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  • richardmitnick 7:45 pm on April 26, 2018 Permalink | Reply
    Tags: , DESY FLASH free-electron laser at Germany’s Deutsches Elektronen-Synchrotron, Flowing sheets of liquid just 100 water molecules thick that persist for days in a vacuum, Images of samples suspended in water with two types of light – infrared and ‘soft’, LBNL ALS, , Researchers used X-ray pulses to heat the liquid sheets to thousands of degrees to simulate the extremely warm dense form of water present in giant planets like Jupiter, , The nozzle is a tiny glass chip with three microscopic channels, There are many mysteries in those big planets and they’re important for understanding the evolution of our planetary system as well as others, Thin free-flowing sheets 100 times thinner than any produced before, X-Ray Scientists Create Tiny Super-Thin Sheets of Flowing Water that Shimmer Like Soap Bubbles   

    From SLAC: “X-Ray Scientists Create Tiny, Super-Thin Sheets of Flowing Water that Shimmer Like Soap Bubbles” 


    SLAC Lab

    April 26, 2018
    Glennda Chui

    The liquid sheets – less than 100 water molecules thick – will let researchers probe chemical, physical and biological processes, and even the nature of water itself, in a way they could never do before.

    1
    This tiny glass chip creates super-thin sheets of flowing liquid for X-ray experiments at SLAC’s X-ray laser, LCLS. A stream of liquid flowing through the middle channel is shaped by flows of gas coming in from the channels on either side. (Dawn Harmer/SLAC National Accelerator Laboratory.)

    Water is an essential ingredient for life as we know it, making up more than half of the adult human body and up to 90 percent of some other living things. But scientists trying to examine tiny biological samples with certain wavelengths of light haven’t been able to observe them in their natural, watery environments because the water absorbs too much of the light.

    Now there’s a way around that problem: A team led by scientists at the Department of Energy’s SLAC National Accelerator Laboratory turned tiny liquid jets that carry samples into the path of an X-ray beam into thin, free-flowing sheets, 100 times thinner than any produced before. They’re so thin that X-rays pass through them unhindered, so images of the samples they carry come out clear.

    The new method opens new windows on critical processes in chemistry, physics and biology, including the nature of water itself, the researchers said in an April 10 report in Nature Communications.

    The method was developed at SLAC’s X-ray free-electron laser, the Linac Coherent Light Source (LCLS), but they said it can also work in experiments with synchrotron light sources, tabletop lasers and electron beams.

    SLAC/LCLS

    3
    A series of movies shows how increasing flows of gas that shape a stream of liquid affects the formation of liquid sheets and their soap-bubble-like sheen.

    “This opens up possibilities in a lot of fields,” said SLAC staff scientist Jake Koralek, who led the research with Daniel DePonte, leader of the LCLS Sample Environment Department.

    “Until now, we haven’t been able to make images of samples suspended in water with two types of light – infrared and ‘soft’, lower-energy X-rays – that are important for studying basic processes in physics, chemistry and biology, including the physics of water,” Koralek said.

    “The new nozzle we developed, which can create flowing sheets of liquid just 100 water molecules thick that persist for days in a vacuum, solves that problem. The sheets can even be used to image samples with electron beams that resolve even smaller details.”

    Shaping Liquid with Gas

    The nozzle is a tiny glass chip with three microscopic channels. A stream of liquid flows through the middle channel, shaped by flows of gas coming in from the channels on either side. This particular nozzle was made with photolithography, a technique used to manufacture computer chips, but it could also be crafted with 3-D printing, the researchers noted.

    As the scientists turn up the speed of the gas flow, the liquid stream spreads into a series of sheets whose width and thickness can be precisely controlled. The sheet closest to the nozzle is the widest and thinnest; the farther they get from the nozzle, the narrower and thicker the sheets become until they finally merge into a cylindrical stream.

    53
    These images show the formation of tiny sheets of liquid shaped by jets of gas from a nozzle developed at SLAC. Top: As the gas flow increases, the liquid sheets become bigger. Bottom: The nozzle produces a series of liquid sheets; the one closest to the nozzle is the widest and thinnest. Each sheet is perpendicular to the previous one, so we are seeing the second and fourth sheets from the side.

    The sheets shimmer like soap bubbles in a variety of colors, the result of light reflecting off both the front and back surfaces of the sheet. And just as the contour lines on a topographic map mark differences in elevation, the hue and spacing of a sheet’s ever-changing bands of color indicate how thick it is and how much the thickness changes from one point to another.

    “It’s a very flexible and reliable design for creating both ultrathin and slightly thicker liquid sheets, which can be desirable for some applications” said Linda Young, a distinguished fellow at DOE’s Argonne National Laboratory and professor at the University of Chicago who was not involved in the study.

    She said she will be using the nozzle to make slightly thicker sheets of water for an LCLS study of how water molecules behave after one of their electrons has been ripped away. These ionized water molecules persist for only a few hundred femtoseconds, or millions of a billionth of a second, and “the X-rays provide a completely new and clean wayto monitor their electronic response in their natural environment, so that’s why we’re excited about it,” Young said.

    A New Way to Study Extreme Forms of Water

    The liquid sheets have already been used in experiments that explore the properties of water in extreme environments like those on giant planets, said co-author Siegfried Glenzer, a SLAC professor and head of the lab’s High Energy Density Science Division.

    Those experiments were performed with the FLASH free-electron laser at Germany’s Deutsches Elektronen-Synchrotron (DESY).

    7
    DESY FLASH free-electron laser at Germany’s Deutsches Elektronen-Synchrotron.

    Researchers used X-ray pulses to heat the liquid sheets to thousands of degrees to simulate the extremely warm, dense form of water present in giant planets like Jupiter. Then they measured the reflectivity and conductivity of the super-hot water with optical laser pulses in the instant before the water vaporized. These measurements could only be made on a flat sheet of water.

    “There are many mysteries in those big planets and they’re important for understanding the evolution of our planetary system as well as others,” Glenzer said. “This is a beautiful tool for studying water itself, and in the future we will also study other materials that we can mix into it.”

    8
    A SLAC research team at the LCLS experimental station where they carried out experiments with the sheet-forming nozzle this week. From left: Paper co-authors Zhijiang Chen, Stefan Moeller, Siegfried Glenzer, Jake Koralek and Chandra Curry and area manager Bob Sublett of the LCLS Sample Environment Department. (Dawn Harmer/SLAC National Accelerator Laboratory)

    The team measured the thickness of the sheets with a beam of infrared light at the Advanced Light Source at the DOE’s Lawrence Berkeley National Laboratory, and also demonstrated that the sheets could be used for infrared spectroscopy, where light absorbed by a material reveals its chemical makeup.

    LBNL/ALS

    LCLS and the Advanced Light Source are DOE Office of Science user facilities. In addition to researchers from SLAC, Berkeley Lab and DESY, scientists from the ELI Beamlines Institute of Physics of the Czech Academy of Sciences, Dartmouth College, the University of Alberta in Canada and the European X-ray Free-Electron Laser Facility (European XFEL) in Germany contributed to this work. Major funding came from the DOE Office of Science and the National Institutes of Health, National Institute of General Medical Sciences.

    See the full article here .

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    SLAC Campus
    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 11:27 am on April 4, 2018 Permalink | Reply
    Tags: , , , LBNL ALS, , Scientists confirm water trapped inside diamonds deep below Earth’s surface,   

    From University of Chicago: “Scientists confirm water trapped inside diamonds deep below Earth’s surface” 

    U Chicago bloc

    University of Chicago

    March 30, 2018
    Karen Mellen

    1
    Researchers working at Argonne National Laboratory have identified a form of water trapped within diamonds that crystallized deep in the Earth’s mantle. (Pictured: Rough diamond in kimberlite.) Copyright Getty Images.

    Water occurs naturally as far as at least 250 miles below the Earth’s surface, according to a study published in Science last week by researchers from the University of Chicago and others. The discovery, which relies on extremely bright X-ray beams from the Advanced Photon Source at Argonne National Laboratory, could change our understanding of how water circulates deep in the Earth’s mantle and how heat escapes from the lower regions of our planet.


    ANL/APS

    The researchers identified a form of water known as Ice-VII, which was trapped within diamonds that crystallized deep in the Earth’s mantle. This is the first time Ice-VII has been discovered in a natural sample, making the compound a new mineral accepted by the International Mineralogical Association.

    The study is the latest in a long line of research projects at the Advanced Photon Source, a massive X-ray facility used by thousands of researchers every year, which have shed light on the composition and makeup of the deep Earth. Humans cannot explore these regions directly, so the Advanced Photon Source lets them use high-powered X-ray beams to analyze inclusions in diamonds formed in the deep Earth.

    2
    UChicago researchers involved in the work at Argonne’s Advanced Photon Source included (from left): Vitali Prakapenka, Tony Lanzirotti, Matt Newville, Eran Greenberg and Dongzhou Zhang. (Photo by Rick Fenner / Argonne National Laboratory).

    “We are interested in those inclusions because they tell us about the chemical composition and conditions in the deep Earth when the diamond was formed,” said Antonio Lanzirotti, a UChicago research associate professor and co-author on the study.

    In this case, researchers analyzed rough, uncut diamonds mined from regions in China and Africa. Using an optical microscope, mineralogists first identified inclusions, or impurities, which must have formed when the diamond crystallized. But to positively identify the composition of these inclusions, mineralogists needed a stronger instrument: the University of Chicago’s GeoSoilEnviroCARS’s beam lines at the Advanced Photon Source.

    Thanks to the very high brightness of the X-rays, which are a billion times more intense than typical X-ray machines, scientists can determine the molecular or atomic makeup of specimens that are only micrometers across. When the beam of X-rays hits the molecules of the specimen, they scatter into unique patterns that reveal their molecular makeup.

    What the team identified was surprising: water, in the form of ice.

    The composition of the water is the same as the water that we drink and use every day, but in a cubic crystalline form—the result of the extremely high pressure of the diamond.

    This form of water, Ice-VII, was created in the lab decades ago, but this study was the first to confirm that it also forms naturally. Because of the pressure required for diamonds to form, the scientists know that these specimens formed between 410 and 660 kilometers (250 to 410 miles) below the Earth’s surface.

    The researchers said the significance of the study is profound because it shows that flowing water is present much deeper below the Earth’s surface than originally thought. Going forward, the results raise a number of important questions about how water is recycled in the Earth and how heat is circulated. Oliver Tschauner, the lead author on the study and a mineralogist at University of Nevada in Las Vegas, said the discovery can help scientists create new, more accurate models of what’s going on inside the Earth, specifically how and where heat is generated under the Earth’s crust. This may help scientists better understand one of the driving mechanisms for plate tectonics.

    ___________________________________________________________
    “[T]hanks to the amazing technical capabilities of the Advanced Photon Source, this team of researchers was able to pinpoint and study the exact area on the diamonds that trapped the water”
    Stephen Streiffer, associate laboratory director for photon sciences
    ___________________________________________________________

    “This wasn’t easy to find,” said Vitali Prakapenka, a UChicago research professor and a co-author of the study. “People have been searching for this kind of inclusion for a long time.”

    For now, the team is wondering whether the mineral Ice-VII will be renamed, now that it is officially a mineral. This is not the first mineral to be identified thanks to research done at the Advanced Photon Source GSECARS beamlines: Bridgmanite, the Earth’s most abundant mineral and a high-density form of magnesium iron silicate, was researched extensively there before it was named. Tschauner was a lead author on that study, too.

    “In this study, thanks to the amazing technical capabilities of the Advanced Photon Source, this team of researchers was able to pinpoint and study the exact area on the diamonds that trapped the water,” said Stephen Streiffer, Argonne associate laboratory director for photon sciences and director of the Advanced Photon Source. “That area was just a few microns wide. To put that in context, a human hair is about 75 microns wide.

    “This research, enabled by partners from the University of Chicago and the University of Nevada, Las Vegas, among other institutions, is just the latest example of how the APS is a vital tool for researchers across scientific disciplines,” he said.

    Other GSECARS co-authors are Eran Greenberg, Dongzhou Zhang and Matt Newville.

    In addition to the University of Chicago and UNLV, other institutions cited in the study include the California Institute of Technology, China University of Geosciences, the University of Hawaii at Manoa and the Royal Ontario Museum, Toronto. Data also was collected at Carnegie Institute of Washington’s High Pressure Collaborative Access Team at the Advanced Photon Source and the Advanced Light Source at Lawrence Berkeley National Lab.

    LBNL/ALS

    LBNL Advanced Light Source storage ring

    See the full article here .

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    An intellectual destination

    One of the world’s premier academic and research institutions, the University of Chicago has driven new ways of thinking since our 1890 founding. Today, UChicago is an intellectual destination that draws inspired scholars to our Hyde Park and international campuses, keeping UChicago at the nexus of ideas that challenge and change the world.

     
  • richardmitnick 3:12 pm on March 21, 2018 Permalink | Reply
    Tags: , , , LBNL ALS,   

    From LBNL: “News Center COSMIC Impact: Next-Gen X-ray Microscopy Platform Now Operational” 

    Berkeley Logo

    Berkeley Lab

    March 21, 2018

    A next-generation X-ray beamline now operating at the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) brings together a unique set of capabilities to measure the properties of materials at the nanoscale.

    Called COSMIC, for Coherent Scattering and Microscopy, this X-ray beamline at Berkeley Lab’s Berkeley Lab’s Advanced Light Source (ALS) allows scientists to probe working batteries and other active chemical reactions, and to reveal new details about magnetism and correlated electronic materials.

    1
    From left to right: Advanced Light Source scientists Tony Warwick, Sujoy Roy, and David Shapiro at the COSMIC beamline. (Credit: Lori Tamura/Berkeley Lab)

    LBNL/ALS

    COSMIC has two branches that focus on different types of X-ray experiments: one for X-ray imaging experiments and one for scattering experiments. In both cases, X-rays interact with a sample and are measured in a way that provides, structural, chemical, electronic, or magnetic information about samples.

    The beamline is also intended as an important technological bridge toward the planned ALS upgrade, dubbed ALS-U, that would maximize its capabilities.

    Now, after a first-year ramp-up during which staff tested and tuned its components, the scientific results from its earliest experiments are expected to get published in journals later this year.

    A study published earlier this month in the journal Nature Communications, based primarily on work at a related ALS beamline, successfully demonstrated a technique known as ptychographic computed tomography that mapped the location of reactions inside lithium-ion batteries in 3-D. That experiment tested the instrumentation that is now permanently installed at the COSMIC imaging facility.

    A next-generation X-ray beamline now operating at the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) brings together a unique set of capabilities to measure the properties of materials at the nanoscale.

    Called COSMIC, for Coherent Scattering and Microscopy, this X-ray beamline at Berkeley Lab’s Berkeley Lab’s Advanced Light Source (ALS) allows scientists to probe working batteries and other active chemical reactions, and to reveal new details about magnetism and correlated electronic materials.

    COSMIC has two branches that focus on different types of X-ray experiments: one for X-ray imaging experiments and one for scattering experiments. In both cases, X-rays interact with a sample and are measured in a way that provides, structural, chemical, electronic, or magnetic information about samples.

    The beamline is also intended as an important technological bridge toward the planned ALS upgrade, dubbed ALS-U, that would maximize its capabilities.

    Now, after a first-year ramp-up during which staff tested and tuned its components, the scientific results from its earliest experiments are expected to get published in journals later this year.

    A study published earlier this month in the journal Nature Communications, based primarily on work at a related ALS beamline, successfully demonstrated a technique known as ptychographic computed tomography that mapped the location of reactions inside lithium-ion batteries in 3-D. That experiment tested the instrumentation that is now permanently installed at the COSMIC imaging facility.

    “This scientific result came out of the R&D effort leading up to COSMIC,” said David Shapiro, a staff scientist in the Experimental Systems Group (ESG) at Berkeley Lab’s ALS and the lead scientist for COSMIC’s microscopy experiments.

    That result was made possible by ALS investments in R&D, and collaborations with the University of Illinois at Chicago and with Berkeley Lab’s Center for Advanced Mathematics for Energy Research Applications (CAMERA), he noted.

    3
    X-rays strike a scintillator material at the COSMIC beamline, causing it to glow. (Credit: Simon Morton/Berkeley Lab)

    “We aim to provide an entirely new class of tools for the materials sciences, as well as for environmental and life sciences,” Shapiro said. Ptychography achieves spatial resolution finer than the X-ray spot size by phase retrieval from coherent diffraction data, and “The ALS has done this with world-record spatial resolution in two and now three dimensions,” he added.

    The ptychographic tomography technique that researchers used in this latest study allowed them to view the chemical states within individual nanoparticles. Young-Sang Yu, lead author of the study and an ESG scientist, said, “We looked at a piece of a battery cathode in 3-D with a resolution that was unprecedented for X-rays. This provides new insight into battery performance both at the single-particle level and across statistically significant portions of a battery cathode.”

    COSMIC is focused on a range of “soft” or low-energy X-rays that are particularly well-suited for analysis of chemical composition within materials

    Ptychographic tomography can be particularly useful for looking at cellular components as well as batteries or other chemically diverse materials in extreme detail. Shapiro said that the X-ray beam at COSMIC is focused to a spot about 50 nanometers (billionths of a meter) in diameter; however, ptychography can enhance the spatial resolution routinely by a factor of 10 or more. The current work was performed with a 120-nanometer beam that achieved a 3-D resolution of about 11 nanometers.

    COSMIC’s X-ray beam is also brighter than the ALS beamline that was used to test its instrumentation, and it will become even brighter once ALS-U is complete. This brightness can translate to an even higher nanoscale resolution, and can also enable far more precision in time-dependent experiments.

    Making efficient use of this brightness requires fast detectors, which are developed by the ALS detector group. The current detector can operate at a data rate of up to 400 megabytes per second and can now generate a few terabytes of data per day – enough to store about 500 to 1,000 feature-length movies. Next-generation detectors, to be tested shortly, will produce data 100 times faster.

    “We are expecting to be the most data-intensive beamline at the ALS, and an important component of COSMIC is the development of advanced mathematics and computation able to quickly reconstruct information from the data as it is collected,” Shapiro said.

    To develop these tools COSMIC coupled with CAMERA, which was created to bring state-of-the-art mathematics and computing to DOE scientific facilities.

    CAMERA Director James Sethian said, “Building real-time advanced algorithms and the high-performance ptychographic reconstruction code for COSMIC has been a highly successful multiyear effort between mathematicians, computer scientists, software engineers, software experts, and beamline scientists.”

    The code the team developed to improve ptychographic imaging at COSMIC, dubbed SHARP, is now available to all light sources across the DOE complex. For COSMIC, the SHARP code runs on a dedicated graphics processing unit (GPU) cluster managed by Berkeley Lab’s High Performance Computing Services.

    Besides ptychography, COSMIC is also equipped for experiments that use X-ray photon correlation spectroscopy, or XPCS, a technique that is useful for studying fluctuations in materials associated with exotic magnetic and electronic properties.

    COSMIC enables scientists to see such fluctuations occurring in milliseconds, or thousandths of a second, compared to time increments of multiple seconds or longer at predecessor beamlines. A new COSMIC endstation with applied magnetic field and cryogenic capabilities is now being built, with early testing set to begin this summer.

    Scientists have already used COSMIC’s imaging capabilities to explore a range of nanomaterials, battery anode and cathode materials, cements, glasses, and magnetic thin films, Shapiro said.

    “We’re still in the mode of learning and tuning, but the performance is fantastic so far,” he said. He credited the ALS crew, led by ESG scientist Tony Warwick, for working quickly to bring COSMIC up to speed. “It’s pretty remarkable to get to such high performance in such a short amount of time.”

    The ALS is a DOE Office of Science User Facility. Development and deployment of the COSMIC beamline was supported by the DOE Office of Science.

    See the full article here .

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  • richardmitnick 12:53 pm on March 5, 2018 Permalink | Reply
    Tags: , , , , , LBNL ALS, , Pyrene   

    From LBNL: “Chemical Sleuthing Unravels Possible Path to the Formation of Life’s Building Blocks in Space” 

    Berkeley Logo

    Berkeley Lab

    March 5, 2018
    Glenn Roberts Jr.
    geroberts@lbl.gov
    (510) 486-5582

    Experiments at Berkeley Lab’s Advanced Light Source reveal how a hydrocarbon called pyrene could form near stars.

    LBNL/ALS

    1
    The atomic structure of pyrene molecules (upper left and upper right) are represented in an artist’s rendering of an asteroid belt, with carbon atoms shown in black and hydrogen atoms in white. A new study shows chemical steps for how pyrene, a type of hydrocarbon found in some meteorite samples, could form in space. (Credit: NASA-JPL-Caltech, Wikimedia Commons).

    Scientists have used lab experiments to retrace the chemical steps leading to the creation of complex hydrocarbons in space, showing pathways to forming 2-D carbon-based nanostructures in a mix of heated gases.

    The latest study, which featured experiments at the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab), could help explain the presence of pyrene, which is a chemical compound known as a polycyclic aromatic hydrocarbon, and similar compounds in some meteorites.

    A team of scientists, including researchers from Berkeley Lab and UC Berkeley, participated in the study, published March 5 in the Nature Astronomy journal. The study was led by scientists at the University of Hawaii at Manoa and also involved theoretical chemists at Florida International University.

    “This is how we believe some of the first carbon-based structures evolved in the universe,” said Musahid Ahmed, a scientist in Berkeley Lab’s Chemical Sciences Division who joined other team members to perform experiments at Berkeley Lab’s Advanced Light Source (ALS).

    “Starting off from simple gases, you can generate one-dimensional and two-dimensional structures, and pyrene could lead you to 2-D graphene,” Ahmed said. “From there you can get to graphite, and the evolution of more complex chemistry begins.”

    Pyrene has a molecular structure composed of 16 carbon atoms and 10 hydrogen atoms. Researchers found that the same heated chemical processes that give rise to the formation of pyrene are also relevant to combustion processes in vehicle engines, for example, and the formation of soot particles.

    The latest study builds on earlier work that analyzed hydrocarbons with smaller molecular rings that have also been observed in space, including in Saturn’s moon Titan – namely benzene and naphthalene.

    Ralf I. Kaiser, one of the study’s lead authors and a chemistry professor at the University of Hawaii at Manoa, said, “When these hydrocarbons were first seen in space, people got very excited. There was the question of how they formed.” Were they purely formed through reactions in a mix of gases, or did they form on a watery surface, for example?

    Ahmed said there is an interplay between astronomers and chemists in this detective work that seeks to retell the story of how life’s chemical precursors formed in the universe.

    “We talk to astronomers a lot because we want their help in figuring out what’s out there,” Ahmed said, “and it informs us to think about how it got there.”

    Kaiser noted that physical chemists, on the other hand, can help shine a light on reaction mechanisms that can lead to the synthesis of specific molecules in space.

    2
    A researcher handles a fragment and a test tube sample of the Murchison meteorite, which has been shown to contain a a variety of hydrocarbons and amino acids, in this photo from a previous, unrelated study at Argonne National Laboratory. Experiments at Berkeley Lab are helping to retrace the chemical steps by which complex hydrocarbons like pyrene could form in the Murchison meteorite and other meteorites. (Credit: Argonne National Laboratory)

    Pyrene belongs to a family known as polycyclic aromatic hydrocarbons, or PAHs, that are estimated to account for about 20 percent of all carbon in our galaxy. PAHs are organic molecules that are composed of a sequence of fused molecular rings. To explore how these rings develop in space, scientists work to synthesize these molecules and other surrounding molecules known to exist in space.

    Alexander M. Mebel, a chemistry professor at Florida International University who participated in the study, said, “You build them up one ring at a time, and we’ve been making these rings bigger and bigger. This is a very reductionist way of looking at the origins of life: one building block at a time.”

    For this study, researchers explored the chemical reactions stemming from a combination of a complex hydrocarbon known as the 4-phenanthrenyl radical, which has a molecular structure that includes a sequence of three rings and contains a total of 14 carbon atoms and nine hydrogen atoms, with acetylene (two carbon atoms and two hydrogen atoms).

    Chemical compounds needed for the study were not commercially available, said Felix Fischer, an assistant professor of chemistry at UC Berkeley who also contributed to the study, so his lab prepared the samples. “These chemicals are very tedious to synthesize in the laboratory,” he said.

    At the ALS, researchers injected the gas mixture into a microreactor that heated the sample to a high temperature to simulate the proximity of a star. The ALS generates beams of light, from infrared to X-ray wavelengths, to support a range of science experiments by visiting and in-house researchers.

    The mixture of gases was jetted out of the microreactor through a tiny nozzle at supersonic speeds, arresting the active chemistry within the heated cell. The research team then focused a beam of vacuum ultraviolet light from the synchrotron on the heated gas mixture that knocked away electrons (an effect known as ionization).

    They then analyzed the chemistry taking place using a charged-particle detector that measured the varied arrival times of particles that formed after ionization. These arrival times carried the telltale signatures of the parent molecules. These experimental measurements, coupled with Mebel’s theoretical calculations, helped researchers to see the intermediate steps of the chemistry at play and to confirm the production of pyrene in the reactions.

    Mebel’s work showed how pyrene (a four-ringed molecular structure) could develop from a compound known as phenanthrene (a three-ringed structure). These theoretical calculations can be useful for studying a variety of phenomena, “from combustion flames on Earth to outflows of carbon stars and the interstellar medium,” Mebel said.

    Kaiser added, “Future studies could study how to create even larger chains of ringed molecules using the same technique, and to explore how to form graphene from pyrene chemistry.”

    3
    A reaction pathway that can form a hydrocarbon called pyrene through a chemical method known as hydrogen-abstraction/acetylene-addition, or HACA, is shown at the top. At bottom, some possible steps by which pyrene can form more complex hydrocarbons via HACA (red) or another mechanism (blue) called hydrogen abstraction – vinylacetylene addition (HAVA). (Credit: Long Zhao, Ralf I. Kaiser, et al./Nature Astronomy, DOI: 10.1038/s41550-018-0399-y)

    Other experiments conducted by team members at the University of Hawaii will explore what happens when researchers mix hydrocarbon gases in icy conditions and simulate cosmic radiation to see whether that may spark the creation of life-bearing molecules.

    “Is this enough of a trigger?” Ahmed said. “There has to be some self-organization and self-assembly involved” to create life forms. “The big question is whether this is something that, inherently, the laws of physics do allow.”

    The study was supported by the U.S. Department of Energy’s Office Sciences, and UC Berkeley, the University of Hawaii, Florida International University, and the National Science Foundation.

    The ALS is a DOE Office of Science User Facility.

    See the full article here .

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  • richardmitnick 1:10 pm on January 16, 2018 Permalink | Reply
    Tags: , LBNL ALS, , X-Rays Reveal ‘Handedness’ in Swirling Electric Vortices   

    From LBNL: “X-Rays Reveal ‘Handedness’ in Swirling Electric Vortices” 

    Berkeley Logo

    Berkeley Lab

    January 15, 2018
    Glenn Roberts Jr.
    geroberts@lbl.gov
    (510) 486-5582

    1
    Just as people can be left-handed or right-handed, scientists have observed chirality or “handedness” in swirling electric vortices in a layered material. (Credit: Pixabay)

    Scientists used spiraling X-rays at the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) to observe, for the first time, a property that gives handedness to swirling electric patterns – dubbed polar vortices – in a synthetically layered material.

    This property, also known as chirality, potentially opens up a new way to store data by controlling the left- or right-handedness in the material’s array in much the same way magnetic materials are manipulated to store data as ones or zeros in a computer’s memory.

    Researchers said the behavior also could be explored for coupling to magnetic or optical (light-based) devices, which could allow better control via electrical switching.

    Chirality is present in many forms and at many scales, from the spiral-staircase design of our own DNA to the spin and drift of spiral galaxies; it can even determine whether a molecule acts as a medicine or a poison in our bodies.

    A molecular compound known as d-glucose, for example, which is an essential ingredient for human life as a form of sugar, exhibits right-handedness. Its left-handed counterpart, l-glucose, though, is not useful in human biology.

    “Chirality hadn’t been seen before in this electric structure,” said Elke Arenholz, a senior staff scientist at Berkeley Lab’s Advanced Light Source (ALS), which is home to the X-rays that were key to the study, published Jan. 15 in the journal Proceedings of the National Academy of Sciences.

    LBNL/ALS

    The experiments can distinguish between left-handed chirality and right-handed chirality in the samples’ vortices. “This offers new opportunities for fundamentally new science, with the potential to open up applications,” she said.

    “Imagine that one could convert a right-handed form of a molecule to its left-handed form by applying an electric field, or artificially engineer a material with a particular chirality,” said Ramamoorthy Ramesh, a faculty senior scientist in Berkeley Lab’s Materials Sciences Division and associate laboratory director of the Lab’s Energy Technologies Area, who co-led the latest study.

    Ramesh, who is also a professor of materials science and physics at UC Berkeley, custom-made the novel materials at UC Berkeley.

    Padraic Shafer, a research scientist at the ALS and the lead author of the study, worked with Arenholz to carry out the X-ray experiments that revealed the chirality of the material.

    The samples included a layer of lead titanate (PbTiO3) and a layer of strontium titanate (SrTiO3) sandwiched together in an alternating pattern to form a material known as a superlattice. The materials have also been studied for their tunable electrical properties that make them candidates for components in precise sensors and for other uses.

    2
    This diagram shows the setup for the X-ray experiment that explored chirality, or handedness, in a layered material. The blue and red spirals at upper left show the X-ray light that was used to probe the material. The X-rays scattered off of the layers of the material (arrows at upper right and associated X-ray images at top), allowing researchers to measure chirality in swirling electrical vortices within the material. (Credit: Berkeley Lab)

    Neither of the two compounds show any handedness by themselves, but when they were combined into the precisely layered superlattice, they developed the swirling vortex structures that exhibited chirality.

    “Chirality may have additional functionality,” Shafer said, when compared to devices that use magnetic fields to rearrange the magnetic structure of the material.

    The electronic patterns in the material that were studied at the ALS were first revealed using a powerful electron microscope at Berkeley Lab’s National Center for Electron Microscopy, a part of the Lab’s Molecular Foundry, though it took a specialized X-ray technique to identify their chirality.

    “The X-ray measurements had to be performed in extreme geometries that can’t be done by most experimental equipment,” Shafer said, using a technique known as resonant soft X-ray diffraction that probes periodic nanometer-scale details in their electronic structure and properties.

    Spiraling forms of X-rays, known as circularly polarized X-rays, allowed researchers to measure both left-handed and right-handed chirality in the samples.

    Arenholz, who is also a faculty member of the UC Berkeley Department of Materials Science & Engineering, added, “It took a lot of time to understand the results, and a lot of modeling and discussions.” Theorists at the University of Cantabria in Spain and their network of computational experts performed calculations of the vortex structures that aided in the interpretation of the X-ray data.

    The same science team is pursuing studies of other types and combinations of materials to test the effects on chirality and other properties.

    “There is a wide class of materials that could be substituted,” Shafer said, “and there is the hope that the layers could be replaced with even higher functionality materials.”

    Researchers also plan to test whether there are new ways to control the chirality in these layered materials, such as by combining materials that have electrically switchable properties with those that exhibit magnetically switchable properties.

    “Since we know so much about magnetic structures,” Arenholz said, “we could think of using this well-known connection with magnetism to implement this newly discovered property into devices.”

    The Advanced Light Source and the Molecular Foundry are both DOE Office of Science User Facilities.

    Also participating in the research were scientists from the UC Berkeley Department of Electrical Engineering and Computer Sciences, the Institute of Materials Science of Barcelona, the University of the Basque Country, and the Luxembourg Institute of Science and Technology. The work was supported by the U.S. Department of Energy Office of Science, the National Science Foundation, the Luxembourg National Research Fund, the Spanish Ministry of Economy and Competitiveness, and the Gordon and Betty Moore Foundation.

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  • richardmitnick 2:06 pm on December 12, 2017 Permalink | Reply
    Tags: Electric car makers are intensely interested in lithium-rich battery cathodes that could significantly increase driving range, LBNL ALS, Scientists Discover Path to Improving Game-Changing Battery Electrode, ,   

    From SLAC: “Scientists Discover Path to Improving Game-Changing Battery Electrode” 


    SLAC Lab

    Electric car makers are intensely interested in lithium-rich battery cathodes that could significantly increase driving range. A new study opens a path to making them live up to their promise.

    1
    Electric car makers are intensely interested in lithium-rich battery cathodes that could significantly increase driving range. A new study opens a path to making them live up to their promise. (Stanford University/3Dgraphic)

    2
    SLAC and Stanford researchers at an SSRL beamline used for battery research. From left: SLAC staff scientists Apurva Mehta and Kevin Stone; Stanford graduate students Will Gent and Kipil Lim; and SLAC distinguished staff scientist Mike Toney. (Dawn Harmer/SLAC National Accelerator Laboratory)

    December 12, 2017
    If you add more lithium to the positive electrode of a lithium-ion battery – overstuff it, in a sense ­– it can store much more charge in the same amount of space, theoretically powering an electric car 30 to 50 percent farther between charges. But these lithium-rich cathodes quickly lose voltage, and years of research have not been able to pin down why – until now.

    After looking at the problem from many angles, researchers from Stanford University, two Department of Energy national labs and the battery manufacturer Samsung created a comprehensive picture of how the same chemical processes that give these cathodes their high capacity are also linked to changes in atomic structure that sap performance.

    “This is good news,” said William E. Gent, a Stanford University graduate student and Siebel Scholar who led the study. “It gives us a promising new pathway for optimizing the voltage performance of lithium-rich cathodes by controlling the way their atomic structure evolves as a battery charges and discharges.”

    Michael Toney, a distinguished staff scientist at SLAC National Accelerator Laboratory and a co-author of the paper, added, “It is a huge deal if you can get these lithium-rich electrodes to work because they would be one of the enablers for electric cars with a much longer range. There is enormous interest in the automotive community in developing ways to implement these, and understanding what the technological barriers are may help us solve the problems that are holding them back.”

    The team’s report appears today in Nature Communications.

    The researchers studied the cathodes with a variety of X-ray techniques at SLAC’s Stanford Synchrotron Radiation Lightsource (SSRL) and Lawrence Berkeley National Laboratory’s Advanced Light Source (ALS).

    SLAC/SSRL

    LBNL/ALS

    Theorists from Berkeley Lab’s Molecular Foundry, led by David Prendergast, were also involved, helping the experimenters understand what to look for and explain their results.

    The cathodes themselves were made by Samsung Advanced Institute of Technology using commercially relevant processes, and assembled into batteries similar to those in electric vehicles.

    “This ensured that our results represented an understanding of a cutting-edge material that would be directly relevant for our industry partners,” Gent said. As an ALS doctoral fellow in residence, he was involved in both the experiments and the theoretical modelling for the study.

    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 9:28 am on November 13, 2017 Permalink | Reply
    Tags: , , Fuel Cell X-Ray Study Details Effects of Temperature and Moisture on Performance, , , LBNL ALS,   

    From LBNL: “Fuel Cell X-Ray Study Details Effects of Temperature and Moisture on Performance” 

    Berkeley Logo

    Berkeley Lab

    November 13, 2017
    Glenn Roberts Jr.
    geroberts@lbl.gov
    (510) 486-5582

    1
    This animated 3-D rendering (view larger size), generated by an X-ray-based imaging technique at Berkeley Lab’s Advanced Light Source, shows tiny pockets of water (blue) in a fibrous sample. The X-ray experiments showed how moisture and temperature can affect hydrogen fuel-cell performance. (Credit: Berkeley Lab)

    Like a well-tended greenhouse garden, a specialized type of hydrogen fuel cell – which shows promise as a clean, renewable next-generation power source for vehicles and other uses – requires precise temperature and moisture controls to be at its best. If the internal conditions are too dry or too wet, the fuel cell won’t function well.

    But seeing inside a working fuel cell at the tiny scales relevant to a fuel cell’s chemistry and physics is challenging, so scientists used X-ray-based imaging techniques at the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) and Argonne National Laboratory to study the inner workings of fuel-cell components subjected to a range of temperature and moisture conditions.

    The research team, led by Iryna Zenyuk, a former Berkeley Lab postdoctoral researcher now at Tufts University, included scientists from Berkeley Lab’s Energy Storage and Distributed Resources Division and the Advanced Light Source (ALS), an X-ray source known as a synchrotron.

    LBNL/ALS

    The ALS lets researchers image in 3-D at high resolution very quickly, allowing them to look inside working fuel cells in real-world conditions. The team created a test bed to mimic the temperature conditions of a working polymer-electrolyte fuel cell that is fed hydrogen and oxygen gases and produces water as a byproduct.

    “The water management and temperature are critical,” said Adam Weber, a staff scientist in the Energy Technologies Area at Berkeley Lab and deputy director for a multi-lab fuel cell research effort, the Fuel Cell Consortium for Performance and Durability (FC-PAD).

    The study has been published online in the journal Electrochimica Acta.

    2
    Temperature-controlled X-ray experiments on fuel-cell components were conducted at Berkeley Lab’s Advanced Light Source (bottom left) and Argonne National Laboratory’s Advanced Photon Source (bottom right).

    ANL/APS

    The computer renderings (top) show the specialized sample holder, which included a heating element near the top and cooling coils at the base. (Credit: Berkeley Lab)

    The research aims to find the right balance of humidity and temperature within the cell, and how water moves out of the cell.

    Controlling how and where water vapor condenses in a cell, for example, is critical so that it doesn’t block incoming gases that facilitate chemical reactions.

    “Water, if you don’t remove it, can cover the catalyst and prevent oxygen from reaching the reaction sites,” Weber said. But there has to be some humidity to ensure that the central membrane in the cell can efficiently conduct ions.

    The research team used an X-ray technique known as micro X-ray computed tomography to record 3-D images of a sample fuel cell measuring about 3 to 4 millimeters in diameter.

    “The ALS lets us image in 3-D at high resolution very quickly, allowing us to look inside working fuel cells in real-world conditions,” said Dula Parkinson, a research scientist at the ALS who participated in the study.

    The sample cell included thin carbon-fiber layers, known as gas-diffusion layers, which in a working cell sandwich a central polymer-based membrane coated with catalyst layers on both sides. These gas-diffusion layers help to distribute the reactant chemicals and then remove the products from the reactions.

    Weber said that the study used materials that are relevant to commercial fuel cells. Some previous studies have explored how water wicks through and is shed from fuel-cell materials, and the new study added precise temperature controls and measurements to provide new insight on how water and temperature interact in these materials.

    Complimentary experiments at the ALS and at Argonne’s Advanced Photon Source, a synchrotron that specializes in a different range of X-ray energies, provided detailed views of the water evaporation, condensation, and distribution in the cell during temperature changes.

    “It took the ALS to explore the physics of this,” Weber said, “so we can compare this to theoretical models and eventually optimize the water management process and thus the cell performance,” Weber said.

    The experiments focused on average temperatures ranging from about 95 to 122 degrees Fahrenheit, with temperature variations of 60 to 80 degrees (hotter to colder) within the cell. Measurements were taken over the course of about four hours. The results provided key information to validate water and heat models that detail fuel-cell function.

    3
    Water clusters in sample fuel-cell components shrink over time in this sequence of images, produced by a 3-D imaging technique known as micro X-ray computed tomography. The water clusters were contained in a fibrous membrane that was exposed to different temperatures. The mean temperature began at about 104 degrees Fahrenheit and was gradually increased to about 131 degrees Fahrenheit. The top side of the images was the hotter side of the sample, and the bottom of the images was the colder side. (Credit: Berkeley Lab)

    This test cell included a hot side designed to show how water evaporates at the site of the chemical reactions, and a cooler side to show how water vapor condenses and drives the bulk of the water movement in the cell.

    While the thermal conductivity of the carbon-fiber layers – their ability to transfer heat energy – decreased slightly as the moisture content declined, the study found that even the slightest degree of saturation produced nearly double the thermal conductivity of a completely dry carbon-fiber layer. Water evaporation within the cell appears to dramatically increase at about 120 degrees Fahrenheit, researchers found.

    The experiments showed water distribution with millionths-of-a-meter precision, and suggested that water transport is largely driven by two processes: the operation of the fuel cell and the purging of water from the cell.

    The study found that larger water clusters evaporate more rapidly than smaller clusters. The study also found that the shape of water clusters in the fuel cell tend to resemble flattened spheres, while voids imaged in the carbon-fiber layers tend to be somewhat football-shaped.

    There are also some ongoing studies, Weber said, to use the X-ray-based imaging technique to look inside a full subscale fuel cell one section at a time.

    “There are ways to stitch together the imaging so that you get a much larger field of view,” he said. This process is being evaluated as a way to find the origin of failure sites in cells through imaging before and after testing. A typical working subscale fuel cell measures around 50 square centimeters, he added.

    Other researchers participating in this study were from Tufts University, Argonne National Laboratory, and the Norwegian University of Science and Technology. The work was supported by the U.S. Department of Energy’s Fuel Cell Technologies Office and Office of Energy Efficiency and Renewable Energy, and the National Science Foundation.

    The Advanced Light Source and the Advanced Photon Source are DOE Office of Science User Facilities that are open to visiting scientists from around the U.S. and world.

    See the full article here .

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  • richardmitnick 12:55 pm on June 26, 2017 Permalink | Reply
    Tags: 1T’-WTe2, , , , LBNL ALS, , , , ,   

    From LBNL: “2-D Material’s Traits Could Send Electronics R&D Spinning in New Directions” 

    Berkeley Logo

    Berkeley Lab

    June 26, 2017
    Glenn Roberts Jr
    geroberts@lbl.gov
    (510) 486-5582

    1
    This animated rendering shows the atomic structure of a 2-D material known as 1T’-WTe2 that was created and studied at Berkeley Lab’s Advanced Light Source. (Credit: Berkeley Lab.)

    An international team of researchers, working at the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) and UC Berkeley, fabricated an atomically thin material and measured its exotic and durable properties that make it a promising candidate for a budding branch of electronics known as “spintronics.”

    The material – known as 1T’-WTe2 – bridges two flourishing fields of research: that of so-called 2-D materials, which include monolayer materials such as graphene that behave in different ways than their thicker forms; and topological materials, in which electrons can zip around in predictable ways with next to no resistance and regardless of defects that would ordinarily impede their movement.

    At the edges of this material, the spin of electrons – a particle property that functions a bit like a compass needle pointing either north or south – and their momentum are closely tied and predictable.

    2
    A scanning tunneling microscopy image of a 2-D material created and studied at Berkeley Lab’s Advanced Light Source (orange, background). In the upper right corner, the blue dots represent the layout of tungsten atoms and the red dots represent tellurium atoms. (Credit: Berkeley Lab.)

    This latest experimental evidence could elevate the material’s use as a test subject for next-gen applications, such as a new breed of electronic devices that manipulate its spin property to carry and store data more efficiently than present-day devices. These traits are fundamental to spintronics.

    The material is called a topological insulator because its interior surface does not conduct electricity, and its electrical conductivity (the flow of electrons) is restricted to its edges.

    “This material should be very useful for spintronics studies,” said Sung-Kwan Mo, a physicist and staff scientist at Berkeley Lab’s Advanced Light Source (ALS) who co-led the study, published today in Nature Physics.

    LBNL/ALS

    “We’re excited about the fact that we have found another family of materials where we can both explore the physics of 2-D topological insulators and do experiments that may lead to future applications,” said Zhi-Xun Shen, a professor in Physical Sciences at Stanford University and the Advisor for Science and Technology at SLAC National Accelerator Laboratory who also co-led the research effort.

    “This general class of materials is known to be robust and to hold up well under various experimental conditions, and these qualities should allow the field to develop faster,” he added.

    The material was fabricated and studied at the ALS, an X-ray research facility known as a synchrotron. Shujie Tang, a visiting postdoctoral researcher at Berkeley Lab and Stanford University, and a co-lead author in the study, was instrumental in growing 3-atom-thick crystalline samples of the material in a highly purified, vacuum-sealed compartment at the ALS, using a process known as molecular beam epitaxy.

    The high-purity samples were then studied at the ALS using a technique known as ARPES (or angle-resolved photoemission spectroscopy), which provides a powerful probe of materials’ electron properties.

    3
    Beamline 10.0.1 at Berkeley Lab’s Advanced Light Source enables researchers to both create and study atomically thin materials. (Credit: Roy Kaltschmidt/Berkeley Lab.)

    “After we refined the growth recipe, we measured it with ARPES. We immediately recognized the characteristic electronic structure of a 2-D topological insulator,” Tang said, based on theory and predictions. “We were the first ones to perform this type of measurement on this material.”

    But because the conducting part of this material, at its outermost edge, measured only a few nanometers thin – thousands of times thinner than the X-ray beam’s focus – it was difficult to positively identify all of the material’s electronic properties.

    So collaborators at UC Berkeley performed additional measurements at the atomic scale using a technique known as STM, or scanning tunneling microscopy. “STM measured its edge state directly, so that was a really key contribution,” Tang said.

    The research effort, which began in 2015, involved more than two dozen researchers in a variety of disciplines. The research team also benefited from computational work at Berkeley Lab’s National Energy Research Scientific Computing Center (NERSC).

    NERSC Cray Cori II supercomputer

    LBL NERSC Cray XC30 Edison supercomputer

    Two-dimensional materials have unique electronic properties that are considered key to adapting them for spintronics applications, and there is a very active worldwide R&D effort focused on tailoring these materials for specific uses by selectively stacking different types.

    “Researchers are trying to sandwich them on top of each other to tweak the material as they wish – like Lego blocks,” Mo said. “Now that we have experimental proof of this material’s properties, we want to stack it up with other materials to see how these properties change.”

    A typical problem in creating such designer materials from atomically thin layers is that materials typically have nanoscale defects that can be difficult to eliminate and that can affect their performance. But because 1T’-WTe2 is a topological insulator, its electronic properties are by nature resilient.

    “At the nanoscale it may not be a perfect crystal,” Mo said, “but the beauty of topological materials is that even when you have less than perfect crystals, the edge states survive. The imperfections don’t break the key properties.”

    Going forward, researchers aim to develop larger samples of the material and to discover how to selectively tune and accentuate specific properties. Besides its topological properties, its “sister materials,” which have similar properties and were also studied by the research team, are known to be light-sensitive and have useful properties for solar cells and for optoelectronics, which control light for use in electronic devices.

    The ALS and NERSC are DOE Office of Science User Facilities. Researchers from Stanford University, the Chinese Academy of Sciences, Shanghai Tech University, POSTECH in Korea, and Pusan National University in Korea also participated in this study. This work was supported by the Department of Energy’s Office of Science, the National Science Foundation, the National Science Foundation of China, the National Research Foundation (NRF) of Korea, and the Basic Science Research Program in Korea.

    See the full article here .

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  • richardmitnick 8:41 am on June 23, 2017 Permalink | Reply
    Tags: , , Building blocks of bacteria, LBNL ALS, , Organelle’s protein shell, ,   

    From LBNL: “Study Sheds Light on How Bacterial Organelles Assemble” 

    Berkeley Logo

    Berkeley Lab

    June 22, 2017
    Sarah Yang
    scyang@lbl.gov
    (510) 486-4575

    1
    Cheryl Kerfeld and Markus Sutter handle crystallized proteins at Berkeley Lab’s Advanced Light Source. (Credit: Marilyn Chung/Berkeley Lab)

    2
    Researchers at Berkeley Lab and MSU have obtained the first atomic-level view of an intact bacterial microcompartment, shown here. Credit: Markus Sutter/Berkeley Lab and MSU


    Scientists with joint appointments at DOE’s Lawrence Berkeley National Laboratory and Michigan State University reveal the building blocks of bacteria. (Video Credit: Michigan State University)

    Scientists are providing the clearest view yet of an intact bacterial microcompartment, revealing at atomic-level resolution the structure and assembly of the organelle’s protein shell.

    The work, led by scientists at the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) and Michigan State University (MSU), will appear in the June 23 issue of the journal Science. They studied the organelle shell of an ocean-dwelling slime bacteria called Haliangium ochraceum.

    “It’s pretty photogenic,” said corresponding author Cheryl Kerfeld, a Berkeley Lab structural biologist with a joint appointment as a professor at the MSU-DOE Plant Research Laboratory. “But more importantly, it provides the very first picture of the shell of an intact bacterial organelle membrane. Having the full structural view of the bacterial organelle membrane can help provide important information in fighting pathogens or bioengineering bacterial organelles for beneficial purposes.”

    These organelles, or bacterial microcompartments (BMCs), are used by some bacteria to fix carbon dioxide, Kerfeld noted. Understanding how the microcompartment membrane is assembled, as well as how it lets some compounds pass through while impeding others, could contribute to research in enhancing carbon fixation and, more broadly, bioenergy. This class of organelles also helps many types of pathogenic bacteria metabolize compounds that are not available to normal, non-pathogenic microbes, giving the pathogens a competitive advantage.

    The contents within these organelles determine their specific function, but the overall architecture of the protein membranes of BMCs are fundamentally the same, the authors noted. The microcompartment shell provides a selectively permeable barrier which separates the reactions in its interior from the rest of the cell. This enables higher efficiency of multi-step reactions, prevents undesired interference, and confines toxic compounds that may be generated by the encapsulated reactions.

    Unlike the lipid-based membranes of eukaryotic cells, bacterial microcompartments (BMCs) have polyhedral shells made of proteins.

    “What allows things through a membrane is pores,” said study lead author Markus Sutter, MSU senior research associate and affiliate scientist at Berkeley Lab’s Molecular Biophysics and Integrated Bioimaging (MBIB) division. “For lipid-based membranes, there are membrane proteins that get molecules across. For BMCs, the shell is already made of proteins, so the shell proteins of BMCs not only have a structural role, they are also responsible for selective substrate transfer across the protein membrane.”

    Earlier studies revealed the individual components that make up the BMC shell, but imaging the entire organelle was challenging because of its large mass of about 6.5 megadaltons, roughly equivalent to the mass of 6.5 million hydrogen atoms. This size of protein compartment can contain up to 300 average-sized proteins.

    The researchers were able to show how five different kinds of proteins formed three different kinds of shapes: hexagons, pentagons and a stacked pair of hexagons, which assembled together into a 20-sided icosahedral shell.

    The intact shell and component proteins were crystallized at Berkeley Lab, and X-ray diffraction data were collected at Berkeley Lab’s Advanced Light Source and the Stanford Synchrotron Radiation Lightsource, both DOE Office of Science User Facilities.

    LBNL/ALS

    SLAC/SSRL

    The study authors said that by using the structural data from this paper, researchers can design experiments to study the mechanisms for how the molecules get across this protein membrane, and to build custom organelles for carbon capture or to produce valuable compounds.

    Other co-authors of the study are Basil Greber, an affiliate of Berkeley Lab’s MBIB division and a UC Berkeley postdoctoral fellow in the California Institute for Quantitative Biosciences, and Clement Aussignargues, a postdoctoral fellow at the MSU-DOE Plant Research Laboratory.

    See the full article here .

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  • richardmitnick 5:08 pm on June 12, 2017 Permalink | Reply
    Tags: , , LBNL ALS, Researchers Find a Surprise Just Beneath the Surface in Carbon Dioxide Experiment   

    From LBNL: “Researchers Find a Surprise Just Beneath the Surface in Carbon Dioxide Experiment” 

    Berkeley Logo

    Berkeley Lab

    Caltech

    June 12, 2017
    Glenn Roberts Jr.
    geroberts@lbl.gov
    (510) 486-5582

    Berkeley Lab, Caltech team combines theory, X-ray experiments to explain what’s at work in copper catalyst

    1
    Scientists are seeking ways to reduce environmentally harmful levels of carbon dioxide from vehicle emissions and other sources by improving chemical processes that convert carbon dioxide gas into ethanol (molecular structure shown here) for use in liquid fuels, for example. X-ray experiments at Berkeley Lab have helped to show what’s at work in the early stages of chemical reactions that convert carbon dioxide and water into ethanol. (Credit: Wikimedia Commons)

    While using X-rays to study the early stages of a chemical process that can reformulate carbon dioxide into more useful compounds, including liquid fuels, researchers were surprised when the experiment taught them something new about what drives this reaction.

    An X-ray technique at the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab), coupled with theoretical work by a team at the California Institute of Technology, Pasadena (Caltech), revealed how oxygen atoms embedded very near the surface of a copper sample had a more dramatic effect on the early stages of the reaction with carbon dioxide than earlier theories could account for.

    This information could prove useful in designing new types of materials to further enhance reactions and make them more efficient in converting carbon dioxide into other products. Large concentrations of carbon dioxide are harmful to health and the environment, so researchers have been pursuing ways to remove it from the atmosphere and safely store it or chemically convert it into more beneficial forms.

    1
    This false-color scanning electron microscopy image shows microscopic details on the surface of a copper foil that was used as a catalyst in a chemical reaction studied at Berkeley Lab’s Advanced Light Source [ALS]. The scale bar represents 50 microns, or millionths of a meter. (Credit: Berkeley Lab)

    LBNL/ALS

    To explain what was at work, the research team developed computer models, and revised existing theories to explain what they were witnessing in experiments. Their results were published online June 12 in the Proceedings of the National Academy of Sciences journal.

    Copper is a common catalyst – a material used to activate and speed up chemical reactions – and, although it is not efficient, it aids in the production of ethanol when exposed to carbon dioxide and water. In the studied reaction, the copper helps to chemically break down and reassemble carbon dioxide and water molecules into other molecules.

    “We found more than we thought we were going to find from this fundamental investigation,” said Ethan Crumlin, a scientist at Berkeley Lab’s Advanced Light Source (ALS) who co-led the study with Joint Center for Artificial Photosynthesis (JCAP) researchers Junko Yano, at Berkeley Lab, and William Goddard III, at Caltech.

    The ALS is an X-ray research facility known as a synchrotron that has dozens of experimental beam lines for exploring a wide range of microscopic properties in matter, and JCAP is focused on how to convert carbon dioxide, water, and sunlight into renewable fuels.

    “Having oxygen atoms just beneath the surface – a suboxide layer – is a critical aspect to this,” Crumlin said. The X-ray work brought new clarity in determining the right amount of this subsurface oxygen – and its role in interactions with carbon dioxide gas and water – to improve the reaction.

    “Understanding this suboxide layer, and the suboxide in contact with water, is integral in how water interacts with carbon dioxide” in this type of reaction, he added.

    Goddard and his colleagues at Caltech worked closely with Berkeley Lab researchers to develop and refine a quantum mechanics theory that fit the X-ray observations and explained the electronic structure of the molecules in the reaction.

    “This was a good looping, iterative process,” Crumlin said. “Just being curious and not settling for a simple answer paid off. It all started coming together as a cohesive story.”

    Goddard said, “This back-and forth between theory and experiment is an exciting aspect of modern research and an important part of the JCAP strategy to making fuels from carbon dioxide.” The Caltech team used computers to help understand how electrons and atoms rearrange themselves in the reaction.

    At Berkeley Lab’s ALS, researchers enlisted an X-ray technique known as APXPS (ambient pressure X-ray photoelectron spectroscopy as they exposed a thin foil sheet of a specially treated copper – known as Cu(111) – to carbon dioxide gas and added water at room temperature. In proceeding experiments they heated the sample slightly in oxygen to vary the concentration of embedded oxygen in the foil, and used X-rays to probe the early stages of how carbon dioxide and water synergistically react with different amounts of subsurface oxide at the surface of the copper.

    2
    In this atomic-scale illustration, trace amounts of oxygen (red) just beneath a copper (blue) surface, play a key role in driving a catalytic reaction in which carbon dioxide (black and red molecules) and water (red and white molecules) interact in the beginning stages of forming ethanol. Carbon dioxide molecules hover at the copper surface and then bend to accept hydrogen atoms from the water molecules. X-ray experiments at Berkeley Lab’s Advanced Light Source [ALS] helped researchers to understand the role of subsurface oxygen in this process. (Credit: Berkeley Lab)

    The X-ray studies, planned and performed by Marco Favaro, the lead author of the study, revealed how carbon dioxide molecules collide with the surface of the copper, then hover above it in a weakly bound state. Interactions with water molecules serve to bend the carbon dioxide molecules in a way that allows them to strip hydrogen atoms away from the water molecules. This process eventually forms ethanol, a type of liquid fuel.

    “The modest amount of subsurface oxygen helps to generate a mixture of metallic and charged copper that can facilitate the interaction with carbon dioxide and promote further reactions when in the presence of water,” Crumlin said.

    Copper has some shortcomings as a catalyst, Yano noted, and it is currently difficult to control the final product a given catalyst will generate.

    “If we know what the surface is doing, and what the model is for this chemical interaction, then there is a way to mimic this and improve it,” Yano said. The ongoing work may also help to predict the final output of a given catalyst in a reaction. “We know that copper works – what about different copper surfaces, copper alloys, or different types of metals and alloys?”

    [The question remains.]

    See the full article here .

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