New software aids design of 3-D DNA structures

Recent demonstrations of the ability to build complex 3-D shapes from DNA (this post and previous work by William Shih and collaborators published in Science August 2009 abstract) create demand for an easier way to design complex shapes from folded DNA strands. Now new software facilitates designing three dimensional shapes using scaffolded DNA origami. Physorg.com points to this written by Anne Trafton, MIT News Office “Origami: Not just for paper anymore“:

… A major hurdle to [designing complex curved and bent structures from a folded DNA strand] has been automation of the design process. Now a team at MIT, led by biological engineer Mark Bathe, has developed software that makes it easier to predict the three-dimensional shape that will result from a given DNA template. While the software doesn’t fully automate the design process, it makes it considerably easier for designers to create complex 3-D structures, controlling their flexibility and potentially their folding stability.

“We ultimately seek a design tool where you can start with a picture of the complex three-dimensional shape of interest, and the algorithm searches for optimal sequence combinations,” says Bathe, the Samuel A. Goldblith Assistant Professor of Applied Biology. “In order to make this technology for nanoassembly available to the broader community — including biologists, chemists, and materials scientists without expertise in the DNA origami technique — the computational tool needs to be fully automated, with a minimum of human input or intervention.”

Bathe and his colleagues described their new software in the Feb. 25 issue of Nature Methods. In that paper [abstract], they also provide a primer on creating DNA origami with collaborator Hendrik Dietz at the Technische Universitaet Muenchen. “One bottleneck for making the technology more broadly useful is that only a small group of specialized researchers are trained in scaffolded DNA origami design,” Bathe says.

… “DNA is in many ways better suited to self-assembly than proteins, whose physical properties are both difficult to control and sensitive to their environment,” Bathe says.

Bathe’s new software program interfaces with a software program from Shih’s lab called caDNAno, which allows users to manually create scaffolded DNA origami from a two-dimensional layout. The new program, dubbed CanDo, takes caDNAno’s 2-D blueprint and predicts the ultimate 3-D shape of the design. This resulting shape is often unintuitive, Bathe says, because DNA is a flexible object that twists, bends and stretches as it folds to form a complex 3-D shape.

A PDF of the paper has been made available by the Dietz Lab at TU Munich here. An accompanying editorial “Into the fold” [abstract, full text requires free registration] gives a one-page overview of DNA origami and its potential applications. It points to the above paper and a paper [abstract] from Shih and his colleagues on purifying DNA nanostructures with improved yield of intact structures, and it discusses what is yet needed for DNA origami to reach its full potential: other and longer DNA single strands to use as scaffolds, improved methods to chemically conjugate functional groups to specific DNA sites, and a “top-down design solution” to fully automate design. Now we know what developments to watch for!

Caltech researchers design a new nanomesh material

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Top: A scanning electron microscope image shows the grid of tiny holes in the nanomesh material. Bottom: In this drawing, each sphere represents a silicon atom in the nanomesh. The colorful bands show the temperature differences on the material, with red being hotter and blue being cooler.

(PhysOrg.com) -- Computers, light bulbs, and even people generate heat?energy that ends up being wasted. With a thermoelectric device, which converts heat to electricity and vice versa, you can harness that otherwise wasted energy. Thermoelectric devices are touted for use in new and efficient refrigerators, and other cooling or heating machines. But present-day designs are not efficient enough for widespread commercial use or are made from rare materials that are expensive and harmful to the environment.

Researchers at the California Institute of Technology (Caltech) have developed a new type of material?made out of silicon, the second most abundant element in Earth's crust?that could lead to more efficient thermoelectric devices. The material?a type of nanomesh?is composed of a thin film with a grid-like arrangement of tiny holes. This unique design makes it difficult for heat to travel through the material, lowering its thermal conductivity to near silicon's theoretical limit. At the same time, the design allows electricity to flow as well as it does in unmodified silicon.

"In terms of controlling thermal conductivity, these are pretty sophisticated devices," says James Heath, the Elizabeth W. Gilloon Professor and professor of chemistry at Caltech, who led the work. A paper about the research will be published in the October issue of the journal Nature Nanotechnology.

A major strategy for making thermoelectric materials energy efficient is to lower the thermal conductivity without affecting the electrical conductivity, which is how well electricity can travel through the substance. Heath and his colleagues had previously accomplished this using silicon nanowires?wires of silicon that are 10 to 100 times narrower than those currently used in computer microchips. The nanowires work by impeding heat while allowing electrons to flow freely.

In any material, heat travels via phonons?quantized packets of vibration that are akin to photons, which are themselves quantized packets of light waves. As phonons zip along the material, they deliver heat from one point to another. Nanowires, because of their tiny sizes, have a lot of surface area relative to their volume. And since phonons scatter off surfaces and interfaces, it is harder for them to make it through a nanowire without bouncing astray. As a result, a nanowire resists heat flow but remains electrically conductive.

But creating narrower and narrower nanowires is effective only up to a point. If the nanowire is too small, it will have so much relative surface area that even electrons will scatter, causing the electrical conductivity to plummet and negating the thermoelectric benefits of phonon scattering.

To get around this problem, the Caltech team built a nanomesh material from a 22-nanometer-thick sheet of silicon. (One nanometer is a billionth of a meter.) The silicon sheet is converted into a mesh?similar to a tiny window screen?with a highly regular array of 11- or 16-nanometer-wide holes that are spaced just 34 nanometers apart.

Instead of scattering the phonons traveling through it, the nanomesh changes the way those phonons behave, essentially slowing them down. The properties of a particular material determine how fast phonons can go, and it turns out that?in silicon at least?the mesh structure lowers this speed limit. As far as the phonons are concerned, the nanomesh is no longer silicon at all. "The nanomesh no longer behaves in ways typical of silicon," says Slobodan Mitrovic, a postdoctoral scholar in chemistry at Caltech. Mitrovic and Caltech graduate student Jen-Kan Yu are the first authors on the Nature Nanotechnology paper.

When the researchers compared the nanomesh to the nanowires, they found that?despite having a much higher surface-area-to-volume ratio?the nanowires were still twice as thermally conductive as the nanomesh. The researchers suggest that the decrease in thermal conductivity seen in the nanomesh is indeed caused by the slowing down of phonons, and not by phonons scattering off the mesh's surface. The team also compared the nanomesh to a thin film and to a grid-like sheet of silicon with features roughly 100 times larger than the nanomesh; both the film and the grid had thermal conductivities about 10 times higher than that of the nanomesh.

Although the electrical conductivity of the nanomesh remained comparable to regular, bulk silicon, its thermal conductivity was reduced to near the theoretical lower limit for silicon. And the researchers say they can lower it even further. "Now that we've showed that we can slow the phonons down," Heath says, "who's to say we can't slow them down a lot more?"

The researchers are now experimenting with different materials and arrangements of holes in order to optimize their design. "One day, we might be able to engineer a material where you not only can slow the phonons down, but you can exclude the phonons that carry heat altogether," Mitrovic says. "That would be the ultimate goal."