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  • richardmitnick 5:46 am on April 21, 2016 Permalink | Reply
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    From Stanford: “Peering deep into materials with ultrafast science” 

    Stanford University Name
    Stanford University

    March 31, 2016 [Just appeared in social media]
    Glenn Roberts Jr.

    1
    New techniques developed at SLAC and Stanford allow scientists to observe changes at the nanoscale that occur in fractions of a second in response to light. This artist’s conception depicts the first step in the photovoltaic response that light produces in lead titanate.

    Laser light exposes the properties of materials used in batteries and electronics

    Creating the batteries or electronics of the future requires understanding materials that are just a few atoms thick and that change their fundamental physical properties in fractions of a second. Cutting-edge facilities at SLAC National Accelerator Laboratory and Stanford University have allowed researchers like Aaron Lindenberg to visualize properties of these nanoscale materials at ultrafast time scales.

    In one experiment, a team led by Lindenberg showed atoms shifting in trillionths of a second to produce a wrinkle in a 3-atom-thick sample of a material that might someday be used in flexible electronics. Another study observed semiconductor crystals — called “quantum dots” because they defy classical physics at the nanoscale — expand and shrink in response to ultrafast pulses of laser light.

    2
    A three-atom-thick material wrinkles in response to a laser pulse. Understanding these dynamic ripples could provide crucial clues for the development of next-generation solar cells, electronics and catalysts.

    Revealing such intriguing properties at the nanoscale gives clues about the fundamental nature of materials and how they perform in applications we rely on for energy or information.

    “Even though some of these materials are completely embedded in everyday technologies, not a lot is understood about how they work,” says Lindenberg, who is an associate professor of materials science and engineering and of photon science. He is also a principal investigator for two SLAC/Stanford joint institutes — Stanford Institute for Materials and Energy Sciences and Stanford PULSE Institute.

    “Part of the reason some phenomena are not well understood is because they happen so fast – in billionths, trillionths or even quadrillionths of a second. For the first time, we have tools that allow us to see these things,” he says.

    Working at the intersection of materials science and engineering, Lindenberg and his team have a particular focus on finding promising materials for next-generation electronics, light-based data storage technologies and energy applications.

    “There are a broad range of new properties that emerge at the nanoscale,” Lindenberg says. “The tiniest samples, with just tens or hundreds of atoms, can have nearly flawless structures that make them ideal test tubes for very fundamental questions about what happens when a material transforms.”

    The team uses different types of laser light at SLAC and Stanford labs to learn how simple tweaks in the size, shape and design of materials can change their basic properties in unexpected ways, which could lead to new applications. Taking advantage of the powerful X-rays at SLAC facilities, including the Linac Coherent Light Source [LCLS] and the Stanford Synchrotron Radiation Lightsource [SSRL] , they explore ultrafast changes in nanoscale samples.

    SLAC/LCLS
    SLAC/LCLS

    SLAC/SSRL
    SLAC/SSRL

    “We are trying to understand how electrons or atoms move in materials, which in turn determines, for example, the efficiency of solar cells and other energy-related materials, and how materials switch between different forms,” he says. “Ultrafast techniques allow you to see these kinds of things in a completely new way.”

    See the full article here .

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

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  • richardmitnick 10:21 am on March 15, 2016 Permalink | Reply
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    From SLAC: “X-ray Studies at SLAC and Berkeley Lab Aid Search for Ebola Cure” 


    SLAC Lab

    March 14, 2016
    No writer credit

    Research Reveals Structures That Could Be Key to Preventing Infection

    q
    TPC1 channel that Ebola and related filoviruses use to infect cells.

    In experiments carried out partly at the Department of Energy’s SLAC National Accelerator Laboratory, scientists have determined in atomic detail how a potential drug molecule fits into and blocks a channel in cell membranes that Ebola and related filoviruses need to infect victims’ cells.

    The study by researchers at University of California, San Francisco marks an important step toward finding a cure for Ebola and other diseases that depend on the channel. The results were published March 9 in Nature.

    “There are no effective treatments for filovirus infections in humans,” said UCSF postdoctoral researcher Alex Kintzer, who performed the study with Professor Robert Stroud. “With these new structures, pharmaceutical chemists can now design new candidate drug molecules that would be more efficient and effective in blocking the channel and defeating these viruses.”

    To determine the structures, Kintzer first made crystals containing many copies of the target channel protein, called TPC1, bound to the potential drug molecule, Ned-19.

    The researchers then exposed the crystals to intense X-rays at two DOE Office of Science User Facilities – SLAC’s Stanford Synchrotron Radiation Lightsource (SSRL) and the Advanced Light Source (ALS) at Lawrence Berkeley National Laboratory.

    SLAC SSRL
    SSRL at SLAC

    LBL ALS interior
    ALS at LBL

    Analyzing the patterns and intensities of the X-rays that diffract from the crystals enables researchers to determine their atomic structures.

    Isolating TPC1 from its complex membrane structure is a difficult process that often results in loosely packed crystals that produce faint diffraction patterns, and finding crystals that diffracted well enough to determine the atomic structure of TPC1 required extensive analysis. SSRL’s Beam Line 12-2 was crucial to the successful analysis of these crystals, because its bright X-rays are particularly well-suited for biomedical diffraction studies, and its pixel-array detector is 1,000 times faster than conventional detectors in logging data.

    “These features of Beam Line 12-2 were especially important in enabling Alex to rapidly analyze the diffraction of his challenging crystals,” said Ana Gonzalez, SSRL’s Macromolecular Crystallography User Support Group leader, who helped Kintzer take full advantage of the beamline’s capabilities.

    Even so, the project involved testing about 6,900 crystals during more than 36 sessions at SSRL and ALS. It took nearly four years to complete, from planning to publication.

    One interesting aspect of this study is that the specific TPC1 sample the researchers used did not come from a human or lab animal. Rather, it was from the cells of a weedy Eurasian annual plant related to broccoli (called mouse-ear cress, or Arabidopsis thaliana) that researchers have used as a model species for studying cell activities and genetics since the mid-1940s. (In 2000, for example, A. thaliana’s genome was the very first plant genome to be sequenced.)

    “It’s common in this field to use well-studied non-human components that have similar genetic sequences, structures and functional properties,” Kintzer said.

    Future research plans include determining the structure of human TPC1 and investigating other molecules that may treat or cure other diseases that exploit that channel’s function.

    “For example, TPC1 function also plays important roles in the progression of diabetes, obesity, fatty liver disease, heart disease and such neurodegenerative disorders as Parkinson’s disease,” Kintzer said. “We hope our work will eventually lead to more effective medicines for treating these diseases as well.”

    The research was supported by the National Institutes of Health (NIH) and the Sandler Foundation. Funding for the SSRL Structural Molecular Biology Program is provided by the DOE Office of Science and the NIH National Institute of General Medical Sciences (NIGMS). The Berkeley Center for Structural Biology is supported by NIGMS and the Howard Hughes Medical Institute.

    Citation: A. Kintzer and R. Stroud, Nature, 9 March 2016 (10.1038/nature17194).

    See the full article here .

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  • richardmitnick 8:11 am on November 17, 2015 Permalink | Reply
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    From SLAC: “X-ray Microscope Reveals ‘Solitons,’ a Special Type of Magnetic Wave” 


    SLAC Lab

    November 16, 2015

    Scientists Hope to Control its Properties to Create a New Form of Electronics

    1
    X-rays at SSRL (purple) measure a special type of magnetic wave, called a spin wave soliton, that has the ability to hold its shape as it moves across a magnetic material. The arrows, like reorienting compass needles, represent localized changes in the material’s magnetic orientation. (SLAC National Accelerator Laboratory)

    Researchers used a powerful, custom-built X-ray microscope at the Department of Energy’s SLAC National Accelerator Laboratory to directly observe the magnetic version of a soliton, a type of wave that can travel without resistance. Scientists are exploring whether such magnetic waves can be used to carry and store information in a new, more efficient form of computer memory that requires less energy and generates less heat.

    Magnetic solitons are remarkably stable and hold their shape and strength as they travel across a magnetic material, just as tsunamis maintain their strength and form while traversing the ocean. This offers an advantage over materials used in modern electronics, which require more energy to move data due to resistance, which causes them to heat up.

    In experiments at SLAC’s Stanford Synchrotron Radiation Lightsource [SSRL] , a DOE Office of Science User Facility, researchers captured the first X-ray images of solitons and a mini-movie of solitons that were generated by hitting a magnetic material with electric current to excite rippling magnetic effects. Results from two independent experiments were published Nov. 16 in Nature Communications and Sept. 17 in Physical Review Letters.

    SLAC SSRL Tunnel
    SSRL

    “Magnetism has been used for navigation for thousands of years and more recently to build generators, motors and data storage devices,” said co-author Hendrik Ohldag, a scientist at SSRL. “However, magnetic elements were mostly viewed as static and uniform. To push the limits of energy efficiency in the future we need to understand better how magnetic devices behave on fast timescales at the nanoscale, which is why we are using this dedicated ultrafast X-ray microscope.”

    “This is an exciting observation because it shows that small magnetic waves – known as spin-waves – can add up to a large one in a magnet,” explains Andrew Kent, a professor of physics at New York University and a senior author for one of the studies.. “A specialized X-ray method that can focus on particular magnetic elements with very high resolution enabled this discovery and should enable many more insights into this behavior.”

    Solitons are a form of spin waves, which are disturbances that propagate in a magnetic material as a patterned, rippling response in the material’s electrons. This response is related to the spin of electrons, a fundamental particle property that can be thought of as either “up” or “down” – like the head or tail sides of a coin.

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    An ultrafast camera coupled to a custom-built X-ray microscope at SLAC’s Stanford Synchrotron Radiation Lightsource allowed researchers to produce a six-frame “movie” of the soliton’s motion. It took about 12 hours to record enough X-ray data to produce the movie. (Stefano Bonetti/Stockholm University)

    In 1834 John Scott Russell, a Scottish civil engineer and shipbuilder, first described his observation of the soliton phenomenon in a boat-produced wave that held a uniform shape for over a mile as it traveled down a canal. Solitons had for decades been theorized to occur in magnets, but it took a specialized X-ray microscope like the one at SLAC to directly observe the effect.

    “We built a microscope that allowed us to look at these magnetic waves in a new way,” said Stefano Bonetti, the leading author of the study published in Nature Communications. Bonetti is a Stanford University postdoctoral fellow now at Stockholm University. “With this new microscope, we can actually see them moving,” he said. “We can see things directly.”

    An ultrafast camera coupled to the microscope allowed researchers to record six images that were compiled in sequence to form a “movie” of the soliton’s motion. It took about 12 hours to record enough X-ray data to produce the movie.

    The high resolution of the X-ray microscope revealed an anomaly in the spin-wave effects: While researchers expected the soliton to fully flip the local magnetic alignment of the material, like a compass switching from north to south, they found that the soliton caused the material’s magnetic orientation to change only slightly.

    “We would expect to see this reverse, or flip,” Bonetti said. “But it didn’t reverse – it just tilted about 25 degrees. The situation is not as simple as people thought.”

    Also, in one of the experiments researchers saw the soliton split in two: it was expected to take a spherical or circular form, but instead appeared split down the middle, as if an approaching ocean wave had split into two separate waves that were mirror images of each other. “In the simulations we were using before, we were blind to this possibility,” Bonetti said.

    More experiments are needed to understand both the tilting effect and the way that the soliton can split into a mirrored form, Bonetti said. Simulations could help researchers learn how to convert the mirrored pattern of the soliton into a more uniformly symmetrical shape, he said, or to understand how to use the split form for data applications.

    Researchers from Stanford University; SIMES, the Stanford Institute for Materials and Energy Sciences at SLAC; University of Barcelona in Spain; KTH Royal Institute of Technology in Sweden; New York University; HGST, a Western Digital Company; and Emory University in Georgia also contributed to the study. The work was supported by Everspin Technologies, the DOE Office of Science, the Knut and Alice Wallenberg Foundation, the Swedish Research Council, the Catalan Government, the National Science Foundation, the Forsk Foundation, the European Commission, the U.S. Army Research Office and Brookhaven National Laboratory.

    Citations: S. Bonetti, et al., Nature Communications, 16 November 2015 (10.1038/NCOMMS9889)

    D. Backes, et al., Physical Review Letters, 17 September 2015 (10.1103/PhysRevLett.115.127205)

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  • richardmitnick 4:23 am on February 19, 2015 Permalink | Reply
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    From SLAC: “Semiconductor Works Better when Hitched to Graphene” 


    SLAC Lab

    February 18, 2015

    Experiments at SLAC Show Potential for Graphene-based Organic Electronic Devices

    Graphene – a one-atom-thick sheet of carbon with highly desirable electrical properties, flexibility and strength – shows great promise for future electronics, advanced solar cells, protective coatings and other uses, and combining it with other materials could extend its range even further.

    Experiments at the Department of Energy’s SLAC National Accelerator Laboratory looked at the properties of materials that combine graphene with a common type of semiconducting polymer. They found that a thin film of the polymer transported electric charge even better when grown on a single layer of graphene than it does when placed on a thin layer of silicon.

    1
    A material made of semiconducting polymer placed on top of graphene conducts electric charge extremely well and may enable new electronic devices. This work was featured on the cover of the journal Advanced Functional Materials. (David Barbero)

    “Our results are among the first to measure the charge transport in these materials in the vertical direction – the direction that charge travels in organic photovoltaic devices like solar cells or in light-emitting diodes,” said David Barbero of Umeå University in Sweden, leader of the international research team that performed the experiments at SLAC’s Stanford Synchrotron Radiation Lightsource (SSRL), a DOE Office of Science User Facility. “The result was somewhat expected, because graphene and silicon have different crystalline structures and electrical properties.”

    But the team also discovered something very unexpected, he said.

    Although it was widely believed that a thinner polymer film should enable electrons to travel faster and more efficiently than a thicker film, Barbero and his team discovered that a polymer film about 50 nanometers thick conducted charge about 50 times better when deposited on graphene than the same film about 10 nanometers thick.

    2
    Studies conducted at the Stanford Synchrotron Radiation Lightsource revealed that when deposited atop graphene, a thicker polymer film (top) conducted charge significantly better than a thinner polymer film (bottom). This is likely because the orientation of the polymer crystallites within the thick film allows the formation of a continuous pathway for the charge to flow. (David Barbero)

    The team concluded that the thicker film’s structure, which consists of a mosaic of crystallites oriented at different angles, likely forms a continuous pathway of interconnected crystals. This, they theorize, allows for easier charge transport than in a regular thin film, whose thin, plate-like crystal structures are oriented parallel to the graphene layer.

    By better controlling the thickness and crystalline structure of the semiconducting film, it may be possible to design even more efficient graphene-based organic electronic devices.

    “The fields most likely to benefit from this work are probably next-generation photovoltaic devices and flexible electronic devices,” said Barbero. “Because graphene is thin, lightweight and flexible, there are a number of potential applications.”

    See the full article here.

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  • richardmitnick 5:32 pm on February 13, 2015 Permalink | Reply
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    From SLAC: “Scientists Get First Glimpse of a Chemical Bond Being Born” 


    SLAC Lab

    February 12, 2015

    Scientists have used an X-ray laser at the Department of Energy’s SLAC National Accelerator Laboratory to get the first glimpse of the transition state where two atoms begin to form a weak bond on the way to becoming a molecule.

    1
    This illustration shows atoms forming a tentative bond, a moment captured for the first time in experiments with an X-ray laser at SLAC National Accelerator Laboratory. The reactants are a carbon monoxide molecule, left, made of a carbon atom (black) and an oxygen atom (red), and a single atom of oxygen, just to the right of it. They are attached to the surface of a ruthenium catalyst, which holds them close to each other so they can react more easily. When hit with an optical laser pulse, the reactants vibrate and bump into each other, and the carbon atom forms a transitional bond with the lone oxygen, center. The resulting carbon dioxide molecule detaches and floats away, upper right. The Linac Coherent Light Source (LCLS) X-ray laser probed the reaction as it proceeded and allowed the movie to be created. (SLAC National Accelerator Laboratory)

    This fundamental advance, reported Feb. 12 in Science Express and long thought impossible, will have a profound impact on the understanding of how chemical reactions take place and on efforts to design reactions that generate energy, create new products and fertilize crops more efficiently.

    “This is the very core of all chemistry. It’s what we consider a Holy Grail, because it controls chemical reactivity,” said Anders Nilsson, a professor at the SLAC/Stanford SUNCAT Center for Interface Science and Catalysis and at Stockholm University who led the research. “But because so few molecules inhabit this transition state at any given moment, no one thought we’d ever be able to see it.”


    Anders Nilsson, a professor at SLAC and at Stockholm University, explains how scientists used an X-ray laser to watch atoms form a tentative bond, and why that’s important.

    The experiments took place at SLAC’s Linac Coherent Light Source (LCLS), a DOE Office of Science User Facility. Its brilliant, strobe-like X-ray laser pulses are short enough to illuminate atoms and molecules and fast enough to watch chemical reactions unfold in a way never possible before.

    Researchers used LCLS to study the same reaction that neutralizes carbon monoxide (CO) from car exhaust in a catalytic converter. The reaction takes place on the surface of a catalyst, which grabs CO and oxygen atoms and holds them next to each other so they pair up more easily to form carbon dioxide.

    In the SLAC experiments, researchers attached CO and oxygen atoms to the surface of a ruthenium catalyst and got reactions going with a pulse from an optical laser. The pulse heated the catalyst to 2,000 kelvins – more than 3,000 degrees Fahrenheit – and set the attached chemicals vibrating, greatly increasing the chance that they would knock into each other and connect.

    The team was able to observe this process with X-ray laser pulses from LCLS, which detected changes in the arrangement of the atoms’ electrons – subtle signs of bond formation – that occurred in mere femtoseconds, or quadrillionths of a second.

    “First the oxygen atoms get activated, and a little later the carbon monoxide gets activated,” Nilsson said. “They start to vibrate, move around a little bit. Then, after about a trillionth of a second, they start to collide and form these transition states.”

    ‘Rolling Marbles Uphill’

    The researchers were surprised to see so many of the reactants enter the transition state – and equally surprised to discover that only a small fraction of them go on to form stable carbon dioxide. The rest break apart again.

    “It’s as if you are rolling marbles up a hill, and most of the marbles that make it to the top roll back down again,” Nilsson said. “What we are seeing is that many attempts are made, but very few reactions continue to the final product. We have a lot to do to understand in detail what we have seen here.”

    Theory played a key role in the experiments, allowing the team to predict what would happen and get a good idea of what to look for. “This is a super-interesting avenue for theoretical chemists. It’s going to open up a completely new field,” said report co-author Frank Abild-Pedersen of SLAC and SUNCAT.

    A team led by Associate Professor Henrik Öström at Stockholm University did initial studies of how to trigger the reactions with the optical laser. Theoretical spectra were computed under the leadership of Stockholm Professor Lars G.M. Pettersson, a longtime collaborator with Nilsson.

    Preliminary experiments at SLAC’s Stanford Synchrotron Radiation Lightsource (SSRL), another DOE Office of Science User Facility, also proved crucial. Led by SSRL’s Hirohito Ogasawara and SUNCAT’s Jerry LaRue, they measured the characteristics of the chemical reactants with an intense X-ray beam so researchers would be sure to identify everything correctly at the LCLS, where beam time is much more scarce. “Without SSRL this would not have worked,” Nilsson said.

    The team is already starting to measure transition states in other catalytic reactions that generate chemicals important to industry.

    “This is extremely important, as it provides insight into the scientific basis for rules that allow us to design new catalysts,” said SUNCAT Director and co-author Jens Nørskov.

    Researchers from LCLS, Helmholtz-Zentrum Berlin for Materials and Energy, University of Hamburg, Center for Free Electron Laser Science, University of Potsdam, Fritz-Haber Institute of the Max Planck Society, DESY and University of Liverpool also contributed to the research. The research was funded by the DOE Office of Science, the Swedish National Research Council, the Knut and Alice Wallenberg Foundation, the Volkswagen Foundation and the German Research Foundation (DFG) Center for Ultrafast Imaging.

    See the full article here.

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  • richardmitnick 5:18 am on February 4, 2015 Permalink | Reply
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    From SLAC: “Record Keeping Helps Bacteria’s Immune System Fight Invaders” 


    SLAC Lab

    February 3, 2015

    Bacteria have a sophisticated means of defending themselves, and they need it: more viruses infect bacteria than any other biological entity.

    Two experiments undertaken at the Department of Energy’s SLAC National Accelerator Laboratory provide new insight at the heart of bacterial adaptive defenses in a system called CRISPR, short for Clustered Regularly Interspaced Short Palindromic Repeat.

    This portion of bacteria’s immune system works as a record keeper, taking note of attacking viruses’ identities and storing that information by integrating fragments of the virus’ DNA into its own DNA. In this way, CRISPRs maintain genetic records of previously encountered viruses, making it easier for the bacteria’s immune system to send out complexes that destroy viral invaders by identifying and cutting up the recognized DNA sequences.

    The studies published last year in Science not only reveal important information about how bacteria repel attacking viruses, but also could potentially improve the prevention of disease in humans. Researchers are currently studying ways of preventing and treating cystic fibrosis, blood disorders and HIV by harnessing the CRISPR system to replace one version of a gene with another or to add a working copy for a mutated gene.

    Scientists studied one particular CRISPR-associated complex called Cascade using bright X-rays at SLAC’s Stanford Synchrotron Radiation Lightsource (SSRL)., a DOE Office of Science User Facility. In the bacteria Escherichia coli, 11 proteins assemble together with an RNA guide that helps Cascade target invading DNA sequences. Once Cascade confirms that the target DNA is from an invader, a molecular signal recruits a nuclease called Cas3 to finish off the invader by chewing it up.

    1`
    An overview of the crystal structure of Cascade, showing each gene in a different color. The red ribbon represents the RNA guide. (Ryan N. Jackson et al.)

    SLAC SSRL TunnelSLAC SSRL

    Previous work by Blake Wiedenheft, the Montana State University assistant professor of microbiology and immunology who led one of the studies, and his colleagues revealed Cascade’s seahorse-shaped architecture, but studies undertaken at SSRL now reveal how all the parts of this machine assemble into a functional surveillance machine that patrols the intracellular environment for invading DNA.

    2
    A simplified representation of the Cascade RNA guide (green) forming an under-wound ribbon-like structure with invading viral DNA (orange). (Scott Bailey et al.)

    “Determining high-resolution structures of large macromolecules remains challenging,” Wiedenheft said. “Several technical aspects of SSRL, including intensity of light, ability to focus the beam, and shutterless X-ray detector made these results possible.”

    The studies also revealed that Cascade’s RNA guide does not twist together with the viral DNA to form a helix, as was expected. Instead, they form an under-wound ribbon-like structure.

    “A high-resolution structure is essentially a molecular blueprint of a biological machine,” said Wiedenheft. Determining the structure of this complex “is a technical accomplishment that provides the first molecular explanation of how all the parts assemble into a functional surveillance machine.”

    See the full article here.

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  • richardmitnick 4:27 pm on January 29, 2015 Permalink | Reply
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    From SLAC: “X-ray Study Reveals Division of Labor in Cell Health Protein” 


    SLAC Lab

    January 28, 2015
    Identical Substructures in ‘TH Protein’ Couple Two Crucial Cellular Functions

    1
    A recent study performed in part at SLAC’s SSRL X-ray facility has provided new insights into how the critical mitochondrial enzyme transhydrogenase, or TH, works in a key process that maintains healthy cells. The crystal structure of TH shows two copies of the molecule (left and right), each of which contains three domains (I, II, III). Structural asymmetry is observed for domain III: One of the structures is facing up (green) to catalyze the production of NADPH from its precursor (black spheres); the other is facing down (magenta) towards the transmembrane domain II to facilitate the transit of a proton. Labels “in” and “out” denote the mitochondrial matrix and the space outside the inner mitochondrial membrane, respectively. (C. David Stout/The Scripps Research Institute)

    Researchers working in part at the Department of Energy’s SLAC National Accelerator Laboratory have discovered that a key protein for cell health, which has recently been linked to diabetes, cancer and other diseases, can multitask by having two identical protein parts divide labor.

    The TH enzyme, short for transhydrogenase, is a crucial protein for most forms of life. In humans and other higher organisms, it works within mitochondria – tiny, double-hulled oxygen reactors inside cells that help power most cellular processes.

    “Despite its importance, TH has been one of the least studied mitochondrial enzymes,” said C. David Stout, a scientist at The Scripps Research Institute whose group led the research. The new study, published Jan. 9 in Science, is an important step toward understanding how this protein manages to perform two crucial cellular tasks at the same time.

    Two Crucial Processes

    As a mitochondrion burns oxygen, it pumps protons out of its innermost compartment, or matrix. Part of the TH protein extends through the membrane that surrounds the matrix; it allows a one-by-one flow of protons back through the membrane. This proton influx, in turn, is linked to the production of NADPH, a compound crucial for defusing oxygen radicals that are harmful to cells.

    But how do TH enzymes couple proton transport and NADPH production? Although Stout’s laboratory and others have previously described portions of the TH enzyme that protrude from the membrane into the mitochondrial matrix, a precise understanding of TH’s mechanism has been elusive. The enzyme has an exceptionally loose structure that makes it hard to evaluate by X-ray crystallography, the standard tool for determining structures of large proteins.

    “Key details we’ve been lacking include the structure of TH’s transmembrane portion, and the way in which the parts assemble into the whole enzyme,” said Josephine H. Leung, a graduate student in the Stout laboratory who was the lead author of the new study.

    For the first time, the team was now able to determine precise details of the transmembrane portion using X-rays from SLAC’s Stanford Synchrotron Radiation Lightsource (SSRL) and Argonne National Laboratory’s Advanced Photon Source (APS), both DOE Office of Science User Facilities. Together with X-ray and electron microscopy data of the whole protein, the study provided major clues as to how TH works.

    SLAC SSRL
    SLAC SSRL

    ANL APS interior

    Flipping Functions

    The analysis revealed that two identical copies of TH are bound together in what is called a dimer, and that one copy appears to be involved in proton transport while the other takes part in NADPH production. “Our new study helps clear up some mysteries – suggesting how the enzyme structure might harness protons and indicating that its two sides are able to alternate functions, always staying in balance,” Stout said.

    Attached to TH’s transmembrane structure, just inside the mitochondrial matrix, is the “domain III” structure, which binds NADPH’s precursor molecule during NADPH synthesis. Previously, scientists did not understand how two such structures could work side by side in the TH dimer and not interfere with each other’s activity.

    The new data suggest that these side-by-side structures are highly flexible and always have different orientations.

    “Our most striking finding was that the two domain III structures are not symmetric – one of them faces up while the other faces down,” said Leung.

    In particular, one of the structures is apparently oriented to catalyze the production of NADPH, while the other is turned towards the membrane, perhaps to facilitate transit of a proton. The new structural model indicates that with each proton transit, the two domain III structures flip and switch their functions. “We suspect that the passage of the proton is what somehow causes this flipping of the domain III structures,” said Leung.

    But much work remains to be done to determine TH’s precise structure and mechanism. For example, the new structural data provide evidence of a likely proton channel in the TH transmembrane region, but show only a closed conformation of that structure. “We suspect that this channel can have another, open conformation that lets the proton pass through, so that’s one of the details we want to study further,” said Leung.

    Research funding for the SSRL Structural Molecular Biology Program was provided by the DOE Office of Biological and Environmental Research and the National Institutes of Health, National Institute of General Medical Sciences.

    See the full article here.

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


    SLAC Lab

    December 19, 2014

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

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

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

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

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

    SLAC SSRL
    SSRL

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

    Tracking Down Electrons

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

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

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

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

    Evidence of Competition

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

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

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

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

    Remaining Mysteries

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

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

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

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

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

    See the full article here.

    Please help promote STEM in your local schools.

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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 5:52 pm on December 8, 2014 Permalink | Reply
    Tags: , , Flu Viruses, , SLAC SSRL   

    From SLAC: “Study May Help Slow the Spread of Flu” 


    SLAC Lab

    December 8, 2014

    X-rays Show How Flu Antibody Binds to Viruses

    An important study conducted in part at the Department of Energy’s SLAC National Accelerator Laboratory may lead to new, more effective vaccines and medicines by revealing detailed information about how a flu antibody binds to a wide variety of flu viruses.

    f
    A false color image of an influenza virus particle, or “virion.” (Centers for Disease Control/Cynthia Goldsmith)

    The flu virus infects millions of people each year. While for most this results in an unproductive and uncomfortable week or two, the flu also contributes to many deaths in the average flu season. And while vaccines are effective in preventing the flu, they require almost yearly reformulation to keep up with the constantly changing virus.

    A team of researchers from The Scripps Research Institute, Fujita Health University and Osaka University studied both samples of flu virus components and an anti-flu antibody. The antibody, called F045-092, was already known to neutralize the flu by connecting to the region of the flu virus that binds to host cells, so it can no longer bind to its target and cause infection.

    f
    Top: The antibody F045-092 inserts a loop (purple) into the region of the flu virus (blue) that would otherwise bind to host cells to initiate infection. With the antibody connected, the flu virus is unable to bind to its target and cannot cause infection. Bottom: Without the antibody present, the flu virus (blue) binds to a host cell receptor (yellow). (Peter Lee et al.)

    “There are patches of the virus that are more hypervariable than others,” said Peter Lee, a postdoctoral research associate at The Scripps Research Institute and first author of the paper. “But the flu always binds to host cells within the same region, and so that binding site needs to be functionally conserved. That makes it a site of vulnerability.”

    The team used the X-ray beams at SLAC’s Stanford Synchrotron Radiation Lightsource (SSRL) and Argonne National Laboratory’s Advanced Photon Source (APS), both DOE Office of Science User Facilities, to view the structure of the antibody bound to one subtype of the flu virus called H3N2. They discovered that the antibody inserts a loop into the binding site of the virus, which would otherwise attach to a receptor in a host cell. Additional experimental data showed that F045-092 binds a wide variety of strains and subtypes, including all H3 avian and human viruses from 1963 to 2011 that were tested.

    SLAC SSRL
    SSRL at SLAC

    ANL APS interior
    Argonne National Laboratory’s Advanced Photon Source

    This understanding of the antibody’s structural details and binding modes offers new insight for future structure-based drug discovery and novel avenues for designing future vaccines.

    But the only way to achieve those goals is for many groups of scientists to work together, Lee said. “Our lab is very focused on the structure of the virus and antibodies, while there are lots of other labs focused on everything from small protein design to vaccine design,” he said. “Hopefully we can use this structural information and join together as one big team to tackle the flu.”

    SSRL’s Structural Molecular Biology program is supported by the National Institutes of Health and the Office of Biological and Environmental Research of the U.S. Department of Energy.

    See the full article here.

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    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 4:40 pm on November 21, 2014 Permalink | Reply
    Tags: , , , , SLAC SSRL,   

    From SLAC: “Robotics Meet X-ray Lasers in Cutting-edge Biology Studies” 


    SLAC Lab

    November 21, 2014

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

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

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

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

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

    SLAC LCLS
    SLAC LCLS

    A New Way to Study Biology

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

    SLAC SSRL
    SLAC SSRL

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

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

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

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

    Early Successes

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

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

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

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

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

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

    Team Effort

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

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

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

    See the full article here.

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    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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