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

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

    Berkeley Logo

    Berkeley Lab

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

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

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


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

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

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

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

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

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

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

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

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

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

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

    LBNL/ALS

    SLAC/SSRL

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

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

    See the full article here .

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  • richardmitnick 8:22 am on June 23, 2017 Permalink | Reply
    Tags: , , , How a Single Chemical Bond Balances Cells Between Life and Death, Protein cytochrome c, , SLAC SSRL, ,   

    From SLAC: “How a Single Chemical Bond Balances Cells Between Life and Death” 


    SLAC Lab

    June 22, 2017
    Amanda Solliday

    1
    An optical laser (green) excites the iron-containing active site of the protein cytochrome c, and then an X-ray laser (white) probes the iron a few femtoseconds to picoseconds later. The critical iron-sulfur bond is broken as the optical laser heats the protein, and rebinds as the system cools. (Greg Stewart/SLAC National Accelerator Laboratory)

    Slight changes in the machinery of a cell determine whether it lives or begins a natural process known as programmed cell death. In many forms of life—from bacteria to humans—a single chemical bond in a protein called cytochrome c can make this call. As long as the bond is intact, the protein transfers electrons needed to produce energy through respiration. When the bond breaks, the protein switches gear and triggers the breakdown of mitochondria, the structures that power the cell’s activities.

    For the first time, scientists have measured exactly how much energy cytochrome c puts into maintaining that bond in a state where it’s strong enough to endure, but easy enough to break when the cell’s life span is ending.

    They used intense X-rays from two facilities, the Linac Coherent Light Source (LCLS) X-ray free-electron laser and the Stanford Synchrotron Radiation Lightsource (SSRL) at the Department of Energy’s SLAC National Accelerator Laboratory.

    SLAC/LCLS

    SLAC/SSRL

    The collaboration, led by Edward Solomon, professor of chemistry at Stanford University and of photon science at SLAC, published their results today in Science.

    “This is a very general yet extremely important process in biochemistry, and with an X-ray laser we now have insight into how this regulation works,” says Roberto Alonso-Mori, LCLS staff scientist and a co-author of the study. “These are processes that are going on a million-fold in our bodies and everywhere there is life.”

    The study marks the first time that anyone has been able to experimentally quantify how the rigid structure of the cytochrome c molecule supports this crucial bond between iron and sulfur atoms in what’s known as an entatic state, where the protein maintains a bond that is just strong enough to perform both of its jobs, says Michael Mara, lead author of the study and a former postdoctoral researcher at Stanford University, now at University of California, Berkeley.

    “This was important because we had shown the bond is weak and shouldn’t be present at room temperature in the absence of the protein constraints,” says Solomon. “But the protein is able to contribute energy to keep this bond intact for electron transfer. In this LCLS experiment, we determined exactly how much energy the rest of the protein contributes to maintaining the bond: about 4 kcal/mol that is derived from an adjacent hydrogen bond network.”

    “We were able to show how nature tunes this system to change the properties on a fundamental level and perform two very different functions,” Mara says. “The energy contribution by cytochrome c is really at a sweet spot. It makes me wonder what sort of similar effects you might see in other protein systems, and it makes us realize that there is exciting new science on the horizon.”

    Ultrafast Changes

    Cytochrome c is present in a wide range of life forms and contributes to both cellular respiration and programmed cell death, the pathway to the natural end of a cell’s life cycle. How exactly the state of the bond relates to these two functions had not yet been demonstrated or quantified.

    Scientists knew from earlier studies that a particular iron-sulfur bond is key. When iron in the protein binds to sulfur contained in one of the protein’s amino-acid building blocks, cytochrome c participates in electron transfer. By transferring electrons, the protein helps generate energy needed for biological processes that maintain life.

    But when cytochrome c encounters cardiolipin, a lipid present in the membrane of the cell’s mitochondria, the iron-sulfur bond breaks, and the protein becomes an enzyme that creates holes in the mitochondria’s outer membrane – the first step in programmed cell death.

    These changes occur incredibly fast, in less than 20 picoseconds, so the experiment required ultrafast pulses of X-rays generated by LCLS to take snapshots of the process.

    “We photoexcited the iron atoms in the protein’s active site—which contains an iron-rich compound known as heme—with an ultrafast laser before probing it with the LCLS X-ray pulses at different time delays,” says Alonso-Mori.

    Each 50-femtosecond laser pulse heated the heme by a couple of hundred degrees. X-ray pulses from LCLS took images of what happened as the heat traveled from the iron to other parts of the protein. After 100 femtoseconds, the iron-sulfur bond would break, only to form again once the sample cooled. Watching this process allowed the scientists to measure energy fluctuations in real time and better understand how this critical bond forms and breaks.

    “The entatic state concept is really interesting, but you have to come up with creative ways to demonstrate and quantify it,” says Ryan Hadt, a former Stanford University doctoral student on an Enrico Fermi Fellowship at Argonne National Laboratory who together with his advisor, Professor Solomon, came up with the idea for the experiment and co-wrote the initial proposal around the time LCLS first came online in 2009.

    “Our research group was excited about this new instrument and wanted to use it to do a definitive experiment,” Hadt adds.

    A Question Raised by Earlier Work

    This experiment builds on an earlier study [JACS] conducted at SSRL that found that the iron-sulfur bond was quite weak, says Thomas Kroll, staff scientist at SSRL and lead author of this prior study.

    In the latest study, spectroscopy at SSRL also built the framework for the LCLS pump-probe experiment. It allowed the scientists to compare what the molecule originally looked like to how it changed when the temperature rose.

    “It’s important to understand how these proteins actually work,” Kroll says. “Because if you don’t understand how they work, how can we create better medicines in an informed and controlled way?”

    Knowledge of cytochrome c’s function is also valuable to the fields of bioenergy and environmental science, since it is a critically important protein in bacteria and plants.

    The DOE Office of Science and the National Institute of General Medical Sciences of the National Institutes of Health supported this research. The Structural Molecular Biology program at SSRL is funded by DOE Office of Science and the National Institutes of Health, National Institute of General Medical Sciences. LCLS and SSRL are DOE Office of Science User Facilities.

    See the full article here .

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    SLAC is a multi-program laboratory exploring frontier questions in photon science, astrophysics, particle physics and accelerator research. Located in Menlo Park, California, SLAC is operated by Stanford University for the DOE’s Office of Science.
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  • richardmitnick 8:52 pm on June 1, 2017 Permalink | Reply
    Tags: Assembled arenavirus glycoprotein, , Hemorrhagic fever viruses, , , , SLAC SSRL, Tripod Shape Key to Future Vaccine Design, Up to 90 percent fatal in pregnant women,   

    From SLAC: “SLAC X-Ray Beam Helps Uncover Blueprint for Lassa Virus Vaccine” 


    SLAC Lab

    June 1, 2017

    1
    The molecular structure of a Lassa virus protein provides the blueprints for vaccine design. (Ollmann Saphire Lab/The Scripps Research Institute)

    2
    Erica Ollmann Saphire, professor of Immunology and Microbial Science at The Scripps Research Institute, during a visit of the Kenema Government Hospital, Sierra Leone, to study Lassa virus. (Kathryn Hastie/The Scripps Research Institute)

    3
    An antibody from a human survivor (turquoise) is shown inactivating a Lassa virus surface protein. (Ollmann Saphire Lab/The Scripps Research Institute)

    A decade-long search ends at the Stanford Synchrotron Radiation Lightsource, where researchers from The Scripps Research Institute emerge with a clear picture of how the deadly Lassa virus enters human cells.

    SLAC/SSRL

    Before Ebola virus ever struck West Africa, locals were continually on the lookout for another deadly pathogen: Lassa virus. With thousands dying from Lassa every year – and the potential for the virus to cause even larger outbreaks – researchers are committed to designing a vaccine to stop it.

    Now a team of scientists from The Scripps Research Institute (TSRI) has solved the structure of the viral machinery that Lassa virus uses to enter human cells.

    X-ray beams from the Stanford Synchrotron Radiation Lightsource (SSRL) at the Department of Energy’s SLAC National Accelerator Laboratory gave the team the final piece in a puzzle they sought to solve for over 10 years.

    Their study, published today in Science, is the first to show a key piece of the viral structure, called the surface glycoprotein, for any member of the deadly arenavirus family, and the new structure provides a blueprint to design a Lassa virus vaccine.

    “This was a tenacious effort – over a decade – to conquer a global threat,” said Erica Ollmann Saphire, a professor of Immunology and Microbial Science from TSRI and senior author of the new study.

    X-ray data for this study was collected at SLAC and the DOE’s Argonne National Laboratory.

    For the SLAC experiments, the researchers used a station at SSRL, a DOE Office of Science User Facility that has a strong program in biological X-ray crystallography. In this method, scientists prompt biological molecules to align and form a crystal, which they then study with powerful X-rays. The way the X-rays scatter off the crystal reveals the structure of the molecules inside – in 3-D and with atomic detail.

    “I am proud of SSRL’s strong partnership with TSRI and our involvement in this project that utilized the bright X-ray microbeams and high level of automation at Beam Line 12-2 to obtain the necessary data,” said SSRL senior staff scientist Aina Cohen. “This structure provides key information towards engineering an effective vaccine against Lassa, enabling the infected to combat the immunosuppressive traits of this virus, which is estimated to kill tens of thousands of people each year.”

    It Started with a Thesis

    The effort began with TSRI staff scientist Kathryn Hastie, the lead author of the study. In 2007, then a grad student in Ollmann Saphire’s lab, she told her thesis committee she wanted to solve the structure of the assembled arenavirus glycoprotein, something never done before. She hoped to create a map of the target on the virus where antibodies need to attack – a key step in developing a vaccine.

    Such maps can be obtained with X-ray crystallography, but the method depends on having a stable protein. Yet, all the Lassa virus glycoprotein wanted to do was fall apart.

    The problem was that glycoproteins are made up of smaller subunits. Other viruses have bonds that hold the subunits together, “like a staple,” Hastie said. Arenaviruses don’t have that staple; instead, the subunits just floated away from each other whenever Hastie tried to work with them.

    Another challenge was to recreate part of the viral lifecycle in the lab – a stage when Lassa’s glycoprotein gets clipped into two subunits. “We had to figure out how to get the subunits to be sufficiently clipped, which is necessary to make the biologically functional assembly, and also where to put an engineered staple to make sure they stayed together,” Hastie said.

    Partnering with West Africa

    As Hastie tackled those challenges from her lab bench in San Diego, staff at the Kenema Government Hospital in Sierra Leone labored on the front lines of the ongoing fight against Lassa.

    Until the 2014–15 Ebola virus outbreak, Kenema was the only hospital in the world to have a special ward dedicated to treating hemorrhagic fever viruses. Staff at the clinic – from the nurses to the ambulance drivers – are all Lassa survivors, which gives them immunity to the disease. The TSRI scientists have a long-term collaboration with Kenema as part of a research program run by Tulane University that provided them with antibodies from survivors of Lassa fever. These antibodies could inactivate the virus, and they provided lifesaving protection to animal models. These were the kinds of antibodies researchers are hoping to elicit with a future Lassa virus vaccine.

    In 2009, Hastie got to visit Kenema on a trip with Ollmann Saphire.

    “I had been working on the project for two years with very little success at that point,” Hastie said. “Going to West Africa showed me how important it was to keep going.”

    Like Ebola virus, Lassa fever starts with flu-like symptoms and can lead to debilitating vomiting, neurological problems and even hemorrhaging from the eyes, gums and nose. The disease is 50 to 70 percent fatal—and up to 90 percent fatal in pregnant women.

    “Studying Lassa is critically important. Hundreds of thousands of people are infected with the virus every year, and it is the viral hemorrhagic fever that most frequently comes to the United States and Europe,” said Ollmann Saphire. “Kate’s study needed to be done.”

    Tripod Shape Key to Future Vaccine Design

    By creating mutant versions of important parts of the molecule, Hastie engineered a version of the Lassa virus surface glycoprotein that didn’t fall apart. She then used this model glycoprotein as a sort of magnet to find antibodies in patient samples that could bind with the glycoprotein to neutralize the virus.

    With this latest study she solved the structure of the Lassa virus glycoprotein, bound to a neutralizing antibody from a human survivor.

    Her structure showed that the glycoprotein has two parts. She compared the shape to an ice cream cone and a scoop of ice cream. A subunit called GP2 forms the cone, and the GP1 subunit sits on top. They work together when they encounter a host cell. GP1 binds to a host cell receptor, and GP2 starts the fusion process to enter that cell.

    The new structure also showed a long structure hanging off the side of GP1—like a drip of melting ice cream running down the cone. This “drip” holds the two subunits together in their pre-fusion state.

    Zooming in even closer, Hastie discovered that three of the GP1-GP2 pairs come together like a tripod. This arrangement appears to be unique to Lassa virus. Other viruses, such as influenza and HIV, also have three-part proteins (called trimers) at this site, but their subunits come together to form a pole, not a tripod. The structure is also important because it can be used as a model to conquer related viruses throughout the Americas, Europe and Africa for which no equivalent structure yet exists.

    “It was great to see exactly how Lassa was different from other viruses,” said Hastie. “It was a tremendous relief to finally have the structure.”

    This tripod arrangement offers a path for vaccine design. The scientists found that 90 percent of the effective antibodies in Lassa patients targeted the spot where the three GP subunits came together. These antibodies locked the subunits together, preventing the virus from gearing up to enter a host cell.

    A future vaccine would likely have the greatest chance of success if it could trigger the body to produce antibodies to target the same site.

    Ollmann Saphire explained that Hastie accomplished something unique in structural biology. “The research started from scratch with the native, wild-type viruses in patients in a remote clinic—and went all the way to developing a basis for vaccine design. And the work was done almost entirely by one woman.”

    Moving Forward with a Lassa Vaccine

    The next step is to test a vaccine that will prompt the immune system to target Lassa’s glycoprotein.

    As director of the Viral Hemorrhagic Fever Immunotherapeutic Consortium, Ollmann Saphire is already coordinating with her partners at Tulane and Kenema to bring a vaccine to patients.

    The Coalition for Epidemic Preparedness Innovations, an international collaboration that includes the Wellcome Trust and the World Health Organization as partners, has recently named a vaccine for Lassa virus as one of its three top priorities. “The community is keenly interested in making a Lassa vaccine, and we think we have the best template to do that,” said Ollmann Saphire.

    She added that with Hastie’s techniques for solving arenavirus structures, researchers can now get a closer look at other hemorrhagic fever viruses, which cause death, neurological diseases and even birth defects around the world.

    Ollmann Saphire added that beamlines such as 12-2 at SSRL, which provided the X-ray beam used to finally determine the Lassa virus glycoprotein structure, along with its recent detector upgrades, are essential for ongoing advances in structural biology.

    “This research highlights the power of crystallographic techniques that rely on advanced synchrotron facilities to combat the most challenging biological problems. The support of the DOE’s Office of Science Biological and Environmental Research, the National Institutes of Health and private institutions such as TSRI enables us to make these resources available to the wider biomedical community,” Cohen said.

    In addition to Ollmann Saphire and Hastie, the following authors contributed: Michelle A. Zandonatti of TSRI; James E. Robinson and Robert F. Garry of Tulane University; Lara M. Kleinfelter and Kartik Chandran of the Albert Einstein College of Medicine; and Megan L. Heinrich, Megan M. Rowland and Luis M. Branco of Zalgen Labs.

    5
    The new study included (left to right) first author Kathryn M. Hastie, senior author Erica Ollmann Saphire and co-author Michelle A. Zandonatti of The Scripps Research Institute. (Photo by Madeline McCurry-Schmidt.)

    The study was supported by the National Institutes of Health and an Investigators in Pathogenesis of Infectious Diseases Award from the Burroughs Wellcome Fund. Research funding for the SSRL Structural Molecular Biology Program was provided by the DOE Office of Science and the National Institutes of Health, National Institute of General Medical Sciences.

    See the full article here .

    See the Scripps press release here .

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  • richardmitnick 3:55 pm on April 17, 2017 Permalink | Reply
    Tags: , , , , , , , SLAC SSRL,   

    From SLAC: “SLAC’s X-ray Laser Glimpses How Electrons Dance with Atomic Nuclei in Materials” 


    SLAC Lab

    September 22, 2016

    Studies Could Help Design and Control Materials with Intriguing Properties, Including Novel Electronics, Solar Cells and Superconductors.

    From hard to malleable, from transparent to opaque, from channeling electricity to blocking it: Materials come in all types. A number of their intriguing properties originate in the way a material’s electrons “dance” with its lattice of atomic nuclei, which is also in constant motion due to vibrations known as phonons.

    This coupling between electrons and phonons determines how efficiently solar cells convert sunlight into electricity. It also plays key roles in superconductors that transfer electricity without losses, topological insulators that conduct electricity only on their surfaces, materials that drastically change their electrical resistance when exposed to a magnetic field, and more.

    At the Department of Energy’s SLAC National Accelerator Laboratory, scientists can study these coupled motions in unprecedented detail with the world’s most powerful X-ray laser, the Linac Coherent Light Source (LCLS). LCLS is a DOE Office of Science User Facility.

    SLAC/LCLS

    1
    An illustration shows how laser light excites electrons (white spheres) in a solid material, creating vibrations in its lattice of atomic nuclei (black and blue spheres). SLAC’s LCLS X-ray laser reveals the ultrafast “dance” between electrons and vibrations that accounts for many important properties of materials. (SLAC National Accelerator Laboratory)

    “It has been a long-standing goal to understand, initiate and control these unusual behaviors,” says LCLS Director Mike Dunne. “With LCLS we are now able to see what happens in these materials and to model complex electron-phonon interactions. This ability is central to the lab’s mission of developing new materials for next-generation electronics and energy solutions.”

    LCLS works like an extraordinary strobe light: Its ultrabright X-rays take snapshots of materials with atomic resolution and capture motions as fast as a few femtoseconds, or millionths of a billionth of a second. For comparison, one femtosecond is to a second what seven minutes is to the age of the universe.

    Two recent studies made use of these capabilities to study electron-phonon interactions in lead telluride, a material that excels at converting heat into electricity, and chromium, which at low temperatures has peculiar properties similar to those of high-temperature superconductors.

    Turning Heat into Electricity and Vice Versa

    Lead telluride, a compound of the chemical elements lead and tellurium, is of interest because it is a good thermoelectric: It generates an electrical voltage when two opposite sides of the material have different temperatures.

    “This property is used to power NASA space missions like the Mars rover Curiosity and to convert waste heat into electricity in high-end cars,” says Mariano Trigo, a staff scientist at the Stanford PULSE Institute and the Stanford Institute for Materials and Energy Sciences (SIMES), both joint institutes of Stanford University and SLAC. “The effect also works in the opposite direction: An electrical voltage applied across the material creates a temperature difference, which can be exploited in thermoelectric cooling devices.”

    Mason Jiang, a recent graduate student at Stanford, PULSE and SIMES, says, “Lead telluride is exceptionally good at this. It has two important qualities: It’s a bad thermal conductor, so it keeps heat from flowing from one side to the other, and it’s also a good electrical conductor, so it can turn the temperature difference into an electric current. The coupling between lattice vibrations, caused by heat, and electron motions is therefore very important in this system. With our study at LCLS, we wanted to understand what’s naturally going on in this material.”

    In their experiment, the researchers excited electrons in a lead telluride sample with a brief pulse of infrared laser light, and then used LCLS’s X-rays to determine how this burst of energy stimulated lattice vibrations.

    2
    This illustration shows the arrangement of lead and tellurium atoms in lead telluride, an excellent thermoelectric that efficiently converts heat into electricity and vice versa. In its normal state (left), lead telluride’s structure is distorted and has a relatively large degree of lattice vibrations (blurring). When scientists hit the sample with a laser pulse, the structure became more ordered (right). The results elucidate how electrons couple with these distortions – an interaction that is crucial for lead telluride’s thermoelectric properties. (SLAC National Accelerator Laboratory)

    “Lead telluride sits at the precipice of a coupled electronic and structural transformation,” says principal investigator David Reis from PULSE, SIMES and Stanford. “It has a tendency to distort without fully transforming – an instability that is thought to play an important role in its thermoelectric behavior. With our method we can study the forces involved and literally watch them change in response to the infrared laser pulse.”

    The scientists found that the light pulse excites particular electronic states that are responsible for this instability through electron-phonon coupling. The excited electrons stabilize the material by weakening certain long-range forces that were previously associated with the material’s low thermal conductivity.

    “The light pulse actually walks the material back from the brink of instability, making it a worse thermoelectric,” Reis says. “This implies that the reverse is also true – that stronger long-range forces lead to better thermoelectric behavior.”

    The researchers hope their results, published July 22 in Nature Communications, will help them find other thermoelectric materials that are more abundant and less toxic than lead telluride.

    Controlling Materials by Stimulating Charged Waves

    The second study looked at charge density waves – alternating areas of high and low electron density across the nuclear lattice – that occur in materials that abruptly change their behavior at a certain threshold. This includes transitions from insulator to conductor, normal conductor to superconductor, and from one magnetic state to another.

    These waves don’t actually travel through the material; they are stationary, like icy waves near the shoreline of a frozen lake.

    “Charge density waves have been observed in a number of interesting materials, and establishing their connection to material properties is a very hot research topic,” says Andrej Singer, a postdoctoral fellow in Oleg Shpyrko’s lab at the University of California, San Diego. “We’ve now shown that there is a way to enhance charge density waves in crystals of chromium using laser light, and this method could potentially also be used to tweak the properties of other materials.”

    This could mean, for example, that scientists might be able to switch a material from a normal conductor to a superconductor with a single flash of light. Singer and his colleagues reported their results on July 25 in Physical Review Letters.

    The research team used the chemical element chromium as a simple model system to study charge density waves, which form when the crystal is cooled to about minus 280 degrees Fahrenheit. They stimulated the chilled crystal with pulses of optical laser light and then used LCLS X-ray pulses to observe how this stimulation changed the amplitude, or height, of the charge density waves.

    “We found that the amplitude increased by up to 30 percent immediately after the laser pulse,” Singer says. “The amplitude then oscillated, becoming smaller and larger over a period of 450 femtoseconds, and it kept going when we kept hitting the sample with laser pulses. LCLS provides unique opportunities to study such process because it allows us to take ultrafast movies of the related structural changes in the lattice.”

    Based on their results, the researchers suggested a mechanism for the amplitude enhancement: The light pulse interrupts the electron-phonon interactions in the material, causing the lattice to vibrate. Shortly after the pulse, these interactions form again, which boosts the amplitude of the vibrations, like a pendulum that swings farther out when it receives an extra push.

    A Bright Future for Studies of the Electron-Phonon Dance

    Studies like these have a high priority in solid-state physics and materials science because they could pave the way for new materials and provide new ways to control material properties.

    With its 120 ultrabright X-ray pulses per second, LCLS reveals the electron-phonon dance with unprecedented detail. More breakthroughs in the field are on the horizon with LCLS-II – a next-generation X-ray laser under construction at SLAC that will fire up to a million X-ray flashes per second and will be 10,000 times brighter than LCLS.

    “LCLS-II will drastically increase our chances of capturing these processes,” Dunne says. “Since it will also reveal subtle electron-phonon signals with much higher resolution, we’ll be able to study these interactions in much greater detail than we can now.”

    Other research institutions involved in the studies were University College Cork, Ireland; Imperial College London, UK; Duke University; Oak Ridge National Laboratory; RIKEN Spring-8 Center, Japan; University of Tokyo, Japan; University of Michigan; and University of Kiel, Germany. Funding sources included DOE Office of Science; Science Foundation Ireland; Volkswagen Foundation, Germany; and Federal Ministry of Education and Research, Germany. Preliminary X-ray studies on lead telluride were performed at SLAC’s Stanford Synchrotron Radiation Lightsource (SSRL), a DOE Office of Science User Facility, and at the Spring-8 Angstrom Compact Free-electron Laser (SACLA), Japan.

    SLAC/SSRL

    SACLA Free-Electron Laser Riken Japan


    his movie introduces LCLS-II, a future light source at SLAC. It will generate over 8,000 times more light pulses per second than today’s most powerful X-ray laser, LCLS, and produce an almost continuous X-ray beam that on average will be 10,000 times brighter. (SLAC National Accelerator Laboratory)

    See the full article here .

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  • richardmitnick 2:45 pm on February 23, 2017 Permalink | Reply
    Tags: , , Instrument finds new earthly purpose, , , SLAC SSRL, Spectrometry, ,   

    From Symmetry: “Instrument finds new earthly purpose” 

    Symmetry Mag

    Symmetry

    02/23/17
    Amanda Solliday

    1
    Nordlund and his colleagues—Sangjun Lee, a SLAC postdoctoral research fellow, and Jamie Titus, a Stanford University doctoral student (pictured above at SSRL, from left: Lee, Titus and Nordlund)—have already used the transition-edge-sensor spectrometer at SSRL to probe for nitrogen impurities in nanodiamonds and graphene, as well as closely examine the metal centers of proteins and bioenzymes, such as hemoglobin and photosystem II. The project at SLAC was developed with 
support by the Department of Energy’s Laboratory Directed Research and Development.
    Andy Freeberg, SLAC National Accelerator Laboratory

    Detectors long used to look at the cosmos are now part of X-ray experiments here on Earth.

    Modern cosmology experiments—such as the BICEP instruments and the in Antarctica—rely on superconducting photon detectors to capture signals from the early universe.

    BICEP 3 at the South Pole
    BICEP 3 at the South Pole

    Keck Array
    Keck Array at the South Pole

    These detectors, called transition edge sensors, are kept at temperatures near absolute zero, at only tenths of a Kelvin. At this temperature, the “transition” between superconducting and normal states, the sensors function like an extremely sensitive thermometer. They are able to detect heat from cosmic microwave background radiation, the glow emitted after the Big Bang, which is only slightly warmer at around 3 Kelvin.

    Scientists also have been experimenting with these same detectors to catch a different form of light, says Dan Swetz, a scientist at the National Institute of Standards and Technology. These sensors also happen to work quite well as extremely sensitive X-ray detectors.

    NIST scientists, including Swetz, design and build the thin, superconducting sensors and turn them into pixelated arrays smaller than a penny. They construct an entire X-ray spectrometer system around those arrays, including a cryocooler, a refrigerator that can keep the detectors near absolute zero temperatures.

    2

    TES array and cover shown with penny coin for scale.
    Dan Schmidt, NIST

    Over the past several years, these X-ray spectrometers built at the NIST Boulder MicroFabrication Facility have been installed at three synchrotrons at US Department of Energy national laboratories: the National Synchrotron Light Source at Brookhaven National Laboratory, the Advanced Photon Source [APS] at Argonne National Laboratory and most recently at the Stanford Synchrotron Radiation Lightsource [SSRL] at SLAC National Accelerator Laboratory.

    BNL NSLS-II Interior
    BNL NSLS-II Interior

    ANL APS interior
    ANL APS interior

    SLAC/SSRL
    SLAC/SSRL

    Organizing the transition edge sensors into arrays made a more powerful detector. The prototype sensor—built in 1995—consisted of only one pixel.

    These early detectors had poor resolution, says physicist Kent Irwin of Stanford University and SLAC. He built the original single-pixel transition edge sensor as a postdoc. Like a camera, the detector can capture greater detail the more pixels it has.

    “It’s only now that we’re hitting hundreds of pixels that it’s really getting useful,” Irwin says. “As you keep increasing the pixel count, the science you can do just keeps multiplying. And you start to do things you didn’t even conceive of being possible before.”

    Each of the 240 pixels is designed to catch a single photon at a time. These detectors are efficient, says Irwin, collecting photons that may be missed with more conventional detectors.

    Spectroscopy experiments at synchrotrons examine subtle features of matter using X-rays. In these types of experiments, an X-ray beam is directed at a sample. Energy from the X-rays temporarily excites the electrons in the sample, and when the electrons return to their lower energy state, they release photons. The photons’ energy is distinctive for a given chemical element and contains detailed information about the electronic structure.

    As the transition edge sensor captures these photons, every individual pixel on the detector functions as a high-energy-resolution spectrometer, able to determine the energy of each photon collected.

    The researchers combine data from all the pixels and make note of the pattern of detected photons across the entire array and each of their energies. This energy spectrum reveals information about the molecule of interest.

    These spectrometers are 100 times more sensitive than standard spectrometers, says Dennis Nordlund, SLAC scientist and leader of the transition edge sensor project at SSRL. This allows a look at biological and chemical details at extremely low concentrations using soft (low-energy) X-rays.

    “These technology advances mean there are many things we can do now with spectroscopy that were previously out of reach,” Nordlund says. “With this type of sensitivity, this is when it gets really interesting for chemistry.”

    The early experiments at Brookhaven looked at bonding and the chemical structure of nitrogen-bearing explosives. With the spectrometer at Argonne, a research team recently took scattering measurements on high-temperature superconducting materials.

    “The instruments are very similar from a technical standpoint—same number of sensors, similar resolution and performance,” Swetz says. “But it’s interesting, the labs are all doing different science with the same basic equipment.”

    At NIST, Swetz says they’re working to pair these detectors with less intense light sources, which could enable researchers to do X-ray experiments in their personal labs.

    There are plans to build transition-edge-sensor spectrometers that will work in the higher energy hard X-ray region, which scientists at Argonne are working on for the next upgrade of Advanced Photon Source.

    To complement this, the SLAC and NIST collaboration is engineering spectrometers that will handle the high repetition rate of X-ray laser pulses such as LCLS-II, the next generation of the free-electron X-ray laser at SLAC. This will require faster readout systems. The goal is to create a transition-edge-sensor array with as many as 10,000 pixels that can capture more than 10,000 pulses per second.

    Irwin points out that the technology developed for synchrotrons, LCLS-II and future cosmic-microwave-background experiments provides shared benefit.

    “The information really keeps bouncing back and forth between X-ray science and cosmology,” Irwin says

    See the full article here .

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    Symmetry is a joint Fermilab/SLAC publication.


     
  • 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.

    1
    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.

    2
    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.

    1
    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.”

    1
    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” 

    Caltech Logo

    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.

    1
    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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