David Kirkpatrick

May 12, 2010

DNA-based logic chips

Very cool and very fascinating in terms of extreme mass production.

The release:

DNA could be backbone of next generation logic chips

IMAGE: This is Duke University’s Chris Dwyer.

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DURHAM, N.C. – In a single day, a solitary grad student at a lab bench can produce more simple logic circuits than the world’s entire output of silicon chips in a month.

So says a Duke University engineer, who believes that the next generation of these logic circuits at the heart of computers will be produced inexpensively in almost limitless quantities. The secret is that instead of silicon chips serving as the platform for electric circuits, computer engineers will take advantage of the unique properties of DNA, that double-helix carrier of all life’s information.

In his latest set of experiments, Chris Dwyer, assistant professor of electrical and computer engineering at Duke’s Pratt School of Engineering, demonstrated that by simply mixing customized snippets of DNA and other molecules, he could create literally billions of identical, tiny, waffle-looking structures.

Dwyer has shown that these nanostructures will efficiently self-assemble, and when different light-sensitive molecules are added to the mixture, the waffles exhibit unique and “programmable” properties that can be readily tapped. Using light to excite these molecules, known as chromophores, he can create simple logic gates, or switches.

These nanostructures can then be used as the building blocks for a variety of applications, ranging from the biomedical to the computational.

IMAGE: This is a closeup of a waffle.

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“When light is shined on the chromophores, they absorb it, exciting the electrons,” Dwyer said. “The energy released passes to a different type of chromophore nearby that absorbs the energy and then emits light of a different wavelength. That difference means this output light can be easily differentiated from the input light, using a detector.”

Instead of conventional circuits using electrical current to rapidly switch between zeros or ones, or to yes and no, light can be used to stimulate similar responses from the DNA-based switches – and much faster.

“This is the first demonstration of such an active and rapid processing and sensing capacity at the molecular level,” Dwyer said. The results of his experiments were published online in the journal Small. “Conventional technology has reached its physical limits. The ability to cheaply produce virtually unlimited supplies of these tiny circuits seems to me to be the next logical step.”

DNA is a well-understood molecule made up of pairs of complimentary nucleotide bases that have an affinity for each other. Customized snippets of DNA can cheaply be synthesized by putting the pairs in any order. In their experiments, the researchers took advantage of DNA’s natural ability to latch onto corresponding and specific areas of other DNA snippets.

Dwyer used a jigsaw puzzle analogy to describe the process of what happens when all the waffle ingredients are mixed together in a container.

“It’s like taking pieces of a puzzle, throwing them in a box and as you shake the box, the pieces gradually find their neighbors to form the puzzle,” he said. “What we did was to take billions of these puzzle pieces, throwing them together, to form billions of copies of the same puzzle.”

IMAGE: These are many waffles.

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In the current experiments, the waffle puzzle had 16 pieces, with the chromophores located atop the waffle’s ridges. More complex circuits can be created by building structures composed of many of these small components, or by building larger waffles. The possibilities are limitless, Dwyer said.

In addition to their use in computing, Dwyer said that since these nanostructures are basically sensors, many biomedical applications are possible. Tiny nanostructures could be built that could respond to different proteins that are markers for disease in a single drop of blood.


Dwyer’s research is supported by the National Science Foundation, the Air Force Research Laboratory, the Defense Advanced Research Projects Agency and the Army Research Office. Other members of the Duke team were Constantin Pistol, Vincent Mao, Viresh Thusu and Alvin Lebeck

August 11, 2008

Digital Matter project gets $3M

From KurzweilAI.net:

$3 million grant awarded to build ‘digital matter’
KurzweilAI.net, Aug.10, 2008

Research in diamond mechanosynthesis (DMS) — building diamond nanostructures atom by atom using scanning probe microscopy — just received a major boost with a $3 million grant from the U.K. Engineering and Physical Sciences Research Council, awarded to Professor Philip Moriarty at the University of Nottingham for a “Digital Matter” project, the Nanofactory Collaboration plans to announce Monday.

Diamond mechanosynthesis with computer-automated tooltip (artist’s impression)

The Nottingham work grew out of continuing discussions since 2005 on DMS between Moriarty and Robert A. Freitas Jr., a Senior Research Fellow at the Institute for Molecular Manufacturing (IMM).

“Diamond mechanosynthesis is the key technology that will let us fabricate atomically precise diamond products, including molecular computers, microbivores, and a host of other molecular machines,” said IMM Senior Fellow Ralph Merkle in an email interview. Merkle co-founded the Nanofactory Collaboration with Freitas in 2001 to pursue molecular manufacturing via DMS.

“There’s a body of theoretical work that says diamond mechanosynthesis is feasible, including specific computational chemistry analyses of specific reactions and specific reaction pathways. Now we have to make it happen in the lab, and Moriarty’s work is the first step along this path.”

In April 2008, Freitas and Merkle published the results of a comprehensive three-year project to computationally analyze a complete set of DMS reaction sequences and an associated minimal set of tooltips that could be used to build basic diamond and graphene (e.g., carbon nanotube) structures. These structures include all of the tools themselves, along with the necessary tool recharging reactions.

Moriarty is interested in testing the viability of positionally controlled atom-by-atom fabrication of diamondoid materials as described in the Freitas-Merkle minimal toolset theory paper. Moriarty’s efforts will be the first time that specific predictions made by sophisticated computational chemistry software in the area of mechanosynthesis will be rigorously tested by experiment.

His work also directly addresses the requirement for “proof of principle” mechanosynthesis experiments requested in the 2006 National Nanotechnology Initiative (NNI) review, in the 2007 Battelle/Foresight nanotechnology roadmap, and by EPSRC’s Strategic Advisor for Nanotechnology, Richard Jones (Physics, Sheffield University, U.K.).

Also see:
Mechanosynthesis toolset is important new step toward the nanofactory