DOE News
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    The DOE Science News Source is a Newswise initiative to promote research news from the Office of Science of the DOE to the public and news media.
    • 2019-12-02 15:15:16
    • Article ID: 723336

    Science Snapshots - microbiome matchmakers, solid-liquid interfaces, undersea earthquakes

    • Credit: Artem Baskin, Jonathon Larson/Berkeley Lab

      Infrared light is focused onto the sharp metallic tip of an atomic force microscope, enabling the acquisition of vibrational spectra from a graphene-liquid interface.

    • Credit: iStock/spawns

      A unique neural network architecture called mmvec (microbe-metabolite vectors) has made it possible to accurately infer the interactions between the microbes that are present in a community and the metabolites they produce.

    • Credit: Nate Lindsey

      Researchers employed 20 kilometers (pink) of a 51-kilometer undersea fiber-optic cable, normally used to communicate with an off-shore science node (MARS, Monterey Accelerated Research System), as a seismic array to study the fault zones under Monterey Bay. During the four-day test, the scientists detected a magnitude 3.5 earthquake 45 kilometers away in Gilroy, and mapped previously uncharted fault zones (yellow circle).

    A Matchmaker for Microbiomes
    New tool will enable important insights into the microbial communities in the environment and inside our bodies

    By Aliyah Kovner

    Microbiomes play essential roles in the natural processes that keep the planet and our bodies healthy, so it’s not surprising that scientists’ investigations into these diverse microbial communities are leading to advances in medicine, sustainable agriculture, cheap water purification methods, and environmental cleanup technology, just to name a few. However, trying to determine which microbes contribute to an important geochemical or physiological reaction is both incredibly challenging and slow-going, because the task involves analyzing enormous datasets of genetic and metabolic information to match the compounds mediating a process to the microbes that produced them.

    But now, researchers have devised a new way to sort through the information overload.

    Writing in Nature Methods, a team led by UC San Diego describes a neural network-based approach called microbe-metabolite vectors (mmvec), which uses probabilities to identify the most likely relationship of co-occurring microbes and metabolites. The team demonstrates how mmvec can outperform traditional correlation-based approaches by applying mmvec to datasets from two well-studied microbiomes types – those found in desert soils and cystic fibrosis patients’ lungs – and gives a taste of how the approach could be used in the future by revealing relationships between microbially-produced metabolites and inflammatory bowel disease. 

    “Previous statistical tools used to estimate microbe-metabolite correlations performed comparably to random chance,” said Marc Van Goethem, a postdoctoral researcher who is one of three study authors from Berkeley Lab. “Their poor performance led to the detection of spurious relationships and missed many true relationships. Mmvec is a powerful new tool that accurately links metabolite and microbial abundances to solve this problem. There could be wide-ranging applications from clinical trials to environmental engineering. Ultimately, mmvec will allow us to begin moving away from simple pattern recognition towards unravelling mechanisms.”

    When Solids and Liquids Meet: In Nanoscale Detail
    Infrared technique at Berkeley Lab’s Advanced Light Source probes active chemistry at the solid-liquid interface

    By Glenn Roberts Jr.

    How a liquid interacts with the surface of a solid is important in batteries and fuel cells, chemical production, corrosion phenomena, and many biological processes.

    To better understand this solid-liquid interface, researchers at Berkeley Lab developed a platform to explore these interactions under real conditions (“in situ”) at the nanoscale using a technique that combines infrared light with an atomic force microscopy (AFM) probe. The results were published in the journal Nano Letters.

    The team explored the interaction of graphene with several liquids, including water and a common battery electrolyte fluid. Graphene is an atomically thin form of carbon. Its single-layer atomic structure gives the material some unique properties, including incredible mechanical strength and high electrical conductivity.

    Researchers used a beam of infrared light produced at Berkeley Lab’s Advanced Light Source and they focused it at the tip of an AFM probe that scanned across a section of graphene in contact with the liquids. The infrared technique provides a nondestructive way to explore the active nanoscale chemistry of the solid-liquid interface.

    By measuring the infrared light scattered from the probe’s tip, researchers collected details about the chemical compounds and the concentration of charged particles along the solid-liquid interface. The same technique, which revealed hidden features at this interface that were not seen using conventional methods, can be used to explore a range of materials and liquids.

    Researchers from the Lab’s Materials Sciences Division, Molecular Foundry, and Energy Storage and Distributed Resources Division participated in the study. The Molecular Foundry and Advanced Light Source are DOE Office of Science user facilities.

    More info:

    Infrared Nanospectroscopy at Graphene–Liquid Interfaces

    Underwater Telecom Cables Make Superb Seismic Network
    Experiment shows undersea fiber optic cable can act as earthquake detectors

    Adapted from a news release by UC Berkeley:

    Fiber-optic cables that constitute a global undersea telecommunications network could one day help scientists study offshore earthquakes and the geologic structures hidden deep beneath the ocean surface. In a recent paper in the journal Science, researchers from UC Berkeley, Lawrence Berkeley National Laboratory (Berkeley Lab), Monterey Bay Aquarium Research Institute (MBARI), and Rice University describe an experiment that turned 20 kilometers of undersea fiber-optic cable into the equivalent of 10,000 seismic stations along the ocean floor. During their four-day experiment in Monterey Bay, they recorded a 3.5 magnitude quake and seismic scattering from underwater fault zones. Their technique, which they had previously tested with fiber-optic cables on land, could provide much-needed data on quakes that occur under the sea, where few seismic stations exist, leaving 70% of Earth’s surface without earthquake detectors.

    “This is really a study on the frontier of seismology, the first time anyone has used offshore fiber-optic cables for looking at these types of oceanographic signals or for imaging fault structures,” said Jonathan Ajo-Franklin, a geophysics professor at Rice University in Houston and a faculty scientist at Berkeley Lab. “One of the blank spots in the seismographic network worldwide is in the oceans.”

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    New composite material revs up pursuit of advanced electric vehicles

    New composite material revs up pursuit of advanced electric vehicles

    Scientists at Oak Ridge National Laboratory used new techniques to create a composite that increases the electrical current capacity of copper wires, providing a new material that can be scaled for use in ultra-efficient, power-dense electric vehicle traction motors.

    Not Your Average Refinery

    Not Your Average Refinery

    PNNL researchers outline how to convert stranded biomass to sustainable fuel using electrochemical reduction reactions in mini-refineries powered by renewable energy.

    Supercooled Water Is a Stable Liquid, Scientists Show for the First Time

    Supercooled Water Is a Stable Liquid, Scientists Show for the First Time

    First-ever measurements provide evidence that supercooled liquid water exists in two distinct structures that co-exist and vary in proportion dependent on temperature

    New Calculation Refines Comparison of Matter with Antimatter

    New Calculation Refines Comparison of Matter with Antimatter

    An international collaboration of theoretical physicists has published a new calculation relevant to the search for an explanation of the predominance of matter over antimatter in our universe. The new calculation gives a more accurate prediction for the likelihood with which kaons decay into a pair of electrically charged pions vs. a pair of neutral pions.

    Digging into soil organic matter

    Digging into soil organic matter

    A new study found patterns in how soil organic matter forms across a wide range of climate types. Understanding how soils break down or preserve organic matter is important because organic matter plays a central role in the kind of services soils can provide, such as whether they make good agricultural soils or if they can sequester carbon to slow climate change.

    Quirky Response to Magnetism Presents Quantum Physics Mystery

    Quirky Response to Magnetism Presents Quantum Physics Mystery

    The search is on to discover new states of matter, and possibly new ways of encoding, manipulating, and transporting information. One goal is to harness materials' quantum properties for communications that go beyond what's possible with conventional electronics. Topological insulators--materials that act mostly as insulators but carry electric current across their surface--provide some tantalizing possibilities. Scientists at Brookhaven Lab describe one such material that should be right just right for making qubits. But this material doesn't obey the rules.

    High-precision electrochemistry: The new gold standard in fuel cell catalyst development

    High-precision electrochemistry: The new gold standard in fuel cell catalyst development

    As part of an international collaboration, scientists at Argonne National Laboratory have made a pivotal discovery that could extend the lifetime of fuel cells that power electric vehicles by eliminating the dissolution of platinum catalysts.

    Scientists probe the chemistry of a single battery electrode particle both inside and out

    Scientists probe the chemistry of a single battery electrode particle both inside and out

    Cracks and chemical reactions on a battery particle's surface can sap its ability to store and release energy. Scientists probed a single charged particle the size of a red blood cell to see how interior and surface damage influence each other.

    Quantum light squeezes the noise out of microscopy signals

    Quantum light squeezes the noise out of microscopy signals

    Researchers at Oak Ridge National Laboratory used quantum optics to advance state-of-the-art microscopy and illuminate a path to detecting material properties with greater sensitivity than is possible with traditional tools.

    Exploring Oxidative Pathways in Nuclear Fuel

    Exploring Oxidative Pathways in Nuclear Fuel

    An international team used PNNL microscopy to answer questions about how uranium dioxide--used in nuclear power plants--might behave in long-term storage.


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    DOE Funding Boosts Artificial Intelligence Research at Jefferson Lab

    DOE Funding Boosts Artificial Intelligence Research at Jefferson Lab

    Two physicists at DOE's Jefferson Lab have secured $2.16 million in funding for projects that harness the power of data analytics to make the work of studying the universe down to its smallest subatomic parts faster and more efficient.

    Argonne National Laboratory and AT&T extend climate resiliency project nationwide

    Argonne National Laboratory and AT&T extend climate resiliency project nationwide

    Argonne and AT&T have been working together to project risks from changing climate on America's Southeastern region. Today they've announced that they're extending their analysis to cover the entire contiguous U.S.

    Key Partners Mark Launch of Electron-Ion Collider Project

    Key Partners Mark Launch of Electron-Ion Collider Project

    U.S. Department of Energy (DOE) Undersecretary for Science Paul Dabbar, leaders from DOE's Brookhaven National Laboratory (Brookhaven Lab) and Thomas Jefferson National Accelerator Facility (Jefferson Lab), and elected officials from New York State and Virginia today commemorated the start of the Electron-Ion Collider project.

    Fermilab scientist Vladimir Shiltsev elected to Academia Europaea

    Fermilab scientist Vladimir Shiltsev elected to Academia Europaea

    Widely recognized for his work in accelerator beam physics, Shiltsev is one of 361 individuals elected to Academia Europaea, which promotes a wider appreciation of the value of European scholarship and research.

    PPPL physicist Hutch Neilson receives award for decades of leadership on national and international fusion experiments

    PPPL physicist Hutch Neilson receives award for decades of leadership on national and international fusion experiments

    Hutch Neilson, a physicist at PPPL who is head of ITER Projects, has received the 2020 Institute of Electrical and Electronics Engineers' (IEEE) Nuclear & Plasma Sciences Society (NPSS) Merit Award for decades of achievements, including collaborations with fusion experiments around the world from the Wendelstein 7-X (W7-X) stellarator in Germany to the international ITER experiment in the south of France.

    Virtual internships for physics students present challenges, build community

    Virtual internships for physics students present challenges, build community

    Summer is usually the time when student interns flock to PPPL to learn about fusion and plasma physics at a national laboratory. But because of the coronavirus pandemic, this year's students participated virtually from their homes around the country.

    Argonne cuts ribbon on expanded Materials Engineering Research Facility to enhance nation's future manufacturing competitiveness

    Argonne cuts ribbon on expanded Materials Engineering Research Facility to enhance nation's future manufacturing competitiveness

    Leaders from DOE and Argonne cut the ribbon on a new era of manufacturing -- science and technology that will accelerate commercialization of complex materials and chemicals critically important to U.S. competitiveness.

    DOE provides $21 million to advance diagnostics on the flagship fusion facility at PPPL

    DOE provides $21 million to advance diagnostics on the flagship fusion facility at PPPL

    New funding will upgrade key diagnostics on the National Spherical Tokamak Experiment-Upgrade, the flagship facility at PPPL.

    Lead Lab Selected for Next-Generation Cosmic Microwave Background Experiment

    Lead Lab Selected for Next-Generation Cosmic Microwave Background Experiment

    The largest collaborative undertaking yet to explore the relic light emitted by the infant universe has taken a step forward with the U.S. DOE's selection of Berkeley Lab to lead the partnership of national labs, universities, and other institutions that are joined in the effort to carry out the DOE roles and responsibilities.

    Jonathan Jarvis wins prestigious DOE award for development of next-generation particle beam cooling and control

    Jonathan Jarvis wins prestigious DOE award for development of next-generation particle beam cooling and control

    This award, totaling $2.5 million, will fund the development of a faster particle beam cooling method as well as the implementation of machine learning advancements to optimally control the system.


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    Harvesting Energy from Light using Bio-inspired Artificial Cells

    Harvesting Energy from Light using Bio-inspired Artificial Cells

    Scientists designed and connected two different artificial cells to each other to produce molecules called ATP (adenosine triphosphate).

    Engineering Living Scaffolds for Building Materials

    Engineering Living Scaffolds for Building Materials

    Bone and mollusk shells are composite systems that combine living cells and inorganic components. This allows them to regenerate and change structure while also being very strong and durable. Borrowing from this amazing complexity, researchers have been exploring a new class of materials called engineered living materials (ELMs).

    Excavating Quantum Information Buried in Noise

    Excavating Quantum Information Buried in Noise

    Researchers developed two new methods to assess and remove error in how scientists measure quantum systems. By reducing quantum "noise" - uncertainty inherent to quantum processes - these new methods improve accuracy and precision.

    How Electrons Move in a Catastrophe

    How Electrons Move in a Catastrophe

    Lanthanum strontium manganite (LSMO) is a widely applicable material, from magnetic tunnel junctions to solid oxide fuel cells. However, when it gets thin, its behavior changes for the worse. The reason why was not known. Now, using two theoretical methods, a team determined what happens.

    When Ions and Molecules Cluster

    When Ions and Molecules Cluster

    How an ion behaves when isolated within an analytical instrument can differ from how it behaves in the environment. Now, Xue-Bin Wang at Pacific Northwest National Laboratory devised a way to bring ions and molecules together in clusters to better discover their properties and predict their behavior.

    Tune in to Tetrahedral Superstructures

    Tune in to Tetrahedral Superstructures

    Shape affects how the particles fit together and, in turn, the resulting material. For the first time, a team observed the self-assembly of nanoparticles with tetrahedral shapes.

    Tracing Interstellar Dust Back to the Solar System's Formation

    Tracing Interstellar Dust Back to the Solar System's Formation

    This study is the first to confirm dust particles pre-dating the formation of our solar system. Further study of these materials will enable a deeper understanding of the processes that formed and have since altered them.

    Investigating Materials that Can Go the Distance in Fusion Reactors

    Investigating Materials that Can Go the Distance in Fusion Reactors

    Future fusion reactors will require materials that can withstand extreme operating conditions, including being bombarded by high-energy neutrons at high temperatures. Scientists recently irradiated titanium diboride (TiB2) in the High Flux Isotope Reactor (HFIR) to better understand the effects of fusion neutrons on performance.

    Better 3-D Imaging of Tumors in the Breast with Less Radiation

    Better 3-D Imaging of Tumors in the Breast with Less Radiation

    In breast cancer screening, an imaging technique based on nuclear medicine is currently being used as a successful secondary screening tool alongside mammography to improve the accuracy of the diagnosis. Now, a team is hoping to improve this imaging technique.

    Microbes are Metabolic Specialists

    Microbes are Metabolic Specialists

    Scientists can use genetic information to measure if microbes in the environment can perform specific ecological roles. Researchers recently analyzed the genomes of over 6,000 microbial species.


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