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  • richardmitnick 4:34 pm on November 24, 2014 Permalink | Reply
    Tags: , , Oak Ridge National Laboratory   

    From ORNL: “Materials researchers get first look at atom-thin boundaries” 


    Oak Ridge National Laboratory

    November 24, 2014
    Morgan McCorkle
    Communications and Media Relations

    Scientists at the Department of Energy’s Oak Ridge National Laboratory have made the first direct observations of a one-dimensional boundary separating two different, atom-thin materials, enabling studies of long-theorized phenomena at these interfaces.

    Theorists have predicted the existence of intriguing properties at one-dimensional (1-D) boundaries between two crystalline components, but experimental verification has eluded researchers because atomically precise 1-D interfaces are difficult to construct.

    Theorists have predicted the existence of intriguing properties at one-dimensional (1-D) boundaries between two crystalline components, but experimental verification has eluded researchers because atomically precise 1-D interfaces are difficult to construct.

    “While many theoretical studies of such 1-D interfaces predict striking behaviors, in our work we have provided the first experimental validation of those interface properties,” said ORNL’s An-Ping Li.

    The new Nature Communications study builds on work by ORNL and University of Tennessee scientists published in Science earlier this year that introduced a method to grow different two-dimensional materials – graphene and boron nitride – into a single layer only one atom thick.

    graphene is an atomic-scale honeycomb lattice made of carbon atoms

    The team’s materials growth technique unlocked the ability to study the 1-D boundary and its electronic properties in atomic resolution. Using scanning tunneling microscopy, spectroscopy and density-functional calculations, the researchers first obtained a comprehensive picture of spatial and energetic distributions of the 1-D interface states.

    “In three-dimensional (3-D) systems, the interface is embedded so you cannot get a real-space view of the complete interface – you can only look at a projection of that plane,” said Jewook Park, ORNL postdoctoral researcher and the lead author of the work. “In our case, the 1-D interface is completely accessible to real-space study,”

    “The combination of scanning tunneling microscopy and the first principles theory calculations allows us to distinguish the chemical nature of the boundary and evaluate the effects of orbital hybridization at the junction,” said ORNL’s Mina Yoon, a theorist on the team.

    The researchers’ observations revealed a highly confined electric field at the interface and provided an opportunity to investigate an intriguing phenomenon known as a “polar catastrophe,” which occurs in 3-D oxide interfaces. This effect can cause atomic and electron reorganization at the interface to compensate for the electrostatic field resulting from materials’ different polarities.

    “This is the first time we have been able to study the polar discontinuity effect in a 1-D boundary,” Li said.

    Although the researchers focused on gaining a fundamental understanding of the system, they note their study could culminate in applications that take advantage of the 1-D interface.

    “For instance, the 1-D chain of electrons could be exploited to pass a current along the boundary,” Li said. “It could be useful for electronics, especially for ultra-thin or flexible devices.”

    The team plans to continue examining different aspects of the boundary including its magnetic properties and the effect of its supporting substrate.

    The study is published as Spatially resolved one-dimensional boundary states in graphene–hexagonal boron nitride planar heterostructures. Coauthors are ORNL’s Jewook Park, Jaekwang Lee, Corentin Durand, Changwon Park, Bobby Sumpter, Arthur Baddorf, Mina Yoon and An-Ping Li; the University of Tennessee’s Lei Liu, Ali Mohsin, and Gong Gu; and Central Methodist University’s Kendal Clark.

    This research was conducted in part at the Center for Nanophase Materials Sciences and the National Energy Research Scientific Computing Center, both DOE Office of Science User Facilities. The research was supported by DOE’s Office of Science, ORNL’s Laboratory Directed Research and Development program, the National Science Foundation and DARPA.

    See the full article here.

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    ORNL is managed by UT-Battelle for the Department of Energy’s Office of Science. DOE’s Office of Science is the single largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time.


  • richardmitnick 7:15 pm on October 14, 2014 Permalink | Reply
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    From ORNL: “New ORNL electric vehicle technology packs more punch in smaller package” 


    Oak Ridge National Laboratory

    Oct. 14, 2014
    Media Contact: Ron Walli

    Using 3-D printing and novel semiconductors, researchers at the Department of Energy’s Oak Ridge National Laboratory have created a power inverter that could make electric vehicles lighter, more powerful and more efficient.

    At the core of this development is wide bandgap material made of silicon carbide with qualities superior to standard semiconductor materials. Power inverters convert direct current into the alternating current that powers the vehicle. The Oak Ridge inverter achieves much higher power density with a significant reduction in weight and volume.

    “Wide bandgap technology enables devices to perform more efficiently at a greater range of temperatures than conventional semiconductor materials,” said ORNL’s Madhu Chinthavali, who led the Power Electronics and Electric Machinery Group on this project. “This is especially useful in a power inverter, which is the heart of an electric vehicle.”

    Specific advantages of wide bandgap devices include: higher inherent reliability; higher overall efficiency; higher frequency operation; higher temperature capability and tolerance; lighter weight, enabling more compact systems; and higher power density.

    Additive manufacturing helped researchers explore complex geometries, increase power densities, and reduce weight and waste while building ORNL’s 30-kilowatt prototype inverter.

    ORNL’s 30-kilowatt power inverter offers greater reliability and power in a compact package.

    “With additive manufacturing, complexity is basically free, so any shape or grouping of shapes can be imagined and modeled for performance,” Chinthavali said. “We’re very excited about where we see this research headed.”

    Using additive manufacturing, researchers optimized the inverter’s heat sink, allowing for better heat transfer throughout the unit. This construction technique allowed them to place lower-temperature components close to the high-temperature devices, further reducing the electrical losses and reducing the volume and mass of the package.

    Another key to the success is a design that incorporates several small capacitors connected in parallel to ensure better cooling and lower cost compared to fewer, larger and more expensive “brick type” capacitors.

    The research group’s first prototype, a liquid-cooled all-silicon carbide traction drive inverter, features 50 percent printed parts. Initial evaluations confirmed an efficiency of nearly 99 percent, surpassing DOE’s power electronics target and setting the stage for building an inverter using entirely additive manufacturing techniques.

    Building on the success of this prototype, researchers are working on an inverter with an even greater percentage of 3-D printed parts that’s half the size of inverters in commercially available vehicles. Chinthavali, encouraged by the team’s results, envisions an inverter with four times the power density of their prototype.

    Others involved in this work, which was to be presented today at the Second Institute of Electrical and Electronics Engineers Workshop on Wide Bandgap Power Devices and Applications in Knoxville, were Curt Ayers, Steven Campbell, Randy Wiles and Burak Ozpineci.

    Research for this project was conducted at ORNL’s National Transportation Research Center and Manufacturing Demonstration Facility, DOE user facilities, with funding from DOE’s Office of Energy Efficiency and Renewable Energy.

    See the full article here.

    ORNL is managed by UT-Battelle for the Department of Energy’s Office of Science. DOE’s Office of Science is the single largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time.


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  • richardmitnick 1:55 pm on October 13, 2014 Permalink | Reply
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    From ORNL: “Unlocking enzyme synthesis of rare sugars to create drugs with fewer side effects” 


    Oak Ridge National Laboratory

    September 26, 2014
    Katie Bethea, 865.576.8039

    A team led by the U.S. Department of Energy’s Oak Ridge National Laboratory has unlocked the enzymatic synthesis process of rare sugars, which are useful in developing drugs with low side effects using a process more friendly to the environment.

    In a paper published in Structure, the research team reported the pioneering use of neutron and X-ray crystallography and high performance computing to study how the enzyme D-xylose isomerase, or XI, can cause a biochemical reaction in natural sugar to produce rare sugars. Unlike drugs made from natural sugar compounds, drugs made from rare sugars do not interfere with cellular processes. As a result, rare sugars have important commercial and biomedical applications as precursors for the synthesis of different antiviral and anti-cancer drugs with fewer side effects.

    An artist’s rendering of the enzyme D-xylose isomerase as it isomerizes L-arabinose into rare sugars not found in nature. The enzyme acts as a filter by capturing and performing catalysis only on the high-energy 5S1 conformation of L-arabinose, while remaining inactive on other more abundant sugar conformations. Neutron macromolecular crystallography has unequivocally demonstrated how this high-energy conformer of L-arabinose binds in the enzyme active site and is converted to the linear intermediate form. Simulations provide evidence for the experimental results. Image credit: Genevieve Martin/ORNL

    “The goal of this study is to dramatically improve the performance of enzymes that can be used by the pharmaceutical industry to synthesize drug precursors,” said ORNL’s Andrey Kovalevsky, the lead author of the study. “We’re trying to find a new way to do enzyme design – neutron studies combined with high performance computing could be an elegant means to do that.”

    Enzymes speed up reactions in organisms, ultimately making life itself possible, and are increasingly used by industry to synthesize value-added compounds. Biotechnological syntheses are “greener” than other techniques that use heavy metal chemical catalysts and large amounts of organic solvents. However, many natural enzymes are not very well suited for industrial processes. XI, for example, is used effectively for the production of high-fructose corn syrup from starch in the food industry, but its applications in the pharmaceutical industry are limited by its performance. Researchers in the pharmaceutical industry want to engineer mutations in enzymes to improve reactions. But first, they have to understand how the enzymes work.

    “We had no idea how the enzyme, D-xylose isomerase, binds its non-physiological substrate – natural sugar L-arabinose,” said Kovalevsky. “You have to know how an enzyme binds its substrate to engineer mutations to improve binding and reaction.”

    Using X-ray and neutron crystallography combined with theoretical calculations, the team figured out how the enzyme isomerizes L-arabinose into the rare sugar L-ribulose and then epimerizes the latter into another rare sugar L-ribose. Importantly, L-ribose is the enantiomer, a mirror image, of the ubiquitous D-ribose that is a building block of DNA and RNA.

    “We found, completely unexpectedly, that the enzyme binds the substrate L-arabinose –an abundant natural sugar found in plants– in a very high energy geometry in the active site, which explained the xylose isomerase’s poor efficiency with the substrate and provided us with clues on how we can re-engineer it to improve its activity,” said Kovalevsky.

    Combining crystallographic observations and computation, the team saw the XI enzyme isomerize the sugar L-arabinose when bound to the active site. is the process in which the sugar changes its configuration through a chemical reaction. An enzyme’s active site is the binding place where catalysis is performed on substrates or where inhibitors dock to hinder catalysis. Binding a substrate in a high energy geometry means the efficiency of catalysis would be low, something researchers would like to improve, explained Kovalevsky.

    This is the first time researchers have looked at enzymatic synthesis by combining neutrons, X-rays and high performance computing.

    “Neutron crystallography gives the location of hydrogen atoms, which is important in enzyme reactions where there’s a lot of shuffling of hydrogen around,” said Kovalevsky. “X-rays can’t see those reactions. But once you have the neutron structures and know the hydrogen positions, then your calculations and theoretical models are much more correct.”

    In the past, researchers had to infer the hydrogen atom location from chemical knowledge, which, as experience shows, may be wrong. Now, neutrons show the exact location of the hydrogen atoms so they do not have to guess.

    Calculations can be misleading if hydrogens are placed incorrectly, leading in many cases to the wrong inference from calculations about how enzymes function. Combining neutrons, calculations and simulations gives a more thorough view of the enzymes’ mechanisms and a complete look at how enzymes work.

    Kovalevsky said future simulations will explore the possibility of tailoring the XI active site to bind lower-energy conformations of L-arabinose to improve catalytic activity.

    This research was partially funded through a National Institutes of HealthNational Institute of General Medical Sciences consortium between ORNL and DOE’s Lawrence Berkeley National Laboratory (LBNL). The work was conducted in part at the Los Alamos Neutron Science Center, a National Nuclear Security Administration User Facility at DOE’s Los Alamos National Laboratory., and at the National Energy Research Scientific Computing Center, a DOE Office of Science User Facility at LBNL.

    See the full article here.

    ORNL is managed by UT-Battelle for the Department of Energy’s Office of Science. DOE’s Office of Science is the single largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time.


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  • richardmitnick 2:39 pm on October 2, 2014 Permalink | Reply
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    From ORNL via Cray Supercomputer Co.: “Q&A: Diving Deep Into Our Solar System” 


    Oak Ridge National Laboratory

    October 1, 2014
    Anthony Mezzacappa

    Anthony Mezzacappa, director of the University of Tennessee–Oak Ridge National Laboratory Joint Institute for Computational Sciences, and a team of computational astrophysicists are conducting one of the largest supernova simulations to date on ORNL’s “Titan” supercomputer. Titan, which is a hybrid Cray® XK7™ supercomputer, is managed by the Oak Ridge Leadership Computing Facility on behalf of the Department of Energy. Dr. Mezzacappa answers our questions about his team’s work on Titan.

    Cray Titan at ORNL

    Q: Why is understanding what triggers a supernova explosion so important?

    A: Supernovae are ultimately responsible for why you and I are here. The class of supernova that our team studies is known as core-collapse supernovae [Type II], and this type of supernova is arguably the most important source of elements in the universe. Core-collapse supernovae are the death throes of massive stars (by massive stars, I’m referring to stars of eight to 10 solar masses and greater). Supernovae are basically stellar explosions that obliterate these stars, leaving the core behind. They are responsible for the lion’s share of elements in the periodic table between oxygen and iron, including the oxygen you breath and the calcium in your bones, and they are believed to be responsible for half the elements heavier than iron. So through supernova explosions, we’re tied to the cosmos in an intimate way.

    Twenty years ago, astronomers witnessed one of the brightest stellar explosions in more than 400 years. The titanic supernova, called SN 1987A, blazed with the power of 100 million suns for several months following its discovery on Feb. 23, 1987. Observations of SN 1987A, made over the past 20 years by NASA’s Hubble Space Telescope and many other major ground- and space-based telescopes, have significantly changed astronomers’ views of how massive stars end their lives. Astronomers credit Hubble’s sharp vision with yielding important clues about the massive star’s demise.

    This Hubble telescope image shows the supernova’s triple-ring system, including the bright spots along the inner ring of gas surrounding the exploded star. A shock wave of material unleashed by the stellar blast is slamming into regions along the inner ring, heating them up, and causing them to glow. The ring, about a light-year across, was probably shed by the star about 20,000 years before it exploded.

    NASA Hubble Telescope
    NASA/ESA HUbble

    Q: Why is supernova research critical to the progression of astrophysics?

    A: In addition to releasing a lot of the elements that make up ourselves and the nature around us, core-collapse supernovae give birth to neutron stars, which can become pulsars or black holes. So these supernovae are also responsible for the birth of other important objects in the universe that we want to understand.

    Another reason to study supernovae as a key component of astrophysics is that we can actually use supernovae as nuclear physics laboratories. With supernovae, we’re dealing with very high-density physics, with systems that are rich in neutrons and conditions that are difficult to produce in a terrestrial lab. We can use supernova models in conjunction with observations to understand fundamental nuclear physics.

    In all these ways, the “supernova problem,” as we call it, is certainly one of the most important and most challenging problems in astrophysics being answered today.

    Q: Back in 2003, what role did the simulations done on “Phoenix,” the Cray® X1E™ supercomputer, have on supernova research?

    A: The simulations back in 2002, which we published in 2003, led to the discovery of the SASI, or standing accretion shock instability.

    Phoenix was a magnificent machine, and we got a lot of science out of it. On Phoenix, we discovered the SASI and learned that the supernova shock wave, which generates the supernova, is unstable and this instability distorts its shape. The shock wave will become prolate or oblate (cigar-like or pancake-like), which has important ramifications for how these stars explode.

    I think if you take a look at supernova theory from about 1980 and onward, the results we see in our 2D and basic 3D models suggest the SASI is the missing link in obtaining supernova explosions in models that have characteristics commensurate with observations.

    Q: The work in 2003 unlocked the key SASI simulation result that was recently proven through observation. Can you explain the importance of that breakthrough now?

    A: As an x-ray observatory, NuSTAR — which delivered these supporting observations — can see the x-rays emitted from the decay of titanium-44. The reason titanium-44 is so important is because it is produced very deep in the explosion, so it can provide more information about the explosion mechanism than other radiative signatures.


    The map of the titanium-44 x-rays gave researchers a map of the explosion and, as such, it gave us a fingerprint, if you will, of the explosion dynamics, which was consistent with the active presence of the SASI. This is a rare example of a computational discovery being made before there was observational evidence to support it because these latest NuSTAR observations occurred a decade after the SASI was simulated on Phoenix. I think computational discovery is likely to happen more often as models develop and the machines they run on develop with them.

    Q: There are still some nuances in supernova research that aren’t explained by SASI. What is being done to fill in those gaps?

    A: Since the SASI was discovered, all supernova groups have considered the SASI an integral part of supernova dynamics. There is some debate on its importance to the supernova explosion mechanism. Some experts believe it’s there but it’s subcritical to other phenomenon; however, everyone believes it’s there and needs to be understood. I think, when all is said and done, we’ll find the SASI is integral to the explosion mechanism.

    The key thing is that Mother Nature works in three dimensions, and earlier simulations have been in 2D. The simulation we are running on Titan now is among the first multiphysics, 3D simulations ever performed.

    It’s not even a nuance so much as if you’re trying to understand the role of the SASI and other parts of the explosion mechanism, it has to be done in 3D — an endeavor which is only now beginning.

    Q: How is working with Titan unlocking better ways to simulate supernova activity?

    A: Unlike earlier 2D simulations, the Titan simulations will model all the important physical properties of a dying massive star in 3D, included gravity, neutrino transport and interaction, and fluid instability.

    For gravity, we’re modeling gravitational fields dictated by the general relativistic theory of gravity (or [Albert] Einstein’s theory of gravity). It’s very important that models include calculations for relativistic gravity rather than Newtonian gravity, which you would use to understand the orbits of the planets around the sun, for instance, although even here a deeper description in terms of Einstein’s theory of gravity can be given.

    Second, the model includes neutrinos. We believe neutrinos actually power these explosions. They are nearly massless particles that behave like radiation in this system and emerge from the center of the supernova. The center of the supernova is like a neutrino bulb radiating at 1045 watts, and it’s energizing the shock wave by heating the material underneath the wave. There’s a lot of energy in neutrinos, but you only have to tap into a fraction of that energy to generate a supernova.

    So neutrinos likely power these explosive events, and their production, transport and interaction with the stellar material has to be modeled very carefully.

    Finally, the stellar material is fluid-like, and because you have a heat source (the neutrinos) below that stellar material, convection is going to occur. If you heat a pot of water on the stove, the bubbles that occur during boiling are less dense than the water around them — that’s an instability and that’s why those bubbles rise. Convection is a similar instability that develops. The shock wave is a discontinuity in the stellar fluid, and the SASI is an instability of this shock wave. So convection and the SASI are both operative and are the main fluid instabilities we must model.

    Those are the main components. There are other properties — rotation, magnetic fields, thermonuclear reactions and more — that are important for understanding the formation of elements as well as the explosion mechanism, and these will all be modeled on Titan.

    Q: What are some of the core goals that make up the INCITE project?

    A: The current Titan simulation is representative of supernovae that originate in stars of about 15 solar masses. Later, we will do other runs on Titan at different solar masses — 10, 20, 25. Fifteen solar masses is in the middle of the range of stellar masses we believe result in supernovae, and we’ll compare it to observed supernovae whose progenitor mass is determined to have been at or near 15 solar masses.

    This INCITE project is focusing on how the explosion mechanism works, which is not just limited to the SASI. When we run the model we’ll wait to see: Does it explode? If it does, was it a weak or a robust explosion? Was the explosion energy commensurate with observed energies for stars of that solar mass? What kind of neutron star is left behind after the explosion?

    Q: If you had to sum up the value of this supernova research, considering everything that has been learned from 2003′s simulations to today, what would you say has been the most important lesson?

    A: I would say the most important lesson is that computation is a critical mode of discovery. It is arguably the best tool to understand phenomena that are nonlinear and have many interconnected components. It is very difficult to understand phenomena like core-collapse supernovae analytically with pencil and paper. The SASI had to be discovered computationally because it’s a nonlinear phenomenon. Computation is not just about getting the details. You don’t go into computation knowing the answer but wanting to get the details; there is discovery and surprise in computation. And there’s no better example of that than the discovery of the SASI.

    In addition to his role as the director of ORNL’s Joint Institute for Computational Sciences, Anthony Mezzacappa is the Newton W. and Wilma C. Thomas chair and a professor in the department of physics and astronomy at the University of Tennessee. He is also ORNL corporate fellow emeritus. The team simulating a core-collapse supernova on Titan includes Mezzacappa, Steve Bruenn of Florida Atlantic University, Bronson Messer and Raph Hix of ORNL, Eric Lentz and Austin Harris of the University of Tennessee, Knoxville, and John Blondin of North Carolina State University.

    See the full article here.

    ORNL is managed by UT-Battelle for the Department of Energy’s Office of Science. DOE’s Office of Science is the single largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time.


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  • richardmitnick 1:17 pm on September 2, 2014 Permalink | Reply
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    From ORNL: “ORNL scientists uncover clues to role of magnetism in iron-based superconductors” 


    Oak Ridge National Laboratory

    September 1, 2014
    Morgan McCorkle, 865.574.7308,

    New measurements of atomic-scale magnetic behavior in iron-based superconductors by researchers at the Department of Energy’s Oak Ridge National Laboratory and Vanderbilt University are challenging conventional wisdom about superconductivity and magnetism.

    ORNL scientists used scanning transmission electron microscopy to measure atomic-scale magnetic behavior in several families of iron-based superconductors.

    The study published in Advanced Materials provides experimental evidence that local magnetic fluctuations can influence the performance of iron-based superconductors, which transmit electric current without resistance at relatively high temperatures.

    “In the past, everyone thought that magnetism and superconductivity could not coexist,” said ORNL’s Claudia Cantoni, the study’s first author. “The whole idea of superconductors is that they expel magnetic fields. But in reality things are more complicated.”

    Superconductivity is strongly suppressed by the presence of long-range magnetism – where atoms align their magnetic moments over large volumes – but the ORNL study suggests that rapid fluctuations of local magnetic moments have a different effect. Not only does localized magnetism exist, but it is also correlated with a high critical temperature, the point at which the material becomes superconducting.

    “One would think for superconductivity to exist, not only the long-range order but also the local magnetic moments would have to die out,” Cantoni said. “We saw instead that if one takes a fast ‘picture’ of the local moment, it is actually at its maximum where superconductivity is at its maximum. This indicates that a large local moment is good for superconductivity.”

    The ORNL-led team used a combination of scanning transmission electron microscopy and electron energy loss spectroscopy to characterize the magnetic properties of individual atoms. Other experimental techniques have not been able to capture information on the local magnetic moments in sufficient detail.

    “This kind of measurement of magnetic moments is usually done with more bulk-sensitive techniques, which means they look at the average of the material,” Cantoni said. “When you use the average, you might not get the right answer.”

    The team’s four-year comprehensive study analyzed compounds across several families of iron-based superconductors, revealing universal trends among the different samples. The researchers were able to figure out the total number and distribution of electrons in atomic energy levels that determine the local magnetic moments.

    “We find this number remains constant for all the members of this family,” Cantoni said. “The number of electrons doesn’t change — what changes are the positions and distribution of electrons in different levels. This is why the magnetic moment differs across families.”

    The ORNL scientists also say the technique they demonstrated on iron-based superconductors could be useful in studies of other technologically interesting materials in fields such as electronics and data storage.

    “Electron microscopy has long been an imaging technique that gives you a lot of crystal structure information; now we’re trying to go beyond to get the electronic structure,” Cantoni said. “Not only do we want to know what atoms are where, but what the electrons in those atoms are doing.”

    The study’s coauthors are ORNL’s Claudia Cantoni, Jonathan Mitchell, Andrew May, Michael McGuire, Juan-Carlos Idrobo, Tom Berlijn, Matthew Chisholm, Elbio Dagotto, Wu Zhou, Athena Safa-Sefat and Brian Sales, and the University of Tennessee’s Stephen Pennycook. The research is published as Orbital occupancy and charge doping in iron-based superconductors.

    This research was conducted in part at the Center for Nanophase Materials Sciences, a DOE Office of Science User Facility. The research at ORNL was supported by the DOE’s Office of Science. Collaborators Idrobo and Zhou at Vanderbilt University were supported by the National Science Foundation.

    See the full article here.

    ORNL is managed by UT-Battelle for the Department of Energy’s Office of Science. DOE’s Office of Science is the single largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time.


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  • richardmitnick 10:29 am on July 23, 2014 Permalink | Reply
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    From DOE Pulse: “Ames Lab scientist hopes to improve rare earth purification process” 


    July 21, 2014
    Austin Kreber, 515.987.4885,

    Using the second fastest supercomputer in the world, a scientist at the U.S. Department of Energy’s Ames Laboratory is attempting to develop a more efficient process for purifying rare-earth materials.

    Dr. Nuwan De Silva, a postdoctoral research associate at the Ames Laboratory’s Critical Materials Institute, said CMI scientists are honing in on specific types of ligands they believe will only bind with rare-earth metals. By binding to these rare metals, they believe they will be able to extract just the rare-earth metals without them being contaminated with other metals.

    Nuwan De Silva, scientist at the Ames
    Laboratory, is developing software to help improve purification of rare-earth materials. Photo credit: Sarom Leang

    Rare-earth metals are used in cars, phones, wind turbines, and other devices important to society. De Silva said China now produces 80-90 percent of the world’s supply of rare-metals and has imposed export restrictions on them. Because of these new export limitations, many labs, including the CMI, have begun trying to find alternative ways to obtain more rare-earth metals.

    Rare-earth metals are obtained by extracting them from their ore. The current extraction process is not very efficient, and normally the rare-earth metals produced are contaminated with other metals. In addition the rare-earth elements for various applications need to be separated from each other, which is a difficult process, one that is accomplished through a solvent extraction process using an aqueous acid solution.

    CMI scientists are focusing on certain types of ligands they believe will bind with just rare-earth metals. They will insert a ligand into the acid solution, and it will go right to the metal and bind to it. They can then extract the rare-earth metal with the ligand still bound to it and then remove the ligand in a subsequent step. The result is a rare-earth metal with little or no contaminants from non rare-earth metals. However, because the solution will still contain neighboring rare-earth metals, the process needs to be repeated many times to separate the other rare earths from the desired rare-earth element.

    The ligand is much like someone being sent to an airport to pick someone up. With no information other than a first name — “John” — finding the right person is a long and tedious process. But armed with a description of John’s appearance, height, weight, and what he is doing, finding him would be much easier. For De Silva, John is a rare-earth metal, and the challenge is developing a ligand best adapted to finding and binding to it.

    To find the optimum ligand, De Silva will use Titan to search through all the possible candidates. First, Titan has to discover the properties of a ligand class. To do that, it uses quantum-mechanical (QM) calculations. These QM calculations take around a year to finish.

    ORNL Titan Supercomputer

    Once the QM calculations are finished, Titan uses a program to examine all the parameters of a particular ligand to find the best ligand candidate. These calculations are called molecular mechanics (MM). MM calculations take about another year to accomplish their task.

    “I have over 2,500,000 computer hours on Titan available to me so I will be working with it a lot,” De Silva said. “I think the short term goal of finding one ligand that works will take two years.”

    The CMI isn’t the only lab working on this problem. The Institute is partnering with Oak Ridge National Laboratory, Lawrence Livermore National Laboratory and Idaho National Laboratory as well as numerous other partners. “We are all in constant communication with each other,” De Silva said.

    See the full article here.

    DOE Pulse highlights work being done at the Department of Energy’s national laboratories. DOE’s laboratories house world-class facilities where more than 30,000 scientists and engineers perform cutting-edge research spanning DOE’s science, energy, National security and environmental quality missions. DOE Pulse is distributed twice each month.

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  • richardmitnick 12:36 pm on July 21, 2014 Permalink | Reply
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    From Oak Ridge Lab: “‘Engine of Explosion’ Discovered at OLCF now Observed in Nearby Supernova Remnant’ 


    Oak Ridge National Laboratory

    May 6, 2014
    Katie Elyce Jones

    Data gathered with high-energy x-ray telescope support the SASI model—a decade later

    Back in 2003, researchers using the Oak Ridge Leadership Computing Facility’s (OLCF’s) first supercomputer, Phoenix, started out with a bang. Astrophysicists studying core-collapse [Type II]supernovae—dying massive stars that violently explode after running out of fuel—asked themselves what mechanism triggers explosion and a fusion chain reaction that releases all the elements found in the universe, including those that make up the matter around us?

    “This is really one of the most important problems in science because supernovae give us all the elements in nature,” said Tony Mezzacappa of the University of Tennessee–Knoxville.

    Leading up to the 2003 simulations on Phoenix, one-dimensional supernovae models simulated a shock wave that pushes stellar material outward, expanding to a certain radius before, ultimately, succumbing to gravity. The simulations did not predict that stellar material would push beyond the shock wave radius; instead, infalling matter from the fringes of the expanding star tamped the anticipated explosion. Yet, humans have recorded supernovae explosions throughout history.

    “There have been a lot of supernovae observations,” Mezzacappa said. “But these observations can’t really provide information on the engine of explosion because you need to observe what is emitted from deep within the supernova, such as gravitational waves or neutrinos. It’s hard to do this from Earth.”

    Then simulations on Phoenix offered a solution: the SASI, or standing accretion shock instability, a sloshing of stellar material that destabilizes the expanding shock and helps lead to an explosion.

    “Once we discovered the SASI, it became very much a part of core-collapse supernova theory,” Mezzacappa said. “People feel it is an important missing ingredient.”

    The SASI provided a logical answer supported by other validated physics models, but it was still theoretical because it had only been demonstrated computationally.

    Now, more than a decade later, researchers mapping radiation signatures from the Cassiopeia A supernova with NASA’s NuSTAR high-energy x-ray telescope array have published observational evidence that supports the SASI model.


    Cass A
    Cas A
    A false color image off Cassiopeia using observations from both the Hubble and Spitzer telescopes as well as the Chandra X-ray Observatory (cropped).
    Courtesy NASA/JPL-Caltech

    “What they’re seeing are x-rays that come from the radioactive decay of Titanium-44 in Cas A,” Mezzacappa said.

    Because Cassiopeia A is only 11,000 light-years away within the Milky Way galaxy (relatively nearby in astronomical distances), NuSTAR is capable of detecting Ti-44 located deep in the supernova ejecta. Mapping the radiative signature of this titanium isotope provides information on the supernova’s engine of explosion.

    “The distribution of titanium is what suggests that the supernova ‘sloshes’ before it explodes, like the SASI predicts,” Mezzacappa said.

    This is a rare example of simulation predicting a physical phenomenon before it is observed experimentally.

    “Usually it’s the other way around. You observe something experimentally then try to model it,” said the OLCF’s Bronson Messer. “The SASI was discovered computationally and has now been confirmed observationally.”

    The authors of the Nature letter that discusses the NuSTAR results cite Mezzacappa’s 2003 paper introducing the SASI in The Astrophysical Journal, which was coauthored by John Blondin and Christine DeMarino, as a likely model to describe the Ti-44 distribution.

    Despite observational support for the SASI, researchers are uncertain whether the SASI is entirely responsible for triggering a supernova explosion or if it is just part of the explanation. To further explore the model, Mezzacappa’s team, including the Innovative and Novel Computational Impact on Theory and Experiment (INCITE) project’s principal investigator Eric Lentz, are taking supernovae simulations to the next level on the OLCF’s 27-petaflop Titan supercomputer located at Oak Ridge National Laboratory.

    ORNL Titan Supercomputer
    Titan at ORNL

    “The role of the SASI in generating explosion and whether or not the models are sufficiently complete to predict the course of explosion is the important question now,” Mezzacappa said. “The NuSTAR observation suggests it does aid in generating the explosion.”

    Although the terascale runs that predicted the SASI in 2003 were in three dimensions, they did not include much of the physics that can now be solved on Titan. Today, the team is using 85 million core hours and scaling to more than 60,000 cores to simulate a supernova in three dimensions with a fully physics-based model. The petascale Titan simulation, which will be completed later this year, could be the most revealing supernova explosion yet—inside our solar system anyway.

    ORNL is managed by UT-Battelle for the Department of Energy’s Office of Science. DOE’s Office of Science is the single largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time.

    See the full article here.


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  • richardmitnick 5:44 pm on May 7, 2014 Permalink | Reply
    Tags: , , , , Oak Ridge National Laboratory,   

    From Oak Ridge: “World’s Most Powerful Accelerator Comes to Titan with a High-Tech Scheduler” 


    Oak Ridge National Laboratory

    May 6, 2014
    Leo Williams

    The people who found the Higgs boson have serious data needs, and they’re meeting some of them on the Oak Ridge Leadership Computing Facility’s (OLCF’s) flagship Titan system.


    Researchers with the ATLAS experiment at Europe’s Large Hadron Collider (LHC) have been using Titan since December, according to Ken Read, a physicist at Oak Ridge National Laboratory and the University of Tennessee. Read, who works with another LHC experiment, known as ALICE, noted that much of the challenge has been in integrating ATLAS’s advanced scheduling and analysis tool, PanDA, with Titan.


    CERN LHC particles

    PanDA (for Production and Distributed Analysis) manages all of ATLAS’s data tasks from a server located at CERN, the European Organization for Nuclear Research. The job is daunting, with the workflow including 1.8 million computing jobs each day distributed among 100 or so computing centers spread across the globe.

    PanDA is able to match ATLAS’s computing needs seamlessly with disparate systems in its network, making efficient use of resources as they become available.

    In all, PanDA manages 150 petabytes of data (enough to hold about 75 million hours of high-definition video), and its needs are growing rapidly—so rapidly that it needs access to a supercomputer with the muscle of Titan, the United States’ most powerful system.

    “For ATLAS, access to the leadership computing facilities will help it manage a hundredfold increase in the amount of data to be processed,” said ATLAS developer Alexei Klimentov of Brookhaven National Laboratory. PanDA was developed in the United States under the guidance of Kaushik De of the University of Texas at Arlington and Torre Wenaus from Brookhaven National Laboratory.

    “Our grid resources are overutilized,” Klimentov said. “It’s a question of where we can find resources and use them opportunistically. We cannot scale the grid 100 times.”

    In order to integrate with Titan, PanDA team developers Sergey Panitkin from BNL and Danila Oleynik from UTA redesigned parts of the PanDA system on Titan responsible for job submission on remote sites (known as “Pilot”) and gave PanDA new capability to collect information about unused worker nodes on Titan. This allows PanDA to precisely define the size and duration of jobs submitted to Titan according to available free resources. This work was done in collaboration with OLCF technical staff.

    The collaboration holds potential benefits for OLCF as well as for ATLAS.

    In the first place, PanDA’s ability to efficiently match available computing time with high-priority tasks holds great promise for a leadership system such as Titan. While the OLCF focuses on projects that can use most, if not all, of Titan’s 18,000-plus computing nodes, there are occasionally a relatively small numbers of nodes sitting idle for one or several hours. They sit idle because there are not enough of them—or they don’t have enough time—to handle a leadership computing job. A scheduler that can occupy those nodes with high-priority tasks would be very valuable.

    “Today, if we use 90 or 92 percent of available hours, we think that is high utilization,” said Jack Wells, director of science at the OLCF. “That’s because of inefficiencies in scheduling big jobs. If we have a flexible workflow to schedule jobs for backfill, it would mean higher utilization of Titan for science.”

    PanDA is also highly skilled at finding needles in haystacks, as it showed during the search for the Higgs boson.

    According to the Standard Model of particle physics, the field associated with the Higgs is necessary for other particles to have mass. The boson is also very massive itself and decays almost instantly; this means it can be created and detected only by a very high-energy facility. In fact, it has, so far, been found definitively only at the LHC, which is the world’s most powerful particle accelerator.

    The Standard Model of elementary particles, with the three generations of matter, gauge bosons in the fourth column, and the Higgs boson in the fifth.

    But while high energy was necessary for identifying the Higgs, it was not sufficient. The LHC creates 800 million collisions between protons each second, yet it creates a Higgs boson only once every one to two hours. In other words, it takes 4 trillion collisions, more or less, to create a Higgs. And it takes PanDA to manage ATLAS’s data processing workflow in sifting through the data and finding it.

    PanDA’s value to high-performance computing is widely recognized. The Department of Energy’s offices of Advanced Scientific Computing Research and High Energy Physics are, in fact, funding a project known as Big PanDA to expand the tool beyond high-energy physics to be used by other communities.

    See the full article here.

    ORNL is managed by UT-Battelle for the Department of Energy’s Office of Science. DOE’s Office of Science is the single largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time.


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  • richardmitnick 10:57 am on August 13, 2013 Permalink | Reply
    Tags: , , , , Oak Ridge National Laboratory   

    From ORNL Lab: “Neutrons’ view of hydrogen yields insight into HIV drug design” 

    ORNL-led study demonstrates relevance of neutrons in biomedical research

    August 13, 2013
    Morgan McCorkle

    “A new study from an international team led by the Department of Energy’s Oak Ridge National Laboratory is guiding drug designers toward improved pharmaceuticals to treat HIV. The scientists used neutrons and x-rays to study the interactions between HIV protease, a protein produced by the HIV virus, and an antiviral drug commonly used to block virus replication.

    An ORNL-led team used neutrons to study the interactions between HIV protease, a protein produced by the HIV virus, and an antiviral drug called amprenavir commonly used to block virus replication. The magenta mesh is the neutron scattering density map showing the exact locations of hydrogen atoms bound to oxygen atoms. The blue dashed lines represent the strongest hydrogen bonds between the drug and the enzyme. This knowledge will help researchers improve the drug’s chemistry and increase its effectiveness.No image credit.

    Using neutrons from the Institut Laue-Langevin in Grenoble, France, the researchers gained a never-before-seen view of hydrogen bonds that connect the HIV protease and the drug. Unlike x-rays, neutrons can easily detect the position of hydrogen atoms.

    ‘Knowing where hydrogen atoms are located gives researchers a much better idea about the nature and strength of the interactions,’ said lead author Andrey Kovalevsky of ORNL. ‘By applying neutron crystallography we have effectively increased the clarity of this picture, because hydrogen atoms become visible in the neutron structures. Using neutrons, we are now able to see every atom in a protein-drug complex, all the way to the smallest atom in nature.’

    The research, published in the Journal of Medicinal Chemistry, presents drug designers with a set of new potential sites for the improvement of the drug’s surface chemistry to significantly strengthen the binding, thereby increasing the effectiveness of the drugs and reducing the necessary dosages.”

    See the full article here.


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  • richardmitnick 6:12 pm on April 3, 2013 Permalink | Reply
    Tags: , , , Oak Ridge National Laboratory   

    From ORNL: “ORNL microscopy uncovers “dancing” silicon atoms in graphene” 

    April 3, 2013
    Morgan McCorkle

    “Jumping silicon atoms are the stars of an atomic scale ballet featured in a new Nature Communications study from the Department of Energy’s Oak Ridge National Laboratory.

    Oak Ridge National Laboratory researchers used electron microscopy to document the ‘dancing’ motions of silicon atoms, pictured in white, in a graphene sheet.

    The ORNL research team documented the atoms’ unique behavior by first trapping groups of silicon atoms, known as clusters, in a single-atom-thick sheet of carbon called graphene. The silicon clusters, composed of six atoms, were pinned in place by pores in the graphene sheet, allowing the team to directly image the material with a scanning transmission electron microscope.

    The ‘dancing’ movement of the silicon atoms was caused by the energy transferred to the material from the electron beam of the team’s microscope.

    ‘It’s not the first time people have seen clusters of silicon,’ said coauthor Juan Carlos Idrobo. ‘The problem is when you put an electron beam on them, you insert energy into the cluster and make the atoms move around. The difference with these results is that the change that we observed was reversible. We were able to see how the silicon cluster changes its structure back and forth by having one of its atoms ‘dancing’ between two different positions.'”

    See the full article here.


    ORNL is managed by UT-Battelle for the Department of Energy’s Office of Science. DOE’s Office of Science is the single largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time.


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