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  • richardmitnick 7:06 am on September 2, 2016 Permalink | Reply
    Tags: , , , Linsey Seitz, SIMES, SLAC SSRL, ,   

    From SLAC: Women in STEM – “SLAC, Stanford Team Finds a Tough New Catalyst for Use in Renewable Fuels Production” Linsey Seitz 


    SLAC Lab

    September 1, 2016

    Discovery Could Make Water-splitting Reaction Cheaper, More Efficient

    Researchers at Stanford University and the Department of Energy’s SLAC National Accelerator Laboratory have developed a tough new catalyst that carries out a solar-powered reaction 100 times faster than ever before, works better as time goes on and stands up to acid.

    And because it requires less of the rare and costly metal iridium, it could bring down the cost of a process that mimics photosynthesis by using sunlight to split water molecules – a key step in a renewable, sustainable pathway to produce hydrogen or carbon-based fuels that can power a broad range of energy technologies.

    The team published their results today in the journal Science.

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    A simulation shows one possible way that a highly active iridium oxide layer could form on the surface of a strontium iridium oxide catalyst. Experiments by SLAC and Stanford researchers showed that strontium atoms (green spheres) left the top layer through a corrosion process during the catalyst’s first two hours of operation. The top layer then rearranged itself and became much better at accelerating chemical reactions. Follow-up X-ray studies at SLAC will examine these surface changes in more detail. (C.F. Dickens/Stanford University)

    A Multi-pronged Search

    The discovery of the catalyst – a very thin film of iridium oxide layered on top of strontium iridium oxide – was the result of an extensive search by three groups of experts for a more efficient way to accelerate the oxygen evolution reaction, or OER, which is half of a two-step process for splitting water with sunlight.

    “The OER has been a real bottleneck, particularly in acidic conditions,” said Thomas Jaramillo, an associate professor at SLAC and Stanford and deputy director of the SUNCAT Center for Interface Science and Catalysis. “The only reasonably active catalysts we know that can survive those harsh conditions are based on iridium, which is one of the rarest metals on Earth. If we want to bring down the cost of such a pathway for making fuels from renewable sources and carry it out on a much larger scale, we need to develop catalyst materials that are more active and that use little or no iridium.”

    The search started with SUNCAT theorists, who used computers to explore a database of materials and find the ones with the most potential to do exactly what was needed. Catalysts accelerate chemical reactions without being used up in the process, and databases like this one have become an important tool for designing catalysts to order, rather than testing thousands of materials in a time-consuming, trial-and-error approach.

    Based on the results, a team led by SLAC Staff Scientist Yasuyuki Hikita and SLAC/Stanford Professor Harold Hwang, both investigators with the Stanford Institute for Materials and Energy Sciences (SIMES), synthesized one of the catalyst candidates, strontium iridium oxide. Linsey Seitz, a PhD student in Jaramillo’s group and first author of the report, investigated the material’s properties.

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    Stanford PhD student Linsey Seitz investigated the properties of a tough new catalyst material that carries out a key water-splitting reaction in acid. She is now a Helmholtz postdoctoral fellow at the Karlsruhe Institute of Technology in Germany. (Jesse D. Benck/Stanford University)

    3
    Sample of a new catalyst material created by SLAC and Stanford researchers. It’s 100 times better than previous catalysts at accelerating the oxygen-evolving reaction in acid, a key step in a pathway for making sustainable fuels. (Linsey Seitz/Stanford University)

    4
    Images made with an atomic force microscope show variations in the height of the catalyst’s surface before (left) and after its first 30 hours of operation. The observed changes in surface texture reflect strontium atoms leaving the top layers of the material during operation, forming a very catalytically active thin film of iridium oxide. (L. Seitz et. al., Science)

    A Surprising Improvement

    To the team’s surprise, this catalyst worked even better than expected, and kept improving over the first two hours of operation. Experiments probing the surface of the material indicated that a corrosion process released strontium atoms into the surrounding fluid during this initial period. This left a film of iridium oxide just a few atomic layers thick that was much more active than the original material, and 100 times more efficient at promoting the OER than any other acid-stable catalyst known to date.

    “A lot of materials do this type of thing – surfaces can be very dynamic, changing during the course of a reaction – but in this case the catalyst changes in a way that gives you excellent performance in acid,” Jaramillo said. “This is unusual, because under these conditions most materials are either poor catalysts or they completely fall apart, or both.”

    The researchers still don’t know exactly why this surface layer is so active, although the theorists, including SUNCAT graduate students Colin Dickens and Charlotte Kirk, have provided some ideas. Jaramillo’s group will be taking a closer look at the catalyst with X-ray beams at SLAC’s Stanford Synchrotron Radiation Lightsource, a DOE Office of Science User Facility, to determine exactly how the atoms on the surface rearrange themselves and why this boosts the catalyst’s performance.

    SLAC SSRL Tunnel
    SLAC SSRL

    “To make a commercially viable catalyst we will need to reduce the amount of iridium in the material even more,” said Jens Nørskov, director of SUNCAT and a professor at SLAC and Stanford. “But there are many possibilities, and this gives us some very good leads.”

    SUNCAT and SIMES are joint institutes of Stanford and SLAC. Major funding for the project came from the DOE Office of Science.

    See the full article here .

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  • richardmitnick 12:28 pm on August 30, 2016 Permalink | Reply
    Tags: A Virtual Flight Through a Catalyst Particle Finds Evidence of Poisoning, , Fluid catalytic cracking (FCC), SLAC SSRL   

    From SLAC: “A Virtual Flight Through a Catalyst Particle Finds Evidence of Poisoning” 


    SLAC Lab

    August 30, 2016

    At SLAC Synchrotron, Two X-ray Techniques Give a 3-D View of Why Catalysts Used in Gasoline Production Go Bad
    August 30, 2016


    This visualization of the experimental data shows how scientists mapped the distribution of chemical elements in a single fluid catalytic cracking (FCC) particle and merged it with structural information about the pore networks. Because of the high resolution at which they mapped the catalyst, they were able to look deep into the pores and learn more about the metal poisoning reaction. The changing colors of the “fog” inside the pores reflect the changing chemistry. (SLAC National Accelerator Laboratory)

    Merging two powerful 3-D X-ray techniques, a team of researchers from the Department of Energy’s SLAC National Accelerator Laboratory and Utrecht University in the Netherlands revealed new details of a process known as metal poisoning that clogs the pores of catalyst particles used in gasoline production, causing them to lose effectiveness.

    The team combined their data to produce a video that shows the chemistry of this aging process and takes the viewer on a virtual flight through the pores of a catalyst particle. The results were published today in Nature Communications.

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    This illustration depicts concentrations of chemical elements at five different points in a catalyst pore channel. The zigzag represents the pore channel, which was reconstructed from X-ray microscopy imaging. The colors show the chemical composition, detected with X-ray fluorescence. This information was combined in a model that simulates the aging of the catalyst pore network. (SLAC National Accelerator Laboratory)

    The particles, known as fluid catalytic cracking or FCC particles, are used in oil refineries to “crack” large molecules that are left after distillation of crude oil into smaller molecules, such as gasoline. Those oil molecules flow through the catalyst particles in tiny pores and passageways, which ensure accessibility to the active domains where chemical reactions can take place. But while the catalyst material is not consumed in the reaction and in theory could be recycled indefinitely, the pores clog up and the particles slowly lose effectiveness. Worldwide, about 400 reactor systems refine oil into gasoline, accounting for about 40 to 50 percent of today’s gasoline production, and each system requires 10 to 40 tons of fresh FCC catalysts daily.

    Finding new clues about how FCCs age out could be key to improving gasoline production. But the new technique also has potential for understanding the workings of materials for powering cars of the future, according to Yijin Liu, a lead author on the paper and staff scientist at SLAC’s Stanford Synchrotron Radiation Lightsource (SSRL), a DOE Office of Science User Facility.

    SLAC SSRL Tunnel
    SLAC SSRL

    “The model we created by combining these two imaging methods can readily be applied to studies of rapid changes in the pore networks of similarly structured materials, such as batteries, fuel cells and underground geological formations,” he said.

    Two Perspectives Complete the Picture

    To design materials for tomorrow’s energy solutions, scientists must understand how they work at multiple scales invisible to the human eye.

    In a previous study at SSRL, the team took a series of two-dimensional images of catalyst particles at various angles and used software they developed to combine them into three-dimensional images of whole particles showing the distribution of elements in catalysts at various ages.

    For the new study, the researchers examined an FCC particle recovered from a refinery using two different 3-D X-ray imaging techniques at two experimental stations, or beamlines, at SSRL.

    One technique, called X-ray fluorescence, provided a detailed profile of the particle’s chemical elements. The other, X-ray transmission microscopy, captured the nanoscale structure of the particle, including fine details about the porous network where metal poisoning can best be observed.

    “The high-resolution microscopy data provided a map of the pores, and the high sensitivity of X-ray fluorescence showed us where metals in the refining fluids were poisoning the catalyst, which appeared as a colored fog in our visualization,” Liu said.

    The results of the study highlight the importance of having multiple techniques to study a single sample at a facility like SSRL. “There was a lot of development on the beamlines to make it possible to register the data in 3-D at this very fine scale,” Liu said. He heads up one of the two beamlines used in the research, which allows him to understand the strength and the limitations of both imaging methods.

    “Understanding catalyst performance requires interrogating catalyst function from multiple perspectives,” SSRL Director Kelly Gaffney said. “The results of this exciting research effort highlight the value of integrating disparate X-ray imaging methods to build a deeper understanding of materials function.”

    A Model for Understanding Material Dynamics

    Going beyond the observation of the experimental data visualized in the video, the scientists developed a model explaining how the accumulation of metals poisons the efficiency of the catalyst.

    “We used an analogy between electrical resistance and the degree of pore blockage, between two points in the particle using the new combined data. We then applied formulas well-known in electrical engineering to explain accessibility through the pore network, but also how it changes when metals are blocking pores,” said the study’s co-lead researcher Florian Meirer, assistant professor of inorganic chemistry and catalysis at Utrecht University.

    The resulting model simulates the aging of the catalyst, allows scientists to quantify this virtual aging, and helps them predict the collapse of its transportation network.

    “The model explains for the first time how this happens in a connective manner, which is a big step toward improving the design of such catalysts. Furthermore, this novel approach can be applied to a broad range of other materials that involve the transport of fluids or gases, such as battery electrodes,” said Bert Weckhuysen, professor of inorganic chemistry and catalysis at Utrecht University.

    Other researchers who contributed to this work were SSRL’s Courtney Krest and Samuel Webb. This work was supported by the NWO Gravitation program, Netherlands Center for Multiscale Catalytic Energy Conversion, and a European Research Council Advanced Grant.

    See the full article here .

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  • richardmitnick 9:31 am on July 29, 2016 Permalink | Reply
    Tags: , Scientists Create Plasma-Printed Sensors to Monitor Astronaut Health on Long Space Trips, SLAC SSRL   

    From SLAC: “SLAC X-ray Studies Help NASA Develop Printable Electronics for Mars Mission” 


    SLAC Lab

    July 28, 2016

    Scientists Create Plasma-Printed Sensors to Monitor Astronaut Health on Long Space Trips.

    1
    The plasma jet printer consists of a glass nozzle with two copper electrodes connected to a power supply. (Universities Space Research Association at NASA Ames Research Center)

    Plans begin decades in advance for a tremendous effort such as the first manned mission to Mars. The details are as fine – and essential – as how astronauts will breathe and eat and track their health.

    “There’s no doubt that the transportation is taken care of. The spacecraft will be developed,” says Ram Gandhiraman, a scientist with Universities Space Research Association at NASA Ames Research Center. “But how are you going to sustain astronauts for one year or more? Equipment wears out, and supplies need replenished. This is work that also needs to be done.”

    To help prepare for the endeavor, Gandhiraman is creating a tool that will allow astronauts to craft materials in space using a jet of plasma – an energized gas of free electrons and ions. (Plasma is the fourth state of matter, joining the more familiar solid, liquid and gas.)

    The plasma jet can spray tiny semiconductor particles onto cheap, flexible surfaces, such as paper or cloth, and form wearable electronic circuits. Astronauts can use these sensors to track their health and also the environment. The sensors contain small semiconductors tailored to detect biomolecules, such as dopamine and serotonin, as well as gases like ammonia in the environment.

    The NASA team brings the sensors to SLAC’s Stanford Synchrotron Radiation Lightsource (SSRL), a DOE Office of Science User Facility, to look at the fine details of the sensors’ surfaces.

    SLAC/SSRL
    SLAC/SSRL

    This characterization allows them to optimize the process for printing sensors with the same quality every time.

    Developing the Printer

    The scientists need to be able to tailor the materials traveling through the plasma and control how they deposit on a surface. Even small defects can make the sensors nonfunctional.

    “This is where X-ray spectroscopy is crucial,” Gandhiraman says.

    Every other month or so, Gandhiraman and his team would analyze sensors at SSRL. While developing the plasma printer, Ram worked closely with SLAC scientist Dennis Nordlund to characterize the newly printed sensors.

    Nordlund would examine the plasma-deposited sensors using X-ray absorption spectroscopy and X-ray photoelectron spectroscopy.

    “These techniques allow us to see what chemical groups are present at the surface of the fabricated sensors,” Nordlund says. “This allows us to extract information about the material on an element-by-element basis, including the part of the chemical structure responsible for reactivity and the content of graphitic carbon – an important form of carbon that conducts well – present in the samples.”

    This helped solve one of Gandhiraman’s major challenges – printing exact copies at such a fine scale.

    “Say we ramp up the voltage or the flow of the plasma jet, then you get different chemistries that result in loss of device performance or sensitivity. What causes the behavior was not clear,” Gandhiraman says. “We needed to go back and forth and do an analysis on materials that we print. We used that information about surface properties to optimize the process here.”

    The plasma-printed nanomaterial forms a dense network of sensor and signal amplification materials better than other printing methods, including screen or aerosol printing. Another advantage: Plasma printing can operate at low temperatures, which means the paper or cloth is not destroyed during the process.

    Plasma Printing in the Lab (and in Space)

    In-space fabrication technology would allow astronauts to create the sensors – which become worn out with use – when the need arises.

    “This printer should be able to use both Martian resources and waste or spent materials to fabricate devices on-demand in space,” Gandhiraman says.

    To make a printer that astronauts can use in space, the researchers needed to engineer the plasma jet with an easy-to-assemble, lightweight set-up. During a demonstration in Gandhiraman’s lab, his research assistant Arlene Lopez turns a valve and gas travels through a plastic tube.

    The gas meets a liquid containing carbon nanotubes, forming a mist that is zapped with electricity flowing between two electrodes. This creates charged plasma.

    The plasma’s excited electrons give off light, and the color depends on the composition of the gas. Today, it’s a blue helium glow.

    In the lab, gas comes from a canister. In space, the Martian atmosphere will provide the needed gas. And instead of plugging into an outlet, solar panels will provide electricity.

    The researchers also had to consider the differences in gravity on Earth and Mars.

    “For space applications, you need to be able to use the printer in micro gravity environment,” Gandhiraman says. “That’s one reason this plasma is very interesting – no matter what environment you have, the electric field will drive the jet through the nozzle.”

    The NASA team plans to collaborate with SLAC to develop even more applications for the versatile plasma jet. The researchers have already shown the jet can be used for sterilizing equipment. Next up – NASA is developing a way to use microbes to recycle metals needed for electronics during long-term missions.

    The plasma jet is being tested to see how well it can print electronics using the metal “bioink” produced by the microbes. SLAC’s X-ray spectroscopy tools will look at the purity of recycled materials and pinpoint any contaminants present. The researchers also plan to look at how the same recycling and printing process might be used here on Earth.

    Citation: R. Gandhiraman et al., Applied Physics Letters, 22 March 2016 DOI: 10.1063/1.4943792; R. Gandhiraman et al., ACS Applied Materials & Interfaces, 25 November 2014 DOI: 10.1021/am5069003

    See the full article here .

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  • richardmitnick 11:51 am on July 20, 2016 Permalink | Reply
    Tags: , , , SLAC SSRL   

    From SLAC: “Stanford, SLAC X-ray Studies Could Help Make LIGO Gravitational Wave Detector 10 Times More Sensitive” 


    SLAC Lab

    July 19, 2016

    Scientists from Stanford University and the Department of Energy’s SLAC National Accelerator Laboratory are using powerful X-rays to study high-performance mirror coatings that could help make the LIGO gravitational wave observatory 10 times more sensitive to cosmic events that ripple space-time.

    LSC LIGO Scientific Collaboration

    Caltech/MIT Advanced aLigo Hanford, WA, USA installation
    Caltech/MIT Advanced aLigo Hanford, WA, USA installation

    Caltech/MIT Advanced aLigo detector installation Livingston, LA, USA
    Caltech/MIT Advanced aLigo detector installation Livingston, LA, USA

    The current version of the Laser Interferometer Gravitational-Wave Observatory, called Advanced LIGO, was the first experiment to directly observe gravitational waves, which were predicted by Albert Einstein 100 years ago. In September 2015, it detected a signal coming from two black holes, each about 30 times heavier than the sun, which merged into a single black hole 1.3 billion years ago. The experiment picked up a similar second event in December 2015.

    “The detection of gravitational waves will fundamentally change our understanding of the universe in years to come,” says Riccardo Bassiri, a physical science research associate at Stanford’s interdisciplinary Ginzton Laboratory. ”Extremely precise mirrors are the heart of LIGO, and their coatings determine the experiment’s sensitivity, or ability to measure gravitational waves. So improving those coatings will make future generations of the experiment even more powerful.”

    Bassiri has teamed up with Apurva Mehta, a staff scientist at SLAC’s Stanford Synchrotron Radiation Lightsource (SSRL), to study the atomic structure of coating materials and develop ideas for better ones. SSRL is a DOE Office of Science User Facility.

    SLAC SSRL Tunnel
    SLAC SSRL

    Since LIGO consists of two nearly identical instruments, located 1,900 miles apart in Hanford, Washington, and Livingston, Louisiana, it can also roughly determine a gravitational wave’s cosmic origin.

    “The effects of gravitational waves on the LIGO detectors are incredibly small, with relative changes in arm length on the order of one thousandth of the diameter of an atomic nucleus,” Bassiri says. “On this scale, random atomic motions in the mirror coatings, known as thermal noise, can obscure signals from gravitational waves.”

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    An experimental setup at SSRL used to study mirror coating materials with the grazing-incidence X-ray pair distribution function (GI-XPDF) technique.

    Understanding Thermal Noise

    All materials exhibit thermal noise to some degree, but some are less noisy than others. LIGO’s mirrors, which are among the least noisy in the world, are coated with thin layers of silica and tantala, oxides of the chemical elements silicon and tantalum.

    Previous research has shown that heating tantala to hundreds of degrees Fahrenheit and adding titanium oxide, or titania, to its layers in a process called doping can lower the thermal noise. However, scientists do not know exactly why.

    “At the moment, we’re only beginning to understand how these treatments affect the atomic structure,” Mehta says. “If we were able to get a better grasp of how a material’s properties are linked to its structure, we might be able to design better materials in a more efficient, controlled way instead of searching for them with a trial-and-error approach.”


    In this video, Stanford’s Riccardo Bassiri explains his work at SSRL, which aims to better understand thermal noise in mirror coatings.

    Applications Beyond LIGO

    The researchers are in the process of testing a number of materials to see how various doping percentages and manufacturing procedures change the medium-range order. Their hope is that this will lead to detailed models of the atomic structures and to theories that can predict how tweaking these structures can yield better material properties.

    “Advanced LIGO and the desire to understand the fundamental physics of gravitational waves are the main drivers for this type of research,” Bassiri says. “But it also has the potential for influencing a whole industry that uses amorphous coating materials for a wide range of applications, from precise atomic clocks to high-performance electronics and computing to corrosion-resistant coatings.”

    The research team includes Stanford Professors Robert Byer and Martin Fejer as well as SLAC scientists Badri Shyam, Kevin Stone and Michael Toney. Other institutions involved in this research are the California Institute of Technology; the University of Glasgow, UK; the University of Oxford, UK; and members of the LIGO scientific collaboration. Funding sources include the National Science Foundation and the Science and Technology Facilities Council, UK.

    3
    SLAC’s Apurva Mehta (left) and Stanford’s Riccardo Bassiri discuss their X-ray experiments at SSRL.

    See the full article here .

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  • richardmitnick 7:28 pm on June 8, 2016 Permalink | Reply
    Tags: , , , SLAC SSRL   

    From Caltech: “Solving Molecular Structures” 

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    Caltech

    06/08/2016
    Lori Dajose

    1
    The various steps of the atomic structure determination by X-ray crystallography are shown from left to right: crystals of the green fluorescent protein variant mPlum; a single mPlum crystal X-ray diffraction pattern obtained at Caltech’s Molecular Observatory; the calculated electron density map (blue) interpreted with the the positioning of all mPlum polypeptide chain atoms (shown in ball-and-stick representation); and the entire atomic structure of mPlum shown in ribbon representation. Credit: Hoelz Laboratory/Caltech

    Determining the chemical formula of a protein is fairly straightforward, because all proteins are essentially long chains of molecules called amino acids. Each chain, however, folds into a unique three-dimensional shape that helps produce the characteristic properties and function of the protein. These shapes are more difficult to determine (or “solve”); scientists traditionally do so using a technique called X-ray crystallography, in which X-rays are shot through a crystallized sample and scatter off the atoms in a distinctive pattern.

    This spring, Caltech students had the opportunity to use the technique to solve protein structures themselves in a new course taught by Professor of Chemistry André Hoelz.

    Although the Institute has a long history in the fields of structural biology and X-ray crystallography, the chance to get hands-on experience with the technique is rare at most universities, Caltech included. Indeed, the method is more commonly performed at specialized facilities with high-energy X-ray beam lines, including the Stanford Synchrotron Radiation Laboratory (SSRL).

    SLAC/SSRL
    SLAC/SSRL

    However, in 2007, thanks to a gift from the Gordon and Betty Moore Foundation, Caltech opened the Molecular Observatory—a dedicated, completely automated radiation beam line at SSRL.

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    Graeme Card examines the sample mount holder in SSRL’s Molecular Observatory for Structural Molecular Biology at Beamline 12. (Courtesy: SLAC)

    “The Molecular Observatory gives us lots of beam time,” notes Hoelz. “Recently, I also received a grant from the Innovation in Education Fund from the Provost’s Office that was matched by the Division of Chemistry and Chemical Engineering, and this allowed me the opportunity to develop this course and train students in a way not commonly found at universities.”

    In the new course, “Macromolecular Structure Determination with Modern X-ray Crystallography Methods” (BMB/Ch 230), Hoelz’s students have been using the Molecular Observatory and other on-campus crystallization resources to solve the structures of various proteins, in particular, variants of green fluorescent proteins (GFPs)—proteins that exhibit bright green fluorescence under certain wavelengths of light. “These proteins are crucial tools in biology because they can be visualized by fluorescence techniques. It’s important to know their physical structure, because it affects the intensity and wavelength at which the protein fluoresces,” says Anders Knight, a first-year graduate student studying protein engineering with Frances Arnold, the Dick and Barbara Dickinson Professor of Chemical Engineering, Bioengineering and Biochemistry, and one of nine students—including two undergraduates—in the inaugural class.

    During the first few weeks of the course, students determined the proper conditions—the pH levels and the mix of salts and buffer solutions—that are required to get a protein to crystallize. These conditions vary from protein to protein, making it tricky to “grow” perfect single crystals of the proteins. “Most of the ones we are working with have known 3-D structures, and they crystallize relatively easily, so they are a great place to start learning about the technique of X-ray crystallography,” Knight says. “But some of us were also given protein variants that had never been crystallized before.”

    Once the students crystallized their proteins, single crystals were mounted in tiny nylon loops that are attached to small metal bases, frozen in liquid nitrogen, and loaded into pucks that were shipped to SSRL. There, the pucks were loaded into a robotic machine—remotely controllable from Caltech and operated by the students—that placed them, one by one, into a powerful X-ray beam. X-rays are scattered at characteristic angles by the electrons within the crystallized samples, generating a diffraction pattern that can be converted into a so-called electron-density map, which is then used to determine the 3-D location of all of the atoms.

    “The electron density map doesn’t exactly show you what the protein’s structure is,” Knight says. “You do have to correctly interpret the electron density map to determine where the protein’s atoms will go. It’s difficult, but this class is designed to give us practice doing that. Collecting data at SSRL was a great learning experience. It was interesting to be able to accurately mount and position the crystals—each smaller than a millimeter—on the beamline from hundreds of miles away. The data collection went fairly quickly, taking around eight minutes.”

    For their final assignment, students will write a mock journal paper about their methods and the final protein structure. Most of the structures had been determined previously, but one student did solve a previously unknown GFP structure, a bright red fluorescent protein called dTomato.

    “dTomato is a product of directed evolution in protein engineering, created by subjecting its parent, DsRed, through several rounds of random genetic mutations,” says Phong Nguyen, a graduate student in the lab of Doug Rees, Roscoe Gilkey Dickinson Professor of Chemistry and Howard Hughes Medical Institute Investigator, and the student who solved the structure of dTomato in Hoelz’s class. “By solving its structure, we can see how directed evolution—a method developed by Frances Arnold to create new proteins using the principles of evolution—changed the protein from its parent. Specifically, we are able to explain how individual mutations contributed to the structural outcome of the protein and consequently to differing chemical and physical properties from the parent. We all are so excited to solve a new structure and contribute knowledge to the field of GFP protein engineering.”

    “Having the Molecular Observatory at Caltech allows us to train students with very sophisticated technology,” says Hoelz, who is now envisioning a second, related course. “Students would learn recombinant protein expression and purification, directly prior to this course, so they can purify the proteins themselves with cutting-edge technology and then go on to determine their 3D structure by X-ray crystallography,” he says.

    “In my opinion, learning by doing is the best way to master how to determine crystal structures and this new course will solidify the strong roots Caltech has in X-ray crystallography,” Hoelz adds. “Not only will this new course accelerate the otherwise slow learning process for this technique, but it will also allow non-structural biology laboratories on campus to determine crystal structures of their favorite proteins using Molecular Observatory, a unique and spectacular facility at Caltech.”

    See the full article here .

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    The California Institute of Technology (commonly referred to as Caltech) is a private research university located in Pasadena, California, United States. Caltech has six academic divisions with strong emphases on science and engineering. Its 124-acre (50 ha) primary campus is located approximately 11 mi (18 km) northeast of downtown Los Angeles. “The mission of the California Institute of Technology is to expand human knowledge and benefit society through research integrated with education. We investigate the most challenging, fundamental problems in science and technology in a singularly collegial, interdisciplinary atmosphere, while educating outstanding students to become creative members of society.”
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  • richardmitnick 5:46 am on April 21, 2016 Permalink | Reply
    Tags: , , , SLAC SSRL   

    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.

    2
    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)

    See the full article here .

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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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    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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