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  • richardmitnick 1:24 pm on February 12, 2018 Permalink | Reply
    Tags: ANL, ATLAS- Argonne Tandem Linac Accelerator System, LBNL Gammasphere,   

    From ANL: “Captured electrons excite nuclei to higher energy states” 

    ANL Lab

    News from Argonne National Laboratory

    February 9, 2018
    Savannah Mitchem

    1
    LBNL Gammosphere
    Argonne scientists and collaborators used the Gammasphere, this powerful gamma ray spectrometer, to help create the right conditions to cause and spot a long-theorized effect called nuclear excitation by electron capture. (Image by Argonne National Laboratory.)

    For the first time, physicists from the U.S. Department of Energy’s (DOE) Argonne National Laboratory and their collaborators, led by a team from the U.S. Army Research Laboratory, demonstrated a long-theorized nuclear effect. This advance tests theoretical models that describe how nuclear and atomic realms interact and may also provide new insights into how star elements are created.

    Physicists first predicted the effect, called nuclear excitation by electron capture (NEEC), over 40 years ago. But scientists had not seen it until now. Using the Argonne Tandem Linac Accelerator System (ATLAS), and Gammasphere, a powerful gamma ray spectrometer, the researchers created the right conditions to cause and spot the behavior.


    Argonne Tandem Linac Accelerator System (ATLAS)

    The NEEC effect occurs when a charged atom captures an electron, giving the atom’s nucleus enough energy to jump to a higher excited state.

    An excited nucleus stays in each energy state for a while before decaying into the state below it, shedding energy in the form of gamma rays. These excited states typically last for much less than a billionth of a second, but in some rare cases, they can live far longer, even for millions of times the age of the universe.

    The longer-lived energy states are called isomers, and to observe the NEEC effect, the researchers produced an isomer with a half-life of about seven hours. In other words, after seven hours of existing in the isomeric energy level, about half of the nuclei of this type will decay.

    The scientists chose to produce this nucleus, called 93Mo, an isotope of molybdenum, because of its unique arrangement of energy levels. “There is an allowed energy level not far above the isomer state,” said the Army Research Laboratory’s Chris Chiara, the study’s lead scientist. “Under normal circumstances, the isomer will decay naturally after about seven hours, but if NEEC occurs, the nucleus is excited out of the isomer to the slightly higher state. That state then quickly decays to a state below the isomer, emitting gamma rays that have distinct energies that we can look for.”

    To make 93Mo, the researchers used ATLAS, a DOE Office of Science User Facility, to accelerate a beam of ions towards the atoms in a target foil where the nuclei of the two fused together. These reactions formed 93Mo in a highly excited state at the center of Gammasphere, which waited to detect evidence of the effect in the form of gamma rays.

    As the 93Mo atoms move through the target material, they bump into atoms that slow them down and strip them of electrons, putting them in a high-charge state. Electrons from the target atoms then fill those vacancies in the 93Mo, and if the electrons have the right energy before the capture, they may excite the nucleus into the next highest state. When this state decays, the nucleus releases a gamma ray that can be traced back to the NEEC reaction.

    The target, made by ATLAS’s in-house target maker, John Greene, played a crucial role in the detection of NEEC. Greene was able to work on the fly, tweaking the target as the scientists learned more about the 93Mo nucleus. With everything in place, the team began to gather data.

    “We detected gamma rays from these reactions over the course of the three-day experiment, and we accumulated around eight billion events in total,” said Mike Carpenter, a group leader at Argonne in charge of Gammasphere. “From these events, we were able to identify around 500 gamma rays that were emitted during the decay of 93Mo that wouldn’t have been released if it weren’t for NEEC.”

    The power and sensitivity of Gammasphere was vital to the experiment’s success. “We made use of a new digital Gammasphere mode, which allowed us to run at a rate about five times higher than would have been possible with the older analog system,” said Chiara. But it was not only the hardware at ATLAS that was important. “As experts in the field of gamma-ray spectroscopy, the Argonne staff provided invaluable scientific and technical support,” he added.

    The team’s success may lead to advances in astronomy and cosmology as it could improve the accuracy of models scientists use to gauge how stars form. The quantities of elements in a star depend largely on the structure and behavior of nuclei. Over long periods, and with vast numbers of atoms interacting, the survival — or destruction — of specific isomers can have a cumulative influence. Taking the NEEC effect into account could improve our understanding of what stars are made of and how they evolve.

    Scientists at the Army Research Laboratory are also interested in possible future applications for the controlled release of nuclear energy from isomers via the NEEC effect. If scientists and engineers could harness this energy, it might help develop power sources with 100,000 times greater energy per unit mass than chemical batteries.

    The results of the experiment were published in a paper titled Isomer depletion as experimental evidence of nuclear excitation by electron capture, on February 8 in Nature.

    Other Argonne co-authors include physicists Robert Janssens (now at the University of North Carolina at Chapel Hill/Triangle Universities Nuclear Laboratory), Darek Seweryniak and Shaofei Zhu.

    The work was funded by DOE’s Office of Science, the U.S. Army Research Laboratory, the National Science Foundation, the Australian Research Council and the Polish National Science Centre.

    The U.S. Army Research Laboratory is part of the U.S. Army Research, Development and Engineering Command (RDECOM), which has the mission to provide innovative research, development and engineering to produce capabilities that provide decisive overmatch to the Army against the complexities of the current and future operating environments in support of the joint warfighter and the nation. RDECOM is a major subordinate command of the U.S. Army Materiel Command.

    See the full article here .

    Please help promote STEM in your local schools.
    STEM Icon
    Stem Education Coalition
    Argonne National Laboratory seeks solutions to pressing national problems in science and technology. The nation’s first national laboratory, Argonne conducts leading-edge basic and applied scientific research in virtually every scientific discipline. Argonne researchers work closely with researchers from hundreds of companies, universities, and federal, state and municipal agencies to help them solve their specific problems, advance America’s scientific leadership and prepare the nation for a better future. With employees from more than 60 nations, Argonne is managed by UChicago Argonne, LLC for the U.S. Department of Energy’s Office of Science. For more visit http://www.anl.gov.

    The Advanced Photon Source at Argonne National Laboratory is one of five national synchrotron radiation light sources supported by the U.S. Department of Energy’s Office of Science to carry out applied and basic research to understand, predict, and ultimately control matter and energy at the electronic, atomic, and molecular levels, provide the foundations for new energy technologies, and support DOE missions in energy, environment, and national security. To learn more about the Office of Science X-ray user facilities, visit http://science.energy.gov/user-facilities/basic-energy-sciences/.

    Argonne is managed by UChicago Argonne, LLC for the U.S. Department of Energy’s Office of Science

    Argonne Lab Campus

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  • richardmitnick 2:45 pm on January 27, 2018 Permalink | Reply
    Tags: ANL, , Breaking bad metals with neutrons, , , , , ,   

    From ANL: “Breaking bad metals with neutrons” 

    ANL Lab

    News from Argonne National Laboratory

    January 11, 2018
    Ron Walli

    `
    A comparison of the theoretical calculations (top row) and inelastic neutron scattering data from ARCS at the Spallation Neutron Source (bottom row) shows the excellent agreement between the two. The three figures represent different slices through the four-dimensional scattering volumes produced by the electronic excitations. (Image by Argonne National Laboratory.)

    By exploiting the properties of neutrons to probe electrons in a metal, a team of researchers led by the U.S. Department of Energy’s (DOE) Argonne National Laboratory has gained new insight into the behavior of correlated electron systems, which are materials that have useful properties such as magnetism or superconductivity.

    The research, to be published in Science, shows how well scientists can predict the properties and functionality of materials, allowing us to explore their potential to be used in novel ways.

    “Our mission from the Department of Energy is to discover and then understand novel materials that could form the basis for completely new applications,” said lead author Ray Osborn, a senior scientist in Argonne’s Neutron and X-ray Scattering Group.

    Osborn and his colleagues studied a strongly correlated electron system (CePd3) using neutron scattering to overcome the limitations of other techniques and reveal how the compound’s electrical properties change at high and low temperatures. Osborn expects the results to inspire similar research.

    “Being able to predict with confidence the behavior of electrons as temperatures change should encourage a much more ambitious coupling of experimental results and models than has been previously attempted,” Osborn said.

    “In many metals, we consider the mobile electrons responsible for electrical conduction as moving independently of each other, only weakly affected by electron-electron repulsion,” he said. “However, there is an important class of materials in which electron-electron interactions are so strong they cannot be ignored.”

    Scientists have studied these strongly correlated electron systems for more than five decades, and one of the most important theoretical predictions is that at high temperatures the electron interactions cause random fluctuations that impede their mobility.

    “They become ‘bad’ metals,” Osborn said. However, at low temperatures, the electronic excitations start to resemble those of normal metals, but with much-reduced electron velocities.

    The existence of this crossover from incoherent random fluctuations at high temperature to coherent electronic states at low temperature had been postulated in 1985 by one of the co-authors, Jon Lawrence, a professor at the University of California, Irvine. Although there is some evidence for it in photoemission experiments, Argonne co-author Stephan Rosenkranz noted that it is very difficult to compare these measurements with realistic theoretical calculations because there are too many uncertainties in modeling the experimental intensities.

    The team, based mainly at Argonne and other DOE laboratories, showed that neutrons probe the electrons in a different way that overcomes the limitations of photoemission spectroscopy and other techniques.

    Making this work possible are advances in neutron spectroscopy at DOE’s Spallation Neutron Source (SNS) at Oak Ridge National Laboratory, a DOE Office of Science User Facility, and the United Kingdom’s ISIS Pulsed Neutron Source, which allow comprehensive measurements over a wide range of energies and momentum transfers. Both played critical roles in this study.

    ORNL Spallation Neutron Source


    ORNL Spallation Neutron Source

    2
    STFC ISIS Pulsed Neutron Source.

    “Neutrons are absolutely essential for this research,” Osborn said. “Neutron scattering is the only technique that is sensitive to the whole spectrum of electronic fluctuations in four dimensions of momentum and energy, and the only technique that can be reliably compared to realistic theoretical calculations on an absolute intensity scale.”

    With this study, these four-dimensional measurements have now been directly compared to calculations using new computational techniques specially developed for strongly correlated electron systems. The technique, known as Dynamical Mean Field Theory, defines a way of calculating electronic properties that include strong electron-electron interactions.

    Osborn acknowledged the contributions of Eugene Goremychkin, a former Argonne scientist who led the data analysis, and Argonne theorist Hyowon Park, who performed the calculations. The agreement between theory and experiments was “truly remarkable,” Osborn said.

    Looking ahead, researchers are optimistic about closing the gap between the results of condensed matter physics experiments and theoretical models.

    “How do you get to a stage where the models are reliable?” Osborn said. “This paper shows that we can now theoretically model even extremely complex systems. These techniques could accelerate our discovery of new materials.”

    Other Argonne authors of the paper, titled Coherent Band Excitations in CePd3: A Comparison of Neutron Scattering and ab initio Theory, are Park and John-Paul Castellan of the Materials Science Division. Also contributing to this work were researchers at the Joint Institute for Nuclear Research in Russia; the University of Illinois at Chicago; Karlsruhe Institute of Technology in Germany; Oak Ridge National Laboratory; Los Alamos National Laboratory and the University of California at Irvine.

    Research at Argonne and Los Alamos was funded by DOE’s Materials Sciences and Engineering Division of the Office of Basic Energy Sciences. Research at Oak Ridge’s SNS was supported by the Scientific User Facilities Division of the Office of Basic Energy Sciences. Neutron experiments were performed at the SNS and the ISIS Pulsed Neutron Source, Rutherford Appleton Laboratory in the UK. Blues, a high-performance computing cluster operated by the Laboratory Computing Resource Center at Argonne, also contributed to this research.

    See the full article here .

    Please help promote STEM in your local schools.
    STEM Icon
    Stem Education Coalition
    Argonne National Laboratory seeks solutions to pressing national problems in science and technology. The nation’s first national laboratory, Argonne conducts leading-edge basic and applied scientific research in virtually every scientific discipline. Argonne researchers work closely with researchers from hundreds of companies, universities, and federal, state and municipal agencies to help them solve their specific problems, advance America’s scientific leadership and prepare the nation for a better future. With employees from more than 60 nations, Argonne is managed by UChicago Argonne, LLC for the U.S. Department of Energy’s Office of Science. For more visit http://www.anl.gov.

    The Advanced Photon Source at Argonne National Laboratory is one of five national synchrotron radiation light sources supported by the U.S. Department of Energy’s Office of Science to carry out applied and basic research to understand, predict, and ultimately control matter and energy at the electronic, atomic, and molecular levels, provide the foundations for new energy technologies, and support DOE missions in energy, environment, and national security. To learn more about the Office of Science X-ray user facilities, visit http://science.energy.gov/user-facilities/basic-energy-sciences/.

    Argonne is managed by UChicago Argonne, LLC for the U.S. Department of Energy’s Office of Science

    Argonne Lab Campus

     
  • richardmitnick 2:16 pm on December 22, 2017 Permalink | Reply
    Tags: ANL, , , ,   

    From ANL: “A catalytic balancing act “ 

    Argonne Lab
    News from Argonne National Laboratory

    1
    Argonne scientists and their collaborators have used a new and counterintuitive approach to balance three important factors — activity, stability and conductivity — in a new catalyst designed for splitting water. (Image by Argonne National Laboratory.)

    Balance forms the foundation for a happy life or a healthy diet. For scientists working to design new catalysts to create renewable energy, balancing different materials and their properties is equally important. (Catalysts help accelerate chemical reactions.)

    In a new study Nature Communications, researchers from the U.S. Department of Energy’s (DOE) Argonne National Laboratory, Johns Hopkins University, Drexel University and several universities in South Korea used a new and counterintuitive approach to create a better catalyst that supports one of the reactions involved in splitting water into hydrogen and oxygen. Scientists plan to use the generated hydrogen as a clean fuel.

    ______________________________________________________
    “Finding a material that works well for energy conversion or storage is like creating a happy marriage.” – Nenad Markovic, Argonne materials scientist and study author.
    ______________________________________________________

    By first creating an alloy of two of the densest naturally occurring elements and then removing one, the scientists reshaped the remaining material’s structure so that it better balanced three factors important for chemical reactions: activity, stability and conductivity.

    “Finding a material that works well for energy conversion or storage is like creating a happy marriage,” said Nenad Markovic, an Argonne materials scientist and author of the study. “In our case, we found that a dynamic partnership between two different materials helped us integrate competing concerns.”

    Scientists searching for new catalysts have scoured the periodic table to find the right elements or combinations of elements to maximize a catalyst’s activity in water-splitting reactions, as well as the durability of the active sites on its surface. Finding materials that are both stable and active, however, has been a challenge.

    “More active catalysts tend to be less stable,” Markovic said. “Those that seem to work twice as well usually work only half as long. It is becoming obvious that designing active catalysts is not enough — we need to have not only active, but also stable, materials.”

    For the new catalyst, Markovic and his colleagues turned to iridium, a metal most commonly associated with meteorites. As a thin film, iridium is catalytically active, but as it reacts over time with an electrolyte environment, iridium atoms become oxidized. During this process, some of them leave the catalyst’s surface through corrosion, increasingly impairing its performance.

    The research team worked to prevent the oxidation by reorganizing the iridium’s structure. To help stabilize and activate iridium, they alloyed it with its neighbor on the periodic table, osmium.

    Unlike iridium, osmium is neither catalytically active nor stable, but it did offer a key benefit. After alloying the osmium and iridium together, the researchers then de-alloyed the two metals, leaving behind only a reconfigured structure of three-dimensional iridium nanopores.

    “Without the osmium, the iridium would never achieve this state,” Markovic said. “We needed to introduce and then remove the osmium to get a form of iridium that was both active and stable.”

    Markovic said each nanopore’s enhanced catalytic stability is due to the small volume of electrolyte within a pore becoming quickly saturated with iridium ions so that surface atoms stop dissolving, in much the same way that it is easier to saturate a teacup of water with sugar than a 10-gallon jug.

    While the nanopore’s structure addressed the need for a stable, active catalyst, it was another facet of the iridium’s reconfiguration that helped boost the material’s electron conductivity. Under operational conditions, the porous catalyst actually forms a unique shell of less-conductive iridium oxide around its highly conductive iridium metal interior. This way, electrons can move easily through most of the catalyst to reach the surface, where the water molecule waits on electrons to initiate the water-splitting reaction.

    “Essentially, we’re trying to find a way to send electrons through on the ‘expressway,’ rather than making them take the side roads,” Markovic said. “This core-shell configuration [of the nanoporous material] allows us to do that.”

    See the full article here .

    Please help promote STEM in your local schools.
    STEM Icon
    Stem Education Coalition
    Argonne National Laboratory seeks solutions to pressing national problems in science and technology. The nation’s first national laboratory, Argonne conducts leading-edge basic and applied scientific research in virtually every scientific discipline. Argonne researchers work closely with researchers from hundreds of companies, universities, and federal, state and municipal agencies to help them solve their specific problems, advance America’s scientific leadership and prepare the nation for a better future. With employees from more than 60 nations, Argonne is managed by UChicago Argonne, LLC for the U.S. Department of Energy’s Office of Science. For more visit http://www.anl.gov.

    The Advanced Photon Source at Argonne National Laboratory is one of five national synchrotron radiation light sources supported by the U.S. Department of Energy’s Office of Science to carry out applied and basic research to understand, predict, and ultimately control matter and energy at the electronic, atomic, and molecular levels, provide the foundations for new energy technologies, and support DOE missions in energy, environment, and national security. To learn more about the Office of Science X-ray user facilities, visit http://science.energy.gov/user-facilities/basic-energy-sciences/.

    Argonne is managed by UChicago Argonne, LLC for the U.S. Department of Energy’s Office of Science

    Argonne Lab Campus

     
  • richardmitnick 10:56 am on November 23, 2017 Permalink | Reply
    Tags: ANL, , Buildings of the future may come equipped with windows that can generate their own electricity, Photovoltaics, , Smart window technology, Working solar cell electrodes within a fully assembled device that works like a window   

    From ANL: “Solar cell discovery opens a new window to powering tomorrow’s cities” 

    ANL Lab

    News from Argonne National Laboratory

    November 22, 2017
    Ron Walli

    1
    A team led by Argonne-based researcher Jacqui Cole has reported an advance in smart window technology that could enable cities to move closer to the goal of being energy sustainable. (Image credit: cybrain/ Shutterstock.)

    Buildings of the future may come equipped with windows that can generate their own electricity, thanks to a finding of a team led by Jacqui Cole, a materials scientist from the University of Cambridge, UK, currently based at the U.S. Department of Energy’s (DOE) Argonne National Laboratory.

    For the first time, Cole and colleagues determined the molecular structure of working solar cell electrodes within a fully assembled device that works like a window. The finding, published in Nanoscale, helps advance smart window technology that could enable cities to move closer to the goal of being energy sustainable.

    2
    Credit: Argonne National Laboratory

    The experiments were performed on dye-sensitized solar cells, which are transparent and thus well-suited for use in glass. Attempts to create smart window technologies have been limited by the many unknown molecular mechanisms between the electrodes and electrolyte that combine to determine how the device operates.

    “Most previous studies have modeled the molecular function of these working electrodes without considering the electrolyte ingredients,” Cole said. “Our work shows that these chemical ingredients can clearly influence the performance of solar cells, so we can now use this knowledge to tune the ions to increase photovoltaic efficiency.”

    To make the discovery, Cole — the 1851 Royal Commission 2014 Design Fellow — and her colleagues used neutron reflectometry to probe the function and interplay of the electrolyte ingredients with electrodes of the dye-sensitized solar cells. Neutron reflectometry, similar to X-ray reflectometry techniques, allows scientists to measure the structure of thin films with high resolution. But it was the fact that the tests were performed in a window-like system that made for a significant discovery.

    “Prior research considered the working electrodes outside the device, so there has been no path to determine how the different device components interact,” Cole said. “Our work signifies a huge leap forward as it’s the world’s first example of applying in situ neutron reflectometry to dye-sensitized solar cells.”

    Previous efforts to characterize the dye/titanium dioxide interface in these solar cells have been limited to determining this interfacial structure within an environment exposed to air or in a solvent medium. Because of these constraints, these solar cell environments are essentially artificial with limited relevance for window applications.

    With this discovery, however, Cole and colleagues have moved beyond artificial constraints. In doing so, they can better understand how a thin-film electrode containing titanium dioxide, a naturally occurring compound found in paint, sunscreen and food coloring, can have a huge impact on solar cell efficiency.

    “Our work has shown that certain chemical ingredients, some of which have so far been overlooked, can clearly influence the photovoltaic performance of these solar cells,” Cole said.

    More efficient solar cells like these can move smart window technology closer to the marketplace, said Cole, adding that the science is almost there.

    “We just need a modest boost in performance to make these solar cells competitive,” Cole said, “since price-to-performance governs the economics of the solar cell industry. And manufacturing dye-sensitized solar cells is very cheap relative to other solar cell technologies.”

    Performance-wise, the cells recently broke a world record with a power conversion efficiency of 14.3 percent using a dye-sensitized electrode featuring two co-sensitized metal-free organic dyes. These dyes “promise cheaper, more environmentally friendly synthetic routes and greater molecular design flexibility than their metal-containing counterparts,” according to the paper.

    The discovery was made with colleagues from the University of Cambridge, United Kingdom, the Australian Nuclear Science and Technology Organization and the Rutherford Appleton Laboratory, UK. Researchers are continuing to apply this materials characterization technique to dye-sensitized solar cells, which could reveal further molecular secrets and lead the way to future energy applications.

    See the full article here .

    Please help promote STEM in your local schools.
    STEM Icon
    Stem Education Coalition
    Argonne National Laboratory seeks solutions to pressing national problems in science and technology. The nation’s first national laboratory, Argonne conducts leading-edge basic and applied scientific research in virtually every scientific discipline. Argonne researchers work closely with researchers from hundreds of companies, universities, and federal, state and municipal agencies to help them solve their specific problems, advance America’s scientific leadership and prepare the nation for a better future. With employees from more than 60 nations, Argonne is managed by UChicago Argonne, LLC for the U.S. Department of Energy’s Office of Science. For more visit http://www.anl.gov.

    The Advanced Photon Source at Argonne National Laboratory is one of five national synchrotron radiation light sources supported by the U.S. Department of Energy’s Office of Science to carry out applied and basic research to understand, predict, and ultimately control matter and energy at the electronic, atomic, and molecular levels, provide the foundations for new energy technologies, and support DOE missions in energy, environment, and national security. To learn more about the Office of Science X-ray user facilities, visit http://science.energy.gov/user-facilities/basic-energy-sciences/.

    Argonne is managed by UChicago Argonne, LLC for the U.S. Department of Energy’s Office of Science

    Argonne Lab Campus

     
  • richardmitnick 2:10 pm on August 30, 2017 Permalink | Reply
    Tags: , ANL, , Dealing with massive data, ,   

    From ANL: “Big Bang – The Movie” 

    Argonne Lab
    News from Argonne National Laboratory

    August 24, 2017
    Jared Sagoff
    Austin Keating

    If you have ever had to wait those agonizing minutes in front of a computer for a movie or large file to load, you’ll likely sympathize with the plight of cosmologists at the U.S. Department of Energy’s (DOE) Argonne National Laboratory. But instead of watching TV dramas, they are trying to transfer, as fast and as accurately as possible, the huge amounts of data that make up movies of the universe – computationally demanding and highly intricate simulations of how our cosmos evolved after the Big Bang.

    In a new approach to enable scientific breakthroughs, researchers linked together supercomputers at the Argonne Leadership Computing Facility (ALCF) and at the National Center for Supercomputing Applications (NCSA) at the University of Illinois at Urbana-Champaign (UI). This link enabled scientists to transfer massive amounts of data and to run two different types of demanding computations in a coordinated fashion – referred to technically as a workflow.

    What distinguishes the new work from typical workflows is the scale of the computation, the associated data generation and transfer and the scale and complexity of the final analysis. Researchers also tapped the unique capabilities of each supercomputer: They performed cosmological simulations on the ALCF’s Mira supercomputer, and then sent huge quantities of data to UI’s Blue Waters, which is better suited to perform the required data analysis tasks because of its processing power and memory balance.

    ANL ALCF MIRA IBM Blue Gene Q supercomputer at the Argonne Leadership Computing Facility

    U Illinois Blue Waters Cray supercomputer

    For cosmology, observations of the sky and computational simulations go hand in hand, as each informs the other. Cosmological surveys are becoming ever more complex as telescopes reach deeper into space and time, mapping out the distributions of galaxies at farther and farther distances, at earlier epochs of the evolution of the universe.

    The very nature of cosmology precludes carrying out controlled lab experiments, so scientists rely instead on simulations to provide a unique way to create a virtual cosmological laboratory. “The simulations that we run are a backbone for the different kinds of science that can be done experimentally, such as the large-scale experiments at different telescope facilities around the world,” said Argonne cosmologist Katrin Heitmann. “We talk about building the ‘universe in the lab,’ and simulations are a huge component of that.”

    Not just any computer is up to the immense challenge of generating and dealing with datasets that can exceed many petabytes a day, according to Heitmann. “You really need high-performance supercomputers that are capable of not only capturing the dynamics of trillions of different particles, but also doing exhaustive analysis on the simulated data,” she said. “And sometimes, it’s advantageous to run the simulation and do the analysis on different machines.”

    Typically, cosmological simulations can only output a fraction of the frames of the computational movie as it is running because of data storage restrictions. In this case, Argonne sent every data frame to NCSA as soon it was generated, allowing Heitmann and her team to greatly reduce the storage demands on the ALCF file system. “You want to keep as much data around as possible,” Heitmann said. “In order to do that, you need a whole computational ecosystem to come together: the fast data transfer, having a good place to ultimately store that data and being able to automate the whole process.”

    In particular, Argonne transferred the data produced immediately to Blue Waters for analysis. The first challenge was to set up the transfer to sustain the bandwidth of one petabyte per day.

    Once Blue Waters performed the first pass of data analysis, it reduced the raw data – with high fidelity – into a manageable size. At that point, researchers sent the data to a distributed repository at Argonne, the Oak Ridge Leadership Computing Facility at Oak Ridge National Laboratory and the National Energy Research Scientific Computing Center (NERSC) at Lawrence Berkeley National Laboratory. Cosmologists can access and further analyze the data through a system built by researchers in Argonne’s Mathematics and Computer Science Division in collaboration with Argonne’s High Energy Physics Division.

    Argonne and University of Illinois built one such central repository on the Supercomputing ’16 conference exhibition floor in November 2016, with memory units supplied by DDN Storage. The data moved over 1,400 miles to the conference’s SciNet network. The link between the computers used high-speed networking through the Department of Energy’s Energy Science Network (ESnet). Researchers sought, in part, to take full advantage of the fast SciNET infrastructure to do real science; typically it is used for demonstrations of technology rather than solving real scientific problems.

    “External data movement at high speeds significantly impacts a supercomputer’s performance,” said Brandon George, systems engineer at DDN Storage. “Our solution addresses that issue by building a self-contained data transfer node with its own high-performance storage that takes in a supercomputer’s results and the responsibility for subsequent data transfers of said results, leaving supercomputer resources free to do their work more efficiently.”

    The full experiment ran successfully for 24 hours without interruption and led to a valuable new cosmological data set that Heitmann and other researchers started to analyze on the SC16 show floor.

    Argonne senior computer scientist Franck Cappello, who led the effort, likened the software workflow that the team developed to accomplish these goals to an orchestra. In this “orchestra,” Cappello said, the software connects individual sections, or computational resources, to make a richer, more complex sound.

    He added that his collaborators hope to improve the performance of the software to make the production and analysis of extreme-scale scientific data more accessible. “The SWIFT workflow environment and the Globus file transfer service were critical technologies to provide the effective and reliable orchestration and the communication performance that were required by the experiment,” Cappello said.

    “The idea is to have data centers like we have for the commercial cloud. They will hold scientific data and will allow many more people to access and analyze this data, and develop a better understanding of what they’re investigating,” said Cappello, who also holds an affiliate position at NCSA and serves as director of the international Joint Laboratory on Extreme Scale Computing, based in Illinois. “In this case, the focus was cosmology and the universe. But this approach can aid scientists in other fields in reaching their data just as well.”

    Argonne computer scientist Rajkumar Kettimuthu and David Wheeler, lead network engineer at NCSA, were instrumental in establishing the configuration that actually reached this performance. Maxine Brown from University of Illinois provided the Sage environment to display the analysis result at extreme resolution. Justin Wozniak from Argonne developed the whole workflow environment using SWIFT to orchestrate and perform all operations.

    The Argonne Leadership Computing Facility, the Oak Ridge Leadership Computing Facility, the Energy Science Network and the National Energy Research Scientific Computing Center are DOE Office of Science User Facilities. Blue Waters is the largest leadership-class supercomputer funded by the National Science Foundation. Part of this work was funded by DOE’s Office of Science.

    The National Center for Supercomputing Applications (NCSA) at the University of Illinois at Urbana-Champaign provides supercomputing and advanced digital resources for the nation’s science enterprise. At NCSA, University of Illinois faculty, staff, students, and collaborators from around the globe use advanced digital resources to address research grand challenges for the benefit of science and society. NCSA has been advancing one third of the Fortune 50 for more than 30 years by bringing industry, researchers, and students together to solve grand challenges at rapid speed and scale.

    See the full article here .

    Please help promote STEM in your local schools.
    STEM Icon
    Stem Education Coalition
    Argonne National Laboratory seeks solutions to pressing national problems in science and technology. The nation’s first national laboratory, Argonne conducts leading-edge basic and applied scientific research in virtually every scientific discipline. Argonne researchers work closely with researchers from hundreds of companies, universities, and federal, state and municipal agencies to help them solve their specific problems, advance America’s scientific leadership and prepare the nation for a better future. With employees from more than 60 nations, Argonne is managed by UChicago Argonne, LLC for the U.S. Department of Energy’s Office of Science. For more visit http://www.anl.gov.

    The Advanced Photon Source at Argonne National Laboratory is one of five national synchrotron radiation light sources supported by the U.S. Department of Energy’s Office of Science to carry out applied and basic research to understand, predict, and ultimately control matter and energy at the electronic, atomic, and molecular levels, provide the foundations for new energy technologies, and support DOE missions in energy, environment, and national security. To learn more about the Office of Science X-ray user facilities, visit http://science.energy.gov/user-facilities/basic-energy-sciences/.

    Argonne is managed by UChicago Argonne, LLC for the U.S. Department of Energy’s Office of Science

    Argonne Lab Campus

     
  • richardmitnick 4:24 pm on June 22, 2017 Permalink | Reply
    Tags: ANL, Chicago Quantum Exchange to create technologically transformative ecosystem, Combining strengths in quantum information, ,   

    From U Chicago: “Chicago Quantum Exchange to create technologically transformative ecosystem” 

    U Chicago bloc

    University of Chicago

    June 20, 2017
    Steve Koppes

    1
    UChicago and affiliated laboratories to collaborate on advancing the science and engineering of quantum information. Courtesy of Nicholas Brawand

    The University of Chicago is collaborating with the U.S. Department of Energy’s Argonne National Laboratory and Fermi National Accelerator Laboratory to launch an intellectual hub for advancing academic, industrial and governmental efforts in the science and engineering of quantum information.

    This hub within the Institute for Molecular Engineering, called the Chicago Quantum Exchange, will facilitate the exploration of quantum information and the development of new applications with the potential to dramatically improve technology for communication, computing and sensing. The collaboration will include scientists and engineers from the two national labs and IME, as well as scholars from UChicago’s departments of physics, chemistry, computer science, and astronomy and astrophysics.

    Quantum mechanics governs the behavior of matter at the atomic and subatomic levels in exotic and unfamiliar ways compared to the classical physics used to understand the movements of everyday objects. The engineering of quantum phenomena could lead to new classes of devices and computing capabilities, permitting novel approaches to solving problems that cannot be addressed using existing technology.

    “The combination of the University of Chicago, Argonne National Laboratory and Fermi National Accelerator Laboratory, working together as the Chicago Quantum Exchange, is unique in the domain of quantum information science,” said Matthew Tirrell, dean and founding Pritzker Director of the Institute for Molecular Engineering and Argonne’s deputy laboratory director for science. “The CQE’s capabilities will span the range of quantum information—from basic solid-state experimental and theoretical physics, to device design and fabrication, to algorithm and software development. CQE aims to integrate and exploit these capabilities to create a quantum information technology ecosystem.”

    Serving as director of the Chicago Quantum Exchange will be David Awschalom, UChicago’s Liew Family Professor in Molecular Engineering and an Argonne senior scientist. Discussions about establishing a trailblazing quantum engineering initiative began soon after Awschalom joined the UChicago faculty in 2013 when he proposed this concept, and were subsequently developed through the recruitment of faculty and the creation of state-of-the-art measurement laboratories.

    “We are at a remarkable moment in science and engineering, where a stream of scientific discoveries are yielding new ways to create, control and communicate between quantum states of matter,” Awschalom said. “Efforts in Chicago and around the world are leading to the development of fundamentally new technologies, where information is manipulated at the atomic scale and governed by the laws of quantum mechanics. Transformative technologies are likely to emerge with far-reaching applications—ranging from ultra-sensitive sensors for biomedical imaging to secure communication networks to new paradigms for computation. In addition, they are making us re-think the meaning of information itself.”

    The collaboration will benefit from UChicago’s Polsky Center for Entrepreneurship and Innovation, which supports the creation of innovative businesses connected to UChicago and Chicago’s South Side. The CQE will have a strong connection with a major Hyde Park innovation project that was announced recently as the second phase of the Harper Court development on the north side of 53rd Street, and will include an expansion of Polsky Center activities. This project will enable the transition from laboratory discoveries to societal applications through industrial collaborations and startup initiatives.

    Companies large and small are positioning themselves to make a far-reaching impact with this new quantum technology. Alumni of IME’s quantum engineering PhD program have been recruited to work for many of these companies. The creation of CQE will allow for new linkages and collaborations with industry, governmental agencies and other academic institutions, as well as support from the Polsky Center for new startup ventures.

    This new quantum ecosystem will provide a collaborative environment for researchers to invent technologies in which all the components of information processing—sensing, computation, storage and communication—are kept in the quantum world, Awschalom said. This contrasts with today’s mainstream computer systems, which frequently transform electronic signals from laptop computers into light for internet transmission via fiber optics, transforming them back into electronic signals when they arrive at their target computers, finally to become stored as magnetic data on hard drives.

    IME’s quantum engineering program is already training a new workforce of “quantum engineers” to meet the need of industry, government laboratories and universities. The program now consists of eight faculty members and more than 100 postdoctoral scientists and doctoral students. Approximately 20 faculty members from UChicago’s Physical Sciences Division also pursue quantum research. These include David Schuster, assistant professor in physics, who collaborates with Argonne and Fermilab researchers.

    Combining strengths in quantum information

    The collaboration will rely on the distinctive strengths of the University and the two national laboratories, both of which are located in the Chicago suburbs and have longstanding affiliations with the University of Chicago.

    At Argonne, approximately 20 researchers conduct quantum-related research through joint appointments at the laboratory and UChicago. Fermilab has about 25 scientists and technicians working on quantum research initiatives related to the development of particle sensors, quantum computing and quantum algorithms.

    “This is a great time to invest in quantum materials and quantum information systems,” said Supratik Guha, director of Argonne’s Nanoscience and Technology Division and a professor of molecular engineering at UChicago. “We have extensive state-of-the-art capabilities in this area.”

    Argonne proposed the first recognizable theoretical framework for a quantum computer, work conducted in the early 1980s by Paul Benioff. Today, including joint appointees, Argonne’s expertise spans the spectrum of quantum sensing, quantum computing, classical computing and materials science.

    Argonne and UChicago already have invested approximately $6 million to build comprehensive materials synthesis facilities—called “The Quantum Factory”—at both locations. Guha, for example, has installed state-of-the-art deposition systems that he uses to layer atoms of materials needed for building quantum structures.

    “Together we will have comprehensive capabilities to be able to grow and synthesize one-, two- and three-dimensional quantum structures for the future,” Guha said. These structures, called quantum bits—qubits—serve as the building blocks for quantum computing and quantum sensing.

    2
    Illustration of near-infrared light polarizing nuclear spins in a silicon carbide chip. Courtesy of Peter Allen

    Argonne also has theorists who can help identify problems in physics and chemistry that could be solved via quantum computing. Argonne’s experts in algorithms, operating systems and systems software, led by Rick Stevens, associate laboratory director and UChicago professor in computer science, will play a critical role as well, because no quantum computer will be able to operate without connecting to a classical computer.

    Fermilab’s interest in quantum computing stems from the enhanced capabilities that the technology could offer within 15 years, said Joseph Lykken, Fermilab deputy director and senior scientist.

    “The Large Hadron Collider experiments, ATLAS and CMS, will still be running 15 years from now,” Lykken said. “Our neutrino experiment, DUNE, will still be running 15 years from now. Computing is integral to particle physics discoveries, so advances that are 15 years away in high-energy physics are developments that we have to start thinking about right now.”

    Lykken noted that almost any quantum computing technology is, by definition, a device with atomic-level sensitivity that potentially could be applied to sensitive particle physics experiments. An ongoing Fermilab-UChicago collaboration is exploring the use of quantum computing for axion detection. Axions are candidate particles for dark matter, an invisible mass of unknown composition that accounts for 85 percent of the mass of the universe.

    Another collaboration with UChicago involves developing quantum computer technology that uses photons in superconducting radio frequency cavities for data storage and error correction. These photons are light particles emitted as microwaves. Scientists expect the control and measurement of microwave photons to become important components of quantum computers.

    “We build the best superconducting microwave cavities in the world, but we build them for accelerators,” Lykken said. Fermilab is collaborating with UChicago to adapt the technology for quantum applications.

    Fermilab also has partnered with the California Institute of Technology and AT&T to develop a prototype quantum information network at the lab. Fermilab, Caltech and AT&T have long collaborated to efficiently transmit the Large Hadron Collider’s massive data sets. The project, a quantum internet demonstration of sorts, is called INQNET (INtelligent Quantum NEtworks and Technologies).

    Fermilab also is working to increase the scale of today’s quantum computers. Fermilab can contribute to this effort because quantum computers are complicated, sensitive, cryogenic devices. The laboratory has decades of experience in scaling up such devices for high-energy physics applications.

    “It’s one of the main things that we do,” Lykken said.

    See the full article here .

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

     
  • richardmitnick 5:46 pm on June 20, 2017 Permalink | Reply
    Tags: ANL, , , , Superconducting undulators, ,   

    From LBNL: “R&D Effort Produces Magnetic Devices to Enable More Powerful X-ray Lasers” 

    Berkeley Logo

    Berkeley Lab

    June 20, 2017
    Glenn Roberts Jr.
    geroberts@lbl.gov
    (510) 486-5582

    Berkeley Lab demonstrates a record-setting magnetic field for a prototype superconducting undulator.

    1
    This Berkeley Lab-developed device, a niobium tin superconducting undulator prototype, set a record in magnetic field strength for a device of its kind. This type of undulator could be used to wiggle electron beams to emit light for a next generation of X-ray lasers.
    (Credit: Marilyn Chung/Berkeley Lab)

    Researchers at the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) and Argonne National Laboratory have collaborated to design, build, and test two devices, called superconducting undulators, which could make X-ray free-electron lasers (FELs) more powerful, versatile, compact, and durable.

    X-ray FELs are powerful tools for studying the microscopic structure and other properties of samples, such as proteins that are key to drug design, exotic materials relevant to electronics and energy applications, and chemistry that is central to industrial processes like fuel production.

    The recent development effort was motivated by SLAC National Accelerator Laboratory’s upgrade of its Linac Coherent Light Source (LCLS), the nation’s only X-ray FEL.

    SLAC LCLS-II

    This upgrade, now underway, is known as LCLS-II. All existing X-ray FELS, including both LCLS and LCLS-II, use permanent magnet undulators to generate intense pulses of X-rays. These devices produce X-ray light by passing high-energy bunches of electrons through alternating magnetic fields produced by a series of permanent magnets.

    Superconducting undulators (SCUs) offer another technical solution and are considered among the most promising technologies to improve the performance of the next generation FELs, and of other types of light sources, such as Berkeley Lab’s Advanced Light Source (ALS) and Argonne’s Advanced Photon Source (APS).

    LBNL/ALS

    ANL APS

    SCUs replace the permanent magnets in the undulator with superconducting coils. The prototype SCUs have successfully produced stronger magnetic fields than conventional undulators of the same size. Higher fields, in turn, can produce higher-energy free-electron laser light to open up a broader range of experiments.

    Berkeley Lab’s 1.5-meter-long prototype undulator, which uses a superconducting material known as niobium-tin (Nb3Sn), set a record in magnetic field strength for a device of its design during testing at the Lab in September 2016.

    “This is a much-anticipated innovation,” agreed Wim Leemans, Director, Accelerator Technology and Applied Physics (ATAP) . “Higher performance in a smaller footprint is something that benefits everyone – the laboratories that host the facilities, the funding agencies, and above all, the user community.”

    Argonne’s test of another superconducting material, niobium-titanium, successfully reached its performance goal, and additionally passed a bevy of quality tests. Niobium-titanium has a lower maximum magnetic field strength than niobium-tin, but is further along in its development.

    3
    The superconducting undulator R&D project at Berkeley Lab was a team effort. Among the contributors: (from left) Heng Pan, Jordan Taylor, Soren Prestemon, Ross Schlueter, Diego Arbelaez, Jim Swanson, Ahmet Pekedis, Scott Myers, Tom Lipton, and Xiaorong Wang. (Credit: Marilyn Chung/Berkeley Lab)

    Researchers at the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) and Argonne National Laboratory have collaborated to design, build, and test two devices, called superconducting undulators, which could make X-ray free-electron lasers (FELs) more powerful, versatile, compact, and durable.

    X-ray FELs are powerful tools for studying the microscopic structure and other properties of samples, such as proteins that are key to drug design, exotic materials relevant to electronics and energy applications, and chemistry that is central to industrial processes like fuel production.

    The recent development effort was motivated by SLAC National Accelerator Laboratory’s upgrade of its Linac Coherent Light Source (LCLS), the nation’s only X-ray FEL. This upgrade, now underway, is known as LCLS-II. All existing X-ray FELS, including both LCLS and LCLS-II, use permanent magnet undulators to generate intense pulses of X-rays. These devices produce X-ray light by passing high-energy bunches of electrons through alternating magnetic fields produced by a series of permanent magnets.

    Superconducting undulators (SCUs) offer another technical solution and are considered among the most promising technologies to improve the performance of the next generation FELs, and of other types of light sources, such as Berkeley Lab’s Advanced Light Source (ALS) and Argonne’s Advanced Photon Source (APS).

    SCUs replace the permanent magnets in the undulator with superconducting coils. The prototype SCUs have successfully produced stronger magnetic fields than conventional undulators of the same size. Higher fields, in turn, can produce higher-energy free-electron laser light to open up a broader range of experiments.

    Berkeley Lab’s 1.5-meter-long prototype undulator, which uses a superconducting material known as niobium-tin (Nb3Sn), set a record in magnetic field strength for a device of its design during testing at the Lab in September 2016.

    “This is a much-anticipated innovation,” agreed Wim Leemans, Director, Accelerator Technology and Applied Physics (ATAP) . “Higher performance in a smaller footprint is something that benefits everyone – the laboratories that host the facilities, the funding agencies, and above all, the user community.”

    Argonne’s test of another superconducting material, niobium-titanium, successfully reached its performance goal, and additionally passed a bevy of quality tests. Niobium-titanium has a lower maximum magnetic field strength than niobium-tin, but is further along in its development.
    Photo – The superconducting undulator R&D project at Berkeley Lab was a team effort. Among the contributors: (from left) Heng Pan, Jordan Taylor, Soren Prestemon, Ross Schlueter, Diego Arbelaez, Jim Swanson, Ahmet Pekedis, Scott Myers, Tom Lipton, and Xiaorong Wang. (Credit: Marilyn Chung/Berkeley Lab)

    The superconducting undulator R&D project at Berkeley Lab was a team effort. Among the contributors: (from left) Heng Pan, Jordan Taylor, Soren Prestemon, Ross Schlueter, Diego Arbelaez, Jim Swanson, Ahmet Pekedis, Scott Myers, Tom Lipton, and Xiaorong Wang. (Credit: Marilyn Chung/Berkeley Lab)

    “The superconducting technology in general, and especially with the niobium tin, lived up to its promise of being the highest performer,” said Ross Schlueter, Head of the Magnetics Department in Berkeley Lab’s Engineering Division. “We’re very excited about this world record. This device allows you to get a much higher photon energy” from a given electron beam energy.

    “We have expertise here both in free-electron laser undulators, as demonstrated in our role in leading the construction of LCLS-II’s undulators, and in synchrotron undulator development at the ALS,” noted Soren Prestemon, Director of the Berkeley Center for Magnet Technology (BCMT), which brings together the Accelerator Technology and Applied Physics Division (ATAP) and Engineering Division, to design and build a range of magnetic devices for scientific, medical, and other applications.

    “The Engineering Division has a long history of forefront research on undulators, and this work continues that tradition,” states Henrik von der Lippe, Director, Engineering Division.

    Diego Arbelaez, the lead engineer in the development of Berkeley Lab’s device, said earlier work at the Lab in building superconducting undulator prototypes for a different project were useful in informing the latest design, though there were still plenty of challenges.

    Niobium-tin is a brittle material that cannot be drawn into a wire. For practical use, a pliable wire, which contains the components that will form niobium-tin when heat-treated, is used for winding the undulator coils. The full undulator coil is then heat-treated in a furnace at 1,200 degrees Fahrenheit.

    The niobium-tin wire is wound around a steel frame to form tightly wrapped coils in an alternating arrangement. The precision of the winding is critical for the performance of the device. Arbelaez said, “One of the questions was whether you can maintain precision in its winding even though you are going through these large temperature variations.”

    After the heat treatment, the coils are placed in a mold and impregnated with epoxy to hold the superconducting coils in place. To achieve a superconducting state and demonstrate its record-setting performance, the device was immersed in a bath of liquid helium to cool it down to about minus 450 degrees Fahrenheit.

    4
    Ahmet Pekedis, left, and Diego Arbelaez inspect the completed niobium tin undulator prototype. (Credit: Marilyn Chung/Berkeley Lab)

    Another challenge was in developing a fast shutoff to prevent catastrophic failure during an event known as “quenching.” During a quench, there is a sudden loss of superconductivity that can be caused by a small amount of heat generation. Uncontrolled quenching could lead to rapid heating that might damage the niobium-tin and surrounding copper and ruin the device.

    This is a critical issue for the niobium-tin undulators due to the extraordinary current densities they can support. Berkeley Lab’s Marcos Turqueti led the effort to engineer a quench-protection system that can detect the occurrence of quenching within a couple thousandths of a second and shut down its effects within 10 thousandths of a second.

    Arbelaez also helped devise a system to correct for magnetic-field errors while the undulator is in its superconducting state.

    SLAC’s Paul Emma, the accelerator physics lead for LCLS-II, coordinated the superconducting undulator development effort.

    Emma said that the niobium-tin superconducting undulator developed at Berkeley Lab shows potential but may require more extensive continuing R&D than Argonne’s niobium-titanium prototype. Argonne earlier developed superconducting undulators that are in use at its APS, and Berkeley Lab also hopes to add superconducting undulators at its ALS.

    “With superconducting undulators,” Emma said, “you don’t necessarily lower the cost but you get better performance for the same stretch of undulator.”

    5
    A close-up view of the superconducting undulator prototype developed at Berkeley Lab. To construct the undulator, researchers wound a pliable wire in alternating coils around a steel frame. The pliable wire was baked to form a niobium-tin compound that is very brittle but can achieve high magnetic fields when chilled to superconducting temperatures. (Credit: Marilyn Chung/Berkeley Lab)

    A superconducting undulator of an equivalent length to a permanent magnetic undulator could produce light that is at least two to three times – perhaps up to 10 times – more powerful, and could also access a wider range in X-ray wavelengths, Emma said, producing a more efficient FEL.

    Superconducting undulators also have no macroscopic moving parts, so they could conceivably be tuned more quickly with high precision. Superconductors also are far less prone to damage by high-intensity radiation than permanent-magnet materials, a significant issue in high-power accelerators such as those that will be installed for LCLS-II.

    There appears to be a clear path forward to developing superconducting undulators for upgrades of existing and new X-ray free-electron lasers, Emma said, and for other types of light sources.

    “Superconducting undulators will be the technology we go to eventually, whether it’s in the next 10 or 20 years,” he said. “They are powerful enough to produce the light we are going to need – I think it’s going to happen. People know it’s a big enough step, and we’ve got to get there.”

    James Symons, Berkeley Lab’s Associate Director for Physical Sciences, said, “We look forward to building on this effort by furthering our R&D on superconducting undulator systems.

    The Advanced Light Source, Advanced Photon Source, and Linac Coherent Light Source are DOE Office of Science User Facilities. The development of the superconducting undulator prototypes was supported by the DOE’s Office of Science.”

    See the full article here .

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  • richardmitnick 9:54 am on September 12, 2016 Permalink | Reply
    Tags: ANL, , Protein crystallography,   

    From ANL: “Two protein studies discover molecular secrets to recycling carbon and healing cells” 

    ANL Lab

    News from Argonne National Laboratory

    September 9, 2016
    Kate Thackrey

    1
    Researchers at Argonne modeled the HcaR protein complex, above, a sort of molecular policeman that controls when to activate genes that code for enzymes used by Acinetobacter bacteria to break down compounds for food. Understanding these processes can help scientists develop ideas for converting more carbon in soil. (Image courtesy Kim et al./Journal of Biological Chemistry.)

    Researchers at the U.S. Department of Energy’s (DOE’s) Argonne National Laboratory have mapped out two very different types of protein. One helps soil bacteria digest carbon compounds; the other protects cells from the effects of harmful molecules.

    In order to uncover the structure of these proteins, researchers used a technique called protein crystallography. Like a mosquito trapped in amber, compounds that are crystallized are placed in array in identical positions and ordered so that scientists can target them with X-ray beams and work backwards from the scattering patterns produced to recreate their three-dimensional structures atom by atom.

    Bacterial breakdown

    In the first study, a group of researchers from the Structural Biology Center, which is funded by DOE’s Office of Science, mapped out a protein responsible for breaking down organic compounds in soil bacteria, an important process for recycling carbon in the ecosystem.

    The bacteria used, called Acinetobacter, is located mostly in soil and water habitats, where it helps to change aromatic compounds (named for their ring shape) into forms that can be used as food.

    One of the sources of aromatic compounds found in soil is lignin, a tough polymer that is an essential part of all plants and that’s hard for many organisms to digest.

    “But Acinetobacter can utilize these aromatic compounds as their sole source of carbon,” said Andrzej Joachimiak, who co-authored both studies and is the director of the Structural Biology Center and the Midwest Center for Structural Genomics at Argonne.

    In order for Acinetobacter to break down the aromatic compounds, it needs to produce catabolic enzymes, molecular machines built from an organism’s DNA that break down molecules into smaller parts that can be digested.

    Whether or not membrane transporters and catabolic enzymes are produced falls to the HcaR regulator, a sort of molecular policeman that controls when the genes that code for these enzymes can be activated.

    Joachimiak and his colleagues found that the regulator works in a cycle, activating genes when aromatic compounds are present and shutting genes down when the compounds are used up.

    “By nature it is very efficient,” Joachimiak said. “If you don’t have aromatic compounds inside a cell, the operon is shut down.”

    The research team didn’t stop at mapping out the regulator itself; to discover how the cycle worked, they crystalized the HcaR regulator during interactions with its two major inputs: the aromatic compounds and DNA.

    The group found that when aromatic compounds are not present in the cell, two wings found on either side of the HcaR regulator wrap around the DNA. This action is mirrored on both sides of the regulator, covering the DNA regulatory site and preventing genes from being activated.

    “This is something that has never been seen before,” Joachimiak said.

    When the aromatic compounds are present, however, they attach themselves to the HcaR regulator, making it so stiff that it can no longer grapple with the DNA.

    Joachimiak said that this knowledge could help outside of the lab, with applications such as a sensor for harmful pesticides and as a template for converting more carbon in soil.

    “If we can train bacteria to better degrade lignin and other polymers produced by plants during photosynthesis, more natural carbon sources can be utilized for example for production of biofuels and bioproducts,” Joachimiak said.

    The paper was published earlier this year by the Journal of Biological Chemistry under the title How Aromatic Compounds Block DNA Binding of HcaR Catabolite Regulator. It was supported by the National Institutes of Health and the U.S. Department of Energy (Office of Biological and Environmental Research).

    Protective proteins

    A second paper focuses on a family of proteins identified as DUF89, which stands for “domain unknown function.” This family is conserved across all three branches of the phylogenetic tree, which means that it is likely essential to many life forms.

    DUF89 has been identified as a type of enzyme called a phosphatase, which strips molecules of their phosphate groups. The paper’s authors hypothesized that DUF89 proteins use this ability to save useful proteins in a cell from rogue molecules which could alter their structure, making them useless or destructive.

    The study found that DUF89 proteins use a metal ion, probably manganese, to lure in potentially harmful molecules and a water molecule to break off their phosphate group.

    DUF89 proteins could have an important role in breaking down a specific type of disruptive molecule: sugar. When the concentration of sugar in blood reaches high levels, simple sugars can have unwanted side reactions with proteins and DNA through a process called glycation.

    “We always have to deal with these side reactions that happen in our cells, and when we get older, we have an accumulation of these errors in our cells,” Joachimiak said.

    Joachimiak said that this research could help scientists develop DUF89 treatments from non-human sources as a way to combat glycation in the bloodstream.

    The paper was published on the Nature Chemical Biology website on June 20 under the title A family of metal-dependent phosphatases implicated in metabolite damage-control. Other authors on the paper were from the University of Florida, the University of Toronto, the University of California-Davis and Brookhaven National Laboratory. It was supported by the National Science Foundation, Genome Canada, the Ontario Genomics Institution, the Ontario Research Fund, the Natural Sciences and Engineering Research Council of Canada, the National Institutes of Health, the C.V. Griffin Sr. Foundation and the U.S. Department of Energy (Office of Basic Energy Sciences and Office of Biological and Environmental Research).

    Both studies used X-rays from the Advanced Photon Source, a DOE Office of Science User Facility, using beamlines 19-ID and 19-BM.

    Both also stem from the goal of the Midwest Center for Structural Genomics, which is to discover the structure and function of proteins potentially important to biomedicine.

    Joachimiak said that despite the new findings from these studies, when it comes to understanding what proteins do, we still have a long way to go.

    “When we sequence genomes, we can predict proteins, but when we predict those sequences we can only say something about function for about half of them,” Joachimiak said.

    See the full article here .

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    Argonne National Laboratory seeks solutions to pressing national problems in science and technology. The nation’s first national laboratory, Argonne conducts leading-edge basic and applied scientific research in virtually every scientific discipline. Argonne researchers work closely with researchers from hundreds of companies, universities, and federal, state and municipal agencies to help them solve their specific problems, advance America’s scientific leadership and prepare the nation for a better future. With employees from more than 60 nations, Argonne is managed by UChicago Argonne, LLC for the U.S. Department of Energy’s Office of Science. For more visit http://www.anl.gov.

    The Advanced Photon Source at Argonne National Laboratory is one of five national synchrotron radiation light sources supported by the U.S. Department of Energy’s Office of Science to carry out applied and basic research to understand, predict, and ultimately control matter and energy at the electronic, atomic, and molecular levels, provide the foundations for new energy technologies, and support DOE missions in energy, environment, and national security. To learn more about the Office of Science X-ray user facilities, visit http://science.energy.gov/user-facilities/basic-energy-sciences/.

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  • richardmitnick 11:15 am on September 9, 2016 Permalink | Reply
    Tags: ANL, , Snapshots of molecules,   

    From ANL: “Seeing energized light-active molecules proves quick work for Argonne scientists” 

    ANL Lab

    News from Argonne National Laboratory

    September 8, 2016
    Jared Sagoff

    For people who enjoy amusement parks, one of the most thrilling sensations comes at the top of a roller coaster, in the split second between the end of the climb and the rush of the descent. Trying to take a picture at exactly the moment that the roller coaster reaches its zenith can be difficult because the drop happens so suddenly.

    For chemists trying to take pictures of energized molecules, the dilemma is precisely the same, if not trickier. When certain molecules are excited – like a roller coaster poised at the very top of its run – they often stay in their new state for only an instant before “falling” into a lower energy state.

    1
    To understand how molecules undergo light-driven chemical transformations, scientists need to be able to follow the atoms and electrons within the energized molecule as it rides on the energy “roller coaster.”

    In a recent study, a team of researchers at the U.S. Department of Energy’s (DOE’s) Argonne National Laboratory, Northwestern University, the University of Washington and the Technical University of Denmark used the ultrafast high-intensity pulsed X-rays produced by the Linac Coherent Light Source (LCLS), a DOE Office of Science User Facility at SLAC National Accelerator Laboratory, to take molecular snapshots of these molecules.

    SLAC/LCLS
    SLAC/LCLS

    By using the LCLS, the researchers were able to capture atomic and electronic arrangements within the molecule that had lifetimes as short as 50 femtoseconds – which is about the amount of time it takes light to travel the width of a human hair.

    “We can see changes in these energized molecules which happen incredibly quickly,” said Lin Chen, an Argonne senior chemist and professor of chemistry at Northwestern University who led the research.

    Chen and her team looked the structure of a metalloporphyrin, a molecule similar to important building blocks for natural and artificial photosynthesis. Metalloporphyrins are of interest to scientists who seek to convert solar energy into fuel by splitting water to generate hydrogen or converting carbon dioxide into sugars or other types of fuels.

    Specifically, the research team examined how the metalloporphyrin changes after it is excited with a laser. They discovered an extremely short-lived “transient state” that lasted only a few hundred femtoseconds before the molecule relaxed into a lower energy state.

    “Although we had previously captured the molecular structure of a longer-lived state, the structure of this transient state eluded our detection because its lifetime was too short,” Chen said.

    When the laser pulse hits the molecule, an electron from the outer ring moves into the nickel metal center. This creates a charge imbalance, which in turn creates an instability within the whole molecule. In short order, another electron from the nickel migrates back to the outer ring, and the excited electron falls back into the lower open orbital to take its place.

    “This first state appears and disappears so quickly, but it’s imperative for the development of things like solar fuels,” Chen said. “Ideally, we want to find ways to make this state last longer to enable the subsequent chemical processes that may lead to catalysis, but just being able to see that it is there in the first place is important.”

    The challenge, Chen said, is to prolong the lifetime of the excited state through the design of the metalloporphyrin molecule. “From this study, we gained knowledge of which molecular structural element, such as bond length and planarity of the ring, can influence the excited state property,” Chen said. “With these results we might be able to design a system to allow us to harvest much of the energy in the excited state.”

    A paper based on the research, “Ultrafast excited state relaxation of a metalloporphyrin revealed by femtosecond X-ray absorption spectroscopy,” was published in the June 10 online edition of the Journal of the American Chemical Society.

    The research was funded by the DOE’s Office of Science and by the National Institute of Health.

    See the full article here .

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    Argonne National Laboratory seeks solutions to pressing national problems in science and technology. The nation’s first national laboratory, Argonne conducts leading-edge basic and applied scientific research in virtually every scientific discipline. Argonne researchers work closely with researchers from hundreds of companies, universities, and federal, state and municipal agencies to help them solve their specific problems, advance America’s scientific leadership and prepare the nation for a better future. With employees from more than 60 nations, Argonne is managed by UChicago Argonne, LLC for the U.S. Department of Energy’s Office of Science. For more visit http://www.anl.gov.

    The Advanced Photon Source at Argonne National Laboratory is one of five national synchrotron radiation light sources supported by the U.S. Department of Energy’s Office of Science to carry out applied and basic research to understand, predict, and ultimately control matter and energy at the electronic, atomic, and molecular levels, provide the foundations for new energy technologies, and support DOE missions in energy, environment, and national security. To learn more about the Office of Science X-ray user facilities, visit http://science.energy.gov/user-facilities/basic-energy-sciences/.

    Argonne is managed by UChicago Argonne, LLC for the U.S. Department of Energy’s Office of Science

    Argonne Lab Campus

     
  • richardmitnick 4:00 pm on August 30, 2016 Permalink | Reply
    Tags: A New Leaf: Scientists Turn Carbon Dioxide Back Into Fuel, ANL,   

    From ANL via DOE: “A New Leaf: Scientists Turn Carbon Dioxide Back Into Fuel” 

    ANL Lab

    News from Argonne National Laboratory

    DOE Office of Science

    August 18, 2016 [Just now from DOE in social media.]
    Jared Sagoff, Argonne National Laboratory

    1
    Plants capture CO2 and convert it into sugars that store energy. | Public Domain photo.

    Can we turn carbon dioxide into fuel, rather than a pollutant?

    A group of researchers asked that question and found a way to say yes.

    In a new study [Science] from the U.S. Department of Energy’s Argonne National Laboratory and the University of Illinois at Chicago, researchers were able to convert carbon dioxide into a usable energy source using sunlight. Their process is similar to how trees and other plants slowly capture carbon dioxide from the atmosphere, converting it to sugars that store energy.

    One of the chief challenges of sequestering carbon dioxide is that it is relatively chemically unreactive. “On its own, it is quite difficult to convert carbon dioxide into something else,” said Argonne chemist Larry Curtiss, an author of the study.

    To make carbon dioxide into something that could be a usable fuel, Curtiss and his colleagues needed to find a catalyst — a particular compound that could make carbon dioxide react more readily. When converting carbon dioxide from the atmosphere into a sugar, plants use an organic catalyst called an enzyme; the researchers used a metal compound called tungsten diselenide, which they fashioned into nanosized flakes to maximize the surface area and to expose its reactive edges.

    While plants use their catalysts to make sugar, the Argonne researchers used theirs to convert carbon dioxide to carbon monoxide. Although carbon monoxide is also a greenhouse gas, it is much more reactive than carbon dioxide and scientists already have ways of converting carbon monoxide into usable fuel, such as methanol. “Making fuel from carbon monoxide means travelling ‘downhill’ energetically, while trying to create it directly from carbon dioxide means needing to go ‘uphill,'” said Argonne physicist Peter Zapol, another author of the study.

    Although the reaction to transform carbon dioxide into carbon monoxide is different from anything found in nature, it requires the same basic inputs as photosynthesis. “In photosynthesis, trees need energy from light, water and carbon dioxide in order to make their fuel; in our experiment, the ingredients are the same, but the product is different,” said Curtiss.

    The setup for the reaction is sufficiently similar to nature that the research team was able to construct an “artificial leaf” that could complete the entire three-step reaction pathway. In the first step, incoming photons — packets of light — are converted to pairs of negatively-charged electrons and corresponding positively charged “holes” that then separate from each other. In the second step, the holes react with water molecules, creating protons and oxygen molecules. Finally, the protons, electrons and carbon dioxide all react together to create carbon monoxide and water.

    “We burn so many different kinds of hydrocarbons — like coal, oil or gasoline — that finding an economical way to make chemical fuels more reusable with the help of sunlight might have a big impact,” Zapol said.

    Towards this goal, the study also showed that the reaction occurs with minimal lost energy — the reaction is very efficient. “The less efficient a reaction is, the higher the energy cost to recycle carbon dioxide, so having an efficient reaction is crucial,” Zapol said.

    According to Curtiss, the tungsten diselenide catalyst is also quite durable, lasting for more than 100 hours — a high bar for catalysts to meet.

    See the full article here .

    Please help promote STEM in your local schools.
    STEM Icon
    Stem Education Coalition
    Argonne National Laboratory seeks solutions to pressing national problems in science and technology. The nation’s first national laboratory, Argonne conducts leading-edge basic and applied scientific research in virtually every scientific discipline. Argonne researchers work closely with researchers from hundreds of companies, universities, and federal, state and municipal agencies to help them solve their specific problems, advance America’s scientific leadership and prepare the nation for a better future. With employees from more than 60 nations, Argonne is managed by UChicago Argonne, LLC for the U.S. Department of Energy’s Office of Science. For more visit http://www.anl.gov.

    The Advanced Photon Source at Argonne National Laboratory is one of five national synchrotron radiation light sources supported by the U.S. Department of Energy’s Office of Science to carry out applied and basic research to understand, predict, and ultimately control matter and energy at the electronic, atomic, and molecular levels, provide the foundations for new energy technologies, and support DOE missions in energy, environment, and national security. To learn more about the Office of Science X-ray user facilities, visit http://science.energy.gov/user-facilities/basic-energy-sciences/.

    Argonne is managed by UChicago Argonne, LLC for the U.S. Department of Energy’s Office of Science

    Argonne Lab Campus

     
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