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    • 2018-05-31 11:05:23
    • Article ID: 695383

    From Face Recognition to Phase Recognition: Neural Network Captures Atomic-Scale Rearrangements

    Scientists use approach analogous to facial-recognition technology to track atomic-scale rearrangements relevant to phase changes, catalytic reactions, and more

    • Brookhaven Lab/Stony Brook University physicist Anatoly Frenkel (standing) with postdoc Janis Timoshenko and a photo of their University of Latvia collaborators—Alexei Kuzmin, Juris Purans, Arturs Cintins, and Andris Anspoks—displaying a model of the room-temperature iron structure atop a free-form tree sculpture.

    • Deciphering the changes in the 3D structure of iron (center) upon heating, from top, clockwise: The in situ x-ray absorption experiment generates an extended x-ray absorption fine structure (EXAFS) spectrum that is fed into a neural network to extract the radial distribution function, unique for each material and atomic arrangement.

    UPTON, NY—If you want to understand how a material changes from one atomic-level configuration to another, it’s not enough to capture snapshots of before-and-after structures. It’d be better to track details of the transition as it happens. Same goes for studying catalysts, materials that speed up chemical reactions by bringing key ingredients together; the crucial action is often triggered by subtle atomic-scale shifts at intermediate stages.

    “To understand the structure of these transitional states, we need tools to both measure and identify what happens during the transition,” said Anatoly Frenkel, a physicist with a joint appointment at the U.S. Department of Energy’s Brookhaven National Laboratory and Stony Brook University.

    Frenkel and his collaborators have now developed such a “phase-recognition” tool—or more precisely, a way to extract “hidden” signatures of an unknown structure from measurements made by existing tools. In a paper just published in Physical Review Letters, they describe how they trained a neural network to recognize features in a material’s x-ray absorption spectrum that are sensitive to the arrangement of atoms at a very fine scale. The method helped reveal details of the atomic-scale rearrangements iron undergoes during an important but poorly understood phase change.

    “This network training is similar to how machine learning is used in facial-recognition technology,” Frenkel explained. In that technology, computers analyze thousands of images of faces and learn to recognize key features, or descriptors, and the differences that tell individuals apart. “There is a correlation between some features of the data,” Frenkel explained. “In the language of our x-ray data, the correlations exist between the intensity of different regions of the spectra that also have direct relevance to the underlying structure and the corresponding phase.”

    Network training

    To get the neural network ready for “phase recognition”—that is, to be able to recognize the key spectral features—the scientists needed a training set of images.

    Janis Timoshenko, a postdoctoral fellow working with Frenkel at Stony Brook and lead author on the paper, tackled that challenge. First, he used molecular dynamic simulations to create 3000 realistic structure models corresponding to different phases of iron and different degrees of disorder.

    “In these models, we wanted to account for the dynamic effects, so we define the forces that act between different atoms and we allow the atoms to move around as influenced by these forces,” Timoshenko said. Then, using well-established approaches, he used mathematical calculations to derive the x-ray absorption spectra that would be obtained from each of these 3000 structures.

    “It’s not a problem to simulate a spectrum,” Timoshenko said, “it’s a problem to understand them in the backwards direction—start with the spectrum to get to the structure—which is why we need the neural network!”

    After using Timoshenko’s modeled spectral data to train the network, the scientists put their method to the test using real spectral data collected as iron underwent the phase transition.

    “There are not a lot of experimental methods to monitor this transition, which happens at quite high temperatures,” Timoshenko said. “But our collaborators— Alexei Kuzmin, Juris Purans, Arturs Cintins, and Andris Anspoks from the Institute of Solid State Physics of the University of Latvia, my former institution—performed this really nice experiment at the ELETTRA synchrotron in Italy to collect x-ray absorption data on this phase transition for the first time.”

    The neural network was able to extract the relevant structural information from the x-ray absorption spectrum of iron—in particular, the radial distribution function, which is a measure of the separations between atoms and how likely the various separations are. This function, unique for any material, is the key that can unlock the hidden details of the structure, according to Frenkel. It allowed scientists to quantify changes in the density and coordination of iron atoms in the process of their transition from one atomic arrangement to another.

    Additional applications

    In addition to being useful for studying the dynamics of phase changes, this method could be used to monitor the arrangements of nanoparticles in catalysts and other materials, the scientists say.

    “We know that nanoparticles in catalytic materials change their structure in reaction conditions. It’s really important to understand the transitional structure—why it changes, and how that affects catalytic properties and processes,” Timoshenko said.

    Nanoparticles also often take on structures that lie somewhere between crystalline and amorphous, with structural variations between the surface and the bulk. This method should be able to tease apart those differences so scientists can assess their relevance for material performance.

    The method would also be useful for studying heterogeneous materials (which are made from a combination of particles with different sizes and shapes) and isomers of the same particle (which contain the same number of atoms but differ in their arrangements).

    “No technique can image positions of atoms in three dimensions with such precision to tell what’s the difference between their shapes. But if we measure this radial distribution function, there is a chance to tell them apart—and address important questions about the role of heterogeneity in catalysis,” Frenkel said.

    Brookhaven Lab’s role in this work was funded by the U.S. Department of Energy’s Office of Science and by Laboratory Directed Research and Development funds.

    Brookhaven National Laboratory is supported by the Office of Science of the U.S. Department of Energy. The 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. For more information, please visit science.energy.gov.

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    Missing gamma-ray blobs shed new light on dark matter, cosmic magnetism

    Scientists, including researchers from the Department of Energy's SLAC National Accelerator Laboratory, have compiled the most detailed catalog of such blobs using eight years of data collected with the Large Area Telescope (LAT) on NASA's Fermi Gamma-Ray Space Telescope. The blobs, including 19 gamma-ray sources that weren't known to be extended before, provide crucial information on how stars are born, how they die, and how galaxies spew out matter trillions of miles into space.

    Applying Auto Industry's Fuel-Efficiency Standards to Agriculture Could Net Billions in Corn Sector, Researchers Conclude

    Adopting benchmarks similar to the fuel-efficiency standards used by the auto industry in the production of fertilizer could yield $5-8 billion in economic benefits for the U.S. corn sector alone, researchers have concluded in a new analysis.

    How Animals Use Their Tails to Swish and Swat Away Insects

    A new study shows how animals use their tails to keep mosquitoes at bay by combining a swish that blows away most of the biting bugs and a swat that kills the ones that get through.

    Research on Light-Matter Interaction Could Lead to Improved Electronic and Optoelectronic Devices

    A paper published in Nature Communications by Sufei Shi, assistant professor of chemical and biological engineering at Rensselaer, increases our understanding of how light interacts with atomically thin semiconductors and creates unique excitonic complex particles, multiple electrons, and holes strongly bound together.

    Next-Gen Ultrafast Optical Fiber-Based Electron Gun to Reveal Atomic Motions During Transition State

    A new method enables researchers to directly observe and capture atomic motions at surfaces and interfaces in real time.

    Intense Microwave Pulse Ionizes Its Own Channel Through Plasma

    Researchers experimentally observed the ionization-induced channeling of an intense microwave beam propagating through a neutral gas (>103 Pa).

    Ancient Pigment Can Boost Energy Efficiency

    Egyptian blue, derived from calcium copper silicate, was routinely used on ancient depictions of gods and royalty. Previous studies have shown that when Egyptian blue absorbs visible light, it then emits light in the near-infrared range. Now a team led by researchers at Lawrence Berkeley National Laboratory has confirmed the pigment's fluorescence can be 10 times stronger than previously thought.

    Expanding Fungal Diversity, One Cell at a Time

    Reported October 8, 2018, in Nature Microbiology, a team led by U.S. Department of Energy Joint Genome Institute researchers developed a pipeline to generate genomes from single cells of uncultivated fungi. The approach was tested on several uncultivated species representing early diverging fungi.

    Columbia Engineers Build Smallest Integrated Kerr Frequency Comb Generator

    Optical frequency combs can enable ultrafast processes in physics, biology, and chemistry, as well as improve communication and navigation, medical testing, and security. Columbia Engineers have built a Kerr frequency comb generator that, for the first time, integrates the laser with the microresonator, significantly shrinking the system's size and power requirements. They no longer need to connect separate devices using fiber--they can now integrate it all on compact and energy efficient photonic chips.

    Scientists Present New Clues to Cut Through the Mystery of Titan's Atmospheric Haze

    Experiments at Berkeley Lab helped scientists zero in on a low-temperature chemical mechanism that may help to explain the complex molecular compounds that make up the nitrogen-rich haze layer surrounding Titan, Saturn's largest moon.


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    Prototype Solar Energy, Battery Systems to Fuel Commercialization

    Designing, building and testing prototype systems that show how renewable energy can power devices, such as a weather and soil sensor station, can help bridge the gap between basic science research and commercialization.

    Argonne to Advance High Performance Computing in Manufacturing

    Argonne awarded funding to partner with Industry to advance the use of high performance computing in manufacturing.

    "Invisible Glass" Wins 2018 Create the Future Design Contest Grand Prize

    Scientists from the Center for Functional Nanomaterials developed a technique for making nonreflecting glass, silicon, and plastic surfaces.

    Missouri S&T researchers win multimillion dollar grant to build fast-charging stations for electric cars

    Researchers from Missouri S&T and three private companies will combine their expertise to create charging stations for electric vehicles that could charge a car in less than 10 minutes - matching the time it takes to fill up a conventional vehicle with gasoline."The big problem with electric vehicles is range, and it's not so much range as range anxiety.

    Making batteries store more energy, last longer

    A new solid polymer electrolyte may help make cell phone batteries store more energy and last longer.

    Three Brookhaven Lab Scientists Named Fellows of American Physical Society

    The American Physical Society (APS), the world's largest physics organization, has elected three scientists from the U.S. Department of Energy's (DOE) Brookhaven National Laboratory as 2018 APS fellows.

    Southern Research first to win accreditation under ISO 14034

    Southern Research has become the first organization in the United States to earn accreditation under ISO 14034, a new international standard for evaluating and verifying environmental technologies that was recently adopted by the American National Standards Institute.

    Kawtar Hafidi to head Physical Sciences and Engineering directorate at Argonne

    Physicist Kawtar Hafidi has been appointed Associate Laboratory Director, Physical Sciences and Engineering at the U.S. Department of Energy's (DOE) Argonne National Laboratory.

    Argonne researchers honored by Energy Secretary's awards program

    A select group of researchers from the U.S. Department of Energy's (DOE) Argonne National Laboratory was recently recognized for their contributions to infrastructure security and nuclear nonproliferation at the Secretary's Honor Awards ceremony in Washington, D.C., on August 29.

    PPPL's Sam Cohen earns award at meeting of U.S. government-funded laboratories hosted by PPPL

    PPPL physicist Sam Cohen and a local company win a Federal Laboratory Consortium award for a rocket propulsion technology.


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    How to Make Soot and Stardust

    Scientists unlock mystery that could help reduce emissions of fine particles from combustion engines and other sources.

    Breaking the Symmetry Between Fundamental Forces

    Scientists improve our understanding of the relationship between fundamental forces by re-creating the earliest moments of the universe.

    Water Plays Unexpected Role in Forming Minerals

    Water molecules line up tiny particles to attach and form minerals; understanding how this happens impacts energy extraction and storage along with waste disposal.

    Heavy Particles Get Caught Up in the Flow

    First direct measurement show how heavy particles containing a charm quark get caught up in the flow of early universe particle soup.

    Seeing Between the Atoms

    New detector enables electron microscope imaging at record-breaking resolution.

    Scaling Up Single-Crystal Graphene

    New method can make films of atomically thin carbon that are over a foot long.

    Discovered: Optimal Magnetic Fields Suppress Instabilities in Tokamak Plasmas

    U.S. and Korean scientists show how to find and use beneficial 3-D field perturbations to stabilize dangerous edge-localized modes in plasma.

    New Electron Glasses Sharpen Our View of Atomic-Scale Features

    A new approach to atom probe tomography promises more precise and accurate measurements vital to semiconductors used in computers, lasers, detectors, and more.

    Getting an Up-Close, 3-D View of Gold Nanostars

    Scientists can now measure 3-D structures of tiny particles with properties that hold promise for advanced sensors and diagnostics.

    Small, Short-Lived Drops of Early Universe Matter

    Particle flow patterns suggest even small-scale collisions create drops of early universe quark-gluon plasma.


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