot predict how those parts fit together into a 3-D structure. And since proteins act like locks and keys, the structure is crucial.

At any moment, thousands of computers are working away at calculating how physical forces would cause a protein to fold. But no computer in the world is big enough, and computers may not take the smartest approach. So the UW team tried to make it into a game that people could play and compete. Foldit turns protein-folding into a game and awards points based on the internal energy of the 3-D protein structure, dictated by the laws of physics.

Tens of thousands of players have taken the challenge. The author list for the paper includes an acknowledgment of more than 57,000 Foldit players, which may be unprecedented on a scientific publication.

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“It’s a new kind of collective intelligence, as opposed to individual intelligence, that we want to study,”Popoviç [principal investigator Zoran Popoviç, a UW associate professor of computer science and engineering] said. “We’re opening eyes in terms of how people think about human intelligence and group intelligence, and what the possibilities are when you get huge numbers of people together to solve a very hard problem.”

There’s a more at Nanowerk including a video about the gamers and the scientists. I think most of us take folding for granted and yet it stimulates all kinds of research and ideas.