3-D Dynamic Imaging of Soft Materials

Oct. 3, 2013 — Autumn is usually not such a great time for big special effects movies as the summer blockbusters have faded and those for the holiday season have not yet opened. Fall is more often the time for thoughtful films about small subjects, which makes it perfect for the unveiling of a new movie produced by researchers at the U.S. Department of Energy (DOE)'s Lawrence Berkeley National Laboratory (Berkeley Lab). Through a combination of transmission electron microscopy (TEM) and their own unique graphene liquid cell, the researchers have recorded the three-dimensional motion of DNA connected to gold nanocrystals. This is the first time TEM has been used for 3D dynamic imaging of so-called soft materials.

This schematic of a graphene liquid cell shows multiple liquid pockets containing single nanoparticles, dimers composed of dsDNA bridges in different lengths, and trimers. (Credit: Image courtesy of DOE/Lawrence Berkeley National Laboratory)

 

"Our demonstration of 3D dynamic imaging goes beyond TEM's conventional use in seeing flat, dry samples and opens many exciting opportunities for studying the dynamics of biological macromolecular assemblies and artificial nanostructures," says physicist Alex Zettl, one of the leaders of this research. "These results were made possible by our novel graphene liquid cell, which can meet the challenges of using TEM to image soft materials."
Zettl, who holds joint appointments with Berkeley Lab's Materials Sciences Division and UC Berkeley's Physics Department where he directs the Center of Integrated Nanomechanical Systems, is one of the co-authors of a paper in NANO Letters describing this research. The paper is titled "3D Motion of DNA-Au Nanoconjugates in Graphene Liquid Cell Electron Microscopy."
Paul Alivisatos, Berkeley Lab Director and UC Berkeley's Samsung Distinguished Chair in Nanoscience and Nanotechnology, is the corresponding author. Other authors are Qian Chen, Jessica Smith, Jungwon Park, Kwanpyo Kim, Davy Ho and Haider Rasool.
The term "soft materials" takes in a vast variety of stuff, including DNA, proteins and other biological compounds, plastics, therapeutic drugs, flexible electronics, and certain types of photovoltaics. Despite their ubiquitous presence in our daily lives, soft materials pose many questions because the study of their dynamics at the nanoscale, especially biological systems, has been a challenge. TEM, in which a beam of electrons rather than light is used for illumination and magnification, provides the resolution for such studies but can only be used in a high vacuum as molecules in the air disrupt the electron beam. Since liquids evaporate in high vacuum, samples of soft materials, which have been described as "highly viscous fluids," must be hermetically sealed in special solid containers (called cells) with a viewing window before being imaged with TEM.
In the past, liquid cells featured silicon-based viewing windows whose thickness limited resolution and perturbed the natural state of the soft materials. Zettl and Alivisatos and their respective research groups overcame these limitations with the development of a liquid cell based on a graphene membrane only a single atom thick. This development was done in close cooperation with researchers at the National Center for Electron Microscopy (NCEM), which is located at Berkeley Lab.
"Our graphene liquid cells pushed the spatial resolution of liquid phase TEM imaging to the atomic scale but still focused on growth trajectories of metallic nanocrystals," says lead author Qian Chen, a postdoctoral fellow in Alivisatos's research group. "Now we've adopted the technique to imaging the 3D dynamics of soft materials, starting with double-strand (dsDNA) connected to gold nanocrystals and achieved nanometer resolution."
To create the cell, two opposing graphene sheets are bonded to one another by their van der Waals attraction. This forms a sealed nanoscale chamber and creates within the chamber a stable aqueous solution pocket approximately 100 nanometers in height and one micron in diameter. The single atom thick graphene membrane of the cells is essentially transparent to the TEM electron beam, minimizing the unwanted loss of imaging electrons and providing superior contrast and resolution compared to silicon-based windows. The aqueous pockets allow for up to two minutes of continuous imaging of soft material samples exposed to a 200 kilo Volt imaging electron beam. During this time, soft material samples can freely rotate.
After demonstrating that their graphene liquid cell can seal an aqueous sample solution against a TEM high vacuum, the Berkeley researchers used it to study the types of gold-dsDNA nanoconjugates that have been widely used as dynamic plasmonic probes.
"The presence of double-stranded DNA molecules incorporates the major challenges of studying the dynamics of biological samples with liquid phase TEM," says Alivisatos. "The high-contrast gold nanocrystals facilitate tracking of our specimens."
The Alivisatos and Zettl groups were able to observe dimers, pairs of gold nanoparticles, tethered by a single piece of dsDNA, and trimers, three gold nanoparticles, connected into a linear configuration by two single pieces of dsDNA. From a series of 2D projected TEM images captured while the samples were rotating, the researchers were to reconstruct 3D configuration and motions of the samples as they evolved over time.
"This information would be inaccessible with conventional TEM techniques," Chen says.

 

Diamond 'Super-Earth' May Not Be Quite So Precious

Oct. 8, 2013 — An alien world reported to be the first known planet to consist largely of diamond appears less likely to be of such precious nature, according to a new analysis led by UA graduate student Johanna Teske.

The smallest of several planets in the 55 Cancri system, the former 'diamond planet' is seen orbiting its host star at very close range in this artist's impression. A nearby brown dwarf with its own 'miniature' planetary system is pictured as well. (Credit: Illustration: NASA/JPL-Caltech)

A planet 40 light years from our solar system, believed to be the first-ever discovered planet to consist largely of diamond, may in fact be of less exquisite nature, according to new research led by University of Arizona astronomy graduate student Johanna Teske.
Revisiting public data from previous telescope observations, Teske's team analyzed the available data in more detail and concluded that carbon -- the chemical element diamonds are made of -- appears to be less abundant in relation to oxygen in the planet's host star -- and by extension, perhaps the planet -- than was suggested by a study of the host star published in 2010.
"The 2010 paper found that '55 Cancri,' a star that hosts five planets, has a carbon-to-oxygen ratio greater than one," Teske said. "This observation helped motivate a paper last year about the innermost planet of the system, the 'super-Earth' 55 Cancri e. Using observations of the planet's mass and radius to create models of its interior that assumed the same carbon-to-oxygen ratio of the star, the 2012 paper suggested the planet contains more carbon than oxygen."
"However, our analysis makes this seem less likely because the host star doesn't appear as carbon-rich as previously thought," Teske said.
Observations obtained in 2010, together with simulations astronomers use to model a planet's interior based on data like radius, mass and orbital velocity, had yielded a carbon to oxygen ratio greater than one, in other words, an alien world based on carbon instead of oxygen as most planets are in our solar system, including Earth.
"The sun only has about half as much carbon as oxygen, so a star or a planet with a higher ratio between the two elements, particularly a planet with more carbon than oxygen, is interesting and different from what we have in our solar system," explained Teske, who is graduating this spring with a doctorate from the UA's Department of Astronomy and Steward Observatory.
Based on the previous results, it was suggested that the "diamond planet" is a rocky world with a surface of graphite surrounding a thick layer of diamond instead of water and granite like Earth.
The new research by Teske and collaborators, to be published in the Astrophysical Journal and available online, calls this conclusion in question, making it less likely a hypothetical space probe sent to sample the planet's innards would dig up anything sparkling.
Teske's group found that the planet's host star contains almost 25 percent more oxygen than carbon, about mid way between the Sun and what the previous study suggested.
"In theory, 55 Cancri e could still have a high carbon to oxygen ratio and be a diamond planet, but the host star does not have such a high ratio," Teske said. "So in terms of the two building blocks of information used for the initial 'diamond-planet' proposal -- the measurements of the exoplanet and the measurements of the star -- the measurements of the star no longer verify that."
A so-called super-Earth boasting about twice Earth's diameter and eight times Earth's mass, the "diamond planet," whose official designation is 55 Cancri e, is the smallest member of a five-planet system located in the constellation Cancer. 55 Cancri e races around its host star at such close distance that one year lasts only 18 hours and its surface temperature is more than 3,000 degrees Fahrenheit.
"With rocky worlds like 55 Cancri e, researchers use measurements of a planet's radius, mass and density and basic physical equations governing the internal structure of solid planets to calculate possible compositions of the planet's interior," Teske said.
"This planet is probably rocky or has a large rocky component," she said. "We don't really know if it has an atmosphere."
Since astronomers can't probe the makeups of stars and planets directly, they rely on indirect observational methods such as absorption spectra; each chemical element absorbs light at different wavelengths, in a characteristic pattern that can be used as a fingerprint of that element. By analyzing the absorption spectra of starlight passing through a star's atmosphere, it is possible to deduce what elements are present in the star's atmosphere.
"Instead of using the same absorption lines in the spectrum of the host star as the previous study of 55 Cancri, we looked at more lines of carbon and more lines of oxygen," Teske said. "We find that because this particular host star is cooler than our sun and more metal-rich, the single oxygen line analyzed in the previous study to determine the star's oxygen abundance is more prone to error."
Teske instead relied on several different indicators of the oxygen abundance that were not considered previously. "Averaging all of these measurements together gives us a more complete picture of the oxygen abundance in the star."
Teske pointed out that the 'diamond planet' results hinge on the presumption that a star's composition bears some relation to the composition of its planets, a notion grounded in the idea that planets form from the same material as their host stars. However, as astronomers discover more and more extrasolar systems, a one-size-fits-all formula becomes less likely.
"We still don't know whether our solar system is common or uncommon in the universe," Teske said, "because many of the systems that we are finding have giant gas planets closer to the star, unlike our system where rocky planets dominate the inner orbits and gas giants occur further out."
Given there are so many processes -- most of which are not fully understood -- happening in a planet-forming disk that could influence the composition of planets, Teske said: "At this point, I would honestly be surprised if there was a one-to-one correlation."
"The compositions of planets and stars don't always match," she said, explaining that in a swirling disk of dust and gas giving birth to a star and planets, "you can have pockets where there is a lot of water, meaning an enhancement of oxygen. Or places where water has frozen out, leaving behind carbon species as the dominant gas molecules. So the planets that are accreting gas at those locations in the disk could be more carbon-rich instead of oxygen-rich."
Therefore, room for uncertainty remains, according to the researchers.
"Depending on where 55 Cancri e formed in the protoplanetary disk, its carbon-to-oxygen ratio could differ from that of the host star," Teske said. "It could be higher or lower. But based on what we know at this point, 55 Cancri e is more of a 'diamond in the rough.'"
The study was co-authored by Katia Cunha of Steward Observatory and Observatorio Nacional in Rio de Janeiro, Brazil; Simon Schuler of the University of Tampa, Fla.; Caitlin Griffith of the UA Lunar and Planetary Laboratory; and Verne Smith of the National Optical Astronomy Observatory in Tucson. Teske and Griffith were supported by NASA's Planetary Atmospheres Program.

 

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First Ever Evidence of a Comet Striking Earth

Oct. 8, 2013 — The first ever evidence of a comet entering Earth's atmosphere and exploding, raining down a shock wave of fire which obliterated every life form in its path, has been discovered by a team of South African scientists and international collaborators.

 

An artist's rendition of the comet exploding in Earth's atmosphere above Egypt. (Credit: Terry Bakker)

The discovery has not only provided the first definitive proof of a comet striking Earth, millions of years ago, but it could also help us to unlock, in the future, the secrets of the formation of our solar system.
"Comets always visit our skies -- they're these dirty snowballs of ice mixed with dust -- but never before in history has material from a comet ever been found on Earth," says Professor David Block of Wits University.
The comet entered Earth's atmosphere above Egypt about 28 million years ago. As it entered the atmosphere, it exploded, heating up the sand beneath it to a temperature of about 2,000 degrees Celsius, and resulting in the formation of a huge amount of yellow silica glass which lies scattered over a 6,000 square kilometre area in the Sahara. A magnificent specimen of the glass, polished by ancient jewellers, is found in Tutankhamun's brooch with its striking yellow-brown scarab.
The research, which will be published in Earth and Planetary Science Letters, was conducted by a collaboration of geoscientists, physicists and astronomers including Block, lead author Professor Jan Kramers of the University of Johannesburg, Dr Marco Andreoli of the South African Nuclear Energy Corporation, and Chris Harris of the University of Cape Town.
At the centre of the attention of this team was a mysterious black pebble found years earlier by an Egyptian geologist in the area of the silica glass. After conducting highly sophisticated chemical analyses on this pebble, the authors came to the conclusion that it represented the very first known hand specimen of a comet nucleus, rather than simply an unusual type of meteorite.
Kramers describes this as a moment of career defining elation. "It's a typical scientific euphoria when you eliminate all other options and come to the realisation of what it must be," he said.
The impact of the explosion also produced microscopic diamonds. "Diamonds are produced from carbon bearing material. Normally they form deep in the Earth, where the pressure is high, but you can also generate very high pressure with shock. Part of the comet impacted and the shock of the impact produced the diamonds," says Kramers.
The team have named the diamond-bearing pebble "Hypatia" in honour of the first well known female mathematician, astronomer and philosopher, Hypatia of Alexandria.
Comet material is very elusive. Comet fragments have not been found on Earth before except as microscopic sized dust particles in the upper atmosphere and some carbon-rich dust in the Antarctic ice. Space agencies have spent billions to secure the smallest amounts of pristine comet matter.
"NASA and ESA (European Space Agency) spend billions of dollars collecting a few micrograms of comet material and bringing it back to Earth, and now we've got a radical new approach of studying this material, without spending billions of dollars collecting it," says Kramers.
The study of Hypatia has grown into an international collaborative research programme, coordinated by Andreoli, which involves a growing number of scientists drawn from a variety of disciplines. Dr Mario di Martino of Turin's Astrophysical Observatory has led several expeditions to the desert glass area.
"Comets contain the very secrets to unlocking the formation of our solar system and this discovery gives us an unprecedented opportunity to study comet material first hand," says Block.