From LBL: “First Detailed Microscopy Evidence of Bacteria at the Lower Size Limit of Life”

February 27, 2015
Dan Krotz

This cryo-electron tomography image reveals the internal structure of an ultra-small bacteria cell like never before. The cell has a very dense interior compartment and a complex cell wall. The darker spots at each end of the cell are most likely ribosomes. The image was obtained from a 3-D reconstruction. The scale bar is 100 nanometers. (Credit: Berkeley Lab)

Scientists have captured the first detailed microscopy images of ultra-small bacteria that are believed to be about as small as life can get. The research was led by scientists from the U.S. Department of Energy’s Lawrence Berkeley National Laboratory and the University of California, Berkeley. The existence of ultra-small bacteria has been debated for two decades, but there hasn’t been a comprehensive electron microscopy and DNA-based description of the microbes until now.

The cells have an average volume of 0.009 cubic microns (one micron is one millionth of a meter). About 150 of these bacteria could fit inside an Escherichia coli cell and more than 150,000 cells could fit onto the tip of a human hair.

The scientists report their findings Friday, Feb. 27, in the journal Nature Communications.

The diverse bacteria were found in groundwater and are thought to be quite common. They’re also quite odd, which isn’t a surprise given the cells are close to and in some cases smaller than several estimates for the lower size limit of life. This is the smallest a cell can be and still accommodate enough material to sustain life. The bacterial cells have densely packed spirals that are probably DNA, a very small number of ribosomes, hair-like appendages, and a stripped-down metabolism that likely requires them to rely on other bacteria for many of life’s necessities.

The bacteria are from three microbial phyla that are poorly understood. Learning more about the organisms from these phyla could shed light on the role of microbes in the planet’s climate, our food and water supply, and other key processes.

A lifeline to other cells? Cryo-transmission electron microscopy captured numerous hairlike appendages radiating from the surface of this ultra-small bacteria cell. The scientists theorize the pili-like structures enable the cell to connect with other microbes and obtain life-giving resources. The scale bar is 100 nanometers. (Credit: Berkeley Lab)

“These newly described ultra-small bacteria are an example of a subset of the microbial life on earth that we know almost nothing about,” says Jill Banfield, a Senior Faculty Scientist in Berkeley Lab’s Earth Sciences Division and a UC Berkeley professor in the departments of Earth and Planetary Science and Environmental Science, Policy and Management.

“They’re enigmatic. These bacteria are detected in many environments and they probably play important roles in microbial communities and ecosystems. But we don’t yet fully understand what these ultra-small bacteria do,” says Banfield.

Banfield is a co-corresponding author of the Nature Communications paper with Birgit Luef, a former postdoctoral researcher in Banfield’s group who is now at the Norwegian University of Science and Technology, Trondheim.

“There isn’t a consensus over how small a free-living organism can be, and what the space optimization strategies may be for a cell at the lower size limit for life. Our research is a significant step in characterizing the size, shape, and internal structure of ultra-small cells,” says Luef.

The scientists set out to study bacteria from phyla that lack cultivated representatives. Some of these bacteria have very small genomes, so the scientists surmised the bacteria themselves might also be very small.

To concentrate these cells in a sample, they filtered groundwater collected at Rifle, Colorado through successively smaller filters, down to 0.2 microns, which is the size used to sterilize water. The resulting samples were anything but sterile. They were enriched with incredibly tiny microbes, which were flash frozen to -272 degrees Celsius in a first-of-its-kind portable version of a device called a cryo plunger. This ensured the microbes weren’t damaged in their journey from the field to the lab.

The frozen samples were transported to Berkeley Lab, where Luef, with the help of Luis Comolli of Berkeley Lab’s Life Sciences Division, characterized the cells’ size and internal structure using 2-D and 3-D cryogenic transmission electron microscopy. The images also revealed dividing cells, indicating the bacteria were healthy and not starved to an abnormally small size.

The bacteria’s genomes were sequenced at the Joint Genome Institute, a DOE Office of Science User Facility located in Walnut Creek, California, under the guidance of Susannah Tringe. The genomes were about one million base pairs in length. In addition, metagenomic and other DNA-based analyses of the samples were conducted at UC Berkeley, which found a diverse range of bacteria from WWE3, OP11, and OD1 phyla.

This combination of innovative fieldwork and state-of-the-art microscopy and genomic analysis yielded the most complete description of ultra-small bacteria to date.

Among their findings: Some of the bacteria have thread-like appendages, called pili, which could serve as “life support” connections to other microbes. The genomic data indicates the bacteria lack many basic functions, so they likely rely on a community of microbes for critical resources.

The scientists also discovered just how much there is yet to learn about ultra-small life.

“We don’t know the function of half the genes we found in the organisms from these three phyla,” says Banfield.

The scientists also used the Advanced Light Source, a DOE Office of Science User Facility located at Berkeley Lab, where Hoi-Ying Holman of the Earth Sciences Division helped determine the majority of the cells in the samples were bacteria, not Archaea.

LBL/ALS

The research is a significant contribution to what’s known about ultra-small organisms. Recently, scientists estimated the cell volume of a marine bacterium at 0.013 cubic microns, but they used a technique that didn’t directly measure the cell diameter. There are also prior electron microscopy images of a lineage of Archaea with cell volumes as small as 0.009 cubic microns, similar to these bacteria, including results from some of the same researchers. Together, the findings highlight the existence of small cells with unusual and fairly restricted metabolic capacities from two of the three major branches of the tree of life.

The research was supported by the Department of Energy’s Office of Science.

See the full article here.

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From BNL: “Unusual Electronic State Found in New Class of Unconventional Superconductors”

Brookhaven Lab

December 8, 2014
Karen McNulty Walsh, (631) 344-8350 or Peter Genzer, (631) 344-3174

Finding gives scientists a new group of materials to explore to unlock secrets of some materials’ ability to carry current with no energy loss

A team of scientists from the U.S. Department of Energy’s (DOE) Brookhaven National Laboratory, Columbia Engineering, Columbia Physics and Kyoto University has discovered an unusual form of electronic order in a new family of unconventional superconductors. The finding, described in the journal Nature Communications, establishes an unexpected connection between this new group of titanium-oxypnictide superconductors and the more familiar cuprates and iron-pnictides, providing scientists with a whole new family of materials from which they can gain deeper insights into the mysteries of high-temperature superconductivity.

Team members conducting research at Brookhaven Lab, led by Simon Billinge of Brookhaven and Columbia Engineering (seated), included (l to r) Columbia U graduate student Ben Frandsen and Weiguo Yin, Yimei Zhu, and Emil Bozin of Brookhaven’s Condensed Matter Physics and Materials Science Department. They used the aberation-corrected electron microscope in Zhu’s lab to conduct electron diffraction experiments that were a key component of this study. Collaborators not shown: Hefei Hu, formerly of Brookhaven Lab and now at Intel, Yasumasa Nozaki and Hiroshi Kageyama of Kyoto University, and Yasutomo Uemura of Columbia.

“Finding this new material is a bit like an archeologist finding a new Egyptian pharaoh’s tomb,” said Simon Billinge, a physicist at Brookhaven Lab and Columbia University’s School of Engineering and Applied Science, who led the research team. “As we try and solve the mysteries behind unconventional superconductivity, we need to discover different but related systems to give us a more complete picture of what is going on—just as a new tomb will turn up treasures not found before, giving a more complete picture of ancient Egyptian society.”

Harnessing the power of superconductivity, or the ability of certain materials to conduct electricity with zero energy loss, is one of the most exciting possibilities for creating a more energy-efficient future. But because most superconductors only work at very low temperatures—just a few degrees above absolute zero, or -273 degrees Celsius—they are not yet useful for everyday life. The discovery in the 1980s of “high-temperature” superconductors that work at warmer temperatures (though still not room temperature) was a giant step forward, offering scientists the hope that a complete understanding of what enables these materials to carry loss-free current would help them design new materials for everyday applications. Each new discovery of a common theme among these materials is helping scientists unlock pieces of the puzzle.

One of the greatest mysteries is seeking to understand how the electrons in high-temperature superconductors interact, sometimes trying to avoid each other and at other times pairing up—the crucial characteristic enabling them to carry current with no resistance. Scientists studying these materials at Brookhaven and elsewhere have discovered special types of electronic states, such as “charge density waves,” where charges huddle to form stripes, and checkerboard patterns of charge. Both of these break the “translational symmetry” of the material—the repetition of sameness as you move across the surface (e.g., moving across a checkerboard you move from white squares to black squares).

Another pattern scientists have observed in the two most famous classes of high-temperature superconductors is broken rotational symmetry without a change in translational symmetry. In this case, called nematic order, every space on the checkerboard is white, but the shapes of the spaces are distorted from a square to a rectangle; as you turn round and round on one space, your neighboring space is nearer or farther depending on the direction you are facing. Having observed this unexpected state in the cuprates and iron-pnictides, scientists were eager to see whether this unusual electronic order would also be observed in a new class of titanium-oxypnictide high-temperature superconductors discovered in 2013.

“These titanium-oxypnictide compounds are structurally similar to the other exotic superconductor systems, and they had all the telltale signs of a broken symmetry, such as anomalies in resistivity and thermodynamic measurements. But there was no sign of any kind of charge density wave in any previous measurement. It was a mystery,” said Emil Bozin, whose group at Brookhaven specializes in searching for hidden local broken symmetries. “It was a natural for us to jump on this problem.”

Top: Ripples extending down the chain of atoms breaks translational symmetry (like a checkerboard with black and white squares), which would cause extra spots in the diffraction pattern (shown as red dots in the underlying diffraction pattern). Bottom: Stretching along one direction breaks rotational symmetry but not translational symmetry (like a checkerboard with identical squares but stretched in one of the directions), causing no additional diffraction spots. The experiments proved these new superconductors have the second type of electron density distribution, called a nematic. Image credit: Ben Frandsen

The team searched for the broken rotational symmetry effect, a research question that had been raised by Tomo Uemura of Columbia, using samples provided by his collaborators in the group of Hiroshi Kageyama at Kyoto University. They conducted two kinds of diffraction studies: neutron scattering experiments at the Los Alamos Neutron Science Center (LANSCE) at DOE’s Los Alamos National Laboratory, and electron diffraction experiments using a transmission electron microscope at Brookhaven Lab.

“We used these techniques to observe the pattern formed by beams of particles shot through powder samples of the superconductors under a range of temperatures and other conditions to see if there’s a structural change that corresponds to the formation of this special type of nematic state,” said Ben Frandsen, a graduate student in physics at Columbia and first author on the paper.

The experiments revealed a telltale symmetry breaking distortion at low temperature. A collaborative effort among experimentalists and theorists established the particular nematic nature of the order.

“Critical in this study was the fact that we could rapidly bring to bear multiple complementary experimental methods, together with crucial theoretical insights—something made easy by having most of the expertise in residence at Brookhaven Lab and wonderfully strong collaborations with colleagues at Columbia and beyond,” Billinge said.

The discovery of nematicity in titanium-oxypnictides, together with the fact that their structural and chemical properties bridge those of the cuprate and iron-pnictide high-temperature superconductors, render these materials an important new system to help understand the role of electronic symmetry breaking in superconductivity.

As Billinge noted, “This new pharaoh’s tomb indeed contained a treasure: nematicity.”

This work was supported by the DOE Office of Science, the U.S. National Science Foundation (NSF, OISE-0968226), the Japan Society of the Promotion of Science, the Japan Atomic Energy Agency, and the Friends of Todai Inc.

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One of ten national laboratories overseen and primarily funded by the Office of Science of the U.S. Department of Energy (DOE), Brookhaven National Laboratory conducts research in the physical, biomedical, and environmental sciences, as well as in energy technologies and national security. Brookhaven Lab also builds and operates major scientific facilities available to university, industry and government researchers. The Laboratory’s almost 3,000 scientists, engineers, and support staff are joined each year by more than 5,000 visiting researchers from around the world.Brookhaven is operated and managed for DOE’s Office of Science by Brookhaven Science Associates, a limited-liability company founded by Stony Brook University, the largest academic user of Laboratory facilities, and Battelle, a nonprofit, applied science and technology organization.

From BNL: “Organic Crystal Film Grown on New Substrate Breaks Performance Record”

Brookhaven Lab

November 18, 2014
Laura Mgrdichian

The study is an important step toward realizing mainstream organic electronic devices

Many future electronic devices may be based not on standard conductors and semiconductors but rather on small organic (carbon-based) molecules and polymers. These organic electronics will have several advantages over conventional electronics, including being cheaper to fabricate, physically bendable and flexible, and, in some cases, can be created using printing methods – perhaps even in your own home.

The field of organic electronics is still in its infancy, however, and scientists have much to learn before organic electronic devices are part of our everyday lives. One obstacle researchers have faced is how to successfully grow high-quality crystals of an organic molecule on top of a conventional substrate – without using a complex growth process or chemically modifying the substrate first. Solving this problem is the necessary first step to creating organic electronic circuits and devices.

Organic two-dimensional heterostructure of rubrene/h-BN

Recently, a research group made some significant headway. Working in part at the National Synchrotron Light Source (NSLS), scientists from Columbia University, Harvard University, Brookhaven Lab, and Japan’s National Institute for Materials Science grew a high-quality, high-performing film of rubrene, an organic semiconductor, onto a substrate of hexagonal boron nitride, a layered crystalline material with hexagonally shaped molecular units (similar to graphite carbon). Their work, which they discuss in the May 14, 2014, edition of the journal Advanced Materials, is notable both due to the high-quality crystalline nature of the film and because the substrate is a new player in the field of organic electronics development.

“The interface between the substrate and the molecular film is very important. It governs the initial nucleation during the growth of the film and also has a big impact on how the film will carry charge,” says Columbia researcher Phillip Kim, one of the paper’s authors. “Our film/substrate heterostructure yielded the highest mobility observed yet in similar systems. It is comparable to those of free-standing single crystals and represents a record for organic films grown on any substrates.”

When paired with organic materials, conventional substrates like silicon oxide, glass, and plastic are too disordered at the molecular level and also don’t have molecular structures that are similar enough to the organic compounds. In materials science terms, they lack an “epitaxial” relationship. This discourages proper film growth and results in lower-quality films that lack long-range order. In everyday terms, this is kind of like trying to build a layer of Lego bricks on Lego board that doesn’t have an ordered grid of nubs.

Kim and his colleagues showed that hexagonal boron nitride (h-BN) has many advantages as a substrate for organic electronics. Using an approach called “van der Waals epitaxy,” a method that takes advantage of the weak van der Waals force between molecules, the group grew rubrene films varying from 5 to 1000 nanometers thick. They studied each sample’s structure and charge-carrying ability using several methods.

Atomic force microscopy (AFM) and transmission electron microscopy (TEM) images suggested that the film was formed of large single-crystal domains. Selected area electron diffraction (SAED), which can be performed inside a transmission electron microscope, also confirmed this. But because SAED provides only local structural information, the group used grazing x-ray diffraction at NSLS beamline X9 to get a broader “view” of the structure. The x-ray data showed sharp, intense peaks, indicating that the sample contained a high-quality crystal structure.

To study how the film carries charge, graphene electrical contacts were incorporated into the growth process, resulting in a field-effect transistor structure. Measuring the current across it showed that electrons traveling within it are highly mobile, meaning they don’t run into too many barriers caused by a “choppy” molecular structure.

“Our study highlights the advantages of h-BN and similar materials over commonly used substrates to achieve high-performance organic electronic devices,” said Kim. “More generally, this approach to film growth – van der Waals epitaxy – could be used to fabricate organic/inorganic structures that can be readily expanded to numerous other organic and layered materials for various electronic applications.”

This research was supported by: the Center for Redefining Photovoltaic Efficiency Through Molecule Scale Control, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences; the FAME Center, one of six centers of STARnet, a Semiconductor Research Corporation program sponsored by MARCO and DARPA; the Nano Material Technology Development Program through the National Research Foundation of Korea funded by the Ministry of Science, ICT and Future Planning; the Basic Science Research Program through the National Research Foundation of Korea; the U.S. Department of Energy, Office of Basic Energy Sciences, under the Extreme Science and Engineering Discovery Environment, supported by the National Science Foundation.

See the full article here.

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From BNL:”Growth of an Ultra-thin Layered Structure Offers Surprises”

Brookhaven Lab

September 22, 2014
Laura Mgrdichian

Many new technologies are based on ultra-thin layered structures that are “grown” using precise deposition techniques. Understanding and ultimately controlling this growth at the atomic level – particularly at the interfaces between these layers, where key properties arise – is essential to imparting these structures with properties tailored to possible applications.

Researchers from the University of Vermont recently investigated an example of “heteroepitaxial” growth, in which one material is grown on the surface of a second material that has a similar crystal structure as the first. They studied a system of bismuth ferrite (BiFeO3, or BFO) grown on strontium titanate (SrTiO3, or STO). The research is published in the February 20, 2014, edition of Physical Review Letters.

two
Simulated “maps” for growing bismuth ferrite on strontium titanate

BFO is a target for materials science researchers because of its diverse ferroelectric properties and possible applications in developing technologies such as nonvolatile memory and data storage. At the National Synchrotron Light Source, the researchers discovered that the BFO forms clusters that grow and coalesce into a single layer in an unexpected way. They found that their data agree well with the “interrupted coalescence model” (ICM) of layer growth. This finding was a bit of a surprise, but they propose that the model may be applicable to other layered systems.

NSLS

“In this system, we saw compact, two-dimensional islands come together efficiently over a range of length scales,” said the study’s corresponding scientist, University of Vermont physicist Randall Headrick. “However, the kinetics of the growth process behave more like droplets than what we expected to observe, which was single-layer clusters that grow exponentially in time. This growth mode has implications for the structure of interfaces and ferroelectric domains in these materials, which will have an impact on domain switching in devices.”

Headrick and his colleagues used a technique called sputter deposition to apply the BFO atoms to the STO surface and “watched” the growth of the BFO layer using x-ray diffraction at NSLS beamline X21. They saw the BFO quickly form islands of varying sizes, with an average size of about 20 nanometers. The small clusters retained their compact shape as they coalesced into bigger clusters. But, this coalescence was kinetically “frozen” when the clusters reached a critical size, leading to the formation of large connected irregularly shaped regions. In the spaces between, smaller islands continued to form and dot the area.

The group confirmed these observations by studying the final layered structure with atomic force microscopy and additional x-ray diffraction measurements.

afm
Atomic Force Microscope at Rutgers University

This work was supported by the Office of Basic Energy Sciences within the U.S. Department of Energy’s Office of Science.

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From Stanford: “Stanford engineers help describe key mechanism in energy and information storage”

Stanford University

September 11, 2014
Bjorn Carey

By observing how hydrogen is absorbed into individual palladium nanocubes, Stanford materials scientists have detailed a key step in storing energy and information in nanomaterials. The work could inform research that leads to longer-lasting batteries or higher-capacity memory devices.

block
The palladium nanocubes viewed through a transmission electron microscope. Each black dot is a palladium atom.

The ideal energy or information storage system is one that can charge and discharge quickly, has a high capacity and can last forever. Nanomaterials are promising to achieve these criteria, but scientists are just beginning to understand their challenging mechanisms.

Now, a team of Stanford materials scientists and engineers has provided new insight into the storage mechanism of nanomaterials that could facilitate development of improved batteries and memory devices.

The team, led by Jennifer Dionne, assistant professor of materials science and engineering at Stanford, and consisting of Andrea Baldi, Tarun Narayan and Ai Leen Koh, studied how metallic nanoparticles composed of palladium absorbed and released hydrogen atoms.

Previously, scientists have studied hydrogen absorption in ensembles of metallic nanoparticles, but this approach makes it difficult to infer information about how the individual nanoparticles behave. The new study reveals that behavior by measuring the hydrogen content in individual palladium nanoparticles exposed to increasing pressures of hydrogen gas.

The group’s experimental findings are consistent with a mechanism recently proposed for energy storage in lithium ion batteries, underscoring the interest for the broader scientific community. The work is detailed online in the journal Nature Materials.

The finding was made possible by the use of a specialized transmission electron microscope (TEM) that allowed the team to detect, with near atomic-scale resolution, the process by which hydrogen entered the nanomaterial.

“Electron microscopy must ordinarily be conducted in high vacuum,” said co-author Ai Leen Koh, a research scientist with the Stanford Nano Shared Facilities. “But the unique capabilities of Stanford’s environmental TEM obviates this requirement, enabling the study of individual nanoparticles both in vacuum and while immersed in a reactive gas.”
Stretching metal

The researchers synthesized palladium nanocubes and then dispersed them onto a very thin membrane. After placing the membrane in the TEM, the engineers flowed hydrogen gas past the palladium nanoparticles and gradually increased its pressure.

At sufficiently high pressures of hydrogen, the gas molecules dissociate on the surface of the nanocubes and individual hydrogen atoms enter into the spaces between the palladium crystals. Interestingly, the absorption and desorption processes appear to be quite sudden.

“You can think of it like popcorn,” said co-lead author Tarun Narayan, a graduate student in Dionne’s group. “It’s a very binary process, and a pretty sharp transition. Either the hydrogen is in the palladium or it’s not, and it enters and leaves at predictable pressures. And that’s quite important for a good energy storage system.”

As the hydrogen enters the palladium nanostructure, the material’s volume increases by about 10 percent. This expansion significantly alters the way in which the particle interacts with the electron beam; this disruption indicates the amount of hydrogen absorbed. Because the nanocubes are single-crystalline and effectively “unbound” from the membrane, the researchers were able to study and measure the storage mechanism in unprecedented detail.

“You have to stretch the palladium to put the hydrogen inside, but you have to pay energy to make it stretch,” said Andrea Baldi, a postdoctoral researcher in Dionne’s group. “Knowing that cost is very important for any battery designs, and because our nanostructures are not glued to a substrate, we’re able to quantify that stretch more accurately than ever before.”
Next up: Palladium spheres

Despite the stress of repeated expansion and contraction, the nanocrystals of palladium were not damaged by hydrogen absorption and desorption, as usually happens in larger specimens.

“At the nanoscale, materials behave quite differently than they do in bulk,” said Dionne, the senior author. “Their increased surface area to volume ratio can significantly impact their mechanical flexibility and, consequently, their ability to charge and discharge ions or atoms.”

In particular, this research indicates that nanoparticles can load more easily and at much lower pressures than bulk materials. Further, because they have a higher resistance to elastic stress, the formation of defects in these materials is suppressed.

“Our results suggest that particles in this size regime don’t develop defects even if charged and discharged with hydrogen multiple times,” Narayan said. “Other researchers are starting to see this in lithium ion battery research as well, and we think a lot of what we’ve learned can be applied to that research.”

Because of its fast storage speeds, stability and ease-of-loading, the hydrogenation of palladium is an excellent model system to study general energy and information storage mechanisms. Palladium, however, is not a likely material for widespread energy storage – it is too heavy and expensive. Yet, the researchers believe the results could be replicated with other systems involving storing hydrogen in metals.

The next steps involve applying the newly developed single-particle method to a wide range of nanostructures – spheres and rods, for example – to study how storage can be affected by the shape, size and crystallinity of a nanoparticle. Furthermore, they plan to use the electron microscope to determine exactly where atoms or ions are preferentially absorbed within a singe nanoparticle.

Dionne is an affiliate of the Stanford Institute for Materials and Energy Sciences (SIMES) and SLAC National Accelerator Laboratory. The research was supported by funding from the National Science Foundation, the Air Force Office of Scientific Research, the U.S. Department of Energy, a Young Energy Scientist Fellowship and a Hellman Fellowship.

See the full article here.

Leland and Jane Stanford founded the University to “promote the public welfare by exercising an influence on behalf of humanity and civilization.” Stanford opened its doors in 1891, and more than a century later, it remains dedicated to finding solutions to the great challenges of the day and to preparing our students for leadership in today’s complex world. Stanford, is an American private research university located in Stanford, California on an 8,180-acre (3,310 ha) campus near Palo Alto. Since 1952, more than 54 Stanford faculty, staff, and alumni have won the Nobel Prize, including 19 current faculty members

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From LBL: “Advanced Light Source Sets Microscopy Record”

Berkeley Lab

September 10, 2014
Lynn Yarris (510) 486-5375

A record-setting X-ray microscopy experiment may have ushered in a new era for nanoscale imaging. Working at the U.S. Department of Energy (DOE)’s Lawrence Berkeley National Laboratory (Berkeley Lab), a collaboration of researchers used low energy or “soft” X-rays to image structures only five nanometers in size. This resolution, obtained at Berkeley Lab’s Advanced Light Source (ALS), a DOE Office of Science User Facility, is the highest ever achieved with X-ray microscopy.

LBL ALS

Ptychographic image using soft X-rays of lithium iron phosphate nanocrystal after partial dilithiation. The delithiated region is shown in red.

Using ptychography, a coherent diffractive imaging technique based on high-performance scanning transmission X-ray microscopy (STXM), the collaboration was able to map the chemical composition of lithium iron phosphate nanocrystals after partial dilithiation. The results yielded important new insights into a material of high interest for electrochemical energy storage.

“We have developed diffractive imaging methods capable of achieving a spatial resolution that cannot be matched by conventional imaging schemes,” says David Shapiro, a physicist with the ALS. “We are now entering a stage in which our X-ray microscopes are no longer limited by our optics and we can image at nearly the wavelength of our X-ray light.”

Shapiro is the lead and corresponding author of a paper reporting this research in Nature Photonics. The paper is titled “Chemical composition mapping with nanometer resolution by soft X-ray microscopy.” (See below for a full list of co-authors and their affiliations.)

David Shapiro with the STXM instruments at ALS beamline 5.3.2.1. (Photo by Roy Kaltschmidt)

In ptychography (pronounced tie-cog-raphee), a combination of multiple coherent diffraction measurements is used to obtain 2D or 3D maps of micron-sized objects with high resolution and sensitivity. Because of the sensitivity of soft x-rays to electronic states, ptychography can be used to image chemical phase transformations and the mechanical consequences of those transformations that a material undergoes.

“Until this work, however, the spatial resolution of ptychographic microscopes did not surpass that of the best conventional systems using X-ray zone plate lenses,” says Howard Padmore, leader of the Experimental Systems Group at the ALS and a co-author of the Nature Photonics paper. “The problem stemmed from the fact that ptychography was primarily developed on hard X-ray sources using simple pinhole optics for illumination. This resulted in a low scattering cross-section and low coherent intensity at the sample, which meant that exposure times had to be extremely long, and that mechanical and illumination stabilities were not good enough for high resolution.”

Key to the success of Shapiro, and his collaborators were the use of soft X-rays which have wavelengths ranging between 1 to 10 nanometers, and a special algorithm that eliminated the effect of all incoherent background signals. Ptychography measurements were recorded with the STXM instruments at ALS beamline 11.0.2, which uses an undulator x-ray source, and ALS beamline 5.3.2.1, which uses a bending magnet source. A coherent soft X-ray beam would be focused onto a sample and scanned in 40 nanometer increments. Diffraction data would then be recorded on an X-ray CCD (charge-coupled device) that allowed reconstruction of the sample to very high spatial resolution.

“Throughout the ptychography scans, we maintained the sample and focusing optic in relative alignment using an interferometric feedback system with a precision comparable to the wavelength of the X-ray illumination,” Shapiro says.

Lithium iron phosphate is widely studied for its use as a cathode material in rechargeable lithium-ion batteries. In using their ptychography technique to map the chemical composition of lithium iron phosphate crystals, Shapiro and his collaborators found a strong correlation between structural defects and chemical phase propagation.

“Surface cracking in these crystals was expected,” Shapiro says, “but there is no other means of visualizing the correlation of those cracks with chemical composition at these scales. The ability to visualize the coupling of the kinetics of a phase transformation with the mechanical consequences is critical to designing materials with ultimate durability.”

Shapiro and his colleagues have already begun applying their ptychography technique to the study of catalytic and magnetic films, magnetotactic bacteria, polymer blends and green cements.
In this soft X-ray ptychography set-up, a 60 nm width outer-zone-plate focuses a coherent soft X-ray beam onto the sample, which is scanned in 40 nm increments to ensure overlap of the probed areas.

In this soft X-ray ptychography set-up, a 60 nm width outer-zone-plate focuses a coherent soft X-ray beam onto the sample, which is scanned in 40 nm increments to ensure overlap of the probed areas.

For the chemical mapping of lithium iron phosphate they used the STXM instrument at ALS beamline 5.3.2.1 which required up to 800 milliseconds of exposure to the X-ray beam for each scan. Next year, they anticipate using a new ALS beamline called COSMIC (COherent Scattering and MICroscopy), which will feature a high brightness undulator x-ray source coupled to new high-frame-rate CCD sensors that will cut beam exposure times to only a few milliseconds and provide spatial resolution at the wavelength of the radiation.

In this soft X-ray ptychography set-up, a 60 nm width outer-zone-plate focuses a coherent soft X-ray beam onto the sample, which is scanned in 40 nm increments to ensure overlap of the probed areas. – See more at: http://newscenter.lbl.gov/2014/09/10/advanced-light-source-sets-microscopy-record/#sthash.6DLMbCxp.dpuf

“If visible light microscopes could only achieve a resolution that was 50 times the wavelength of visible light, we would not be able to see most single celled organisms,” Shapiro says. “Where would the life sciences be with such a limitation? We are now approaching the point where we will have X-ray microscopes of comparable quality to today’s visible light instruments for the study of nanomaterials.”

Co-authoring the Nature Photonics paper in addition to Shapiro and Padmore were Young-Sang Yu, Tolek Tyliszczak, Jordi Cabana, Rich Celestre, Weilun Chao, David Kilcoyne, Stefano Marchesini, Tony Warwick and Lee Yang of Berkeley Lab; Konstantin Kaznatcheev of Brookhaven National Laboratory; Shirley Meng of the University of San Diego; and Filipe Maia of Uppsala University in Sweden.

This research was primarily supported by the DOE Office of Science.

See the full article here.

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From SLAC: “Buckyballs and Diamondoids Join Forces in Tiny Electronic Gadget”

SLAC Lab

September 9, 2014
Press Office Contact: Andrew Gordon, agordon@slac.stanford.edu, (650) 926-2282

Scientists Craft Two Exotic Forms of Carbon into a Molecule for Steering Electron Flow

Scientists have married two unconventional forms of carbon – one shaped like a soccer ball, the other a tiny diamond – to make a molecule that conducts electricity in only one direction. This tiny electronic component, known as a rectifier, could play a key role in shrinking chip components down to the size of molecules to enable faster, more powerful devices.

An international team led by researchers at SLAC National Accelerator Laboratory and Stanford University joined two offbeat carbon molecules – diamondoids, the square cages at left, and buckyballs, the soccer-ball shapes at right – to create “buckydiamondoids,” center. These hybrid molecules function as rectifiers, conducting electrons in only one direction, and could help pave the way to molecular electronic devices. (Manoharan Lab/Stanford University)

“We wanted to see what new, emergent properties might come out when you put these two ingredients together to create a ‘buckydiamondoid,’” said Hari Manoharan of the Stanford Institute for Materials and Energy Sciences (SIMES) at the Department of Energy’s SLAC National Accelerator Laboratory. “What we got was a basically a one-way valve for conducting electricity – clearly more than the sum of its parts.”

The research team, which included scientists from Stanford University, Belgium, Germany and Ukraine, reported its results September 9, 2014, in Nature Communications.

Two Offbeat Carbon Characters Meet Up

Many electronic circuits have three basic components: a material that conducts electrons; rectifiers, which commonly take the form of diodes, to steer that flow in a single direction; and transistors to switch the flow on and off. Scientists combined two offbeat ingredients – buckyballs and diamondoids – to create the new diode-like component.

Buckyballs – short for buckminsterfullerenes – are hollow carbon spheres whose 1985 discovery earned three scientists a Nobel Prize in chemistry. Diamondoids are tiny carbon cages bonded together as they are in diamonds, but weighing less than a billionth of a billionth of a carat. Both are subjects of a lot of research aimed at understanding their properties and finding ways to use them.

In 2007, a team led by researchers from SLAC and Stanford discovered that a single layer of diamondoids on a metal surface can efficiently emit a beam of electrons. Manoharan and his colleagues wondered: What would happen if they paired an electron-emitting diamondoid with another molecule that likes to grab electrons? Buckyballs are just that sort of electron-grabbing molecule.

A Very Small Valve for Channeling Electron Flow

For this study, diamondoids were produced in the SLAC laboratory of SIMES researchers Jeremy Dahl and Robert Carlson, who are world experts in extracting the tiny diamonds from petroleum. They were then shipped to Germany, where chemists at Justus-Liebig University figured out how to attach them to buckyballs.

The resulting buckydiamondoids, which are just a few nanometers long, were tested in SIMES laboratories at Stanford. A team led by graduate student Jason Randel and postdoctoral researcher Francis Niestemski used a scanning tunneling microscope to make images of the hybrid molecules and measure their electronic behavior. They discovered the hybrid is an excellent rectifier: The electrical current flowing through the molecule was up to 50 times stronger in one direction, from electron-spitting diamondoid to electron-catching buckyball, than in the opposite direction. This is something neither component can do on its own.

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An image made with a scanning tunneling microscope shows hybrid buckydiamondoid molecules on a gold surface. The buckyball end of each molecule is attached to the surface, with the diamondoid end sticking up; both are clearly visible. The area shown here is 5 nanometers on a side. (H. Manoharan et al, Nature Communications)

Illustration of a buckydiamondoid molecule under a scanning tunneling microscope (STM). The sharp metallic tip of the STM ends in a single atom; as it scans over a sample, electrons tunnel from the tip into the sample. In this study the STM made images of the buckydiamondoids and probed their electronic properties. (SLAC National Accelerator Laboratory)

While this is not the first molecular rectifier ever invented, it’s the first one made from just carbon and hydrogen, a simplicity researchers find appealing, said Manoharan, who is an associate professor of physics at Stanford. The next step, he said, is to see if transistors can be constructed from the same basic ingredients.

“Buckyballs are easy to make – they can be isolated from soot – and the type of diamondoid we used here, which consists of two tiny cages, can be purchased commercially,” he said. “And now that our colleagues in Germany have figured out how to bind them together, others can follow the recipe. So while our research was aimed at gaining fundamental insights about a novel hybrid molecule, it could lead to advances that help make molecular electronics a reality.”

Other research collaborators came from the Catholic University of Louvain in Belgium and Kiev Polytechnic Institute in Ukraine. The primary funding for the work came from the U.S. Department of Energy Office of Science.

See the full article here.

SLAC is a multi-program laboratory exploring frontier questions in photon science, astrophysics, particle physics and accelerator research. Located in Menlo Park, California, SLAC is operated by Stanford University for the DOE’s Office of Science.

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From PNNL: “Birth of a mineral”

PNNL Lab

September 04, 2014
Mary Beckman, PNNL, (509) 375-3688

One of the most important molecules on earth, calcium carbonate crystallizes into chalk, shells and minerals the world over. In a study led by the Department of Energy’s Pacific Northwest National Laboratory, researchers used a powerful microscope that allows them to see the birth of crystals in real time, giving them a peek at how different calcium carbonate crystals form, they report September 5 in Science.

The results might help scientists understand how to lock carbon dioxide out of the atmosphere as well as how to better reconstruct ancient climates.

“Carbonates are most important for what they represent, interactions between biology and Earth,” said lead researcher James De Yoreo, a materials scientist at PNNL. “For a decade, we’ve been studying the formation pathways of carbonates using high-powered microscopes, but we hadn’t had the tools to watch the crystals form in real time. Now we know the pathways are far more complicated than envisioned in the models established in the twentieth century.”

Earth’s Reserve

Calcium carbonate is the largest reservoir of carbon on the planet. It is found in rocks the world over, shells of both land- and water-dwelling creatures, and pearls, coral, marble and limestone. When carbon resides within calcium carbonate, it is not hanging out in the atmosphere as carbon dioxide, warming the world. Understanding how calcium carbonate turns into various minerals could help scientists control its formation to keep carbon dioxide from getting into the atmosphere.

Calcium carbonate deposits also contain a record of Earth’s history. Researchers reconstructing ancient climates delve into the mineral for a record of temperature and atmospheric composition, environmental conditions and the state of the ocean at the time those minerals formed. A better understanding of its formation pathways will likely provide insights into those events.

To get a handle on mineral formation, researchers at PNNL, the University of California, Berkeley, and Lawrence Berkeley National Laboratory [LBNL] examined the earliest step to becoming a mineral, called nucleation. In nucleation, molecules assemble into a tiny crystal that then grows with great speed. Nucleation has been difficult to study because it happens suddenly and unpredictably, so the scientists needed a microscope that could watch the process in real time.

Come to Order

In the 20th century, researchers established a theory that crystals formed in an orderly fashion. Once the ordered nucleus formed, more molecules added to the crystal, growing the mineral but not changing its structure. Recently, however, scientists have wondered if the process might be more complicated, with other things contributing to mineral formation. For example, in previous experiments they’ve seen forms of calcium carbonate that appear to be dense liquids that could be sources for minerals.

Researchers have also wondered if calcite forms from less stable varieties or directly from calcium and carbonate dissolved in the liquid. Aragonite and vaterite are calcium carbonate minerals with slightly different crystal architectures than calcite and could represent a step in calcite’s formation. The fourth form called amorphous calcium carbonate — or ACC, which could be liquid or solid, might also be a reservoir for sprouting minerals.

To find out, the team created a miniature lab under a transmission electron microscope at the Molecular Foundry, a DOE Office of Science User Facility at LBNL. In this miniature lab, they mixed sodium bicarbonate (used to make club soda) and calcium chloride (similar to table salt) in water. At high enough concentrations, crystals grew. Videos of nucleating and growing crystals recorded what happened:

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transmission electron microscope at LBNL

Morphing Minerals

The videos revealed that mineral growth took many pathways. Some crystals formed through a two-step process. For example, droplet-like particles of ACC formed, then crystals of aragonite or vaterite appeared on the surface of the droplets. As the new crystals formed, they consumed the calcium carbonate within the drop on which they nucleated.

Other crystals formed directly from the solution, appearing by themselves far away from any ACC particles. Multiple forms often nucleated in a single experiment — at least one calcite crystal formed on top of an aragonite crystal while vaterite crystals grew nearby.

What the team didn’t see in and among the many options, however, was calcite forming from ACC even though researchers widely expect it to happen. Whether that means it never does, De Yoreo can’t say for certain. But after looking at hundreds of nucleation events, he said it is a very unlikely event.

“This is the first time we have directly visualized the formation process,” said De Yoreo. “We observed many pathways happening simultaneously. And they happened randomly. We were never able to predict what was going to come up next. In order to control the process, we’d need to introduce some kind of template that can direct which crystal forms and where.”

In future work, De Yoreo and colleagues plan to investigate how living organisms control the nucleation process to build their shells and pearls. Biological organisms keep a store of mineral components in their cells and have evolved ways to make nucleation happen when and where needed. The team is curious to know how they use cellular molecules to achieve this control.

This work was supported by the Department of Energy Office of Science.

See the full article here.

Pacific Northwest National Laboratory (PNNL) is one of the United States Department of Energy National Laboratories, managed by the Department of Energy’s Office of Science. The main campus of the laboratory is in Richland, Washington.

PNNL scientists conduct basic and applied research and development to strengthen U.S. scientific foundations for fundamental research and innovation; prevent and counter acts of terrorism through applied research in information analysis, cyber security, and the nonproliferation of weapons of mass destruction; increase the U.S. energy capacity and reduce dependence on imported oil; and reduce the effects of human activity on the environment. PNNL has been operated by Battelle Memorial Institute since 1965.

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From Berkeley Lab: “Shaping the Future of Nanocrystals”

Berkeley Lab

August 21, 2014
Lynn Yarris

The first direct observations of how facets form and develop on platinum nanocubes point the way towards more sophisticated and effective nanocrystal design and reveal that a nearly 150 year-old scientific law describing crystal growth breaks down at the nanoscale.

Researchers with the U.S. Department of Energy (DOE)’s Lawrence Berkeley National Laboratory (Berkeley Lab) used highly sophisticated transmission electron microscopes and an advanced high-resolution, fast-detection camera to capture the physical mechanisms that control the evolution of facets – flat faces – on the surfaces of platinum nanocubes formed in liquids. Understanding how facets develop on a nanocrystal is critical to controlling the crystal’s geometric shape, which in turn is critical to controlling the crystal’s chemical and electronic properties.

“For years, predictions of the equilibrium shape of a nanocrystal have been based on the surface energy minimization proposal by Josiah Willard Gibbs in the 1870s to describe the equilibrium shape of a water droplet,” says Haimei Zheng, a staff scientist in Berkeley Lab’s Materials Sciences Division who led this study. “For nanocrystals, the idea is that during crystal growth, high-energy facets will grow at a higher rate than low-energy facets and eventually disappear, resulting in a nanocrystal whose shape is configured to minimize surface energy.”

The research of Zheng and her collaborators showed that at the molecular level, the geometric shape of nanocrystals during synthesis in solution is actually driven by differences in the mobility of ligands across the surfaces of different facets.

“By choosing ligands that selectively bind on the facets, we should be able to control the shape of the nanocrystal as it grows,” she says. “This would provide a new way to design nanomaterials for advanced applications, including nanostructures for bio-imaging, catalysts for solar conversion, and energy storage.”

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Haimei Zheng and Hong-Gang Liao used TEMs at the National Center for Electron Microscopy and a K2-IS camera to record the first direct observations facet formation in platinum nanocubes. (Photo by Kelly Owen)

Zheng is the corresponding author of a paper in Science titled Facet Development During Platinum Nanocube Growth. Hong-Gang Liao is the lead author. Co-authors are Danylo Zherebetskyy, Huolin Xin, Cory Czarnik, Peter Ercius, Hans Elmlund, Ming Pan and Lin-Wang Wang.

The performance of nanocrystals in such surface-enhanced applications as catalysis, sensing and photo-optics is strongly influenced by shape. While significant advances have been made in the synthesis of nanocrystals featuring a variety of shapes – cube, octahedron, tetrahedron, decahedron, icosahedron, etc., – controlling these shapes is often difficult and unpredictable.

“A major roadblock has been that the atomic pathways of facet development in nanocrystals are mostly unknown due to the lack of direct observation,” Zheng says. “It has been assumed that commonly used surfactants modify the energy of specific facets through preferential adsorption, thereby influencing the relative growth rate of different facets and the shape of the final nanocrystal. However, this assumption was based on post-reaction characterizations that did not account for how facet dynamics evolve during crystal growth.”

As a crystal undergoes growth, its constituent atoms or molecules fan out along specific directional planes whose coordinates are denoted by a three-digit system called the Miller Index. Facets form when the surfaces along different planes grow at different rates. Three of the most critical facets for determining a crystal’s geometric shape are the so-called “low index facets,” which are designated under the Miller Index as {100}, {110} and {111}.

Berkeley Lab researchers found that differences in ligand mobility during crystallization cause the low index facets – {100}, {110} and {111} – to stop growing at different times, resulting in the crystal’s final cubic shape. (Image courtesy of Haimei Zheng group)

Working with platinum, one of the most effective industrial catalysts in use today, Zheng and her collaborators initiated the growth of nanocubes in a thin layer of liquid sandwiched between two silicon nitride membranes. This microfabricated liquid cell can encapsulate and maintain the liquid inside the high vacuum of a transmission electron microscope (TEM) for an extended period of time, enabling in situ observations of single nanoparticle growth trajectories.

“With the liquid cells, we’re able to use TEMs to observe the growth of nanocrystals that remarkably resemble nanocrystals synthesized in flasks,” Zheng says. “We found that the growth rates of all low index facets are similar until the {100} facets stop growing. The {110} facets will continue to grow until they reach two neighboring {100} facets, at which point they form the edge of a cube whose corners will be filled in by the continued growth of {111} facets. The arrested growth of the {100} facets that triggers this process is determined by ligand mobility on the {100} facets, which is much lower than on the {110} and {111} facets.”

For their observations, Zeng and her collaborators were able to use several of the TEMs at Berkeley Lab’s National Center for Electron Microscopy (NCEM), a DOE Office of Science user facility, including the TEAM 0.5 instrument, the world’s most powerful TEM. In addition, they were able to use a K2-IS camera from Gatan, Inc., which can capture electron images directly onto a CMOS sensor at 400 frames per second (fps) with 2K-by-2K pixel resolution.

“The K2-IS camera can also be configured to capture images at up to 1600 fps with appropriate scaling of the field of view, which is critical for observing particles that are moving dynamically in the field of view,” says lead author Liao, a member of Zheng’s research group. “The elimination of the traditional scintillation process during image detection results in significant improvement in both sensitivity and resolution. High resolution imaging is also facilitated by the thin silicon nitride membranes of our liquid cell window, which is about 10 nanometers thick per membrane.”

The lower ligand mobility and arrested growth of selected facets experimentally observed by Zheng and Liao, were supported by ab initio calculations carried out under the leadership of co-author Wang, a senior scientist with the Materials Sciences Division who heads the Computational Material Science and Nano Science group.

“At first, we thought the continued growth in the {111} direction might be a result of higher surface energy on the {111} plane,” says co-author Zherebetskyy, a member of Wang’s group. “The experimental observations forced us to consider alternative mechanisms and our calculations show that the relatively low energy barrier on the {111} plane allow the ligand molecules on that plane to be very mobile.”

Says Wang, “Our collaboration with Haimei Zheng’s group showcases how ab initio calculations can be combined with experimental observations to shed new light on hidden molecular processes.”

Zheng and her group are now in the process of determining whether the ligand mobility in platinum that shaped the formation of cube-shaped nanocrystals also applies to ligands in other nanomaterials and the formation of nanocrystals in other geometric shapes.

This research was supported by the DOE Office of Science.

See the full article here.

A U.S. Department of Energy National Laboratory Operated by the University of California

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From SLAC: “Bringing High-energy X-rays into Better Focus”

SLAC Lab

July 22, 2014
SLAC-invented Etching Process Builds Custom Nanostructures for X-ray Optics

Scientists at the Department of Energy’s SLAC National Accelerator Laboratory have invented a customizable chemical etching process that can be used to manufacture high-performance focusing devices for the brightest X-ray sources on the planet, as well as to make other nanoscale structures such as biosensors and battery electrodes.

“The tools researchers use to manipulate X-rays today are very limited,” said Anne Sakdinawat, an associate staff scientist at SLAC’s Stanford Synchrotron Radiation Lightsource (SSRL) who developed the new “V-MACE” process with Chieh Chang, an SSRL research associate.

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Scanning electron microscope image of a cleaved spiral zone plate, a type of X-ray optic, created using a chemical etching technique that was developed at SLAC. (Chieh Chang, Anne Sakdinawat)

“Our new technique for fabricating high performance X-ray optics involves just a few chemicals in a simple, easy-to-implement, one-step technology,” Sakdinawat said. “It offers significant advantages in many far-ranging applications.” The patent-pending technique is detailed in the June 27 edition of Nature Communications.

Focusing X-rays, particularly higher-energy or “hard” X-rays, is particularly challenging at the nanoscale, though it is key to the success of many scientific studies at two of SLAC’s DOE Office of Science user facilities, SSRL and the Linac Coherent Light Source (LCLS) X-ray laser.

It is also of great interest for commercial applications such as X-ray microscopy, complex electronics, and biomedical devices and imaging tools.

Existing tools for focusing hard X-rays, such as specialized mirrors and sequences of concave metal structures that form lenses, are generally limited in how they can shape the X-ray light. Focusing the highest-energy X-rays to produce crisp images remains a challenge, as the focusing tools themselves generally lack nanoscale precision and sap away much of the X-ray energy.

“It’s been technologically very difficult to fabricate structures that offer both high resolution and high efficiency,” Sakdinawat said, and the effectiveness of the structures, which are examples of X-ray “diffractive optics,” is typically based on the height and precision of their features.

The new fabrication technique is adapted from a process used to create hairlike silicon wires for research on advanced batteries and electronics. It can fabricate structures up to 100 times as tall as they are wide, with dimensions accurate to billionths of a meter. The technique reduces the need to stack multiple layers to create tall structures.

The researchers used the etching technique to build tall, precise X-ray diffractive optics, called zone plates, whose thinly spaced lines, symmetric rings or spiral patterns alternately obstruct or phase-shift X-rays and allow them to pass through in a way that separates and refocuses them. This improves the focus and produces higher-quality images.

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Scanning electron microscope (SEM) image of a zone plate pattern produced using a chemical etching technique invented at SLAC. (Chieh Chang, Anne Sakdinawat)

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This scanning electron microscope image shows a cross-sectional view of a zone plate produced using a patent-pending chemical etching technique called “V-MACE” developed at SLAC. (Chieh Chang, Anne Sakdinawat)

“Basically, this is like an artificial crystal,” Sakdinawat said, diffracting the X-ray light in a predictable pattern, as a crystal would. “You can basically manipulate the light in whatever fashion you want – you can shape the light in different ways,” she said, based on the design of the optics and the needs of the experiment.

Sakdinawat and Chang tested and imaged a sample zone plate at SSRL, and they hope to construct similar plates for use in experiments at SSRL and LCLS.

The same technique can be used to build other types of precise silicon and metal-coated nanostructures, such as filtration devices, thermoelectric devices that can create electricity from heat and components for tiny bio-sensors that can be embedded in the body, and researchers are working to tailor the process to suit the needs of government agencies and corporate partners.

“We’re trying to expand into other fields,” Sakdinawat said. “There are many different applications for this.”

See the full article here.