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  • richardmitnick 3:34 pm on August 22, 2014 Permalink | Reply
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    From Brookhaven Lab: “A Single Diamond Crystal Does the Job” 

    Brookhaven Lab

    August 22, 2014
    Laura Mgrdichian

    X-ray absorption spectroscopy (XAS) is a technique used in many areas of science, from biology to materials science,that allows researchers to uncover information on a sample’s molecular structure and electronic behavior by studying how it absorbs and re-emits x-rays. Recently, a research team working at the National Synchrotron Light Source developed a way to improve certain XAS experiments by replacing a standard experimental component, an x-ray beam monitor, with a diamond-based type that is better performing but has been incompatible with many XAS experiments due to technical roadblocks.

    Brookhaven NSLS
    NSLS at Brookhaven

    x scans
    X-ray absorption spectroscopy (XAS) scans over energy ranges typical of XAS experiments

    The most common type of beam monitor is an ionization chamber, which consists of a gas-filled chamber between two charged electrodes. When x-rays pass through the gas, they ionize the molecules and cause a tiny but measurable current to flow between the electrodes. By calculating backward from the amount of current, researchers can determine the “flux” of the x-ray beam; that is, the total number of x-ray photons passing through a unit area as a function of the beam energy.

    Diamond sensors, which consist of a single diamond crystal, have many advantages over ionization chambers, including faster response times, less leakage current, and smaller size. But even as electronics-grade diamond is more readily available, they have not been commonly used in XAS because they respond poorly during experiments that require scanning over a large energy range. Often the range of the scan includes the Bragg diffraction energies for diamond – x-rays with wavelengths that are diffracted by the diamond rather than transmitted through it. (If the range of the energy scan avoids this value, then diamond sensors can simply be swapped out for ionization chambers.)

    “Measuring XAS data with a diamond sensor through an energy region that produces diffraction peaks yields data that require extensive post-processing,” said the study’s corresponding scientist, Bruce Ravel of the National Institute of Standards and Technology. “We have found a way that diamond sensors can be used, at least for certain XAS experiments, without having to do so much work to the data.”

    Ravel and his colleagues, from Stony Brook University, Brookhaven National Laboratory, and Case Western Reserve University, discovered that coupling the diamond sensor to an optic component known as a “half polycapillary lens” significantly mitigates the diffraction problem. The lens consists of a bundle of tiny glass tubes encased in a steel cylinder, with one end of the tubes drawn into a taper (in a full lens, both ends are tapered). The lens “smears” the x-ray beam before it reaches the diamond sensor, causing the diffraction effect to be far less pronounced.

    “The data we gathered using both the diamond sensor and the lens are of comparable quality as data taken using an ionization chamber and no lens,” said Ravel.

    The results of their investigation have led the group to propose combination devices, with a diamond window placed onto the end of the steel cylinder that encases the glass tubes, instead of the usual beryllium window.

    X-ray data for this study were collected at NSLS beamline X23A2. The paper describing the work is published in the October 2013 issue of Review of Scientific Instruments.

    See the full article here.

    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 8:45 am on August 21, 2014 Permalink | Reply
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    From Astrobiology: “Scientists Detect Evidence of ‘Oceans Worth’ of Water in Earth’s Mantle” 

    Astrobiology Magazine

    Astrobiology Magazine

    Aug 21, 2014
    Andrew Williams

    Researchers have found evidence of a potential “ocean’s worth” of water deep beneath the United States.

    Although not present in a familiar form, the building blocks of water are bound up in rock located deep in the Earth’s mantle, and in quantities large enough to represent the largest water reservoir on the planet, according to the research.

    For many years, scientists have attempted to establish exactly how much water may be cycling between the Earth’s surface and interior reservoirs through the action of plate tectonics. Northwestern University geophysicist Steve Jacobsen and University of New Mexico seismologist Brandon Schmandt have found deep pockets of magma around 400 miles beneath North America — a strong indicator of the presence of H₂O stored in the crystal structure of high-pressure minerals at these depths.

    “The total H₂O content of the planet has long been among the most poorly constrained ‘geochemical parameters’ in Earth science. Our study has found evidence for widespread hydration of the mantle transition zone,” says Jacobsen.

    For at least 20 years geologists have known from laboratory experiments that the Earth’s transition zone — a rocky layer of the Earth’s mantle located between the lower mantle and upper mantle, at depths between 250 and 410 miles — can, in theory, hold about 1 percent of its total weight as H₂O, bound up in minerals called wadsleyite and ringwoodite. However, as Schmandt explains, up until now it has been difficult to figure out whether that potential water reservoir is empty, as many have suggested, or not.

    If there does turn out to be a substantial amount of H₂O in the transition zone, then recent laboratory experiments conducted by Jacobsen indicate there should be large quantities of what he calls “partial melt” in areas where mantle flows downward out of the zone. This water-rich silicate melt is molten rock that occurs at grain boundaries between solid mineral crystals and may account for about 1 percent of the volume of rocks.

    two
    Brandon Schmandt (University of New Mexico, left) and Steve Jacobsen (Northwestern University, right) combined seismic observations from the US-Array with laboratory experiments to detect dehydration melting of hydrous mantle material beneath North America at depths of 700-800 km. Credit: University of New Mexico/Northwestern University

    “Melting occurs because hydrated rocks are carried from the transition zone, where the rocks can hold lots of H₂O, downward into the lower mantle, where the rocks cannot hold as much H₂O. Melting is the way to get rid of the H₂O that won’t fit in the crystal structure present in the lower mantle,” says Jacobsen.

    He adds:

    “When a rock starts to melt, whatever H₂O is bound in the rock will go into the melt right away. So the melt would have much higher H₂O concentration than the remaining solid. We’re not sure how it got there. Maybe it’s been stuck there since early in Earth’s history or maybe it’s constantly being recycled by plate tectonics.”

    Seismic Waves

    Melt strongly affects the speed of seismic waves — the acoustic-like waves of energy that travel through the Earth’s layers as a result of an earthquake or explosion. This is because stiff rocks, like the silicate-rich ones present in the mantle, propagate seismic waves very quickly. According to Schmandt, if just a little melt — even 1 percent or less — is added between the crystal grains of such a rock it causes it to become less stiff, meaning that elastic waves propagate more slowly.

    “We were able to analyse seismic waves from earthquakes to look for melt in the mantle just beneath the transition zone,” says Schmandt.

    “What we found beneath the U.S. is consistent with partial melt being present in areas of downward flow out of the transition zone. Without the presence of H₂O, it is very difficult to explain melting at these depths. This is a good hint that the transition zone H₂O reservoir is not empty, and even if it’s only partially filled that could correspond to about the same mass of H₂O as in Earth’s oceans,” he adds.

    Jacobsen and Schmandt hope that their findings, published in the June issue of the journal Science, will help other scientists to understand how the Earth formed and what its current composition and inner workings are, as well as establish how much water is trapped in mantle rock.

    “I think we are finally seeing evidence for a whole-Earth water cycle, which may help explain the vast amount of liquid water on the surface of our habitable planet. Scientists have been looking for this missing deep water for decades,” says Jacobsen

    Mantle Rock Studies

    The study combined Schmandt’s analysis of seismic data from the USArray, a network of over 2,000 seismometers across the U.S., with Jacobsen’s laboratory experiments, in which he examined the behaviour of mantle rock under conditions designed to simulate the high pressures and temperatures present at 400 miles below the Earth’s surface.

    globe
    Schematic representation of seismometers placed in the US-Array between 2004 and 2014 and used in the study by Schmandt and Jacobsen to detect dehydration melting at the top of the lower mantle beneath North America. Image Credit: NSF-Earthscope

    The USArray is part of Earthscope, a program sponsored by National Science Foundation. Jacobsen’s experiments were conducted at two Department of Energy. user facilities, the Advanced Photon Source of Argonne National Laboratory and the National Synchrotron Light Source at Brookhaven National Laboratory.

    Argonne APS
    APS at Argonne Lab

    Brookhaven NSLS
    NSLS at Brookhaven

    Taken as a whole, their findings produced strong evidence that melting may occur about 400 miles deep in the Earth, with H₂O stored in mantle rocks, such as those containing the mineral ringwoodite, which is likely to be a dominant mineral at those depths.

    Schmandt explains that he made this discovery after carrying out seismic imaging of the boundary between the transition zone and lower mantle. He found evidence that, in areas where “sharp transitions” like melt are present, some earthquake energy had converted from a compressional, or longitudinal wave, to a shear or S-wave. The phase of the converted S-waves in areas where the mantle is flowing down and out of the transition zone indicated a significantly lower velocity than surrounding mantle. The discovery suggests that water from the Earth’s surface can be driven to such great depths by plate tectonics, eventually resulting in the partial melting of the rocks found deep in the mantle.

    “We used many seismic wave conversions to see that many areas beneath the U.S. may have some melt just beneath the transition zone. The next step was comparing these areas to the areas where mantle flow models predict downward flow out of the transition zone,” says Schmandt.

    Ringwoodite

    Schmandt and Jacobsen’s findings build on a discovery reported in March in the journal Nature in which scientists discovered a piece of the blue mineral ringwoodite inside a diamond brought up from a depth of 400 miles by a volcano in Brazil. That tiny piece of ringwoodite — the only sample we have from within the Earth — contained a surprising amount of water bound in solid form in the mineral.

    “Not only was this the first terrestrial ringwoodite ever seen — all other natural ringwoodite examples came from shocked meteorites — but the tiny inclusion of ringwoodite was also full of H₂O, to about 1.5 percent of total weight,” says Jacobsen. “This is about the maximum amount of water that we are able to put into ringwoodite in laboratory experiments.”

    Although the discovery provided direct evidence of water in the deep mantle at about 700 kilometers (434 miles) deep, the diamond sampled only one point of the mantle. Jacobsen explains that the paper expands the search to question how widespread hydration might be throughout the entire transition zone. This is important because the presence of H₂O in the large volumes of rock found at depths of between 410 to 660 kilometers (255 to 410 miles) would “significantly alter our understanding of the composition of the Earth.”

    Crystals of laboratory-grown hydrous ringwoodite, a high-pressure polymorph of olivine that is stable from about 520-660 km depth in the Earth’s mantle. The ringwoodite pictured here contains around one weight percent of H2O, similar to what was inferred in the seismic observations made by Schmandt and Jacobsen. Image Credit: Steve Jacobsen/Northwestern University

    Crystals of laboratory-grown hydrous ringwoodite, a high-pressure polymorph of olivine that is stable from about 520-660 km depth in the Earth’s mantle. The ringwoodite pictured here contains around one weight percent of H2O, similar to what was inferred in the seismic observations made by Schmandt and Jacobsen. Image Credit: Steve Jacobsen/Northwestern University

    “It would double or triple the known amount of H₂O in the bulk Earth. Just 1 to 2 percent H₂O by weight in the transition zone would be equivalent to 2 to 3 times the amount of H₂O in the oceans,” adds Jacobsen.

    Big Questions

    Looking ahead, Jacobsen admits that some big questions remain. For example, if the transition zone is full of H₂O, what does this tell us about the origin of Earth’s water? And is the presence of ringwoodite in a planet’s mantle necessary for a planet to retain enough original water to form oceans? Moreover, how is the H₂O in the transition zone connected to the surface reservoirs? Is the transition zone, if it contains a geochemical reservoir of H₂O larger than the oceans, somehow buffering the amount of liquid water on the Earth’s surface?

    “An analogy could be that of a sponge, which needs to be filled before liquid water can be supported on top. Was water in the transition zone added through plate tectonics early in Earth’s history, or did the oceans de-gas from the mantle until an equilibrium was reached between surface and interior reservoirs?” asks Jacobsen.

    Either way, the research is likely to be of strong interest to astrobiologists largely because water is often so closely linked to the formation of biological life. Remote geochemical analysis could be one way of detecting if such processes occur elsewhere in the universe, and it is likely that such analysis would involve the use of gamma-ray, neutron, and x-ray spectrometers of the type used by the NASA MESSENGER spacecraft for the remote geochemical mapping of Mercury.

    NASA Messenger satellite
    NASA Messenger

    “On other hard to reach planets it’s not practical to apply the type of seismic imaging that I used. So my guess is that geochemical analysis of volcanic rocks from other planetary bodies may be our best way to test whether volatiles are stored in the planet’s interior,” says Schmandt.

    See the full article here.

    NASA

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  • richardmitnick 5:33 am on August 16, 2014 Permalink | Reply
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    From Brookhaven Lab: “Harnessing the Power of Bacteria’s Sophisticated Immune System” 

    Brookhaven Lab

    August 15, 2014
    Karen McNulty Walsh, (631) 344-8350 or Peter Genzer, (631) 344-3174

    Researchers Now Better Understand How Bacteria Can So Quickly Protect Itself From Harm, Could Help Unlock Clues About Antibiotic Resistance

    Bacteria’s ability to destroy viruses has long puzzled scientists, but researchers at the Johns Hopkins Bloomberg School of Public Health say they now have a clear picture of the bacterial immune system and say its unique shape is likely why bacteria can so quickly recognize and destroy their assailants.

    The researchers drew what they say is the first-ever picture of the molecular machinery, known as Cascade, which stands guard inside bacterial cells. To their surprise, they found it contains a two-strand, unencumbered structure that resembles a ladder, freeing it to do its work faster than a standard double-helix would allow.

    The findings, published online Aug. 14 in the journal Science, may also provide clues about the spread of antibiotic resistance, which occurs when bacteria adapt to the point where antibiotics no longer work in people who need them to treat infections, since similar processes are in play. The World Health Organization (WHO) considers antibiotic resistance a major threat to public health around the world.

    “If you understand what something looks like, you can figure out what it does,” says study leader Scott Bailey, PhD, an associate professor in the Bloomberg School’s Department of Biochemistry and Molecular Biology. “And here we found a structure that nobody’s ever seen before, a structure that could explain why Cascade is so good at what it does.”

    For their study, Bailey and his colleagues used something called X-ray crystallography to draw the picture of Cascade, a key component of bacteria’s sophisticated immune system known as CRISPR, an acronym for Clustered Regularly Interspaced Short Palindromic Repeats. Cascade uses the information housed in sequences of RNA as shorthand to identify foreign invaders and kill them.

    crispr
    Diagram of the possible mechanism for CRISPR

    Much of the human immune system is well understood, but until recently scientists didn’t realize the level of complexity associated with the immune system of single-cell life forms, including bacteria. Scientists first identified CRISPR several years ago when trying to understand why bacterial cultures used to make yogurt succumbed to viral infections. Researchers subsequently discovered they could harness the CRISPR bacterial immune system to edit DNA and repair damaged genes. One group, for example, was able to remove viral DNA from human cells infected with HIV.

    Bailey’s work is focused on how Cascade is able to help bacteria fight off viruses called bacteriophages. The Cascade system uses short strands of bacterial RNA to scan the bacteriophage DNA to see if it is foreign or self. If foreign, the cell launches an attack that chews up the invading bacteriophage.

    bac
    The structure of a typical myovirus bacteriophage

    To “see” how this happens, Bailey and his team converted Cascade into a crystalized form. Technicians at the National Synchrotron Light Source at Brookhaven National Laboratory in Upton, New York, and the Stanford Synchrotron Radiation Lightsource then trained high-powered X-rays on the crystals. The X-rays provided computational data to the Bloomberg School scientists allowing them to draw Cascade, an 11-protein machine that only operates if each part is in perfect working order.

    Brookhaven NSLS
    Brookhaven NSLS

    SLAC SSRL
    SLAC SSRL

    What they saw was unexpected. Instead of the RNA and DNA wrapping around each other to form what is known as a double-helix structure, in Cascade the DNA and RNA are more like parallel lines, forming something of a ladder. Bailey says that if RNA had to wrap itself around DNA to recognize an invader – and then unwrap itself to look at the next strand – the process would take too much time to ward off infection. With a ladder structure, RNA can quickly scan DNA.

    ah
    Annie Heroux at NSLS

    In the new study, Bailey says his team determined that the RNA scans the DNA in a manner similar to how humans scan text for a key word. They break long stretches of characters into smaller bite-sized segments, much like words themselves, so they can be spotted more easily.

    Since the CRISPR-Cas system naturally acts as a barrier to the exchange of genetic information between bacteria and bacteriophages, its function can offer clues to how antibiotic resistance develops and ideas for how to keep it from happening.

    “We’re finding more pieces to the puzzle,” Bailey says. “This gives us a better understanding of how these machines find their targets, which may help us harness the CRISPR system as a tool for therapy or manipulation of DNA in a lab setting. And it all started when someone wanted to make yogurt more cheaply.”

    “Crystal structure of a CRISPR RNA-guided surveillance complex bound to a ssDNA target” was written by Sabin Mulepati, Annie Heroux and Scott Bailey.

    This work was funded by a grant from the National Institute of Health’s National Institute of General Medical Sciences (GM097330).

    See the full article here.

    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 8:49 am on August 6, 2014 Permalink | Reply
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    From Brookhaven Lab: “New Method Provides Nanoscale Details of Electrochemical Reactions in Electric Vehicle Battery Materials” 

    Brookhaven Lab

    August 4, 2014
    Karen McNulty Walsh, (631) 344-8350 or Peter Genzer, (631) 344-3174

    Using a new method to track the electrochemical reactions in a common electric vehicle battery material under operating conditions, scientists at the U.S. Department of Energy’s Brookhaven National Laboratory have revealed new insight into why fast charging inhibits this material’s performance. The study also provides the first direct experimental evidence to support a particular model of the electrochemical reaction. The results, published August 4, 2014, in Nature Communications, could provide guidance to inform battery makers’ efforts to optimize materials for faster-charging batteries with higher capacity.

    three
    Jiajun Wang, Karen Chen and Jun Wang prepare a sample for study at NSLS beamline X8C.

    “This is the first time anyone has been able to see that delithiation was happening differently at different spatial locations on an electrode under rapid charging conditions.”
    — Brookhaven physicist Jun Wang

    “Our work was focused on developing a method to track structural and electrochemical changes at the nanoscale as the battery material was charging,” said Brookhaven physicist Jun Wang, who led the research. Her group was particularly interested in chemically mapping what happens in lithium iron phosphate—a material commonly used in the cathode, or positive electrode, of electrical vehicle batteries—as the battery charged. “We wanted to catch and monitor the phase transformation that takes place in the cathode as lithium ions move from the cathode to the anode,” she said.

    Getting as many lithium ions as possible to move from cathode to anode through this process, known as delithiation, is the key to recharging the battery to its fullest capacity so it will be able to provide power for the longest possible period of time. Understanding the subtle details of why that doesn’t always happen could ultimately lead to ways to improve battery performance, enabling electric vehicles to travel farther before needing to be recharged.

    X-ray imaging and chemical fingerprinting

    mapping
    In operando 2D chemical mapping of multi particle lithium iron phosphate cathode during fast charging (top to bottom). The called-out close-up frame shows that as the sample charges, some regions become completely delithiated (green) while others remain completely lithiated (red). This inhomogeneity results in a lower overall battery capacity than can be attained with slower charging, where delithiation occurs more evenly throughout the electrode. No image credit

    Many previous methods used to analyze such battery materials have produced data that average out effects over the entire electrode. These methods lack the spatial resolution needed for chemical mapping or nanoscale imaging, and are likely to overlook possible small-scale effects and local differences within the sample, Wang explained.

    To improve upon those methods, the Brookhaven team used a combination of full- field, nanoscale-resolution transmission x-ray microscopy (TXM) and x-ray absorption near-edge spectroscopy (XANES) at the National Synchrotron Light Source (NSLS), a DOE Office of Science User Facility that provides beams of high-intensity x-rays for studies in many areas of science. These x-rays can penetrate the material to produce both high-resolution images and spectroscopic data—a sort of electrochemical “fingerprint” that reveals, pixel by pixel, where lithium ions remain in the material, where they’ve been removed leaving only iron phosphate, and other potentially interesting electrochemical details.

    The scientists used these methods to analyze samples made up of multiple nanoscale particles in a real battery electrode under operating conditions (in operando). But because there can be a lot of overlap of particles in these samples, they also conducted the same in operando study using smaller amounts of electrode material than would be found in a typical battery. This allowed them to gain further insight into how the delithiation reaction proceeds within individual particles without overlap. They studied each system (multi-particle and individual particles) under two different charging scenarios—rapid (like you’d get at an electric vehicle recharging station), and slow (used when plugging in your vehicle at home overnight).

    Insight into why charging rate matters

    The detailed images and spectroscopic information reveal unprecedented insight into why fast charging reduces battery capacity. At the fast charging rate, the pixel-by-pixel images show that the transformation from lithiated to delithiated iron phosphate proceeds inhomogeneously. That is, in some regions of the electrode, all the lithium ions are removed leaving only iron phosphate behind, while particles in other areas show no change at all, retaining their lithium ions. Even in the “fully charged” state, some particles retain lithium and the electrode’s capacity is well below the maximum level.

    “This is the first time anyone has been able to see that delithiation was happening differently at different spatial locations on an electrode under rapid charging conditions,” Jun Wang said.

    Slower charging, in contrast, results in homogeneous delithiation, where lithium iron phosphate particles throughout the electrode gradually change over to pure iron phosphate—and the electrode has a higher capacity.

    Implications for better battery design

    Scientists have known for a while that slow charging is better for this material, “but people don’t want to charge slowly,” said Jiajun Wang, the lead author of the paper. “Instead, we want to know why fast charging gives lower capacity. Our results offer clues to explain why, and could give industry guidance to help them develop a future fast-charge/high-capacity battery,” he said.

    For example, the phase transformation may happen more efficiently in some parts of the electrode than others due to inconsistencies in the physical structure or composition of the electrode—for example, its thickness or how porous it is. “So rather than focusing only on the battery materials’ individual features, manufacturers might want to look at ways to prepare the electrode so that all parts of it are the same, so all particles can be involved in the reaction instead of just some,” he said.

    The individual-particle study also detected, for the first time, the coexistence of two distinct phases—lithiated iron phosphate and delithiated, or pure, iron phosphate—within single particles. This finding confirms one model of the delithiation phase transformation—namely that it proceeds from one phase to the other without the existence of an intermediate phase.

    “These discoveries provide the fundamental basis for the development of improved battery materials,” said Jun Wang. “In addition, this work demonstrates the unique capability of applying nanoscale imaging and spectroscopic techniques in understanding battery materials with a complex mechanism in real battery operational conditions.”

    The paper notes that this in operando approach could be applied in other fields, such as studies of fuel cells and catalysts, and in environmental and biological sciences.

    Future studies using these techniques at NSLS-II—which will produce x-rays 10,000 times brighter than those at NSLS—will have even greater resolution and provide deeper insight into the physical and electrochemical characteristics of these materials, thus making it possible for scientists to further elucidate how those properties affect performance.

    Yu-chen Karen Chen-Wiegart also contributed to this research. This work was supported by a Laboratory Directed Research and Development (LDRD) project at Brookhaven National Laboratory. The use of the NSLS was supported by the U.S. Department of Energy’s Office of Science.

    See the full article here.

    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 3:45 pm on June 6, 2014 Permalink | Reply
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    From Brookhaven LAB: “Scientists Reveal Details of Calcium ‘Safety-Valve’ in Cells” 

    Brookhaven Lab

    Structure of membrane protein that plays a role in signaling cell death could be new target for anticancer drugs

    June 6, 2014
    Karen McNulty Walsh

    Sometimes a cell has to die—when it’s done with its job or inflicted with injury that could otherwise harm an organism. Conversely, cells that refuse to die when expected can lead to cancer. So scientists interested in fighting cancer have been keenly interested in learning the details of “programmed cell death.” They want to understand what happens when this process goes awry and identify new targets for anticancer drugs.

    The details of one such target have just been identified by a group of scientists from the U.S. Department of Energy’s Brookhaven National Laboratory, Columbia University, New York University, Baylor College of Medicine, Technical University of Munich, and the New York Structural Biology Center. The group, known as the New York Consortium on Membrane Protein Structure (NYCOMPS), used x-rays at Brookhaven Lab’s National Synchrotron Light Source (NSLS) to decipher the atomic level structure of a protein that regulates the level of calcium in cells. The work is described as a research article published in Science June 6, 2014.

    “The accumulation of calcium is a key signaling agent that can trigger programmed cell death, or apoptosis,” explained Wayne Hendrickson of Columbia and Brookhaven, and the director of NYCOMPS as well as a senior author on the paper. “Our study reveals how this protein, embedded in a cellular membrane structure called the endoplasmic reticulum, serves as a molecular safety valve for keeping calcium levels steady. Designing drugs that inhibit this protein would promote cell death, which could be a promising strategy for fighting cancers in which such proteins are overexpressed.”

    cal
    A calcium-leak channel prevents calcium overload in cellular organelles for protection of life. Viewing from within the membrane, the structure is shown as ribbons for the closed-conformation. The di-aspartyl pH-sensor unit and the arginine/aspartate lock are shown as sticks covered by electron densities in magenta.

    3-D Model for Rational Drug Design

    The protein that the scientists studied is a prokaryotic homolog of human “Transmembrane Bax Inhibitor Motif” (TMBIM) proteins, which come in six varieties. TMBIM6 is overexpressed in various cancers—including prostate, breast, glioma, uterine, ovarian, and lung.

    “Our work using the prokaryotic version of this protein has enabled us to construct a three-dimensional model that can be used as a basis for the rational design of possible inhibitor molecules,” said Qun Liu, a scientist at NSLS and NYCOMPS and the lead author on the paper.

    The atomic-level structures were determined using x-ray crystallography at NSLS beamlines X4A and X4C. Interactions of x-rays with the 3-D lattices of the protein molecules produce diffraction patterns from which the 3-D molecular images were derived. The images reveal a novel structure consisting of a centralized helix wrapped by two novel triple-helix sandwiches that traverse the membrane. The central portion can take on an open or closed conformation dependent on the acidity level, or pH. At physiological pH, open and closed conformations exist in equilibrium, maintaining a steady of state of calcium in the cell by allowing gradual leakage of calcium across the membrane through a transient transmembrane pore.

    “This leak is intrinsic to all kinds of cells and is cytoprotective for life, similar to a pressure safety value used in a standard steam boiler for safety assurance,” said Liu.

    The studies reveal in detail how the TMBIM protein senses and responds to changes in acidity to precisely regulate the mechanism.

    “The next step will be to solve crystal structures of the human TMBIM proteins to refine the design of possible inhibitor drugs,” said Liu.

    That work will take place at a new light source nearing completion at Brookhaven known as NSLS-II. That facility, set to start early experiments later this year, will be 10,000 times brighter than NSLS, making it particularly suitable for studies of membrane proteins, which are difficult to crystallize.

    Brookhaven NSLS II Photo
    Brookhaven NSLS II

    The New York Structural Biology Center is working in partnership with Photon Sciences at Brookhaven to build a microdiffraction beamline, called NYX, for advanced studies of biological molecules at NSLS-II.

    This research was supported in part by the National Institutes of Health (NIH) grant GM095315 and GM107462. The NSLS at Brookhaven Lab is a DOE Office of Science user facility, with beamlines X4A and X4C supported by the New York Structural Biology Center.

    See the full article here.

    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 3:49 pm on April 22, 2014 Permalink | Reply
    Tags: , Brookhaven NSLS, , ,   

    From Brookhaven Lab: “Disorder on the Nanoscale May Be Responsible for Solar-cell Efficiency” 

    Brookhaven Lab

    April 22, 2014
    Chelsea Whyte

    In the past few years, perovskite solar cells have made large leaps forward in efficiency, recently achieving energy conversion with up to 16 percent efficiency. These simple and promising devices are easy enough to make and are made up of earth abundant materials, but little work has been done to explore their atomic makeup.

    ml
    Methylammonium lead iodide perovskite

    Researchers at Brookhaven National Laboratory and Columbia University used high-energy x-rays at the National Synchrotron Light Source (NSLS) to characterize the structure of methylammonium lead iodide (MAPbI3) in titanium oxide – the active material in high-performance perovskite solar cells. Their results are reported in a paper published online in Nano Letters on November 22, 2013.

    Brookhaven NSLS
    Brookhaven NSLS

    Photoluminescent properties of these materials are thought to depend sensitively on the degree of structural order and defects. To characterize the structure, the researchers used beamline X17A at NSLS to study samples of the MAPbI3. Atomic pair distribution function analysis of x-ray diffraction data revealed that 30 percent of the material forms a tetragonal perovskite phase, while 70 percent exists in a disordered state. The presence of disordered material correlates with strong changes in the photoluminescence and absorbance spectra.

    This disordered structure has been undetected by conventional x-ray diffraction techniques used in previous studies. “This nanostructure is expected to have a significant impact on the optoelectronic properties and device performance of the perovskites,” said Simon Billinge, coauthor on the paper and a physicist with a joint appointment at Brookhaven National Laboratory and Columbia University.

    For example, the absorption of this composite material, made of both ordered and disordered states, is blue shifted by about 50 meV compared to the bulk perovskite crystalline structure. They also found that disordered MAPbI3 is photoluminescent, while the crystalline material is not.

    This new understanding of the structure of these materials will lead to better deposition and processing methods that may increase the performance and efficiency of future solar cells.

    The high-energy x-ray atomic pair distribution function analysis performed in this paper will be applied to a wide range of even more challenging problems at the higher brightness XPD-2 beamline (PDF) at NSLS-II.

    Brookhaven NSLS II Photo
    NSLS-II at Brookhaven Lab

    See the full article here.

    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 8:16 pm on April 21, 2014 Permalink | Reply
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    From Brookhaven Lab: “A New Approach to Engineering the Materials of the Future” 

    Brookhaven Lab

    April 21, 2014
    Laura Mgrdichian

    Some of the most interesting and fascinating electronic devices that will someday be available to consumers, from paper-thin computers to electronic fabric, will be the result of advanced materials designed by scientists. Indeed, some remarkable discoveries have already been made. To innovate further, scientists must learn how to precisely engineer the chemical structures of materials at the nanoscale in such a way as to yield specific macroscopic properties and functions.

    A research group, jointly working at the National Synchrotron Light Source, has found a new way to do just that. They have synthesized a new class of macromolecules that organize themselves, or “self-assemble,” into various ordered structures with feature sizes smaller than 10 nanometers. Called “giant surfactants,” these large molecules mimic the structural features of small surfactants (substances that significantly lower the surface tension between two liquids, such as detergents), but have been transformed into functional molecular nanoparticles by being “clicked” with polymer chains. The resulting materials are unique because they bridge the gap between small molecule surfactants and traditional block copolymers and thus possess an interesting “duality” in their self-assembly behaviors.

    Brookhaven NSLS
    Brookhaven NSLS

    new
    Transmission electron microscope (TEM) images and GISAXS paEerns (insets) of two giant surfactant thin‐film samples. The TEM images show ordered nanoscale paEerns.

    “This class of materials provides a versatile platform for engineering nanostructures that have features smaller than 10 nanometers, which is a scale that is very relevant to the blueprints of nanotechnology and microelectronics,” said the study’s corresponding scientist Stephen Cheng, a researcher in the University of Akron’s College of Polymer Science and Polymer Engineering. “More broadly, we are also interested in how our results could help advance our understanding of the chemical and physical principles that underlie self-assembly.”

    Surfactants play a huge role in our everyday life, although most people are unaware of them. They are present in household cleaners and soaps, adhesives, paint, ink, plastics, and many, many other products. Naturally, they are a key part of materials research.

    Giant surfactants have the potential to be even more versatile than their smaller counterparts because they have the advantages of both a polymer and a surfactant. They are of particular interest to the electronics industry because they can spontaneously self-assemble into nanodomains just a few nanometers in size. This length scale must be achieved in order to allow the continual downsizing of computer chips but proven very difficult to achieve for conventional technologies. The production of nanopatterned thin films – which are the foundation of modern computer chips – could be directly affected by giant surfactants. If films can be produced with smaller nanoscale features, they could lead to denser, faster computer chips.

    The group used several techniques to study different giant surfactant samples in thin-film form, as well as in bulk form and in solution. These techniques included grazing-incidence small-angle x-ray scattering (GISAXS) at NSLS beamline X9. GISAXS is suited to studying thin film samples that have ordered nanoscale features, typically between 5 and 20 nanometers, and can tell researchers about the shape, size, and orientation of these features, among other information. It is widely used to study self-assembled thin films with nanoscale features.

    This research is published in the June 18, 2013 issue of the Proceedings of the National Academy of Sciences. The team, which includes scientists from the University of Akron, National Tsing Hua University (Taiwan), McMaster University (Canada), and Peking University (China), has also described this research in a pending patent application.

    See the full article here.

    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 12:04 pm on November 19, 2013 Permalink | Reply
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    From Brookhaven Lab: “Infrared Light Fills a ‘Gap’ in Iron-based Superconductor Research” 

    Brookhaven Lab

    November 18, 2013
    Laura Mgrdichian

    Superconductors are a fascinating group of materials in which electrons can flow with almost zero resistance. They have the potential to revolutionize electronics and power distribution, but no existing superconductors have an ideal combination of properties necessary to realize these applications. To design the ideal superconductor, scientists need a complete understanding of the complex, atomic-level electrical and magnetic behaviors that produce the phenomenon.

    Many groups have focused their efforts on “high-temperature” (high-Tc) superconductors that operate at temperatures well above the conventional superconducting materials. Conventional superconductors must be chilled to almost absolute zero (the coldest temperature possible), making them impractical for many applications. The most widely studied high-Tc materials, known as cuprates because they contain layers of copper and oxygen atoms, avoid the ultra-low temperature requirement, but exhibit other properties that limit their practical use.

    Recently, a new family of iron-based superconductors was discovered that do not seem to superconduct in the same way as conventional superconductors or quite like the cuprates. This iron-based family has been found to be quite large and diverse, so physicists are hoping that studying all of its members will yield a clear picture of how they operate, and point the way to a high-Tc material that has other necessary properties.

    graph
    (a) Data taken from 3 to 30K showing the temperature dependence of infrared transmission through the LaFeAsO1-‐xFx thin film, normalized to the transmission at 33K (b) Time-‐resolved infrared transmission data through the sample from about 2K to 15K. The slow (ns) relaxation time indicates the presence of a full superconducting gap.

    In this work, researchers from Brookhaven National Laboratory and the Leibniz Institute for Solid State Physics in Dresden, Germany, investigated an iron pnictide compound composed of lanthanum (La), iron (Fe), arsenic (As), oxygen (O), and an added fluorine (F) “dopant” that replaces about 10 percent of the O atoms. Abbreviated LaFeAsO1-xFx (the ‘x’ denotes the number of F and, therefore, O atoms per molecule), it was the first iron-based superconductor found to operate at temperatures higher than most conventional superconductors. Still, little is known about how it works.

    This work may be a key step in changing that. Using beams of infrared light produced at Brookhaven’s National Synchrotron Light Source, the group discovered evidence that LaFeAsO1-xFx has a full “superconducting gap” – the energy required for electrons in the lowest energy state, the ground state, to “jump” into higher energy levels. This gap is one hallmark of a superconductor and an indicator of its performance under certain conditions. For example, the gap in the cuprates actually disappears for electrons traveling in certain directions.

    “Understanding the details of the gap is essential for unraveling the superconducting mechanism, yet questions about gap structure in this material have persisted even after years of research,” said Brookhaven researcher Xiaoxiang Xi, who was the lead experimenter in the study. “Establishing these details experimentally, as we have done, puts constraints on the possible theories that could explain the origin of the superconductivity in these materials.”

    See the full article here.

    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 11:03 am on November 15, 2013 Permalink | Reply
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    From Brookhaven Lab: “Small Particles, Big Findings” 

    Brookhaven Lab

    November 15, 2013
    Karen McNulty Walsh

    Sometimes big change comes from small beginnings. That’s especially true in the research of Anatoly Frenkel, a professor of physics at Yeshiva University, who is working to reinvent the way we use and produce energy by unlocking the potential of some of the world’s tiniest structures: nanoparticles.

    “The nanoparticle is the smallest unit in most novel materials, and all of its properties are linked in one way or another to its structure,” said Frenkel. “If we can understand that connection, we can derive much more information about how it can be used for catalysis, energy, and other purposes.”

    three
    Eric Stach and Dmitri Zakharov of the CFN with Anatoly Frenkel of Yeshiva University and his postdoc, Yuanyuan Li, sitting at the Titan 80/300 Environmental Transmission Electron Microscope at the CFN.

    “This work could lead to big gains in energy efficiency and cost savings for industrial processes.” — Eric Stach, CFN

    Frenkel is collaborating with materials scientist Eric Stach and others at the U.S. Department of Energy’s Brookhaven National Laboratory to develop new ways to study how nanoparticles behave in catalysts—the “kick-starters” of chemical reactions that convert fuels to useable forms of energy and transform raw materials to industrial products.

    “We are developing a new ‘micro-reactor’ that enables us to explore many aspects of catalytic function using multiple approaches at Brookhaven’s National Synchrotron Light Source (NSLS), the soon-to-be-completed NSLS-II, and the Center for Functional Nanomaterials (CFN),” said Stach, who works at the CFN. “This approach lets us understand multiple aspects of how catalysts work so that we can tweak their design to improve their function. This work could lead to big gains in energy efficiency and cost savings for industrial processes.”

    See the full article here.

    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 9:41 am on November 7, 2013 Permalink | Reply
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    From Brookhaven Lab: “New Camera Reveals How Light Breaks Molecules Apart” 

    Brookhaven Lab

    November 4, 2013
    Andrei Nomerotski and Michael White

    Way beyond pure illumination—from bright sunshine to intense x-rays at the National Synchrotron Light Source (NSLS)—light can pack a powerful punch down at the atomic scale. When light strikes organic compounds bound to certain surfaces, it can split them into atomic and molecular fragments called photoproducts. These fractured pieces offer crucial clues to how and why light breaks some chemical bonds, which is at the core of understanding how solar energy can be used to remove pollutants from the environment.

    Just one organic molecule can break into many photoproducts and capturing each one presents a considerable, time-consuming challenge. We used a highly specialized system—the Pixel Imaging Mass Spectrometry (PImMS) camera—to bring this light-induced process into focus. Results of our experiments using the new PImMS camera to capture these telltale photoproducts were just published in the Journal of Chemical Physics and highlighted in Physics Today. With PImMS performing beautifully, the technology could also be used in research at NSLS-II and the proposed electron-ion collider, eRHIC.

    camera
    From left: Physicist Andrei Nomerotski, Stony Brook University graduate student Matt Kershis, and chemist Michael White use this instrument to prepare organic molecule samples for tests with the new PImMS camera.

    Tracking Photoproducts, Pre-PImMS

    Several years ago, Michael and his colleagues in the Chemistry Department began exploring how ultraviolet (UV) light can cause organic molecules on titanium dioxide surfaces to decompose into photoproducts. This important reaction, called photo-oxidation, removes organic pollutants from air and water and is the basis for windows and building exteriors’ self-cleaning coatings.

    Before PImMS, we used a technique called ion imaging and a conventional imaging camera—with a charge-coupled device (CCD) sensor similar to those in consumer cameras—to track photoproducts that struck a two-dimensional detector. But in this method, each of these many photoproducts must be captured as individual images, requiring multiple sample preparations and time-consuming repetition. We needed a better camera to catch all the action.

    Enter the PImMS Camera

    Fortunately, an Oxford University group—including Andrei, who only recently joined Brookhaven’s Physics Department to work on the Large Synoptic Survey Telescope—developed a new camera capable of conventional imaging while simultaneously measuring the arrival time for each photoproduct that strikes the detector. This information acts much like a photographic time stamp and could essentially reveal all the photoproducts with a single image exposure.

    Now, instead of repeatedly capturing and reading out whole frames, one after another, PImMS records up to four ion arrival times inside each pixel, a bit like multiple exposures on a film camera. We then read out the sensor just once at the very end of the experimental cycle to gather all that information, accelerating the entire process. In fact, the PImMS camera has an effective imaging speed of just 10 nanoseconds—that’s 100,000 times faster than a conventional CCD camera—and experimental cycles can now take 25 percent of the time they used to. The new sensor combines time-of-flight mass spectrometry to identify multiple molecules, and sensitive ion imaging, which revolutionized the field of chemical reaction dynamics.

    See the full article here.

    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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