Best routes found to self-assembling 3-D shapes

Researchers at Brown and Johns Hopkins universities have found optimal configurations for creating 3-D geometric shapes -- like tiny, highly simplified geodesic domes that assemble by themselves. The Brown team developed the algorithmic tools, and the Johns Hopkins team tested selected configurations. The research may lead to advances from drug-delivery containers to 3-D sensors and electronic circuits.

Results published in Proceedings of the National Academy of Sciences.

Material chemists and engineers would love to figure out how to create self-assembling shells, containers or structures that could be used as tiny drug-carrying containers or to build 3-D sensors and electronic devices.

There have been some successes with simple 3-D shapes such as cubes, but the list of possible starting points that could yield the ideal self-assembly for more complex geometric configurations gets long fast. For example, while there are 11 2-D arrangements for a cube, there are 43,380 for a dodecahedron (12 equal pentagonal faces). Creating a truncated octahedron (14 total faces -- six squares and eight hexagons) has 2.3 million possibilities.

"The issue is that one runs into a combinatorial explosion," said Govind Menon, associate professor of applied mathematics at Brown University. "How do we search efficiently for the best solution within such a large dataset? This is where math can contribute to the problem."

In a paper published in the Proceedings of National Academy of Sciences, researchers from Brown and Johns Hopkins University determined the best 2-D arrangements, called planar nets, to create self-folding polyhedra with dimensions of a few hundred microns, the size of a small dust particle. The strength of the analysis lies in the combination of theory and experiment. The team at Brown devised algorithms to cut through the myriad possibilities and identify the best planar nets to yield the self-folding 3-D structures. Researchers at Johns Hopkins then confirmed the nets' design principles with experiments.

"Using a combination of theory and experiments, we uncovered design principles for optimum nets which self-assemble with high yields," said David Gracias, associate professor in of chemical and biomolecular engineering at Johns Hopkins and a co-corresponding author on the paper. "In doing so, we uncovered striking geometric analogies between natural assembly of proteins and viruses and these polyhedra, which could provide insight into naturally occurring self-assembling processes and is a step toward the development of self-assembly as a viable manufacturing paradigm."

"This is about creating basic tools in nanotechnology," said Menon, co-corresponding author on the paper. "It's important to explore what shapes you can build. The bigger your toolbox, the better off you are."

While the approach has been used elsewhere to create smaller particles at the nanoscale, the researchers at Brown and Johns Hopkins used larger sizes to better understand the principles that govern self-folding polyhedra.

The researchers sought to figure out how to self-assemble structures that resemble the protein shells viruses use to protect their genetic material. As it turns out, the shells used by many viruses are shaped like dodecahedra (a simplified version of a geodesic dome like the Epcot Center at Disney World). But even a dodecahedron can be cut into 43,380 planar nets. The trick is to find the nets that yield the best self-assembly. Menon, with the help of Brown undergraduate students Margaret Ewing and Andrew "Drew" Kunas, sought to winnow the possibilities. The group built models and developed a computer code to seek out the optimal nets, finding just six that seemed to fit the algorithmic bill.

The students got acquainted with their assignment by playing with a set of children's toys in various geometric shapes. They progressed quickly into more serious analysis. "We started randomly generating nets, trying to get all of them. It was like going fishing in a lake and trying to count all the species of fish," said Kunas, whose concentration is in applied mathematics. After tabulating the nets and establishing metrics for the most successful folding maneuvers, "we got lists of nets with the best radius of gyration and vertex connections, discovering which nets would be the best for production for the icosahedron, dodecahedron, and truncated octahedron for the first time."

Gracias and colleagues at Johns Hopkins, who have been working with self-assembling structures for years, tested the configurations from the Brown researchers. The nets are nickel plates with hinges that have been soldered together in various 2-D arrangements. Using the options presented by the Brown researchers, the Johns Hopkins's group heated the nets to around 360 degrees Fahrenheit, the point at which surface tension between the solder and the nickel plate causes the hinges to fold upward, rotate and eventually form a polyhedron. "Quite remarkably, just on heating, these planar nets fold up and seal themselves into these complex 3-D geometries with specific fold angles," Gracias said.

"What's amazing is we have no control over the sequence of folds, but it still works," Menon added.

Contributing authors include Shivendra Pandey from Johns Hopkins and Nghi Nguyen from the University of Massachusetts-Amherst. The National Science Foundation funded the research.

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Journal Reference:

S. Pandey, M. Ewing, A. Kunas, N. Nguyen, D. H. Gracias, G. Menon. Algorithmic design of self-folding polyhedra. Proceedings of the National Academy of Sciences, 2011; DOI: 10.1073/pnas.1110857108

Note: If no author is given, the source is cited instead.

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Dinosaur feathers found in Alberta amber

Feathers believed to be from dinosaurs have been found beautifully preserved in Alberta amber.

The primitive, hair-like feathers known as protofeathers likely belonged to theropods — dinosaurs similar to tiny Tyrannosaurus rexes — that roamed the swampy forests of Alberta 80 million years ago, said Alexander P. Wolfe, a University of Alberta earth sciences professor who co-authored the research published Thursday in Science.

The protofeathers don't look like feathers from any modern bird, but are similar to those seen in fossils of therapods. (Science/AAAS)

"Protofeathers aren't known from any modern, existing groups of birds and therefore the most obvious interpretation is that they belong to dinosaurs," he said.

Theropods, which are thought to be closely related to modern birds, were already known to have feathers, based on features surrounding fossils found in China. But a lot of details were lost in the fossilization process.

"The feathers get altered, they get substituted by minerals and you can't see any of the detail," Wolfe said.

"With amber, it's different. We actually have the actual object.… we actually have this protofeather for the first time in the flesh."

The feathers are preserved down to the pigments that show what colour they are and microscopic details of their structure.

Based on the fact that the protofeathers were just single filaments or clumps of filaments, just two centimetres long, the researchers concluded "these had nothing to do with flight," Wolfe said.

Instead, he believes they were used to keep the dinosaurs warm.

A theropod fossil from China shows bristle-like feathers on the head, neck, back and tail. However, many of the details have been obscured by the fossilization process. (Nanjing Institute/Associated Press)

The protofeathers were among a wide range of feathers found in Alberta amber specimens by Ryan McKellar, a researcher who recently completed his PhD under Wolfe's supervision. McKellar's research was initially interested in insects, but stumbled upon some very bird-like feathers in the process of sorting through amber from the Royal Tyrell Museum and the University of Alberta's collection, Wolfe said.

He decided to keep an eye out for other feathers. After sorting through around 4,000 chunks of amber, each less than two centimetres in diameter, he had collected a wide range, from the protofeathers to more complex feathers from the same time period that were most certainly from birds.

Some were downy "like the kind you have in your pillow," Wolfe said. Others look like modern flight feathers. Some also had special features found in diving birds such as grebes.

Wolfe, an expert in amber chemistry, said such birds likely shared the same ecosystem as the dinosaurs — a steamy, "very buggy" coastal forest similar to Florida's everglades, dominated by cypress and cedar-like trees. The remains of the forest were compressed into coal deposits in Alberta where the amber samples were found.

Wolfe said now that the new research, including photographs, has been published, he hopes researchers in other parts of the world where feather dinosaur fossils have been found will start keeping an eye out for dinosaur feathers in amber. He also hopes to do a biochemical analysis on the proteins in the feathers.

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Antibiotic resistance found in ancient bacteria

Modern soil bacteria make a variety of compounds,some of which generate the colours shown above and some of which have antibiotic activity. Gerard Wright/McMaster University

The same genes that make disease-causing bacteria resistant to today's antibiotics have been found in soil bacteria that have remained frozen since woolly mammoths roamed the Earth.

“We’ve shown for the first time that drug resistance is a really old phenomenon and it’s part of the natural ecology of the planet,” said Gerard Wright, a biochemist at McMaster University in Hamilton, Ont.

He led the study that was published online Wednesday in the journal Nature.

Wright said this evidence of ancient genes may explain how today's disease-causing bacteria have so quickly become resistant to modern antibiotics.

He also suggested that these findings, which involved the study of one type of bacteria that lived in one location, in the Yukon, 30,000 years ago, might just be the tip of the iceberg.

“Surely this history goes back millions of years,” he said. “We just don’t have those samples yet.”

Wright had conducted a study five years ago to see how prevalent antibiotic resistance was among common soil bacteria called Actinobacteria, which do not cause disease in humans.

“You know how dirt has that dirty dirt smell? That smell of earth? Well, that’s caused by [this type of] bacteria,” he said.

What he found in that study was that many of these bacteria were resistant to multiple antibiotics. That was true of both bacteria in urban and agricultural sites, as well as those in remote parts of northern Ontario. Still, to be certain the bacteria had never been exposed to human antibiotics, he needed to find bacteria from a pristine environment isolated from the modern world.

Duane Froese, a geologist at the University of Alberta, and Grant Zazula of the Yukon government’s paleontology program, had a solution. They gathered samples of permafrost in the Yukon that was buried under a layer of ash from a volcanic eruption 30,000 years ago.

“Samples taken immediately below that are essentially the same age,” Froese said.

The permafrost contained ice wedges, which form when the ground is so cold that it cracks open allowing water to freeze inside. The wedges can only form at the surface and their presence deep underground shows that the permafrost had never melted since it was buried.

The researchers tested the samples in the lab of Hendrik Poinar, a McMaster University anthropologist who specializes in DNA analysis. They found it contained DNA from ancient mammals, like the mammoths and horses that roamed the Yukon 30,000 years ago, but no modern mammals such as moose or elk. That confirmed that the bacteria was not contaminated with soils from above the ash layer.

The samples also contained DNA for at least a hundred species of bacteria, including Actinobacteria. And the Actinobacteria DNA contained genes that made it resistant to beta-lactam, tetracycline and glycopeptide antibiotics, including vancomycin.

Wright said that’s not surprising, since that type of bacteria is the source of many of those same antibiotics.

“They make probably 80 per cent of the drugs that are currently used today – they also make anti-cancer agents, they make immune suppressants, they are remarkable, remarkable little chemists.”

Permafrost sediments deposited 30,000 years ago in the Klondike area of the Yukon contained bison, horse and mammoth DNA as well as bacterial genes associated with antibiotic resistance. D.G. Froese/University of Alberta That antibiotic resistance likely jumped from the soil bacteria to disease-causing bacteria.

"These environmental bacteria are actually the wellspring of resistant genes that eventually make their way into disease-causing bacteria."

Wright said scientists don’t yet know why soil bacteria have a tendency to make antibiotics and be resistant to antibiotics, but they speculate it may help them compete with other bacteria in an environment crowded with millions of bacterial species.

He said most disease-causing bacteria evolved in the more isolated environments of animals' guts or skin, where they may not have had a need for antibiotic resistance.

The researchers don’t yet know how widespread antibiotic resistance is among other kinds of bacteria.

"We’re very keen to broaden our view of what the sources of resistance are," Wright said. "This is very probably the source of our problems – all the [antibiotic resistance] genes that have emerged in these disease-causing bacteria. So we really need to understand the diversity that exists out there so that we can be prepared for it if and when it emerges in pathogens."

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