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  • richardmitnick 10:06 am on June 23, 2017 Permalink | Reply
    Tags: , BNL NSLS, , , , Improve the performance of fuel cells that run on hydrogen fuel but can be poisoned by CO, , Peking University, Taiyuan University of Technology China   

    From BNL: “New Efficient, Low-Temperature Catalyst for Converting Water and CO to Hydrogen Gas and CO2” 

    Brookhaven Lab

    June 22, 2017
    Karen McNulty Walsh
    kmcnulty@bnl.gov
    (631) 344-8350

    Peter Genzer
    genzer@bnl.gov
    (631) 344-3174

    Low-temperature “water gas shift” reaction produces high levels of pure hydrogen for potential applications, including fuel cells.

    1
    Brookhaven Lab chemists Ping Liu and José Rodriguez helped to characterize structural and mechanistic details of a new low-temperature catalyst for producing high-purity hydrogen gas from water and carbon monoxide. No image credit.

    Scientists have developed a new low-temperature catalyst for producing high-purity hydrogen gas while simultaneously using up carbon monoxide (CO). The discovery—described in a paper set to publish online in the journal Science on Thursday, June 22, 2017—could improve the performance of fuel cells that run on hydrogen fuel but can be poisoned by CO.

    “This catalyst produces a purer form of hydrogen to feed into the fuel cell,” said José Rodriguez, a chemist at the U.S. Department of Energy’s (DOE) Brookhaven National Laboratory. Rodriguez and colleagues in Brookhaven’s Chemistry Division—Ping Liu and Wenqian Xu—were among the team of scientists who helped to characterize the structural and mechanistic details of the catalyst, which was synthesized and tested by collaborators at Peking University in an effort led by Chemistry Professor Ding Ma.

    Because the catalyst operates at low temperature and low pressure to convert water (H2O) and carbon monoxide (CO) to hydrogen gas (H2) and carbon dioxide (CO2), it could also lower the cost of running this so-called “water gas shift” reaction.

    “With low temperature and pressure, the energy consumption will be lower and the experimental setup will be less expensive and easier to use in small settings, like fuel cells for cars,” Rodriguez said.

    The gold-carbide connection

    The catalyst consists of clusters of gold nanoparticles layered on a molybdenum-carbide substrate. This chemical combination is quite different from the oxide-based catalysts used to power the water gas shift reaction in large-scale industrial hydrogen production facilities.

    “Carbides are more chemically reactive than oxides,” said Rodriguez, “and the gold-carbide interface has good properties for the water gas shift reaction; it interacts better with water than pure metals.”

    2
    Wenqian Xu and José Rodriguez of Brookhaven Lab and Siyu Yao, then a student at Peking University but now a postdoctoral research fellow at Brookhaven, conducted operando x-ray diffraction studies of the gold-molybdenum-carbide catalyst over a range of temperatures (423 Kelvin to 623K) at the National Synchrotron Light Source (NSLS) at Brookhaven Lab. The study revealed that at temperatures above 500K, molybdenum-carbide transforms to molybdenum oxide, with a reduction in catalytic activity. No image credit

    “The group at Peking University discovered a new synthetic method, and that was a real breakthrough,” Rodriguez said. “They found a way to get a specific phase—or configuration of the atoms—that is highly active for this reaction.”

    Brookhaven scientists played a key role in deciphering the reasons for the high catalytic activity of this configuration. Rodriguez, Wenqian Xu, and Siyu Yao (then a student at Peking University but now a postdoctoral research fellow at Brookhaven) conducted structural studies using x-ray diffraction at the National Synchrotron Light Source (NSLS) while the catalyst was operating under industrial or technical conditions.

    BNL NSLS

    These operando experiments revealed crucial details about how the structure changed under different operating conditions, including at different temperatures.

    With those structural details in hand, Zhijun Zuo, a visiting professor at Brookhaven from Taiyuan University of Technology, China, and Brookhaven chemist Ping Liu helped to develop models and a theoretical framework to explain why the catalyst works the way it does, using computational resources at Brookhaven’s Center for Functional Nanomaterials (CFN).

    “We modeled different interfaces of gold and molybdenum carbide and studied the reaction mechanism to identify exactly where the reactions take place—the active sites where atoms are binding, and how bonds are breaking and reforming,” she said.

    Additional studies at Oak Ridge National Laboratory’s Center for Nanophase Materials Sciences (CNMS), the Advanced Light Source (ALS) at Lawrence Berkeley National Laboratory, and two synchrotron research facilities in China added to the scientists’ understanding.

    “This is a multipart complex reaction,” said Liu, but she noted one essential factor: “The interaction between the gold and the carbide substrate is very important. Gold usually bonds things very weakly. With this synthesis method we get stronger adherence of gold to molybdenum carbide in a controlled way.”

    That configuration stabilizes the key intermediate that forms as the reaction proceeds, and the stability of that intermediate determines the rate of hydrogen production, she said.

    The Brookhaven team will continue to study this and other carbide catalysts with new capabilities at the National Synchrotron Light Source II (NSLS-II), a new facility that opened at Brookhaven Lab in 2014, replacing NSLS and producing x-rays that are 10,000 times brighter.

    BNL NSLS-II

    With these brighter x-rays, the scientists hope to capture more details of the chemistry in action, including details of the intermediates that form throughout the reaction process to validate the theoretical predictions made in this study.

    The work at Brookhaven Lab was funded by the U.S. DOE Office of Science.

    Additional funders for the overall research project include: the National Basic Research Program of China, the Chinese Academy of Sciences, National Natural Science Foundation of China, Fundamental Research Funds for the Central Universities of China, and the U.S. National Science Foundation.

    NSLS, NSLS-II, CFN, CNMS, and ALS are all DOE Office of Science User Facilities.

    See the full article here .

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    One of ten national laboratories overseen and primarily funded by the Office of Science of the U.S. Department of Energy (DOE), Brookhaven National Laboratory conducts research in the physical, biomedical, and environmental sciences, as well as in energy technologies and national security. Brookhaven Lab also builds and operates major scientific facilities available to university, industry and government researchers. The Laboratory’s almost 3,000 scientists, engineers, and support staff are joined each year by more than 5,000 visiting researchers from around the world. Brookhaven is operated and managed for DOE’s Office of Science by Brookhaven Science Associates, a limited-liability company founded by Stony Brook University, the largest academic user of Laboratory facilities, and Battelle, a nonprofit, applied science and technology organization.
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  • richardmitnick 2:36 pm on December 6, 2016 Permalink | Reply
    Tags: , , , BNL NSLS, , Don DiMarzio,   

    From BNL: “Q&A with CFN User Don DiMarzio” 

    Brookhaven Lab

    December 6, 2016
    Ariana Tantillo
    atantillo@bnl.gov

    1
    Don DiMarzio. No image credit

    Don DiMarzio is an engineering fellow at Northrop Grumman and a senior scientist within the company’s advanced research, development, design, and demonstration group NG Next, where he studies nanomaterials and radio-frequency metamaterials. He is also an adjunct professor at Stony Brook University, where he teaches a nanotechnology class. Since March 2016, he has been using the advanced characterization labs at the Center for Functional Nanomaterials (CFN)—a U.S. Department of Energy (DOE) Office of Science User Facility at Brookhaven Lab—primarily to investigate nanostructures whose self-assembly is directed through DNA scaffolds. CFN physicist Oleg Gang has been developing this DNA-based technique for several years.

    Northrop Grumman is typically known for building aircraft, such as the U.S. Air Force’s B-2 stealth bomber, as well as unmanned autonomous aircraft and satellites. How does basic research come into play?

    About two years ago, Tom Vice, corporate vice president and president of Northrop Grumman Aerospace Systems, began discussing with his leadership team how to reconstitute the basic research activity that had existed in various forms earlier in the company’s history. NG Next, which includes basic research, applied research and technology development, advanced design, and rapid prototyping, emerged from these discussions. The goal of NG Next is to position Northrop Grumman at the cutting edge of science and technology and to attract the best and brightest young talent.

    NG Next’s basic research group is led by Tom Pieronek, vice president of basic research. The group has eight thrusts or topic areas relevant to the aerospace industry. One of these topics is nanomaterials, which is the focus of the Nanomaterials Group, led by Jesse Tice. I belong to this group. Other thrusts within the basic research group include semiconductor materials, plasmonics, and cognitive autonomy. The charter of our basic research organization is to do real science that is nonproprietary and publishable, in collaboration with the nation’s top universities and government labs. Any fundamental new discoveries that we think are promising may be transferred over to our applied research and prototyping groups within NG Next.

    The Center for Functional Nanomaterials (CFN) is one of five U.S. Department of Energy Nanoscale Science Research Centers and is among the many nanoscale facilities located at universities across the United States. What influenced your decision to submit a user proposal to CFN?

    After I got my PhD in solid-state physics, I did a postdoc at Brookhaven’s National Synchrotron Light Source (NSLS) in the late 1980s and really enjoyed working at Brookhaven.

    BNL NSLS
    BNL NSLS Interior
    BNL/NSLS

    After my postdoc, I became a scientist at the Grumman Corporate Research Center in Bethpage, NY, but continued my collaborations with Brookhaven on and off throughout the years.

    When Northrop Grumman leadership began planning for the new basic research group last year, I got involved. Part of my planning and development work for the group included helping to organize workshops—one in nanomaterials and the other in radio-frequency metamaterials—at our regional headquarters in southern California. For these invite-only workshops, the goal was to learn what was at the cutting edge in research, where we should focus our efforts, and who we could collaborate with.

    Our Nanomaterials Workshop provided a broad perspective on cutting-edge research, from nanomaterials synthesis and structures fabrication through fundamental properties and applications. One area that showed great potential was in nanoparticle self-assembly, and one of the major players in that field is the CFN. Although I had been working with various nanotechnologies before the establishment of NG Next, the CFN was either not established yet or our research was both applied and highly proprietary. But with the establishment of the basic research group within NG Next, it became clear that there was a definite opportunity for collaboration, especially considering that the way CFN is set up aligns with NG Next’s charter to publish, make presentations, and collaborate.

    When I learned about CFN physicist Oleg Gang’s work on exploiting DNA to direct the self-assembly of nanoparticles, I became very intrigued. I was particularly impressed with the strength and flexibility of this DNA origami scaffolding to fabricate a wide range of structures relevant for device and materials applications, and the ability to transition these assemblies from “soft” to “hard” while preserving key functionalities. Northrop Grumman sees this work as a potentially ground-breaking area that may lead to revolutionary new fabrication capability for everything from sensor systems to structural composites.

    While most of NG Next’s basic research group is in California, I am here on Long Island (at our Bethpage facility), so CFN is conveniently located near where I work and live. The group in California is currently building out its own labs that will be separate from our traditional applied laboratories. As an existing facility with state-of-the-art equipment and expertise in nanomaterials synthesis, device fabrication, and advanced characterization, CFN was the perfect complement to our West Coast research operations.

    3
    Gold nanoparticles are coordinated by DNA origami octahedron into the prescribed cluster, as obtained from the 3D transmission electron microscopy reconstruction (based on Y. Tian et al. Nature Nanotechnology 10, 637–644, 2015).

    Are you working on any other projects at CFN besides the directed self-assembly?

    In nanomaterials research, I am supporting principal investigators who are using CFN’s advanced characterization tools, particularly those in microscopy, to look at cutting-edge 2D materials like tin selenide (SnSe) and black phosphorous, in collaboration with our university partners.

    For our nanomaterials work, I am also collaborating with an NG Next group involved in plasmonics research, leveraging our DNA assembly work to fabricate new and unique optical structures.

    What are some of the characterization techniques you use at CFN?

    To probe the composition of the DNA-based nanostructures, we focus on small-angle x-ray scattering (SAXS) and transmission electron microscopy (TEM). To probe the chemical states of 2D materials and devices, we use energy-dispersive x-ray spectroscopy and electron energy-loss spectroscopy. In addition to these traditional microscopy techniques, we employ aberration-corrected low-energy electron microscopy (LEEM) and angle-resolved photoemission spectroscopy (ARPES) for some of our 2D materials. This latter technique is important because the band structure, or electronic energy levels, of 2D materials often has directional dependence.

    Your work at CFN sounds like it could also benefit from the advanced characterization methods at the National Synchrotron Light Source II (NSLS-II). Are you collaborating with NSLS-II or do you have plans to?

    BNL NSLS II
    BNL NSLS Interior
    BNL/NSLS-II

    Plans are in the works for experiments at the NSLS-II, building on our current efforts at the CFN. We will be working with CFN scientists Dario Stacchiola and Jerzy Sadowski on the new LEEM/ARPES system during its commissioning in January, and we are evaluating the use of synchrotron SAXS for large-volume data acquisition from nanomaterials for additive manufacturing.

    Our leadership is very supportive of our interactions with Brookhaven’s DOE Office of Science User Facilities and would like to solidify relationships for the long term.

    How has it been coming back to Brookhaven more than 30 years later?

    Even though I work for Northrop Grumman, I feel like I am part of the family here at CFN. I am working at CFN pretty much every day. From the start, CFN leadership has been very accommodating. They helped us get rapid access while we started negotiations on our CRADA [cooperative research and development agreement] and submitted our long-range user proposals for the directed assembly and 2D materials projects.

    Since I arrived, CFN staff scientists have been very helpful with training on laboratory equipment such as the SAXS, TEM, and scanning TEM (STEM) systems. The CFN group leads have been particularly helpful in facilitating timely sample preparation, such as that with the focused-ion beam, and with scheduling the use of characterization tools.

    You mentioned you are at CFN basically every day. What keeps you coming back?

    I feel like a kid in a candy shop here. Everyone who works here is passionate about what they do, so coming in every day is something I look forward to. I have my own spare office, close to the group leaders who I am working with. Although I primarily work with Oleg, I get to interact with many other staff scientists and postdocs, not only through my research but also through my volunteer work at CFN. I am the elected vice chair of the CFN Users’ Executive Committee and co-chair of the 2017 NSLS-II & CFN Joint Users’ Meeting.

    How did you become interested in nanomaterials?

    Years ago, I was doing applied research in photocatalysis involving the use of titanium dioxide nanoparticles to create self-decontaminating surfaces—a DARPA [Defense Advanced Research Projects Agency] project. Subsequently, I got involved in developing lightweight carbon nanotube based electrical cables for Department of Defense applications. The carbon nanotube work is ongoing at Northrop Grumman, with applications for space systems and air platforms. Although these applications are important, my turn to basic research was rooted in the NG Next vision to investigate fundamental phenomena that will enable new game-changing technologies that will have applications to both Northrop Grumman’s traditional customers and future technology marketplaces.

    See the full article here .

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    BNL Campus

    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 4:24 pm on November 18, 2014 Permalink | Reply
    Tags: , BNL NSLS, , ,   

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

    Brookhaven Lab

    November 18, 2014
    Laura Mgrdichian

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

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

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

    im
    Organic two-dimensional heterostructure of rubrene/h-BN

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

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

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

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

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

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

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

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

    See the full article here.

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    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 5:10 pm on September 22, 2014 Permalink | Reply
    Tags: , BNL NSLS, ,   

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

    Brookhaven Lab

    September 22, 2014
    Laura Mgrdichian

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

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

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

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

    BNL NSLS
    BNL NSLS Interior
    NSLS

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

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

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

    afm
    Atomic Force Microscope at Rutgers University

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

    See the full article here.

    BNL Campus

    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 3:34 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.

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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
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    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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