Tag Archives: Brown University

Brown University (US) gets big bucks to study effect on nanomaterials on human health

In over seven years of blogging about nanotechnology, this is the most active funding period for health and environmental effects impacts I’ve seen yet. A Sept. 26, 2015 news item on Azonano features another such grant,

With a new federal grant of nearly $10.8 million over the next five years, Brown University researchers and students in the Superfund Research Program (SRP) will be able to advance their work studying how toxicant exposures affect health, how such exposures occur, how nanotechnologies could contain contamination, and how to make sure those technologies are safe.

A Sept. 24, 2015 Brown University news release, which originated the news item, describes of Brown’s SRP work already underway and how this new grant will support it,

“There is more research to be performed,” said Kim Boekelheide, program director, professor of pathology and laboratory medicine, and fellow of the Institute at Brown for Environment and Society (IBES). “Our scientific theme is integrated biomedical and engineering solutions to regulatory uncertainty, using interdisciplinary approaches to attack the really difficult contamination problems that matter.”

The program is pursuing four integrated projects. In one led by Boekelheide, a team is looking at the physiological effects of exposure to toxicants like trichloroethylene on the male reproductive system. In particular he hopes to find the subtle differences in biomolecular markers in sperm that could allow for very early detection of exposure. Meanwhile in another line of research, Eric Suuberg, professor of engineering, is studying how vapors from toxic material releases can re-emerge from the soil entering into buildings built at or near the polluted sites — and why it is hard to predict the level of exposure that inhabitants of these buildings may suffer.

In another project, Robert Hurt, an IBES fellow, SRP co-primary investigator and professor of engineering, is studying how graphene, an atomically thin carbon material, can be used to block the release and transport of toxicants to prevent human exposures. Hurt is also collaborating with Agnes Kane, an IBES fellow and chair and professor of pathology and laboratory medicine, who is leading a study of nanomaterial effects on human health, so they can be designed and used safely in environmental and other applications.

The program will also continue the program’s community outreach efforts in which they work and share information with communities near the state’s Superfund-designated and Brownfield contaminated sites. Scott Frickel, an IBES fellow and associate professor of sociology, is the new leader of community engagement. The program also includes a research translation core in which researchers share their findings and expertise with the U.S. Environmental Protection Agency, state agencies, and professionals involved in contamination management and cleanup. A training core provides opportunities for interdisciplinary research, field work, and industry “externships” for graduate students in engineering, pathobiology, and social sciences at Brown.

It’s good to see they are integrating social sciences into this project although I hope they aren’t attempting this move as a means to coopt and/or stifle genuine dissent and disagreement by giving a superficial nod to the social sciences and public engagement  while wending on their merry way.

A Venus flower basket sea sponge has strength

Despite being made essentially of glass, the skeleton of the sea sponge known as Venus' flower basket is remarkably strong -- right down to the tiny, hair-like fibers that hold the creatures to the sea floor. Researchers from Brown University have shown that those fibers, called spicules, have an intricate internal structure that is fine-tuned to boost strength. The findings could inform the engineering of human-made materials. Credit: Kesari Lab / Brown University

Despite being made essentially of glass, the skeleton of the sea sponge known as Venus’ flower basket is remarkably strong — right down to the tiny, hair-like fibers that hold the creatures to the sea floor. Researchers from Brown University have shown that those fibers, called spicules, have an intricate internal structure that is fine-tuned to boost strength. The findings could inform the engineering of human-made materials.
Credit: Kesari Lab / Brown University

I’m not sure how anyone saw a flower basket in that sponge but I bow to a more poetic soul. In any event, scientists at Brown University (US) have shown that this sponge has unexpected strength according to an April 6, 2015 news item on ScienceDaily,

Life may seem precarious for the sea sponge known as Venus’ flower basket. Tiny, hair-like appendages made essentially of glass are all that hold the creatures to their seafloor homes. But fear not for these creatures of the deep. Those tiny lifelines, called basalia spicules, are fine-tuned for strength, according to new research led by Brown University engineers.

In a paper published in the Proceedings of the National Academy of Sciences, the researchers show that the secret to spicules’ strength lies in their remarkable internal structure. The spicules, each only 50 microns in diameter, are made of a silica (glass) core surrounded by 10 to 50 concentric cylinders of glass, each separated by an ultra-thin layer of an organic material. The walls of each cylinder gradually decrease in thickness moving from the core toward the outside edge of the spicule.

An April 6, 2015 Brown University news release (also on EurekAlert), which originated the news item, describes the research in more detail,

When Haneesh Kesari, assistant professor of engineering at Brown, first saw this structure, he wasn’t sure what to make of it. But the pattern of decreasing thickness caught his eye.

“It was not at all clear to me what this pattern was for, but it looked like a figure from a math book,” Kesari said. “It had such mathematical regularity to it that I thought it had to be for something useful and important to the animal.”

The lives of these sponges depend on their ability to stay fixed to the sea floor. They sustain themselves by filtering nutrients out of the water, which they cannot do if they’re being cast about with the flow. So it would make sense, Kesari thought, that natural selection may have molded the creatures’ spicule anchors into models of strength — and the thickness pattern could be a contributing factor.

“If it can’t anchor, it can’t survive,” Kesari said. “So we thought this internal structure must be contributing to these spicules being a better anchor.”

To find out, Kesari worked with graduate student Michael Monn to build a mathematical model of the spicules’ structure. Among the model’s assumptions was that the organic layers between the glass cylinders allowed the cylinders to slide against each other.

“We prepared a mechanical model of this system and asked the question: Of all possible ways the thicknesses of the layers can vary, how should they vary so that the spicule’s anchoring ability is maximized?” Kesari said.

The model predicted that the structure’s load capacity would be greatest when the layers decrease in thickness toward the outside, just as was initially observed in actual spicules. Kesari and Monn then worked with James Weaver and Joanna Aizenberg of Harvard’s Wyss Institute for Biologically Inspired Engineering, who have worked with this sponge species for years. The team carefully compared the layer thicknesses predicted by the mechanics model to the actual layer thicknesses in more than a hundred spicule samples from sponges.

The work showed that the predictions made by the model matched very closely with the observed layer thicknesses in the samples. “It appears that the arrangement and thicknesses of these layers does indeed contribute to the spicules’ strength, which helps make them better anchors,” Kesari said.

The researchers say this is the first time to their knowledge that anyone has evaluated the mechanical advantage of this particular arrangement of layers. It could add to the list of useful engineered structures inspired by nature.

“In the engineered world, you see all kinds of instances where the external geometry of a structure is modified to enhance its specific strength — I-beams are one example,” Monn said. “But you don’t see a huge effort focused toward the internal mechanical design of these structures.”

This study, however, suggests that sponge spicules could provide a blueprint for load-bearing beams made stronger from the inside out.

Here’s a link to and a citation for the paper,

New functional insights into the internal architecture of the laminated anchor spicules of Euplectella aspergillum by Michael A. Monn, James C. Weaver, Tianyang Zhang, Joanna Aizenberg, and Haneesh Kesari. Published online before print April 6, 2015, doi: 10.1073/pnas.1415502112 PNAS April 6, 2015

This paper is behind a paywall.

High-order Brownian motion observed

A Nov. 17, 2014 news item on ScienceDaily highlights a new technique for observing Brownian motion,

For the first time, scientists have vividly mapped the shapes and textures of high-order modes of Brownian motions–in this case, the collective macroscopic movement of molecules in microdisk resonators–researchers at Case Western Reserve University report.

To do this, they used a record-setting scanning optical interferometry technique, described in a study published today in the journal Nature Communications.

The new technology holds promise for multimodal sensing and signal processing, and to develop optical coding for computing and other information-processing functions by exploiting the spatially resolved multimode Brownian resonances and their splitting pairs of modes.

A Nov. 17, 2014 Case Western Reserve University news release on EurekAlert, which originated the news item, provides more information about the technique and the research,

Interferometry uses the interference of light waves reflected off a surface to measure distances, a technique invented by Case School of Applied Science physicist Albert A. Michelson (who won the Nobel prize in science in 1907). Michelson and Western Reserve University chemist Edward Morley used the instrument to famously disprove that light traveled through “luminous ether” in 1887, setting the groundwork for Albert Einstein’s theory of relativity.

The technology has evolved since then. The keys to Feng’s new interferometry technique are focusing a tighter-than-standard laser spot on the surface of novel silicon carbide microdisks.

The microdisks, which sit atop pedestals of silicon oxide like cymbals on stands, are extremely sensitive to the smallest fluctuations arising from Brownian motions, even at thermodynamic equilibrium. Hence, they exhibit very small oscillations without external driving forces. These oscillations include fundamental and higher modes, called thermomechanical resonances.

Some of the light from the laser reflects back to a sensor after striking the top surface of the silicon dioxide film. And some of the light is refracted through the film and reflected back on a different path, causing interference in the light waves.

The narrow laser spot scans the disk surface and measures movement, or displacement, of the disk with a sensitivity of about 7 femtometers per square-root of a hertz at room temperature, which researchers believe is a record for interferometric systems. To put that in perspective, the width of a hair is about 40 microns, and a femtometer is 100 million times smaller than a micron.

Although higher frequency modes have small motion amplitudes, the technology enabled the group to spatially map and clearly visualize the first through ninth Brownian modes in the high frequency band, ranging from 5.78 to 26.41 megahertz.

In addition to detecting the shapes and textures of Brownian motions, multimode mapping identified subtle structural imperfections and defects, which are ubiquitous but otherwise invisible, or can’t be quantified most of the time. This capability may be useful for probing the dynamics and propagation of defects and defect arrays in nanodevices, as well as for future engineering of controllable defects to manipulate information in silicon carbide nanostructures

The high sensitivity and spatial resolution also enabled them to identify mode splitting, crossing and degeneracy, spatial asymmetry and other effects that may be used to encode information with increasing complexity. The researchers are continuing to explore the capabilities of the technology.

Here’s a link to and a citation for the paper,

Spatial mapping of multimode Brownian motions in high-frequency ​silicon carbide microdisk resonators by Zenghui Wang, Jaesung Lee & Philip X. -L. Feng. Nature Communications 5, Article number: 5158 doi:10.1038/ncomms6158 Published 17 November 2014

This paper is behind a paywall.

For those who would like a little more information about Brownian motion, there’s this from its Wikipedia entry,

Brownian motion or pedesis (from Greek: πήδησις /pɛ̌ːdɛːsis/ “leaping”) is the random motion of particles suspended in a fluid (a liquid or a gas) resulting from their collision with the quick atoms or molecules in the gas or liquid. The term “Brownian motion” can also refer to the mathematical model used to describe such random movements, which is often called a particle theory.

The Wikipedia entry also includes this gif

This is a simulation of Brownian motion of a big particle (dust particle) that collides with a large set of smaller particles (molecules of a gas) which move with different velocities in different random directions. http://weelookang.blogspot.com/2010/06/ejs-open-source-brownian-motion-gas.html Lookang Author of computer model: Francisco Esquembre, Fu-Kwun and lookang - Own work

This is a simulation of Brownian motion of a big particle (dust particle) that collides with a large set of smaller particles (molecules of a gas) which move with different velocities in different random directions. http://weelookang.blogspot.com/2010/06/ejs-open-source-brownian-motion-gas.html
Lookang Author of computer model: Francisco Esquembre, Fu-Kwun and lookang – Own work

On a tangential and amusing note, Brown University celebrating its 250th anniversary this year (2014) commissioned a Brownian Motion composition as part of its commemoration activities (from a Feb. 21, 2014 Brown University news release),

While Brown University and its neighbors celebrate the University’s first 250 years during the Opening Celebration Friday and Saturday, March 7-8, 2014, some new history will be made as well. On Friday night, the Brown University Wind Symphony will present the world premier of Brownian Motion, a piece commissioned for the semiquincentenary.

Written by the composer and saxophonist Patrick Zimmerli, the commission was funded by Edward Guiliano, a 1972 Brown graduate who was president of the Brown Band and founded the Brown Wind Ensemble during his time on College Hill.

Zimmerli admits to feeling excitement when approached with the commission. “I didn’t go to Brown but I have many connections to people who did, and I was really looking forward to the challenge of writing for an undergraduate wind ensemble, something I’d never done before.”

McGarrell [Matthew McGarrell, director of bands at Brown] and Zimmerli met last summer to talk about the commission for the first time. Aside from sending Zimmerli a few pieces to use as models, McGarrell gave the composer free reign over over everything from the feel to the length of the piece.

The resulting composition, which Zimmerli presented to McGarrell at the beginning of January, is dominated by jazz rhythms, with some nods to vernacular musics, including Caribbean and calypso, mixed in.

“The piece has several different moods but overall it is celebratory,” Zimmerli said. “After all it’s a birthday piece. It’s meant to be challenging but fun for the players.”

Listeners with a link to Brown may also find parts of the work familiar. Zimmerli subtly weaves an early melody known as “Araby’s Daughter” — Brown’s Alma Mater — throughout the piece, building on it until it’s played in its full glory by the French horns toward the end.

For inspiration, Zimmerli did extensive research on Brown’s early history and was intrigued to learn that Brown’s founding was initially opposed by a group of preachers who had a mistrust for those who had been formally educated. The result is a theme — “learning is evil,” a nod to those early roots — that winds its way throughout the song.

“Brown is an amazing example of an institution that has been able to evolve and transform itself from within, and I thought that fact should be celebrated,” said Zimmerli.

Other parts of the song inspired the Brownian Motion name.

“There’s a jagged theme toward the beginning of the piece that is a bit cheeky, even subversive. The way it moves and darts around through the instruments unexpectedly is what eventually led me to the actual title of the piece,” Zimmerli said.

“We knew we wanted to make it special concert,” said McGarrell of the program selections. “We wanted to reach both the Brown community in history, through the alumni, through musical representation, and we wanted to reach out to the extended Brown community in Rhode Island and southeastern New England, through history and intercultural outreach.”

The Brown musicians have been hard at work since the end of January learning Brownian Motion. While technically challenging, McGarrell said the students have been appreciating the skill level required and that “morale has remained high within the group.” Zimmerli arrives on campus on Wednesday, March 5, to help put the finishing touches on the performance.

There is a youtube video (over 60 mins.) of the Brownian Motion March 2014 performance.

Boron as a ‘buckyball’ or borospherene

First there was the borophene (like graphene but using boron rather than carbon) announcement from Brown University in my Jan. 28, 214 posting and now US (Brown University again) and Chinese researchers have developed a boron ‘buckyball’. Coincidentally, this announcement comes just after the 2014 World Cup final (July 13, 2014). Representations of buckyballs always resemble soccer balls. (Note: Germany won.)

From a July 14, 2014 news item on Azonano,

The discovery 30 years ago of soccer-ball-shaped carbon molecules called buckyballs helped to spur an explosion of nanotechnology research. Now, there appears to be a new ball on the pitch.

Researchers from Brown University, Shanxi University and Tsinghua University in China have shown that a cluster of 40 boron atoms forms a hollow molecular cage similar to a carbon buckyball. It’s the first experimental evidence that a boron cage structure—previously only a matter of speculation—does indeed exist.

“This is the first time that a boron cage has been observed experimentally,” said Lai-Sheng Wang, a professor of chemistry at Brown who led the team that made the discovery. “As a chemist, finding new molecules and structures is always exciting. The fact that boron has the capacity to form this kind of structure is very interesting.”

The researchers have provided an illustration of their borospherene,

The carbon buckyball has a boron cousin. A cluster for 40 boron atoms forms a hollow cage-like molecule. Courtesy Brown University

The carbon buckyball has a boron cousin. A cluster for 40 boron atoms forms a hollow cage-like molecule. Courtesy Brown University

A July 9, 2104 Brown University news release (also on EurekAlert), which originated the news item, describes the borosphene’s predecessor, the carbon buckyball, and provides more details about this new molecule,

Carbon buckyballs are made of 60 carbon atoms arranged in pentagons and hexagons to form a sphere — like a soccer ball. Their discovery in 1985 was soon followed by discoveries of other hollow carbon structures including carbon nanotubes. Another famous carbon nanomaterial — a one-atom-thick sheet called graphene — followed shortly after.

After buckyballs, scientists wondered if other elements might form these odd hollow structures. One candidate was boron, carbon’s neighbor on the periodic table. But because boron has one less electron than carbon, it can’t form the same 60-atom structure found in the buckyball. The missing electrons would cause the cluster to collapse on itself. If a boron cage existed, it would have to have a different number of atoms.

Wang and his research group have been studying boron chemistry for years. In a paper published earlier this year, Wang and his colleagues showed that clusters of 36 boron atoms form one-atom-thick disks, which might be stitched together to form an analog to graphene, dubbed borophene. Wang’s preliminary work suggested that there was also something special about boron clusters with 40 atoms. They seemed to be abnormally stable compared to other boron clusters.

Figuring out what that 40-atom cluster actually looks like required a combination of experimental work and modeling using high-powered supercomputers.

On the computer, Wang’s colleagues modeled over 10,000 possible arrangements of 40 boron atoms bonded to each other. The computer simulations estimate not only the shapes of the structures, but also estimate the electron binding energy for each structure — a measure of how tightly a molecule holds its electrons. The spectrum of binding energies serves as a unique fingerprint of each potential structure.

The next step is to test the actual binding energies of boron clusters in the lab to see if they match any of the theoretical structures generated by the computer. To do that, Wang and his colleagues used a technique called photoelectron spectroscopy.

Chunks of bulk boron are zapped with a laser to create vapor of boron atoms. A jet of helium then freezes the vapor into tiny clusters of atoms. The clusters of 40 atoms were isolated by weight then zapped with a second laser, which knocks an electron out of the cluster. The ejected electron flies down a long tube Wang calls his “electron racetrack.” The speed at which the electrons fly down the racetrack is used to determine the cluster’s electron binding energy spectrum — its structural fingerprint.

The experiments showed that 40-atom-clusters form two structures with distinct binding spectra. Those spectra turned out to be a dead-on match with the spectra for two structures generated by the computer models. One was a semi-flat molecule and the other was the buckyball-like spherical cage.

“The experimental sighting of a binding spectrum that matched our models was of paramount importance,” Wang said. “The experiment gives us these very specific signatures, and those signatures fit our models.”

The borospherene molecule isn’t quite as spherical as its carbon cousin. Rather than a series of five- and six-membered rings formed by carbon, borospherene consists of 48 triangles, four seven-sided rings and two six-membered rings. Several atoms stick out a bit from the others, making the surface of borospherene somewhat less smooth than a buckyball.

As for possible uses for borospherene, it’s a little too early to tell, Wang says. One possibility, he points out, could be hydrogen storage. Because of the electron deficiency of boron, borospherene would likely bond well with hydrogen. So tiny boron cages could serve as safe houses for hydrogen molecules.

But for now, Wang is enjoying the discovery.

“For us, just to be the first to have observed this, that’s a pretty big deal,” Wang said. “Of course if it turns out to be useful that would be great, but we don’t know yet. Hopefully this initial finding will stimulate further interest in boron clusters and new ideas to synthesize them in bulk quantities.”

The theoretical modeling was done with a group led by Prof. Si-Dian Li from Shanxi University and a group led by Prof. Jun Li from Tsinghua University. The work was supported by the U.S. National Science Foundation (CHE-1263745) and the National Natural Science Foundation of China.

Here’s a link to and a citation for the paper,

Observation of an all-boron fullerene by Hua-Jin Zhai, Ya-Fan Zhao, Wei-Li Li, Qiang Chen, Hui Bai, Han-Shi Hu, Zachary A. Piazza, Wen-Juan Tian, Hai-Gang Lu, Yan-Bo Wu, Yue-Wen Mu, Guang-Feng Wei, Zhi-Pan Liu, Jun Li, Si-Dian Li, & Lai-Sheng Wang. Nature Chemistry (2014) doi:10.1038/nchem.1999 Published online 13 July 2014

This paper is behind a paywall.

Physics, nanopores, viruses, and DNA

A June 17, 2014 news item on Azonano describes a project which could help scientists decode strands of DNA at top speeds,

Nanopores may one day lead a revolution in DNA sequencing. By sliding DNA molecules one at a time through tiny holes in a thin membrane, it may be possible to decode long stretches of DNA at lightning speeds. Scientists, however, haven’t quite figured out the physics of how polymer strands like DNA interact with nanopores. Now, with the help of a particular type of virus, researchers from Brown University have shed new light on this nanoscale physics.

“What got us interested in this was that everybody in the field studied DNA and developed models for how they interact with nanopores,” said Derek Stein, associate professor of physics and engineering at Brown [Brown University, US] who directed the research. “But even the most basic things you would hope models would predict starting from the basic properties of DNA — you couldn’t do it. The only way to break out of that rut was to study something different.”

A June 16, 2014 Brown University news release (also on EurekAlert), which originated the news item, describes the problems with nanopores,

The concept behind nanopore sequencing is fairly simple. A hole just a few billionths of a meter wide is poked in a membrane separating two pools of salty water. An electric current is applied to the system, which occasionally snares a charged DNA strand and whips it through the pore — a phenomenon called translocation. When a molecule translocates, it causes detectable variations in the electric current across the pore. By looking carefully at those variations in current, scientists may be able to distinguish individual nucleotides — the A’s, C’s, G’s and T’s coded in DNA molecules.

The first commercially available nanopore sequencers may only be a few years away, but despite advances in the field, surprisingly little is known about the basic physics involved when polymers interact with nanopores. That’s partly because of the complexities involved in studying DNA. In solution, DNA molecules form balls of random squiggles, which make understanding their physical behavior extremely difficult.

For example, the factors governing the speed of DNA translocation aren’t well understood. Sometimes molecules zip through a pore quickly; other times they slither more slowly, and nobody completely understands why.

One possible explanation is that the squiggly configuration of DNA causes each molecule to experience differences in drag as they’re pulled through the water toward the pore. “If a molecule is crumpled up next to the pore, it has a shorter distance to travel and experiences less drag,” said Angus McMullen, a physics graduate student at Brown and the study’s lead author. “But if it’s stretched out then it would feel drag along the whole length and that would cause it to go slower.”

The news release then goes on to detail a possible solution to the problem of why DNA translocation varies in speed. Answering this question about DNA translocation could lead to faster and more accurate nanopore sequencing,

The drag effect is impossible to isolate experimentally using DNA, but the virus McMullen and his colleagues studied offered a solution.

The researchers looked at fd, a harmless virus that infects e. coli bacteria. Two things make the virus an ideal candidate for study with nanpores. First, fd viruses are all identical clones of each other. Second, unlike squiggly DNA, fd virus is a stiff, rod-like molecule. Because the virus doesn’t curl up like DNA does, the effect of drag on each one should be essentially the same every time.

With drag eliminated as a source of variation in translocation speed, the researchers expected that the only source of variation would be the effect of thermal motion. The tiny virus molecules constantly bump up against the water molecules in which they are immersed. A few random thermal kicks from the rear would speed the virus up as it goes through the pore. A few kicks from the front would slow it down.

The experiments showed that while thermal motion explained much of the variation in translocation speed, it didn’t explain it all. Much to the researchers’ surprise, they found another source of variation that increased when the voltage across the pore was increased.

“We thought that the physics would be crystal clear,” said Jay Tang, associate professor of physics and engineering at Brown and one of the study’s co-authors. “You have this stiff [virus] with well-defined diameter and size and you would expect a very clear-cut signal. As it turns out, we found some puzzling physics we can only partially explain ourselves.”

The researchers can’t say for sure what’s causing the variation they observed, but they have a few ideas.

“It’s been predicted that depending on where [an object] is inside the pore, it might be pulled harder or weaker,” McMullen said. “If it’s in the center of the pore, it pulls a little bit weaker than if it’s right on the edge. That’s been predicted, but never experimentally verified. This could be evidence of that happening, but we’re still doing follow up work.

The new approach using a virus answered questions while leading to new insights and possibilities (from the news release),

A better understanding of translocation speed could improve the accuracy of nanopore sequencing, McMullen says. It would also be helpful in the crucial task of measuring the length of DNA strands. “If you can predict the translocation speed,” McMullen said, “then you can easily get the length of the DNA from how long its translocation was.”

The research also helped to reveal other aspects of the translocation process that could be useful in designing future devices. The study showed that the electrical current tends to align the viruses head first to the pore, but on occasions when they’re not lined up, they tend to bounce around on the edge of the pore until thermal motion aligns them to go through. However, when the voltage was turned too high, the thermal effects were suppressed and the virus became stuck to the membrane. That suggests a sweet spot in voltage where headfirst translocation is most likely.

None of this is observable directly — the system is simply too small to be seen in action. But the researchers could infer what was happening by looking at slight changes in the current across the pore.

“When the viruses miss, they rattle around and we see these little bumps in the current,” Stein said. “So with these little bumps, we’re starting to get an idea of what the molecule is doing before it slides through. Normally these sensors are blind to anything that’s going on until the molecule slides through.”

That would have been impossible to observe using DNA. The floppiness of the DNA molecule allows it to go through a pore in a folded configuration even if it’s not aligned head-on. But because the virus is stiff, it can’t fold to go through. That enabled the researchers to isolate and observe those contact dynamics.

“These viruses are unique,” Stein said. “They’re like perfect little yardsticks.”

In addition to shedding light on basic physics, the work might also have another application. While the fd virus itself is harmless, the bacteria it infects — e. coli — is not. Based on this work, it might be possible to build a nanopore device for detecting the presence of fd, and by proxy, e. coli. Other dangerous viruses — Ebola and Marburg among them — share the same rod-like structure as fd.

“This might be an easy way to detect these viruses,” Tang said. “So that’s another potential application for this.”

Here’s a link to and a citation for the paper,

Stiff filamentous virus translocations through solid-state nanopores by Angus McMullen, Hendrick W. de Haan, Jay X. Tang, & Derek Stein. Nature Communications 5, Article number: 4171 doi:10.1038/ncomms5171 Published 16 June 2014

This paper is behind a paywall.

Bioceramic armour: tough and clear

This story about a mollusk and its armour eventually led me back to one of my favourite science writers, David L. Chandler at the Massachusetts Institute of Technology (MIT). First, here’s an excerpt from a March 30, 2014 news item on ScienceDaily,

The shells of a sea creature, the mollusk Placuna placenta, are not only exceptionally tough, but also clear enough to read through. Now, researchers at MIT have analyzed these shells to determine exactly why they are so resistant to penetration and damage — even though they are 99 percent calcite, a weak, brittle mineral.

The shells’ unique properties emerge from a specialized nanostructure that allows optical clarity, as well as efficient energy dissipation and the ability to localize deformation, the researchers found. The results are published this week in the journal Nature Materials, in a paper co-authored by MIT graduate student Ling Li and professor Christine Ortiz.

A March 30, 2014 MIT press release (I’m not positive Chandler wrote this but he is the press contact) describes both the engineered bioceramic armour and the mollusk’s naturally occurring armour,

Engineered ceramic-based armor, while designed to resist penetration, often lacks the ability to withstand multiple blows, due to large-scale deformation and fracture that can compromise its structural integrity, Ortiz says. In transparent armor systems, such deformation can also obscure visibility.

Creatures that have evolved natural exoskeletons — many of them ceramic-based — have developed ingenious designs that can withstand multiple penetrating attacks from predators. The shells of a few species, such as Placuna placenta, are also optically clear.

To test exactly how the shells — which combine calcite with about 1 percent organic material — respond to penetration, the researchers subjected samples to indentation tests, using a sharp diamond tip in an experimental setup that could measure loads precisely. They then used high-resolution analysis methods, such as electron microscopy and diffraction, to examine the resulting damage.

The material initially isolates damage through an atomic-level process called “twinning” within the individual ceramic building blocks: A crystal breaks up into a pair of mirror-image regions that share a common boundary, rather like a butterfly’s wings. This twinning process occurs all around the stressed region, helping to form a kind of boundary that keeps the damage from spreading outward.

The MIT researchers found that twinning then activates “a series of additional energy-dissipation mechanisms … which preserve the mechanical and optical integrity of the surrounding material,” Li says. This produces a material that is 10 times more efficient in dissipating energy than the pure mineral, Li adds.

The properties of this natural armor make it a promising template for the development of bio-inspired synthetic materials for both commercial and military applications — such as eye and face protection for soldiers, windows and windshields, and blast shields, Ortiz says.

Huajian Gao, a professor of engineering at Brown University who was not involved in this research, calls it “an excellent and elegant piece of work.” He says it “successfully demonstrates the effectiveness of nanoscale deformation twins in energy dissipation in bioceramics, and should be able to inspire and guide the development of manmade ceramic materials.” He adds, “As a first-of-its-kind [demonstration of] the effectiveness of deformation twins in natural materials, this work should have huge practical impact.”

The work was supported by the National Science Foundation; the U.S. Army Research Office through the MIT Institute for Soldier Nanotechnologies; the National Security Science and Engineering Faculty Fellowships Program; and the Office of the Assistant Secretary of Defense for Research and Engineering.

The researchers have produced an image showing how the mollusk shell reacts to being damaged,

A Scanning Electron Microscope (SEM) image of the region surrounding an indentation the researchers made in a piece of shell from Placuna placenta. The image shows the localization of damage to the area immediately surrounding the stress. Image: Ling Li and James C. Weaver. Courtesy: MIT

A Scanning Electron Microscope (SEM) image of the region surrounding an indentation the researchers made in a piece of shell from Placuna placenta. The image shows the localization of damage to the area immediately surrounding the stress.
Image: Ling Li and James C. Weaver. Courtesy: MIT

Here’s a link to and a citation for the paper,

Pervasive nanoscale deformation twinning as a catalyst for efficient energy dissipation in a bioceramic armour by Ling Li & Christine Ortiz. Nature Materials (2014) doi:10.1038/nmat3920 Published online 30 March 2014

This paper is behind a paywall.

Borophene at Brown University (US)

It’s still theory at this point but researchers at Brown University (Rhode Island, US) have produced experimental proof that a single layer of boron atoms in a lattice reminiscent of  but not identical to a graphene layer is possible. A Jan. 28, 2014 news item on Azonano describes the research,

Researchers from Brown University have shown experimentally that a boron-based competitor to graphene is a very real possibility.

Graphene has been heralded as a wonder material. Made of a single layer of carbon atoms in a honeycomb arrangement, graphene is stronger pound-for-pound than steel and conducts electricity better than copper. Since the discovery of graphene, scientists have wondered if boron, carbon’s neighbor on the periodic table, could also be arranged in single-atom sheets. Theoretical work suggested it was possible, but the atoms would need to be in a very particular arrangement.

Boron has one fewer electron than carbon and as a result can’t form the honeycomb lattice that makes up graphene. For boron to form a single-atom layer, theorists suggested that the atoms must be arranged in a triangular lattice with hexagonal vacancies — holes — in the lattice.

“That was the prediction,” said Lai-Sheng Wang, professor of chemistry at Brown, “but nobody had made anything to show that’s the case.”

Wang and his research group, which has studied boron chemistry for many years, have now produced the first experimental evidence that such a structure is possible. In a paper published on January 20 in Nature Communications, Wang and his team showed that a cluster made of 36 boron atoms (B36) forms a symmetrical, one-atom thick disc with a perfect hexagonal hole in the middle.

Here’s an image that illustrates ‘borophene’,

Caption: This shows a 36-atom cluster of boron, left, arranged as a flat disc with a hexagonal hole in the middle, fits the theoretical requirements for making a one-atom-thick boron sheet, right, a theoretical nanomaterial dubbed "borophene." Credit: Wang Lab / Brown University

Caption: This shows a 36-atom cluster of boron, left, arranged as a flat disc with a hexagonal hole in the middle, fits the theoretical requirements for making a one-atom-thick boron sheet, right, a theoretical nanomaterial dubbed “borophene.”
Credit: Wang Lab / Brown University

The Jan. 27, 2014 Brown University news release (also on EurekAlert), which originated the news item, provides details about how the research was conducted,

The work required a combination of laboratory experiments and computational modeling. In the lab, Wang and his student, Wei-Li Li, probe the properties of boron clusters using a technique called photoelectron spectroscopy. They start by zapping chunks of bulk boron with a laser to create vapor of boron atoms. A jet of helium then freezes the vapor into tiny clusters of atoms. Those clusters are then zapped with a second laser, which knocks an electron out of the cluster and sends it flying down a long tube that Wang calls his “electron racetrack.” The speed at which the electron flies down the racetrack is used to determine the cluster’s electron binding energy spectrum — a readout of how tightly the cluster holds its electrons. That spectrum serves as fingerprint of the cluster’s structure.

Wang’s experiments showed that the B36 cluster was something special. It had an extremely low electron binding energy compared to other boron clusters. The shape of the cluster’s binding spectrum also suggested that it was a symmetrical structure.

To find out exactly what that structure might look like, Wang turned to Zachary Piazza, one of his graduate students specializing in computational chemistry. Piazza began modeling potential structures for B36 on a supercomputer, investigating more than 3,000 possible arrangements of those 36 atoms. Among the arrangements that would be stable was the planar disc with the hexagonal hole.

“As soon as I saw that hexagonal hole,” Wang said, “I told Zach, ‘We have to investigate that.'”

To ensure that they have truly found the most stable arrangement of the 36 boron atoms, they enlisted the help of Jun Li, who is a professor of chemistry at Tsinghua University in Beijing and a former senior research scientist at Pacific Northwest National Laboratory (PNNL) in Richland, Wash. Li, a longtime collaborator of Wang’s, has developed a new method of finding stable structures of clusters, which would be suitable for the job at hand. Piazza spent the summer of 2013 at PNNL working with Li and his students on the B36 project. They used the supercomputer at PNNL to examine more possible arrangements of the 36 boron atoms and compute their electron binding spectra. They found that the planar disc with a hexagonal hole matched very closely with the spectrum measured in the lab experiments, indicating that the structure Piazza found initially on the computer was indeed the structure of B36.

That structure also fits the theoretical requirements for making borophene, which is an extremely interesting prospect, Wang said. The boron-boron bond is very strong, nearly as strong as the carbon-carbon bond. So borophene should be very strong. Its electrical properties may be even more interesting. Borophene is predicted to be fully metallic, whereas graphene is a semi-metal. That means borophene might end up being a better conductor than graphene.

“That is,” Wang cautions, “if anyone can make it.”

Here’s a link to and a citation for the research paper,

Planar hexagonal B36 as a potential basis for extended single-atom layer boron sheets by Zachary A. Piazza, Han-Shi Hu, Wei-Li Li, Ya-Fan Zhao, Jun Li, & Lai-Sheng Wang. Nature Communications 5, Article number: 3113 doi:10.1038/ncomms4113 Published 20 January 2014

This paper is behind a paywall.

Recycling carbon dioxide with gold nanoparticles

Researchers at Brown University (in Providence, Rhode Island) have developed a technique using gold nanoparticles to capture carbon dioxide and turn it into carbon monoxide (from the Oct. 24, 2013 Brown University news release [also on EurekAlert]),

It’s a 21st-century alchemist’s dream: turning Earth’s superabundance of carbon dioxide — a greenhouse gas — into fuel or useful industrial chemicals. Researchers from Brown have shown that finely tuned gold nanoparticles can do the job. The key is maximizing the particles’ long edges, which are the active sites for the reaction.[This paragraph is present only on the Brown website news release]

By tuning gold nanoparticles to just the right size, researchers from Brown University have developed a catalyst that selectively converts carbon dioxide (CO2) to carbon monoxide (CO), an active carbon molecule that can be used to make alternative fuels and commodity chemicals.

“Our study shows potential of carefully designed gold nanoparticles to recycle CO2 into useful forms of carbon,” said Shouheng Sun, professor of chemistry and one of the study’s senior authors. “The work we’ve done here is preliminary, but we think there’s great potential for this technology to be scaled up for commercial applications.”

The scientists were trying to solve a major problem with recycling carbon dioxide when using gold (from the news release),

Converting CO2 to CO isn’t easy. Prior research has shown that catalysts made of gold foil are active for this conversion, but they don’t do the job efficiently. The gold tends to react both with the CO2 and with the water in which the CO2 is dissolved, creating hydrogen byproduct rather than the desired CO.

The Brown research team decided to try gold nanoparticles and had a surprising result (from the news release),

The Brown experimental group, led by Sun and Wenlei Zhu, a graduate student in Sun’s group, wanted to see if shrinking the gold down to nanoparticles might make it more selective for CO2. They found that the nanoparticles were indeed more selective, but that the exact size of those particles was important. Eight nanometer particles had the best selectivity, achieving a 90-percent rate of conversion from CO2 to CO. Other sizes the team tested — four, six, and 10 nanometers — didn’t perform nearly as well.

“At first, that result was confusing,” said Andrew Peterson, professor of engineering and also a senior author on the paper. “As we made the particles smaller we got more activity, but when we went smaller than eight nanometers, we got less activity.”

The researchers investigated further and found a relationship between size and shape which affects the gold nanoparticles’ performance (from the news release),

To understand what was happening, Peterson and postdoctoral researcher Ronald Michalsky used a modeling method called density functional theory. They were able to show that the shapes of the particles at different sizes influenced their catalytic properties.

“When you take a sphere and you reduce it to smaller and smaller sizes, you tend to get many more irregular features — flat surfaces, edges and corners,” Peterson said. “What we were able to figure out is that the most active sites for converting CO2 to CO are the edge sites, while the corner sites predominantly give the by-product, which is hydrogen. So as you shrink these particles down, you’ll hit a point where you start to optimize the activity because you have a high number of these edge sites but still a low number of these corner sites. But if you go too small, the edges start to shrink and you’re left with just corners.”

Now that they understand exactly what part of the catalyst is active, the researchers are working to further optimize the particles. “There’s still a lot of room for improvement,” Peterson said. “We’re working on new particles that maximize these active sites.”

The researchers believe these findings could be an important new avenue for recycling CO2 on a commercial scale.

“Because we’re using nanoparticles, we’re using a lot less gold than in a bulk metal catalyst,” Sun said. “That lowers the cost for making such a catalyst and gives the potential to scale up.”

Here’s a link to and a citation for the research paper,

Monodisperse Au Nanoparticles for Selective Electrocatalytic Reduction of CO2 to CO by Wenlei Zhu, Ronald Michalsky, Önder Metin, Haifeng Lv, Shaojun Guo, Christopher J. Wright, Xiaolian Sun, Andrew A. Peterson, and Shouheng Sun. J. Am. Chem. Soc., DOI: 10.1021/ja409445p Publication Date (Web): October 24, 2013
Copyright © 2013 American Chemical Society

This article is behind a paywall.

Should October 2013 be called ‘the month of graphene’?

Since the Oct. 10-11, 2013 Graphene Flagship (1B Euros investment) launch, mentioned in my preview Oct. 7, 2013 posting, there’ve been a flurry of graphene-themed news items both on this blog and elsewhere and I’ve decided to offer a brief roundup what I’ve found elsewhere.

Dexter Johnson offers a commentary in the pithily titled, Europe Invests €1 Billion to Become “Graphene Valley,” an Oct. 15, 2013 posting on his Nanoclast blog (on the IEEE [Institute of Electrical and Electronics Engineers] website) Note: Links have been removed,

The initiative has been dubbed “The Graphene Flagship,” and apparently it is the first in a number of €1 billion, 10-year plans the EC is planning to launch. The graphene version will bring together 76 academic institutions and industrial groups from 17 European countries, with an initial 30-month-budget of €54M ($73 million).

Graphene research is still struggling to find any kind of applications that will really take hold, and many don’t expect it will have a commercial impact until 2020. What’s more, manufacturing methods are still undeveloped. So it would appear that a 10-year plan is aimed at the academic institutions that form the backbone of this initiative rather than commercial enterprises.

Just from a political standpoint the choice of Chalmers University in Sweden as the base of operations for the Graphene Flagship is an intriguing choice. …

I have to agree with Dexter that choosing Chalmers University over the University of Manchester where graphene was first isolated is unexpected. As a companion piece to reading Dexter’s posting in its entirety and which features a video from the flagship launch, you might want to try this Oct. 15, 2013 article by Koen Mortelmans for Youris (h/t Oct. 15, 2013 news item on Nanowerk),

Andre Konstantin Geim is the only person who ever received both a Nobel and an Ig Nobel. He was born in 1958 in Russia, and is a Dutch-British physicist with German, Polish, Jewish and Ukrainian roots. “Having lived and worked in several European countries, I consider myself European. I don’t believe that any further taxonomy is necessary,” he says. He is now a physics professor at the University of Manchester. …

He shared the Noble [Nobel] Prize in 2010 with Konstantin Novoselov for their work on graphene. It was following on their isolation of microscope visible grapheme flakes that the worldwide research towards practical applications of graphene took off.  “We did not invent graphene,” Geim says, “we only saw what was laid up for five hundred year under our noses.”

Geim and Novoselov are often thought to have succeeded in separating graphene from graphite by peeling it off with ordinary duct tape until there only remained a layer. Graphene could then be observed with a microscope, because of the partial transparency of the material. That is, after dissolving the duct tape material in acetone, of course. That is also the story Geim himself likes to tell.

However, he did not use – as the urban myth goes – graphite from a common pencil. Instead, he used a carbon sample of extreme purity, specially imported. He also used ultrasound techniques. But, probably the urban legend will survive, as did Archimedes’ bath and Newtons apple. “It is nice to keep some of the magic,” is the expression Geim often uses when he does not want a nice story to be drowned in hard facts or when he wants to remain discrete about still incomplete, but promising research results.

Mortelmans’ article fills in some gaps for those not familiar with the graphene ‘origins’ story while Tim Harper’s July 22, 2012 posting on Cientifica’s (an emerging technologies consultancy where Harper is the CEO and founder) TNT blog offers an insight into Geim’s perspective on the race to commercialize graphene with a paraphrased quote for the title of Harper’s posting, “It’s a bit silly for society to throw a little bit of money at (graphene) and expect it to change the world.” (Note: Within this context, mention is made of the company’s graphene opportunities report.)

With all this excitement about graphene (and carbon generally), the magazine titled Carbon has just published a suggested nomenclature for 2D carbon forms such as graphene, graphane, etc., according to an Oct. 16, 2013 news item on Nanowerk (Note: A link has been removed),

There has been an intense research interest in all two-dimensional (2D) forms of carbon since Geim and Novoselov’s discovery of graphene in 2004. But as the number of such publications rise, so does the level of inconsistency in naming the material of interest. The isolated, single-atom-thick sheet universally referred to as “graphene” may have a clear definition, but when referring to related 2D sheet-like or flake-like carbon forms, many authors have simply defined their own terms to describe their product.

This has led to confusion within the literature, where terms are multiply-defined, or incorrectly used. The Editorial Board of Carbon has therefore published the first recommended nomenclature for 2D carbon forms (“All in the graphene family – A recommended nomenclature for two-dimensional carbon materials”).

This proposed nomenclature comes in the form of an editorial, from Carbon (Volume 65, December 2013, Pages 1–6),

All in the graphene family – A recommended nomenclature for two-dimensional carbon materials

  • Alberto Bianco
    CNRS, Institut de Biologie Moléculaire et Cellulaire, Immunopathologie et Chimie Thérapeutique, Strasbourg, France
  • Hui-Ming Cheng
    Shenyang National Laboratory for Materials Science, Institute of Metal Research, Chinese Academy of Sciences, 72 Wenhua Road, Shenyang 110016, China
  • Toshiaki Enoki
    Department of Chemistry, Graduate School of Science and Engineering, Tokyo Institute of Technology, Tokyo, Japan
  • Yury Gogotsi
    Materials Science and Engineering Department, A.J. Drexel Nanotechnology Institute, Drexel University, 3141 Chestnut Street, Philadelphia, PA 19104, USA
  • Robert H. Hurt
    Institute for Molecular and Nanoscale Innovation, School of Engineering, Brown University, Providence, RI 02912, USA
  • Nikhil Koratkar
    Department of Mechanical, Aerospace and Nuclear Engineering, The Department of Materials Science and Engineering, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA
  • Takashi Kyotani
    Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
  • Marc Monthioux
    Centre d’Elaboration des Matériaux et d’Etudes Structurales (CEMES), UPR-8011 CNRS, Université de Toulouse, 29 Rue Jeanne Marvig, F-31055 Toulouse, France
  • Chong Rae Park
    Carbon Nanomaterials Design Laboratory, Global Research Laboratory, Research Institute of Advanced Materials, Department of Materials Science and Engineering, Seoul National University, Seoul 151-744, Republic of Korea
  • Juan M.D. Tascon
    Instituto Nacional del Carbón, INCAR-CSIC, Apartado 73, 33080 Oviedo, Spain
  • Jin Zhang
    Center for Nanochemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China

This editorial is behind a paywall.

Celebrate women in science on Oct. 15, 2013 and participate in a Wikipedia: Ada Lovelace Day 2013 edit-a-thon

Founded in 2009 by Suw Charman-Anderson, Ada Lovelace Day (Oct. 15) is on its way to realizing its goal of bringing more recognition to and celebrating women in science. From Charman-Anderson’s Oct. 15, 2013 posting for the Guardian Science blogs (Note: Links have been removed),

When I started the day five years ago, my goal was to collect these stories not only to inspire girls to study the STEM subjects, but also to provide support to women pursuing careers in these usually male-dominated fields.

Ada Lovelace is the ideal figurehead for this project: She was the world’s first computer programmer, and the first person to realise that a general purpose computing machine such as Charles Babbage’s Analytical Engine could do more than just calculate large tables of numbers. It could, she said, create music and art, given the right inputs. The Analytical Engine, she wrote, “weaves algebraic patterns just as the Jacquard loom weaves flowers and leaves”.

This daughter of “mad, bad and dangerous to know” Lord Byron achieved this distinction despite the fierce prejudices of the 19th Century. Her tutor Augustus De Morgan echoed the accepted view of the time when he said that maths problems presented “a very great tension of mind beyond the strength of a woman’s physical power”.

But Ada persevered in her studies, and De Morgan recognised her brilliance when he said that had she been a man, she would have had the potential to become “an original mathematical investigator, perhaps of first-rate eminence”.

Sydney Brownstone has written an Oct. 15, 2013 article about an Ada Lovelace Day Wikipedia event (on the Fast Company website; Note: Links have been removed),

Take Wikipedia, for example. Despite the fact that our communal encyclopedia provides a wealth of accessible information, women make up fewer than 15% of the project’s editors. (For further information, see the Wikipedia article “Wikipedia: Systemic bias.”) Oftentimes, the lack of gender parity results in a dearth of articles about, or including, important female figures in society. That’s what science journalist and BrainPOP news director Maia Weinstock found when she started editing Wikipedia articles back in 2007: Women who should be included in the STEM (science, technology, engineering, and math) achievement canon were simply missing from the archives. Or, when they were included, their stories were often stubs that left out the magnitude of their contributions.

In attempt to rectify some of these wrongs, Weinstock organized a Wikipedia Edit-a-thon held on last year’s Ada Lovelace day, a holiday dedicated to celebrating achievements of women in STEM fields, named for the pioneering 19th-century scientist (who, thankfully, has an extensive Wikipedia entry). Today [Oct. 15, 2013], Weinstock is organizing another round of editing at Brown University, in which some 40 contributors will help write articles from scratch or expand stubs on women pioneers. [emphasis mine]

In addition to the meetup at Brown University (Rhode Island, US), remote participation is also being encouraged in the Edit-a-thon from 3 pm to 8:30 pm EDT today (Oct. 15, 2013). You can find out more about the event (in person or remote) on this page: Wikipedia:Meetup/Ada Lovelace Edit-a-thon 2013 – Brown.

Brava to all women involved in STEM (science, technology, engineering, and mathematics) everywhere!