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  • richardmitnick 4:24 pm on December 19, 2014 Permalink | Reply
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    From SLAC: “First Direct Evidence that a Mysterious Phase of Matter Competes with High-Temperature Superconductivity” 


    SLAC Lab

    December 19, 2014

    SLAC Study Shows “Pseudogap” Phase Hoards Electrons that Might Otherwise Conduct Electricity with 100 Percent Efficiency

    Scientists have found the first direct evidence that a mysterious phase of matter known as the “pseudogap” competes with high-temperature superconductivity, robbing it of electrons that otherwise might pair up to carry current through a material with 100 percent efficiency.

    The result, led by researchers at Stanford University and the Department of Energy’s SLAC National Accelerator Laboratory, is the culmination of 20 years of research aimed at finding out whether the pseudogap helps or hinders superconductivity, which could transform society by making electrical transmission, computing and other areas much more energy efficient.

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    This illustration shows the complex relationship between high-temperature superconductivity (SC) and a mysterious phase called the pseudogap (PG). Copper oxide materials become superconducting when an optimal number of electrons are removed, leaving positively charged “holes,” and the material is chilled below a transition temperature (blue curve). This causes remaining electrons (yellow) to pair up and conduct electricity with 100 percent efficiency. Experiments at SLAC have produced the first direct evidence that the pseudogap competes for electrons with superconductivity over a wide range of temperatures at lower hole concentrations (SC+PG). At lower temperatures and higher hole concentrations, superconductivity wins out. (SLAC National Accelerator Laboratory)

    The new study definitively shows that the pseudogap is one of the things that stands in the way of getting superconductors to work at higher temperatures for everyday uses, said lead author Makoto Hashimoto, a staff scientist at SLAC’s Stanford Synchrotron Radiation Lightsource (SSRL), the DOE Office of Science User Facility where the experiments were carried out. The results were published in Nature Materials.

    SLAC SSRL
    SSRL

    “Now we have clear, smoking-gun evidence that the pseudogap phase competes with and suppresses superconductivity,” Hashimoto said. “If we can somehow remove this competition, or handle it better, we may be able to raise the operating temperatures of these superconductors.”

    Tracking Down Electrons

    In the experiments, researchers used a technique called angle-resolved photoemission spectroscopy, or ARPES, to knock electrons out of a copper oxide material, one of a handful of materials that superconduct at relatively high temperatures – although they still have to be chilled to at least minus 135 degrees Celsius.

    Plotting the energies and momenta of the ejected electrons tells researchers how they were behaving when they were inside the material. In metals, for instance, electrons freely flow around and between atoms. In insulators, they stick close to their home atoms. And in superconductors, electrons leave their usual positions and pair up to conduct electricity with zero resistance and 100 percent efficiency; the missing electrons leave a characteristic gap in the researchers’ plots.

    But in the mid-1990s, scientists discovered another, puzzling gap in their plots of copper oxide superconductors. This “pseudogap” looked like the one left by superconducting electrons, but it showed up at temperatures too warm for superconductivity to occur. Was it a lead-in to superconducting behavior? A rival state that held superconductivity at bay? Where did it come from? No one knew.

    “It’s a complex, intimate relationship. These two phenomena likely share the same roots but are ultimately antagonistic,” said Zhi-Xun Shen, a professor at SLAC and Stanford and senior author of the study. “When the pseudogap is winning, superconductivity is losing ground.”

    Evidence of Competition

    Shen and his colleagues have been using ARPES to investigate the pseudogap ever since it showed up, refining their techniques over the years to pry more information out of the flying electrons.

    In this latest study, Hashimoto was able to find out exactly what was happening at the moment the material transitioned into a superconducting state. He did this by measuring not only the energies and momenta of the electrons, but the number of electrons coming out of the material with particular energies over a wide range of temperatures, and after the electronic properties of the material had been altered in various ways.

    He discovered clear, strong evidence that at this crucial transition temperature, the pseudogap and superconductivity are competing for electrons. Theoretical calculations by members of the team were able to reproduce this complex relationship.

    “The pseudogap tends to eat away the electrons that want to go into the superconducting state,” explained Thomas Devereaux, a professor at Stanford and SLAC and co-author of the study. “The electrons are busy doing the dance of the pseudogap, and superconductivity is trying to cut in, but the electrons are not letting that happen. Then, as the material goes into the superconducting state, the pseudogap gives up and spits the electrons back out. That’s really the strongest evidence we have that this competition is occurring.”

    Remaining Mysteries

    Scientists still don’t know what causes the pseudogap, Devereaux said: “This remains one of the most important questions in the field, because it’s clearly preventing superconductors from working at even higher temperatures, and we don’t know why.”

    But the results pave new directions for further research, the scientists said.

    “Now we can model the competition between the pseudogap and superconductivity from the theoretical side, which was not possible before,” Hashimoto said. “We can use simulations to reproduce the kinds of features we have seen, and change the variables within those simulations to try to pin down what the pseudogap is.”

    He added, “Competition may be only one aspect of the relationship between the two states. There may be more profound questions – for example, whether the pseudogap is necessary for superconductivity to occur.”

    In addition to SLAC and Stanford, researchers from Lawrence Berkeley National Laboratory, Osaka University, the National Institute of Advanced Industrial Science and Technology in Japan, the Japan Atomic Energy Agency, Tokyo Institute of Technology, University of Tokyo and Cornell University contributed to the study. The research was supported by the DOE Office of Science.

    See the full article here.

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    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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  • richardmitnick 7:35 pm on December 15, 2014 Permalink | Reply
    Tags: , Concrete, X-ray Technology   

    From LBL: “News Center Back to the Future with Roman Architectural Concrete” 

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    Berkeley Lab

    December 15, 2014
    Lynn Yarris (510) 486-5375

    No visit to Rome is complete without a visit to the Pantheon, Trajan’s Markets, the Colosseum, or the other spectacular examples of ancient Roman concrete monuments that have stood the test of time and the elements for nearly two thousand years. A key discovery to understanding the longevity and endurance of Roman architectural concrete has been made by an international and interdisciplinary collaboration of researchers using beams of X-rays at the Advanced Light Source (ALS) of the U.S. Department of Energy (DOE)’s Lawrence Berkeley National Laboratory (Berkeley Lab).

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    LBL ALS interior
    ALS at LBL

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    The concrete walls of Trajan’s Markets in Rome have stood the test of time and the elements for nearly 2,000 years. They have even survived a major earthquake in 1349. (Photo courtesy of Marie Jackson)

    Working at ALS beamline 12.3.2, a superconducting bending magnet X-ray micro-diffraction beamline, the research team studied a reproduction of Roman volcanic ash-lime mortar that had been previously subjected to fracture testing experiments at Cornell University. In the concrete walls of Trajan’s Markets, constructed around 110 CE, this mortar binds cobble-sized fragments of tuff and brick. Through observing the mineralogical changes that took place in the curing of the mortar over a period of 180 days and comparing the results to 1,900 year old samples of the original, the team discovered that a crystalline binding hydrate prevents microcracks from propagating.

    “The mortar resists microcracking through in situ crystallization of platy strätlingite, a durable calcium-alumino-silicate mineral that reinforces interfacial zones and the cementitious matrix,” says Marie Jackson, a faculty scientist with the University of California (UC) Berkeley’s Department of Civil and Environmental Engineering who led this study. “The dense intergrowths of the platy crystals obstruct crack propagation and preserve cohesion at the micron scale, which in turn enables the concrete to maintain its chemical resilience and structural integrity in a seismically active environment at the millennial scale.”

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    (From left) Marie Jackson, Qinfei Li, Martin Kunz and Paulo Monteiro at ALS Beamline 12.3.2 where they conducted a study on ancient Roman concrete. (Photo by Roy Kaltschmidt)

    Jackson, a volcanologist by training who led an earlier study at the ALS on Roman seawater concrete, is the lead author of a paper describing this study in the Proceedings of the National Academy of Sciences (PNAS) titled Mechanical Resilience and Cementitious Processes in Imperial Roman Architectural Mortar. Co-authors of the paper are Eric Landis, Philip Brune, Massimo Vitti, Heng Chen, Qinfei Li, Martin Kunz, Hans-Rudolf Wenk, Paulo Monteiro and Anthony Ingraffea.

    The mortars that bind the concrete composites used to construct the structures of Imperial Rome are of keen scientific interest not just because of their unmatched resilience and durability, but also for the environmental advantages they offer. Most modern concretes are bound by limestone-based Portland cement. Manufacturing Portland cement requires heating a mix of limestone and clay to 1,450 degrees Celsius (2,642 degrees Fahrenheit), a process that releases enough carbon – given the 19 billion tons of Portland cement used annually – to account for about seven-percent of the total amount of carbon emitted into the atmosphere each year.

    Roman architectural mortar, by contrast, is a mixture of about 85-percent (by volume) volcanic ash, fresh water, and lime, which is calcined at much lower temperature than Portland cement. Coarse chunks of volcanic tuff and brick compose about 45-to-55-percent (by volume) of the concrete. The result is a significant reduction in carbon emissions.

    “If we can find ways to incorporate a substantial volumetric component of volcanic rock in the production of specialty concretes, we could greatly reduce the carbon emissions associated with their production also improve their durability and mechanical resistance over time,” Jackson says.

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    Ancient Roman concrete consists of coarse chunks of volcanic tuff and brick bound together by a volcanic ash-lime mortar that resists microcracking, a key to its longevity and endurance. (Photo by Roy Kaltschmidt, Berkeley Lab)

    As part of their study, Jackson and her collaborators at UC Berkeley used ALS beamline 12.3.2 to make X-ray micro-diffraction measurements of slices of the Roman mortar that were only about 0.3 millimeters thick.

    “We obtained X-ray diffractograms for many different points within a given cementitious microstructure,” Jackson says. “This enabled us to detect changes in mineral assemblages that gave precise indications of chemical processes active over very small areas.”

    The mineralogical changes that Jackson and her collaborators observed showed the mortar reproduction gaining strength and toughness over 180 days as calcium-aluminum-silicate-hydrate (C-A-S-H) cementing binder coalesced and strätlingite crystals grew in interfacial zones between volcanic scoria and the mortar matrix. The toughening of these interfacial zones is reflected in the bridging crack morphology, which was measured by co-author Landis at the University of Maine, using computed tomography scans of the fractured mortar specimens. These experimental results correlate well with computations of increasing fracture energy determined by co-author Brune, now at Dupont Technologies. The strätlingite crystals show no corrosion and their smooth surfaces suggest long-term stability, similar to geological strätlingite that persists for hundreds of thousands of years.

    “The in situ crystallization of the strätlingite crystals produces interfacial zones that are very different from any interfacial microstructure observed in Portland cement concretes,” Jackson says. “High porosity along the interfacial zones of inert aggregates in Portland cement concrete creates the sites where crack paths first nucleate and propagate.”

    A future challenge for researchers, Jackson says, will be to “find ways to activate aggregates, as slag or as volcanic ash for example, in innovative concretes so that these can develop strätlingite reinforcements in interfacial zones like the Roman architectural mortars.”

    The fracture testing experiments at Cornell University were led by co-author Ingraffea. The samples of mortar from Trajan’s Markets were provided by co-author Vitti and the Sovrintendenza Capitolina di Roma Capitale. Co-author Kunz is the principal scientist at ALS beamline 12.3.2.

    This research was supported by the National Science Foundation and the Loeb Library at Harvard University. The Advanced Light Source is a DOE Office of Science User Facility.

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  • richardmitnick 6:57 pm on December 8, 2014 Permalink | Reply
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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.

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    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.”

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    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.

    See the full article here.

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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.
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  • richardmitnick 7:51 pm on December 4, 2014 Permalink | Reply
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    From SLAC: “Rattled Atoms Mimic High-temperature Superconductivity” 


    SLAC Lab

    December 4, 2014

    X-ray Laser Experiment Provides First Look at Changes in Atomic Structure that Support Superconductivity

    An experiment at the Department of Energy’s SLAC National Accelerator Laboratory provided the first fleeting glimpse of the atomic structure of a material as it entered a state resembling room-temperature superconductivity – a long-sought phenomenon in which materials might conduct electricity with 100 percent efficiency under everyday conditions.

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    In a high-temperature superconducting material known as YBCO, light from a laser causes oxygen atoms (red) to vibrate between layers of copper oxide that are just two molecules thick. (The copper atoms are shown in blue.) This jars atoms in those layers out of their normal positions in a way that likely favors superconductivity. In this short-lived state, the distance between copper oxide planes within a layer increases, while the distance between the layers decreases. (Jörg Harms/Max Planck Institute for the Structure and Dynamics of Matter)

    Researchers used a specific wavelength of laser light to rattle the atomic structure of a material called yttrium barium copper oxide, or YBCO. Then they probed the resulting changes in the structure with an X-ray laser beam from the Linac Coherent Light Source (LCLS), a DOE Office of Science User Facility.

    SLAC LCLS
    SLAC LCLS Inside
    LCLS at SLAC

    They discovered that the initial exposure to laser light triggered specific shifts in copper and oxygen atoms that squeezed and stretched the distances between them, creating a temporary alignment that exhibited signs of superconductivity for a few trillionths of a second at well above room temperature – up to 60 degrees Celsius (140 degrees Fahrenheit). The scientists coupled data from the experiment with theory to show how these changes in atomic positions allow a transfer of electrons that drives the superconductivity.

    New Views of Atoms in Motion

    “This is a highly interesting state, even though it only exists for a short period of time,” said Roman Mankowsky of the Max Planck Institute for the Structure and Dynamics of Matter in Hamburg, Germany, who was lead author of a report on the experiment in the Dec. 4 print issue of Nature. “When the laser excites the material, it shifts the atoms and changes the structure. We hope these results will ultimately help in the design of new materials to enhance superconductivity.”

    Sustaining such a state at room temperature would revolutionize many fields, making the electrical grid more efficient and enabling more powerful and compact computers. Traditional superconductors operate only at temperatures close to absolute zero. YBCO is one of a handful of materials discovered since 1986 that superconduct at somewhat higher temperatures; but they still have to be chilled to at least minus 135 degrees Celsius in order to sustain superconductivity, and scientists still don’t know what allows these so-called high-temperature superconductors to carry electricity with zero resistance.

    A Powerful Tool for Exploring Superconductivity

    Josh Turner, a SLAC staff scientist who has led other studies of YBCO at the LCLS, said powerful tools such as X-ray lasers have excited new interest in superconductor research by allowing researchers to isolate a specific property that they want to learn more about. This is important because high-temperature superconductors can exhibit a tangle of magnetic, electronic and structural properties that may compete or cooperate as the material moves toward a superconducting state. For example, another recently published LCLS study found that exciting YBCO with the same optical laser light disrupts an electronic order that competes with superconductivity.

    “What LCLS is now showing us is how these different properties change over short times,” Turner said. “We can actually see how the electrons or atoms are moving.”

    Mankowsky said future experiments at LCLS could try to sustain the superconducting state for longer periods, use a combination of experimental techniques to study how other properties evolve in the transition into the superconducting state and explore whether the same structural changes are at work in other high-temperature superconductors.

    Researchers from the National Center for Scientific Research in France, Paul Scherrer Institute in Switzerland, Max Planck Institute for Solid State Research in Germany, Swiss Federal Institute of Technology, College of France, University of Geneva, Oxford University in the United Kingdom, the Center for Free-Electron Laser Science in Germany, and University of Hamburg in Germany also participated in the study. The work was supported by the European Research Council, German Science Foundation, Swiss National Superconducting Center and Swiss National Science Foundation.

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    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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  • richardmitnick 7:30 pm on December 4, 2014 Permalink | Reply
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    From ANL: “Atomic ‘mismatch’ creates nano ‘dumbbells'” 

    News APS at Argonne National Laboratory

    December 4, 2014
    Jared Sagoff

    Like snowflakes, nanoparticles come in a wide variety of shapes and sizes. The geometry of a nanoparticle is often as influential as its chemical makeup in determining how it behaves, from its catalytic properties to its potential as a semiconductor component.

    Thanks to a new study from the U.S. Department of Energy’s (DOE) Argonne National Laboratory, researchers are closer to understanding the process by which nanoparticles made of more than one material – called heterostructured nanoparticles – form. This process, known as heterogeneous nucleation, is the same mechanism by which beads of condensation form on a windowpane.

    Heterostructured nanoparticles can be used as catalysts and in advanced energy conversion and storage systems. Typically, these nanoparticles are created from tiny “seeds” of one material, on top of which another material is grown. In this study, the Argonne researchers noticed that the differences in the atomic arrangements of the two materials have a big impact on the shape of the resulting nanoparticle.

    “Before we started this experiment, it wasn’t entirely clear what’s happening at the interface when one material grows on another,” said nanoscientist Elena Shevchenko of Argonne Center for Nanoscale Materials, a DOE Office of Science user facility.

    In this study, the researchers observed the formation of a nanoparticle consisting of platinum and gold. The researchers started with a platinum seed and grew gold around it. Initially, the gold covered the platinum seed’s surface uniformly, creating a type of nanoparticle known as “core-shell.” However, as more gold was deposited, it started to grow unevenly, creating a dumbbell-like structure.

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    This picture combines a transmission electron microscope image of a nanodumbbell with a gold domain oriented in direction. The seed and gold domains in the dumbbell in the image on the right are identified by geometric phase analysis. Image credit: Soon Gu Kwon.

    Thanks to state-of-the-art X-ray analysis provided by Argonne’s Advanced Photon Source (APS), a DOE Office of Science user facility, the researchers identified the cause of the dumbbell formation as “lattice mismatch,” in which the spacing between the atoms in the two materials doesn’t align.

    “Essentially, you can think of lattice mismatch as having a row of smaller boxes on the bottom layer and larger boxes on the top layer. When you try to fit the larger boxes into the space for a smaller box, it creates an immense strain,” said Argonne physicist Byeongdu Lee.

    While the lattice mismatch is only fractions of a nanometer, the effect accumulates as layer after layer of gold forms on the platinum. The mismatch can be handled by the first two layers of gold atoms – creating the core-shell effect – but afterwards it proves too much to overcome. “The arrangement of atoms is the same in the two materials, but the distance between atoms is different,” said Argonne postdoctoral researcher Soon Gu Kwon. “Eventually, this becomes unstable, and the growth of the gold becomes unevenly distributed.”

    As the gold continues to accumulate on one side of the seed nanoparticle, small quantities “slide” down the side of the nanoparticle like grains of sand rolling down the side of a sand hill, creating the dumbbell shape.

    The advantage of the Argonne study comes from the researchers’ ability to perform in situ observations of the material in realistic conditions using the APS. “This is the first time anyone has been able to study the kinetics of this heterogeneous nucleation process of nanoparticles in real-time under realistic conditions,” said Argonne physicist Byeongdu Lee. “The combination of two X-ray techniques gave us the ability to observe the material at both the atomic level and the nanoscale, which gave us a good view of how the nanoparticles form and transform.” All conclusions made based on the X-ray studies were further confirmed using atomic-resolution microscopy in the group of Professor Robert Klie of the University of Illinois at Chicago.

    This analysis of nanoparticle formation will help to lay the groundwork for the formation of new materials with different and controllable properties, according to Shevchenko. “In order to design materials, you have to understand how these processes happen at a very basic level,” she said.

    The research was funded in part by the National Science Foundation and the University of Illinois at Chicago Research Resources Center.

    An article based on the research, Heterogeneous nucleation and shape transformation of multicomponent metallic nanostructures,” appeared in the Nov. 2 online issue of Nature Materials.

    Argonne National Laboratory seeks solutions to pressing national problems in science and technology. The nation’s first national laboratory, Argonne conducts leading-edge basic and applied scientific research in virtually every scientific discipline. Argonne researchers work closely with researchers from hundreds of companies, universities, and federal, state and municipal agencies to help them solve their specific problems, advance America’s scientific leadership and prepare the nation for a better future.

    With employees from more than 60 nations, Argonne is managed by UChicago Argonne, LLC for the U.S. Department of Energy’s Office of Science. The Office of Science is the single largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time.

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  • richardmitnick 4:24 pm on December 4, 2014 Permalink | Reply
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    From SLAC: “X-ray Laser Reveals How Bacterial Protein Morphs in Response to Light” 


    SLAC Lab

    December 4, 2014

    A Series of Super-Sharp Snapshots Demonstrates a New Tool for Tracking Life’s Chemistry

    Human biology is a massive collection of chemical reactions, from the intricate signaling network that powers our brain activity to the body’s immune response to viruses and the way our eyes adjust to sunlight. All involve proteins, known as the molecules of life; and scientists have been steadily moving toward their ultimate goal of following these life-essential reactions step by step in real time, at the scale of atoms and electrons.

    Now, researchers have captured the highest-resolution snapshots ever taken with an X-ray laser that show changes in a protein’s structure over time, revealing how a key protein in a photosynthetic bacterium changes shape when hit by light. They achieved a resolution of 1.6 angstroms, equivalent to the radius of a single tin atom.

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    This illustration depicts an experiment at SLAC that revealed how a protein from photosynthetic bacteria changes shape in response to light. Samples of the crystallized protein (right), called photoactive yellow protein or PYP, were jetted into the path of SLAC’s LCLS X-ray laser beam (fiery beam from bottom left). The crystallized proteins had been exposed to blue light (coming from left) to trigger shape changes. Diffraction patterns created when the X-ray laser hit the crystals allowed scientists to recreate the 3-D structure of the protein (center) and determine how light exposure changes its shape. (SLAC National Accelerator Laboratory)

    “These results establish that we can use this same method with all kinds of biological molecules, including medically and pharmaceutically important proteins,” said Marius Schmidt, a biophysicist at the University of Wisconsin-Milwaukee who led the experiment at the Department of Energy’s SLAC National Accelerator Laboratory. There is particular interest in exploring the fastest steps of chemical reactions driven by enzymes — proteins that act as the body’s natural catalysts, he said: “We are on the verge of opening up a whole new unexplored territory in biology, where we can study small but important reactions at ultrafast timescales.”

    The results, detailed in a report published online Dec. 4 in Science, have exciting implications for research on some of the most pressing challenges in life sciences, which include understanding biology at its smallest scale and making movies that show biological molecules in motion.

    A New Way to Study Shape-shifting Proteins

    The experiment took place at SLAC’s Linac Coherent Light Source (LCLS), a DOE Office of Science User Facility. LCLS’s X-ray laser pulses, which are about a billion times brighter than X-rays from synchrotrons, allowed researchers to see atomic-scale details of how the bacterial protein changes within millionths of a second after it’s exposed to light.

    SLAC LCLS
    SLAC LCLS Inside
    LCLS at SLAC

    “This experiment marks the first time LCLS has been used to directly observe a protein’s structural change as it happens. It opens the door to reaching even faster time scales,” said Sébastien Boutet, a SLAC staff scientist who oversees the experimental station used in the study. LCLS’s pulses, measured in quadrillionths of a second, work like a super-speed camera to record ultrafast changes, and snapshots taken at different points in time can be compiled into detailed movies.

    The protein the researchers studied, found in purple bacteria and known as PYP for “photoactive yellow protein,” functions much like a bacterial eye in sensing blue light. The mechanism is very similar to that of other receptors in biology, including receptors in the human eye. “Though the chemicals are different, it’s the same kind of reaction,” said Schmidt, who has studied PYP since 2001. Proving the technique works with a well-studied protein like PYP sets the stage to study more complex and biologically important molecules at LCLS, he said.

    Chemistry on the Fly

    In the LCLS experiment, researchers prepared crystallized samples of the protein, and exposed the crystals, each about 2 millionths of a meter long, to blue laser light before jetting them into the LCLS X-ray beam.

    The X-rays produced patterns as they struck the crystals, which were used to reconstruct the 3-D structures of the proteins. Researchers compared the structures of the proteins that had been exposed to light to those that had not to identify light-induced structural changes.

    “In the future we plan to study all sorts of enzymes and other proteins using this same technique,” Schmidt said. “This study shows that the molecular details of life’s chemistry can be followed using X-ray laser crystallography, which puts some of biology’s most sought-after goals within reach.”

    Researchers from the University of Wisconsin-Milwaukee and SLAC were joined by researchers from Arizona State University; Lawrence Livermore National Laboratory; University of Hamburg and DESY in Hamburg, Germany; State University of New York, Buffalo; University of Chicago; and Imperial College in London. The work was supported by the National Science Foundation, National Institutes of Health and Lawrence Livermore National Laboratory.

    See the full article here.

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  • richardmitnick 8:22 pm on December 3, 2014 Permalink | Reply
    Tags: , , , X-ray Technology   

    From SLAC: “SLAC, RadiaBeam Build New Tool to Tweak Rainbows of X-ray Laser Light” 


    SLAC Lab

    December 3, 2014

    ‘Dechirper’ Will Give Scientists More Control Over ‘Color Spectrum’ of LCLS X-ray Pulses

    The Department of Energy’s SLAC National Accelerator Laboratory has teamed up with Santa Monica-based RadiaBeam Systems to develop a device known as a dechirper, which will provide a new way of adjusting the range of energies within single pulses from SLAC’s X-ray laser.

    d
    Design drawing of the outer structure of a dechirper that will be used to tweak the “color range” of light pulses from SLAC’s X-ray laser, LCLS. Two dechirpers will be lined up in front of the LCLS undulator—a magnetic structure that generates ultrabright, ultrafast X-rays from bunches of electrons. (RadiaBeam Systems)

    i
    The inside of the dechirper consists of two parallel, 2-meter-long, flat aluminum rails. Electron bunches will travel through a variable gap between the rails at nearly the speed of light. (RadiaBeam Systems)

    r
    The aluminum rails have comb-like grooves that are half a millimeter deep and a quarter millimeter wide. The electron bunches “sense” the grooves, leading to a change in the energy spread of the X-rays they produce. (RadiaBeam Systems)

    “For many experiments it is important to use a specific X-ray energy so that we can study specific chemical elements in our samples,” says LCLS scientist William Schlotter. “The narrower the energy bandwidth, the more precisely we can study those elements.”

    Tweaking the ‘Color Spectrum’ of X-ray Pulses

    LCLS generates ultrabright and ultrashort X-ray pulses from packets of electrons that travel through a magnetic structure, called an undulator, at almost the speed of light. The properties of the electron bunches determine the characteristics of the X-ray light that they produce.

    un
    Working of the undulator. 1: magnets, 2: electron beam entering from the upper left, 3: synchrotron radiation exiting to the lower right

    Many experiments demand X-ray pulses that last only a few quadrillionths of a second, but it is difficult to make electron bunches this short. Therefore, scientists have turned to nature and adopted a solution reminiscent of a bird’s chirp. They create a spread of energies in the electron bunch, with the tail having more energy than the head. When electron bunches pass through another magnetic device known as a chicane, this so-called “energy chirp” allows lagging electrons in the tail to catch up with the ones in the head, creating shorter electron bunches, and thus shorter X-ray pulses.

    However, since the chirp consists of a spectrum of energies, the X-rays also have multiple energies—a rainbow of X-ray “colors” known as the energy bandwidth. Depending on the type of experiment, this can be an advantage or disadvantage, and researchers would like to have new tools to adjust the energy bandwidth to match their needs.

    As the name suggests, the dechirper’s primary task will be to minimize the chirp, i.e. to make pulses with a smaller spread in X-ray energies. Additionally, the dechirper can do the opposite and make X-ray pulses with a broader energy spectrum. In fact, many users have had a desire for a wider bandwidth since LCLS started operations in 2009, as LCLS scientist Sébastien Boutet points out.

    Precision Tool to Manipulate Electron Bunches

    SLAC scientists first proposed the idea for a dechirper in 2012 and, together with researchers from Lawrence Berkeley National Laboratory, demonstrated its feasibility in a test experiment at the Pohang Accelerator Laboratory in South Korea.

    The LCLS device, whose final design review will take place on Dec. 4, will consist of two flat, parallel aluminum rails, each 2 meters long, with comb-like grooves that are half a millimeter deep and a quarter millimeter wide. Two of these devices will be lined up in front of the undulator, with the electron beam traveling through the gap between the rails.

    Even though the electron bunches will not touch the rails, they will “sense” the grooves. These “bumps” along the electrons’ flight path will create a wake at the tail of the bunch, similar to the wake behind a boat gliding over water. “In this process, the tail loses energy while the front stays the same,” explains accelerator physicist Richard Iverson, the project lead at SLAC, where the technical requirements for the dechirper were specified.

    Varying the gap between the rails changes the effect on the electrons, allowing scientists to adjust the chirp of the electron bunches and, consequently, the energy bandwidth of the X-ray pulses generated in the undulator.

    What may sound like a relatively simple setup poses significant challenges for the manufacturing process. “The dechirper’s grooves are only as wide as three or four human hairs,” says project manager Marcos Ruelas at RadiaBeam, where the device is being designed and constructed. “Moreover, the rails must be very flat and smooth. Over the entire length of 4 meters, their height can only differ by 50 micrometers.” To meet these requirements, each 2-meter rail will be manufactured in four smaller blocks.

    The new device is expected to be installed at SLAC in August 2015. It will not only start providing LCLS users with more flexibility for their experiments, but will also become the test bed for dechirpers at SLAC’s next-generation LCLS-II facility and other X-ray lasers worldwide.

    Other key personnel of the project include Karl Bane, Paul Emma, Timothy Maxwell, Zhirong Huang, Gennady Stupakov and Zhen Zhang from SLAC’s Accelerator Directorate, as well as RadiaBeam’s Pedro Frigola, Mark Harrison and David Martin.

    See the full article here.

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  • richardmitnick 2:29 pm on December 2, 2014 Permalink | Reply
    Tags: , , , X-ray Technology   

    From LBL: “A Better Look at the Chemistry of Interfaces” 

    Berkeley Logo

    Berkeley Lab

    December 2, 2014
    Lynn Yarris (510) 486-5375

    Researchers working at the Advanced Light Source (ALS) of the U.S. Department of Energy (DOE)’s Lawrence Berkeley National Laboratory (Berkeley Lab) have combined key features of two highly acclaimed X-ray spectroscopy techniques into a new technique that offers sub-nanometer resolution of every chemical element to be found at heterogeneous interfaces, such as those in batteries and fuel cells. This new technique is called SWAPPS for Standing Wave Ambient Pressure Photoelectron Spectroscopy, and it combines standing-wave photoelectron spectroscopy (SWPS) with high ambient pressure photoelectron spectroscopy (APPS).

    i
    By utilizing X-ray standing waves to excite photoelectrons, SWAPPS delivers vital information about all the chemical elements at the heterogeneous interfaces found in batteries, fuel cells and other devices.

    “SWAPPS enables us to study a host of surface chemical processes under realistic pressure conditions and for systems related to energy production, such as electrochemical cells, batteries, fuel cells and photovoltaic cells, as well as in catalysis and environmental science,” says Charles Fadley, a physicist who holds joint appointments with Berkeley Lab’s Materials Sciences Division and the University of California Davis, where he is a Distinguished Professor of Physics. “SWAPPS provides all the advantages of the widely used technique of X-ray photoelectron spectroscopy, including element and chemical-state sensitivity, and quantitative analysis of relative concentrations of all species present. However with SWAPPS we don’t require the usual ultrahigh vacuum, which means we can measure the interfaces between volatile liquids and solids.”

    Fadley is one of three corresponding authors of a paper describing SWAPPS in Nature Communications. The paper is titled Concentration and chemical-state profiles at heterogeneous interfaces with sub-nm accuracy from standing-wave ambient-pressure photoemission. The other two corresponding authors are Hendrik Bluhm, with Berkeley Lab’s Chemical Sciences Division, a pioneer in the development of APPS, and Slavomír Nemšák, now with Germany’s Jülich Peter Grünberg Institute. (See below for the complete list of authors).

    team
    (From left) Chuck Fadley, Ioannis Zegkinoglou, Slavomir Nemsak, Osman Karslioglu, Andrey Shavorskiy and Hendrik Bluhm at Beamline 11.0.2 of the Advanced Light Source (photo by Roy Kaltschmidt)

    In terms of energies and wavelengths, X-rays serve as excellent probes of chemical processes. In the alphabet soup of X-ray analytical techniques, two in particular stand out for the study of chemistry at the interface where layers of two different materials or phases of matter meet. The first is SWPS, developed at the ALS by Fadley and his research group, which made it possible for the first time to selectively study buried interfaces in a sample with either soft or hard X-rays. The second is APPS, also developed at the ALS by a team that included Bluhm, which made it possible for the first time to use X-ray photoelectron spectroscopy under pressures and humidities similar to those encountered in natural or practical environments.

    “Heterogeneous processes at solid/gas, liquid/gas and solid/liquid interfaces are ubiquitous in modern devices and technologies but often difficult to study quantitatively,” Bluhm says. “Full characterization requires measuring the depth profiles of chemical composition and state with enhanced sensitivity in narrow interfacial regions at the nanometer scale. By combining features of SWPS and APPS techniques, we can use SWAPPS to measure the elemental and chemical composition of heterogeneous interfaces with sub-nanometer resolution in the direction perpendicular to the interface.”

    Says Fadley, “We believe SWAPPS will deliver vital information about the structure and chemistry of liquid/vapor and liquid/solid interfaces, in particular the electrical double layer whose structure is critical to the operation of batteries, fuel cells and all of electrochemistry, but which is still not understood at a microscopic level.”

    Fadley, Bluhm, Nemšák and their collaborators used their SWAPPS technique to study a model system in which a nanometer layer of an aqueous electrolyte of sodium hydroxide and cesium hydroxide was grown on an iron oxide (hematite) solid. The spatial distributions of the electrolyte ions and the carbon contaminants across the solid/liquid and liquid/gas interfaces were directly probed and absolute concentrations of the chemical species were determined. The observation of binding-energy shifts with depth provided additional information on the bonding and/or depth-dependent potentials in the system.

    “We determined that the sodium ions are located close to the iron oxide/solution interface, while cesium ions are on average not in direct contact with the solid/liquid interface,” Bluhm says. “We also discovered that there are two different kinds of carbon species, one hydrophobic, which is located exclusively in a thin film at the liquid/vapor interface, and a hydrophilic carbonate or carboxyl that is evenly distributed throughout the liquid film.”

    SWAPPS measures the depth profiles of chemical elements with sub-nanometer resolution in the direction perpendicular to the interface, utilizing an X-ray standing wave field that can be tailored to focus on specific depths, i.e., near the surface or near the iron oxide interface.

    SWAPPS measures the depth profiles of chemical elements with sub-nanometer resolution in the direction perpendicular to the interface utilizing an X-ray standing wave field that can be tailored to focus on specific depths, i.e., near the surface or near the iron oxide interface.

    A key to the success of this study was the use of X-ray standing waves to excite the photoelectrons. A standing wave is a vibrational pattern created when two waves of identical wavelength interfere with one another: one is the incident X-ray and the other is the X-ray reflected by a mirror. Interactions between standing waves and core-level electrons reveal much about the depth distributions of each chemical species in a sample.

    “Tailoring the X-ray wave field into a standing wave can be used to achieve greater depth sensitivity in photoelectron spectroscopy,” Fadley says. “Our combination of an oscillatory standing-wave field and the exponential decay of the photoelectron signal at each interface gives us unprecedented depth resolution.”

    In their Nature Communications paper, the authors say that future time-resolved SWAPPS studies using free-electron laser or high-harmonic generation light sources would also permit, via pump-probe methods, looking at the timescales of processes at interfaces on the femtosecond time scale.

    “The range of future applications and measurement scenarios for SWAPPS is enormous,” Fadley says.

    This work was carried out at ALS Beamline 11.0.2, which is operated by Berkeley Lab’s Chemical Sciences Division and hosts two ambient-pressure photoemission spectroscopy endstations.

    In addition to Fadley, Bluhm and Nemšák, other authors of the Nature Communications paper describing SWAPPS were Andrey Shavorskiy, Osman Karslioglu, Ioannis Zegkinoglou, Peter Greene, Edward Burks, Arunothai Rattanachata, Catherine Conlon, Armela Keqi, Farhad Salmassi, Eric Gullikson, See-Hun Yang and Kai Liu.

    This research was primarily funded by the DOE Office of Science. The Advanced Light Source is a DOE Office of Science User Facility.

    See the full article here.

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  • richardmitnick 7:36 pm on November 26, 2014 Permalink | Reply
    Tags: , , , , X-ray Technology   

    From BNL: “X-Ray Powder Diffraction Beamline at NSLS-II Takes First Beam and First Data” 

    Brookhaven Lab

    November 26, 2014
    Chelsea Whyte

    On November 6, Eric Dooryhee walked into a crowd of people excitedly talking at the X-ray Powder Diffraction (XPD) beamline beaming an enormous smile. The group broke into applause for the enormous achievement they had gathered to celebrate: the operators had opened a shutter to the electron storage ring of the National Synchrotron Light Source II and captured light for the first time at the XPD beamline. It was the second beamline at NSLS-II to achieve x-ray beam.

    BNL NSLS II Photo
    BNL NSLS Interior
    BNL NSLS II

    team
    The beamline group at XPD during their open house for first light at the beamline. They are led by Eric Dooryhee, the Powder Diffraction Beamline Group Leader, and Associate Laboratory Director for Photon Sciences and NSLS-II Project Director Steve Dierker. Within the beamline hutch behind them stands the specially designed robotic sample changer, which will allow for high through-put data collection at the beamline.

    “This is a big day for all of us,” said Dooryhee, the Powder Diffraction Beamline Group Leader. The list of acknowledgements he made reflected the huge effort of many support groups across the Photon Sciences Directorate and beyond, that made the milestone possible: administration and procurement staff, surveyors, riggers, carpenters, vacuum specialists, mechanical and electrical utilities technicians, equipment protection and personnel safety staff, x-ray optics metrology experts, scientists, designers, and engineers. “We couldn’t have achieved our first light without the commitment and support of many collaborators around the Lab, including work with Peter Siddons and his group, who are developing several state-of-the-art detectors for XPD.”

    The XPD core team includes Sanjit Ghose, beamline scientist in charge of operating XPD and consolidating its research program; Hengzi Wang, mechanical engineer; John Trunk, beamline technician; Andrew DeSantis, mechanical designer; and Wayne Lewis, controls engineer.

    The complexity of this accomplishment came through when Dooryhee talked about the effort put in by Wayne Lewis, the controls engineer for XPD.

    “How many motors, vacuum gauges and sensors did you have to take ownership of? Hundreds?” Dooryhee asked. Lewis wryly smiled and responded, “Yeah, a few.”

    It was Lewis who ultimately opened the shutter, allowing the white x-ray beam for the first time to travel through a diamond window and several other components until it was purposely intercepted by a beam stop. Both the window and the beamstop emitted a bright fluorescent light once struck by the x-rays, and the x-ray footprint at several locations down the beam pipe could thus be imaged and shown on large screens to everyone present.

    Eventually, once commissioning starts, a monochromator will select one part of the white beam at a particular color (or wavelength). This one-color (monochromatic) x-ray beam will go past the white beam stop and will be reflected off a four-and-a-half-foot long mirror and over to the sample.

    “As we open the shutter, the beam is spot on,” said Dooryhee. “We find the beam is very stable, and we are extremely happy with these start-up conditions, thanks to the work accomplished by the Accelerator Division. This concludes 5 years of preparation and installation, and now is the beginning of a new phase for us. We have to commission the entire beamline with the x-rays on, get beam safely into the experimental station, and transition to science as soon as we can.”

    Part of this “open house” celebration at XPD was a demonstration of the 250-pound robotic sample changer, which will operate within the lead-lined hutch while the x-ray beam is on. This robot will be able to perform unmanned and repetitive collection of data on a variety of sample holders in a reliable, reproducible and fast way. XPD is designed with high throughput efficiency in mind.

    The robot will also enable landmark experiments of radioactive samples, like those proposed by Lynne Ecker of Brookhaven’s Nuclear Science and Technology Department. Ecker was awarded $980,000 from the U.S. Department of Energy’s Nuclear Energy Enabling Technologies program that will enable cross-cutting research at XPD and will fundamentally improve the safety and performance of nuclear reactors.

    “BNL is a truly outstanding environment and our chance with NSLS-II is to interact with very high-level scientific collaborators across the Laboratory, that will enable XPD to host premier work from the Center for Functional Nanomaterials, the Nuclear Energy group, Chemistry, and Physics,” said Dooryhee. “And XPD is also planning to accommodate a part of the high-pressure program at NSLS-II that includes a large volume press and diamond-anvil cells that were previously in use at NSLS, in collaboration with the COMPRES consortium and Stony Brook University.”

    The XPD beamline research will focus on studies of catalysts, batteries, and other functional and technological materials under the conditions of synthesis and operation, and Dooryhee is optimistic about the science to come. He is also excited about the intersection of XPD’s scientific program with Brookhaven’s Laboratory Directed Research and Development (LDRD) program. “Young, active, committed scientists will have access to our beamline, and will help us develop new capabilities. Current LDRD-XPD partnerships have already led to the invention of a novel slit system for probing the sample with x-rays at well controlled locations and are helping develop a new method called “Modulation Enhanced Diffraction.”

    d
    NSLS-II diffraction image

    Just before publication of this feature, Dooryhee reported that the XPD team managed to condition and focus the x-ray monochromatic beam after only three weeks of commissioning. Shown here is the first diffraction image from NSLS-II:

    The very first scientific sample run on XPD is a new material system, “TaSe2-xSx ” — Sulfur-doped Tantalum Selenide — that is being studied by Cedomir Petrovic in the Condensed Matter Physics and Materials Sciences department at Brookhaven.

    At low temperature, electrons in both the pure TaSe2 and TaS2 compounds spontaneously form into charge density waves (CDWs), like ripples on the surface of a pond, but characteristics of the waves (such as the wavelength) are different. The question is, when you vary composition smoothly from one end of the series to the other end (meaning vary x in TaSe2-xSx), how do the waves cross over from one to the other? The surprise is that in between the waves disappear and are replaced by superconductivity – the ability of the material to conduct electricity with no resistance.

    “It is like mixing red paint and white paint, and instead of getting pink you get blue after mixing,” said professor Simon Billinge, joint appointee with Brookhaven and Columbia University, who has been the spokesperson and the chair of the beamline advisory team for the XPD beamline since the inception of the project. “The data from XPD provides crucial information about how the atomic structure varies with composition which is used to understand the delicate interplay of CDW and superconducting behavior in these materials.”

    “As well as being interesting in their own right, these studies at XPD are important to understand the phenomenon of unconventional high-temperature superconductivity, currently our best hope for technological devices for low loss power transmission, where a similar interplay of CDW and superconductivity is seen,” added Dooryhee.

    See the full article here.

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  • richardmitnick 4:40 pm on November 21, 2014 Permalink | Reply
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    From SLAC: “Robotics Meet X-ray Lasers in Cutting-edge Biology Studies” 


    SLAC Lab

    November 21, 2014

    Platform Brings Speed, Precision in Determining 3-D Structure of Challenging Biological Molecules

    Scientists at the Department of Energy’s SLAC National Accelerator Laboratory are combining the speed and precision of robots with one of the brightest X-ray lasers on the planet for pioneering studies of proteins important to biology and drug discovery.

    The new system uses robotics and other automated components to precisely maneuver delicate samples for study with the X-ray laser pulses at SLAC’s Linac Coherent Light Source (LCLS). This will speed efforts to map the 3-D structures of nanoscale crystallized proteins, which are important for designing targeted drugs and synthesizing natural systems and processes.

    s
    This illustration shows an experimental setup used in crystallography experiments at SLAC’s Linac Coherent Light Source X-ray laser. The drum-shaped container at left stores supercooled crystal samples that are fetched by a robotic arm and delivered to another device, called a goniometer. The goniometer moves individual crystals through the X-ray beam, which travels from the pipe at upper left toward the lower right. A detector, right, captures X-ray diffraction patterns produced as the X-rays pass through the crystal samples. (SLAC National Accelerator Laboratory)

    i
    Equipment used in a highly automated X-ray crystallography system at SLAC’s Linac Coherent Light Source X-ray laser. The metal drum at lower left contains liquid nitrogen for cooling crystallized samples studied with LCLS’s intense X-ray pulses. (SLAC National Accelerator Laboratory)

    SLAC LCLS
    SLAC LCLS

    A New Way to Study Biology

    “This is an efficient, highly reliable and automated way to obtain high-resolution 3-D structural information from small sizes and volumes of samples, and from samples that are too delicate to study using other X-ray sources and techniques,” said Aina Cohen, who oversaw the development of the platform in collaboration with staff at LCLS and at SLAC’s Stanford Synchrotron Radiation Lightsource (SSRL), both DOE Office of Science User Facilities.

    SLAC SSRL
    SLAC SSRL

    She is co-leader of the Macromolecular Crystallography group in the Structural Molecular Biology (SMB) program at SSRL, which has used robotic sample-handling systems to run remote-controlled experiments for a decade.

    The new setup at LCLS is described in the Oct. 31 edition of Proceedings of the National Academy of Sciences. It includes a modified version of a “goniometer,” a sample-handling device in use at SSRL and many other synchrotrons, as well as a custom version of an SSRL-designed software package that pinpoints the position of crystals in arrays of samples.

    LCLS, with X-ray pulses a billion times brighter than more conventional sources, has already allowed scientists to explore biological samples too small or fragile to study in detail with other tools. The new system provides added flexibility in the type of samples and sample-holders that can be used in experiments.

    Rather than injecting millions of tiny, randomly tumbling crystallized samples into the path of the pulses in a thin liquid stream – common in biology experiments at LCLS – the goniometer-based system places crystals one at a time into the X-ray pulses. This greatly reduces the number of crystals needed for structural studies on rare and important samples that require a more controlled approach.

    Early Successes

    “This system adapts common synchrotron techniques for use at LCLS, which is very important,” said Henrik Lemke, staff scientist at LCLS. “There is a large community of scientists who are familiar with the goniometer technique.”

    The system has already been used to provide a complete picture of a protein’s structure in about 30 minutes using only five crystallized samples of an enzyme, moved one at a time into the X-rays for a sequence of atomic-scale “snapshots.”

    It has also helped to determine the atomic-scale structures of an oxygen-binding protein found in muscles, and another protein that regulates heart and other muscle and organ functions.

    “We have shown that this system works, and we can further automate it,” Cohen said. “Our goal is to make it easy for everyone to use.”

    Many biological experiments at LCLS are conducted in air-tight chambers. The new setup is designed to work in the open air and can also be used to study room-temperature samples, although most of the samples used in the system so far have been deeply chilled to preserve their structure. One goal is to speed up the system so it delivers samples and measures the resulting diffraction patterns as fast as possible, ideally as fast as LCLS delivers pulses: 120 times a second.

    The goniometer setup is the latest addition to a large toolkit of systems that deliver a variety of samples to the LCLS beam, and a new experimental station called MFX that is planned at LCLS will incorporate a permanent version.

    Team Effort

    Developed through a collaboration of SSRL’s Structural Molecular Biology program and the Stanford University School of Medicine, the LCLS goniometer system reflects increasing cooperation in the science of SSRL and LCLS, Cohen said, drawing upon key areas of expertise for SSRL and the unique capabilities of LCLS. “The combined effort of staff at both experimental facilities was key in this success,” she said.

    In addition to staff at SLAC’s SSRL and LCLS and at Stanford University’s School of Medicine, researchers from SLAC’s Photon Science Directorate, the University of Pittsburgh School of Medicine, Howard Hughes Medical Institute, Montana State University, Lawrence Berkeley National Laboratory and the University of California, San Francisco also participated in this effort.

    The work was supported by the Department of Energy Office of Basic Energy Sciences, the SSRL Structural Molecular Biology Program via the DOE Office of Biological and Environmental Research, and the Biomedical Technology Research Resources program at the National Institute of General Medical Sciences, National Institutes of Health.

    See the full article here.

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