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  • richardmitnick 3:42 pm on February 12, 2018 Permalink | Reply
    Tags: , Aleksandra Dimitrievska, , , , , LBNL, , ,   

    From LBNL- “From Belgrade to Berkeley: A Postdoctoral Researcher’s Path in Particle Physics” 

    Berkeley Logo

    Berkeley Lab

    February 12, 2018

    Berkeley Lab’s Aleksandra Dimitrievska is working on a next-gen particle detector for CERN’s Large Hadron Collider

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    Aleksandra Dimitrievska works on prototype chips for a planned upgrade at CERN’s Large Hadron Collider. (Credit: Marilyn Chung/Berkeley Lab)

    After completing her Ph.D. thesis in calculating the mass of the W boson – an elementary particle that mediates one of the universe’s fundamental forces – physics researcher Aleksandra Dimitrievska is now testing out components for a scheduled upgrade of the world’s largest particle detectors.

    Dimitrievska left the University of Belgrade in Serbia late last year to join the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) as the recipient of an Owen Chamberlain Postdoctoral Fellowship in Experimental Particle Physics & Cosmology in the Lab’s Physics Division. The fellowship will extend up to five years.

    “Before, I was working behind a computer on coding. Now, I am in a clean room making wire bonds on computer chips, so it’s a much different experience,” Dimitrievska said. “I completely feel like a physicist now.”

    The Chamberlain Fellowship was created in 2002 to honor the late Owen Chamberlain, a Berkeley Lab physicist and UC Berkeley professor who received the Nobel Prize in Physics in 1959 for his work on the team that discovered the anti-proton using the Lab’s Bevatron accelerator. He also worked on the development of the time projection chamber, a type of detector that has been widely used in particle physics experiments.

    Dimitrievska’s path toward a career in particle physics led her to CERN’s Large Hadron Collider (LHC), a particle collider with an underground tunnel measuring 17 miles in circumference that is used to accelerate protons up to nearly the speed of light and collide them in detectors to measure the ensuing subatomic fireworks.

    “I started as a summer student at CERN in 2012. After that I went back to Belgrade – my Ph.D. advisor was involved in work on the W boson mass measurement,” she said. He connected her with a CERN team led by French physicist Maarten Boonekamp.

    The W boson and Z boson, which were both discovered in CERN experiments in 1983, are carriers of the “weak force” that is responsible for the particle process triggering fusion in the sun and other stars, the presence of radiation across the universe, and the breakdown of radioactive elements via a process known as beta decay. The W boson can have a positive or negative charge while the Z boson has a neutral charge, and each of these particles has a mass that is heavier than an iron atom.

    But despite such large masses, it has been difficult to pinpoint the W boson’s mass because of the typical noisy mess of other particle processes associated with its creation in collider experiments.

    “This is a really difficult measurement,” Dimitrievska said. The W boson’s mass must be calculated based on indirect measurements – a careful dissection of the data from related particle processes including recoil, in which particles are ejected from other particles in high-energy collisions at the LHC.

    “We started from scratch, one step at a time,” she said, to find the best way to calibrate the W boson measurements. “We tried different approaches and different ideas. The most important things are the uncertainties,” she said, and in finding ways to reduce the uncertainties in the analyses of data from experiments. “It takes a lot of time to really calibrate each source.”

    The team conducting the analysis found that a useful way to measure the W boson is to use measurements of the Z boson for calibration. “You are calibrating the recoil on the Z boson events, and then you extrapolate (measurements) for the W boson,” she said, based in part on the uncertainties in the Z boson measurements.

    The team worked with data from millions of particle collisions that produced candidate W bosons in the 2011 run of the LHC. Ongoing studies will apply the same techniques developed for the 2011 analysis for larger sets of data accumulated at the LHC in 2012, 2015, and 2016. The latest sets of LHC data, because they can involve larger numbers of colliding protons, are even more challenging to pick through in isolating individual particle properties.

    Such painstaking analyses can ultimately test whether the standard model of particle physics, developed through decades of experiments and theories, holds up to increasingly precise measurements.

    In this case, Dimitrievska’s team found good agreement in their measurements with the standard model. “There is no hint of physics beyond the standard model, but this result is important because we have something new to put in front of the theoretical ideas and see where there is place for improvement in the measurements,” she said.

    She added, “The calibration and methods we used will also be used for other measurements at higher energies.”

    The latest measurement, published Feb. 6 in the European Physical Journal C, determined the mass of the W boson to be about 80,370 mega (million) electronvolts, or MeV, with a statistical uncertainty of plus or minus 7 MeV, which is consistent with an average from previous measurements of about 80,385 MeV, with uncertainty at plus or minus 15 MeV. An electronvolt is a unit of energy that is a common measure of mass for subatomic particles.

    Dimitrievska successfully defended her Ph.D. thesis on the W boson mass measurement at the University of Belgrade in December.

    Her current work at Berkeley Lab is focused on testing 2-centimeter-by-1-centimeter prototype computer chips for the planned High-Luminosity LHC at CERN that will produce a higher volume of particle collisions and data.

    “Because we will have more data, the readout system has to be faster,” she said. “Basically, we have to improve everything.”

    2
    Aleksandra Dimitrievska holds a prototype chip for planned detector upgrades at CERN. (Credit: Marilyn Chung/Berkeley Lab)

    The final version of the chips that she is testing will be installed in the inner part of the ATLAS and CMS detectors at CERN and must be radiation-hardened to withstand the constant drumming of high-energy particles. She has used 3-D printers at UC Berkeley to fabricate prototype components related to the chip assemblies she works with.

    “For now, I am just testing if the chips work – how they are collecting data,” she said. A next step for her research group is to set up a particle beam to monitor how the chips perform under simulated experimental conditions.

    As an active member of Berkeley Lab’s ATLAS collaboration team, Dimitrievska also participates remotely in several meetings per week hosted at CERN, and she said she looks forward to the opportunity to work on the LHC upgrade project as it moves forward from its R&D stages to actual fabrication, assembly, and installation.

    “I think this is the really nice part about this work,” she said. “You can see the development of something that you can actually use later. You can participate first in the development of the detector, and then do the analysis and see how it really works.”

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  • richardmitnick 12:37 pm on February 12, 2018 Permalink | Reply
    Tags: , , , , , LBNL,   

    From LBNL: “Solving the Dark Energy Mystery: A New Assignment for a 45-Year-Old Telescope” 

    Berkeley Logo

    Berkeley Lab

    FNAL II photo

    FNAL Art Image
    FNAL Art Image by Angela Gonzales

    Fermilab is an enduring source of strength for the US contribution to scientific research world wide.

    February 12, 2018
    Glenn Roberts Jr.
    geroberts@lbl.gov
    (510) 486-5582

    1
    A view inside the dome at the Mayall Telescope near Tucson, Arizona. The 2-meter corrector barrel atop the telescope will be removed and replaced with a new corrector barrel for the Dark Energy Spectroscopic Instrument (DESI). DESI’s installation will begin soon. (Credit: P. Marenfeld and NOAO/AURA/NSF)

    NOAO/Mayall 4 m telescope at Kitt Peak, Arizona, USA, Altitude 2,120 m (6,960 ft)

    LBNL/DESI Dark Energy Spectroscopic Instrument for the Nicholas U. Mayall 4-meter telescope at Kitt Peak National Observatory near Tucson, Ariz, USA

    Forty-five years ago this month, a telescope tucked inside a 14-story, 500-ton dome atop a mile-high peak in Arizona took in the night sky for the first time and recorded its observations in glass photographic plates.

    Fermilab scientists are managing key elements of the construction, including the heavy mechanical components (including the precise alignment of the structures that hold the lenses), the assembly of the charge-coupled devices, or CCDs, that capture light, and the online databases used for data acquisition. Fermilab is also providing software that maps between the locations of light sources in the sky and the positions of each of the 5,000 robotic fiber positioners that make up the DESI plane, drawing on more than 25 years of experience with the Sloan Digital Sky Survey and the Dark Energy Survey.

    For more information on Fermilab’s role in DESI, please contact Andre Salles at media@fnal.gov or 630-840-3351.

    Today, the dome closes on the previous science chapters of the 4-meter Nicholas U. Mayall Telescope so that it can prepare for its new role in creating the largest 3-D map of the universe. This map could help to solve the mystery of dark energy, which is driving the accelerating expansion of the universe.

    The temporary closure sets in motion the largest overhaul in the telescope’s history and sets the stage for the installation of the Dark Energy Spectroscopic Instrument (DESI), which will begin a five-year observing run next year at the National Science Foundation’s Kitt Peak National Observatory (KPNO) – part of the National Optical Astronomy Observatory (NOAO).

    NOAO Kitt Peak National Observatory on the Tohono O’odham reservation outside Tucson, AZ, USA

    “This day marks an enormous milestone for us,” said DESI Director Michael Levi of the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab), which is leading the project’s international collaboration. “Now we remove the old equipment and start the yearlong process of putting the new stuff on.” More than 465 researchers from about 71 institutions are participating in the DESI collaboration.


    The Life of a Lens: This video chronicles the many steps it took to create a single lens for the Dark Energy Spectroscopic Instrument. (Credit: Google Earth, DESI Collaboration)

    The entire top end of the telescope, which weighs as much as a school bus and houses the telescope’s secondary mirror and a large digital camera, will be removed and replaced with DESI instruments. A large crane will lift the telescope’s top end through the observing slit in its dome.

    Besides providing new insights about the universe’s expansion and large-scale structure, DESI will also help to set limits on theories related to gravity and the formative stages of the universe, and could even provide new mass measurements for a variety of elusive yet abundant subatomic particles called neutrinos.

    “One of the primary ways that we learn about the unseen universe is by its subtle effects on the clustering of galaxies,” said DESI Collaboration Co-Spokesperson Daniel Eisenstein of Harvard University. “The new maps from DESI will provide an exquisite new level of sensitivity in our study of cosmology.”

    The Mayall Telescope has played an important role in many astronomical discoveries, including measurements supporting the discovery of dark energy and establishing the role of dark matter in the universe from measurements of galaxy rotation. Its observations have also been used in determining the scale and structure of the universe. Dark matter and dark energy together are believed to make up about 95 percent of all of the universe’s mass and energy.

    It was one of the world’s largest optical telescopes at the time it was built, and because of its sturdy construction it is perfectly suited to carry the new 9-ton instrument.

    “We started this project by surveying large telescopes to find one that had a suitable mirror and wouldn’t collapse under the weight of such a massive instrument,” said Berkeley Lab’s David Schlegel, a DESI project scientist.

    Arjun Dey, the NOAO project scientist for DESI, explained, “The Mayall was precociously engineered like a battleship and designed with a wide field of view.”

    The expansion of the telescope’s field-of-view will allow DESI to map out about one-third of the sky.

    Brenna Flaugher, a DESI project scientist who leads the Astrophysics Department at Fermi National Accelerator Laboratory, said DESI will transform the speed of science at the Mayall Telescope.

    “The telescope was designed to carry a person at the top who aimed and steered it, but with DESI it’s all automated,” she said. “Instead of one at a time we can measure the velocities of 5,000 galaxies at a time – we will measure more than 30 million of them in our five-year survey.”

    3
    The first of 10 wedge-shaped petals for the DESI project is fully stocked with 500 slender robotic positioners. These positioners will each swivel independently to gather light from a preprogrammed sequence of space objects, including galaxies and quasars. The petals will fit snugly together to form DESI’s focal plane, which will be composed of about 600,000 individual parts. (Credit: DESI Collaboration)

    DESI will use an array of 5,000 swiveling robots, each carefully choreographed to point a fiber-optic cable at a preprogrammed sequence of deep-space objects, including millions of galaxies and quasars, which are galaxies that harbor massive, actively feeding black holes.

    The fiber-optic cables will carry the light from these objects to 10 spectrographs, which are tools that will measure the properties of this light and help to pinpoint the objects’ distance and the rate at which they are moving away from us. DESI’s observations will provide a deep look into the early universe, up to about 11 billion years ago.

    The cylindrical, fiber-toting robots, which will be embedded in a rounded metal unit called a focal plane, will reposition to capture a new exposure of the sky roughly every 20 minutes. The focal plane, which is now being assembled at Berkeley Lab, is expected to be completed and delivered to Kitt Peak this year.

    DESI will scan one-third of the sky and will capture about 10 times more data than a predecessor survey, the Baryon Oscillation Spectroscopic Survey (BOSS). That project relied on a manually rotated sequence of metal plates – with fibers plugged by hand into pre-drilled holes – to target objects.

    All of DESI’s six lenses, each about a meter in diameter, are complete. They will be carefully stacked and aligned in a steel support structure and will ultimately ride with the focal plane atop the telescope.

    Each of these lenses took shape from large blocks of glass. They have criss-crossed the globe to receive various treatments, including grinding, polishing, and coatings. It took about 3.5 years to produce each of the lenses, which now reside at University College London in the U.K. and will be shipped to the DESI site this spring.

    The Mayall Telescope has most recently been enlisted in a DESI-supporting sky survey known as the Mayall z-Band Legacy Survey (MzLS), which is one of four sky surveys that DESI will use to preselect its targeted sky objects. That survey wrapped up just days before the Mayall’s temporary closure, while the others are ongoing.

    Data from these surveys are analyzed at Berkeley Lab’s National Energy Research Scientific Computing Center (NERSC), a DOE Office of Science User Facility. Data from these surveys have been released to the public at legacysurvey.org.

    “We can see about a billion galaxies in the survey images, which is quite a bit of fun to explore,” Schlegel said. “The DESI instrument will precisely measure millions of those galaxies to see the effects of dark energy.”

    Levi noted that there is already a lot of computing work underway at NERSC to prepare for the stream of data that will pour out of DESI once it starts up.

    “This project is all about generating huge quantities of data,” Levi said. “The data will go directly from the telescope to NERSC for processing. We will create hundreds of universes in these computers and see which universe best fits our data.”

    Installation of DESI’s components is expected to begin soon and to wrap up in April 2019, with first science observations planned in September 2019.

    “Installing DESI on the Mayall will put the telescope at the heart of the next decade of discoveries in cosmology,” said Risa Wechsler, DESI Collaboration Co-Spokesperson and associate professor of physics and astrophysics at SLAC National Accelerator Laboratory and Stanford University. “The amazing 3-D map it will measure may solve some of the biggest outstanding questions in cosmology, or surprise us and bring up new ones.”

    More information:
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  • richardmitnick 1:19 pm on January 30, 2018 Permalink | Reply
    Tags: , , Cell differentiation, , , LBNL, Polycomb Repressive Complex 2 (PRC2)   

    From LBNL: “Silencing Is Golden: Scientists Image Molecules Vital for Gene Regulation” 

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    Berkeley Lab

    January 29, 2018
    Dan Krotz
    DAKrotz@lbl.gov
    (510) 486-4019

    1
    Structure of the human Polycomb Repressive Complex 2 (PRC2) bound to cofactors obtained by cryo-electron microscopy. Both cofactors mimic the histone protein tail to stabilize and stimulate the enzymatic activity of PRC2. (Credit: Vignesh Kasinath)

    All the trillions of cells in our body share the same genetic information and are derived from a single, fertilized egg. When this initial cell multiplies during fetal development, its daughter cells become more and more specialized. This process, called cell differentiation, gives rise to all the various cell types, such as nerve, muscle, or blood cells, which are diverse in shape and function and make up tissues and organs. How can the same genetic blueprint lead to such diversity? The answer lies in the way that genes are switched on or off during the course of development.

    Scientists at Lawrence Berkeley National Laboratory (Berkeley Lab) have been studying the molecules that act at the genetic level to give rise to different types of cells. Some of these molecules are a complex of proteins called the Polycomb Repressive Complex 2 (PRC2) that is involved in “silencing” genes so that they are not “read” by the cellular machinery that decodes genetic information, effectively keeping the genetic information in the “off” state.

    In two new studies, a team of researchers led by Eva Nogales, senior faculty scientist in the Molecular Biophysics and Integrated Bioimaging (MBIB) Division, has gained insight into the structure of PRC2 and the ways in which it is regulated to affect gene silencing. Their work was reported on January 18 in the journal Science and on January 29 in Nature Structural and Molecular Biology by Eva Nogales and postdoctoral researchers Vignesh Kasinath and Simon Poepsel.

    Both publications provide a structural framework to understand PRC2 function, and in the case of the latter, the structures are the first to illustrate how a molecule of this type engages with its substrate. The structural descriptions of human PRC2 with its natural partners in the cell lend important insight into the mechanism by which the PRC2 complex regulates gene expression. This information could provide new possibilities for the development of therapies for cancer.

    PRC2 is a gene regulator that is vital for normal development. Genomic DNA is packaged into nucleosomes, which are formed by histone proteins that have DNA wrapped around them. Histone proteins have long polypeptide tails that can be modified by the addition and removal of small chemical groups. These modifications influence the interaction of nucleosomes with each other and other protein complexes in the nucleus. The function of PRC2 in the cell is to make a particular chemical change in one of the histones. The genes in the regions of the genome that have been modified by PRC2 are switched off, or become silenced.

    2
    This montage of the full PRC2 with two nucleosomes is based on the superposition of the cryo-EM maps of PRC2 with and without the nucleosomes to show the consistency of the observed nucleosome binding configuration with the full PRC2 structure. (Credit: Simon Poepsel)

    “Not surprisingly, elaborate mechanisms have evolved to ensure that PRC2 marks the correct regions for silencing at the right time,” said Nogales, who is also a Howard Hughes Medical Investigator and professor of Biochemistry, Biophysics and Structural Biology at the University of California, Berkeley. Failure of this regulation not only impairs the process of development, but also contributes to the reversal of cell differentiation and the uncontrolled cell growth that are the hallmarks of cancer. “Therefore,” Nogales continued, “gaining insight into how PRC2 function is adjusted both in space and time is crucial to understanding cell development.”

    Nogales and her team use structural biology to elucidate how biomolecules, particularly proteins and nucleic acids (DNA, RNA), are organized and combine to form functional biological assemblies. Obtaining detailed insights into their three-dimensional shape will not only help to understand how they function but also how this function is regulated in the cell. These two studies rely on cryo-electron microscopy for imaging the biomolecules, a technique that can see large biomolecules on a very small scale and in multiple conformations. Kasinath and Poepsel, have now solved the structure of PRC2, which provides a framework to understand how this complex is regulated to modify histone proteins.

    The first study, published January 18 in Science by Kasinath, Poepsel, Nogales, and coworkers, visualized the architecture of the complete PRC2 in atomic detail. First author Vignesh Kasinath said, “It took three years of work to obtain this high-resolution structure of all the parts, or subunits, that make up a functional PRC2, as well as visualize how additional protein subunits, called cofactors, may help regulate its activity. Remarkably, both cofactors mimic the histone protein tail in their binding to PRC2 suggesting that cofactors and histone tails together work hand-in-hand to regulate PRC2 function. This structural work holds great promise for new drug development to fight PRC2 dysfunction in cancer.”

    This work is complemented by a second study that presents snapshots of PRC2 binding to the histone proteins that it modifies as a signal for gene silencing. The structures, which have been published in Nature Structural and Molecular Biology on January 29 by Poepsel, Kasinath and Nogales this week, illustrate beautifully the action of this sophisticated complex. “PRC2 can simultaneously engage two nucleosomes,” said Poepsel, first author of this study. “Our cryo-EM images help us understand how the complex can recognize the presence of a histone modification in one nucleosome and place the same tag onto a neighboring nucleosome.” This cascade of activity enables PRC2 to spread this modification over the entire neighboring gene loci, thereby marking it for silencing. Nogales added, “The visualization of such interactions is notoriously hard. We have made an important step forward in our general understanding of how gene regulators can bind to and recognize nucleosomes.”

    PRC2 is essential to gene regulation and expression in all multicellular organisms. The findings from both studies open up tremendous possibilities for combatting cancer while simultaneously expanding our knowledge of gene regulation at a molecular level. “Because PRC2 is deregulated in cancers, it makes a good target for potential therapeutics,” said Nogales. The fundamental understanding of PRC2 arising from these studies will have broad implications in both plant and animal biology.

    This work was funded by the Howard Hughes Medical Institute and Eli Lilly. This research used cryo-electron microscopy (cryo-EM) and made use of the unique resources of the Bay Area Cryo-EM Facility. Image analysis relied on heavy computational work that was carried out at Berkeley Lab’s National Energy Research Scientific Computing Center (NERSC), a DOE Office of Science User Facility.

    NERSC Cray XC40 Cori II supercomputer

    LBL NERSC Cray XC30 Edison supercomputer


    The Genepool system is a cluster dedicated to the DOE Joint Genome Institute’s computing needs. Denovo is a smaller test system for Genepool that is primarily used by NERSC staff to test new system configurations and software.

    NERSC PDSF

    PDSF is a networked distributed computing cluster designed primarily to meet the detector simulation and data analysis requirements of physics, astrophysics and nuclear science collaborations.

    Vignesh Kasinath was supported by a postdoctoral fellowship from Helen Hay Whitney and Simon Poepsel was supported by the Alexander von Humboldt foundation (Germany) as a Feodor-Lynen postdoctoral fellow.

    See the full article here .

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  • richardmitnick 12:54 pm on January 30, 2018 Permalink | Reply
    Tags: , , , , LBNL, , , , ,   

    From LBNL: “Applying Machine Learning to the Universe’s Mysteries” 

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    Berkeley Lab

    Glenn Roberts Jr.
    geroberts@lbl.gov
    (510) 486-5582

    1
    The colored lines represent calculated particle tracks from particle collisions occurring within Brookhaven National Laboratory’s STAR detector at the Relativistic Heavy Ion Collider, and an illustration of a digital brain. The yellow-red glow at center shows a hydrodynamic simulation of quark-gluon plasma created in particle collisions. (Credit: Berkeley Lab)

    BNL/RHIC Star Detector

    Computers can beat chess champions, simulate star explosions, and forecast global climate. We are even teaching them to be infallible problem-solvers and fast learners.

    And now, physicists at the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) and their collaborators have demonstrated that computers are ready to tackle the universe’s greatest mysteries. The team fed thousands of images from simulated high-energy particle collisions to train computer networks to identify important features.

    The researchers programmed powerful arrays known as neural networks to serve as a sort of hivelike digital brain in analyzing and interpreting the images of the simulated particle debris left over from the collisions. During this test run the researchers found that the neural networks had up to a 95 percent success rate in recognizing important features in a sampling of about 18,000 images.

    The study was published Jan. 15 in the journal Nature Communications.

    The researchers programmed powerful arrays known as neural networks to serve as a sort of hivelike digital brain in analyzing and interpreting the images of the simulated particle debris left over from the collisions. During this test run the researchers found that the neural networks had up to a 95 percent success rate in recognizing important features in a sampling of about 18,000 images.

    The next step will be to apply the same machine learning process to actual experimental data.

    Powerful machine learning algorithms allow these networks to improve in their analysis as they process more images. The underlying technology is used in facial recognition and other types of image-based object recognition applications.

    The images used in this study – relevant to particle-collider nuclear physics experiments at Brookhaven National Laboratory’s Relativistic Heavy Ion Collider and CERN’s Large Hadron Collider – recreate the conditions of a subatomic particle “soup,” which is a superhot fluid state known as the quark-gluon plasma believed to exist just millionths of a second after the birth of the universe. Berkeley Lab physicists participate in experiments at both of these sites.

    BNL RHIC Campus

    BNL/RHIC

    LHC

    CERN/LHC Map

    CERN LHC Tunnel

    CERN LHC particles

    “We are trying to learn about the most important properties of the quark-gluon plasma,” said Xin-Nian Wang, a nuclear physicist in the Nuclear Science Division at Berkeley Lab who is a member of the team. Some of these properties are so short-lived and occur at such tiny scales that they remain shrouded in mystery.

    In experiments, nuclear physicists use particle colliders to smash together heavy nuclei, like gold or lead atoms that are stripped of electrons. These collisions are believed to liberate particles inside the atoms’ nuclei, forming a fleeting, subatomic-scale fireball that breaks down even protons and neutrons into a free-floating form of their typically bound-up building blocks: quarks and gluons.

    3
    The diagram at left, which maps out particle distribution in a simulated high-energy heavy-ion collision, includes details on particle momentum and angles. Thousands of these images were used to train and test a neural network to identify important features in the images. At right, a neural network used the collection of images to created this “importance map” – the lighter colors represent areas that are considered more relevant to identify equation of state for the quark-gluon matter created in particle collisions. (Credit: Berkeley Lab)

    Researchers hope that by learning the precise conditions under which this quark-gluon plasma forms, such as how much energy is packed in, and its temperature and pressure as it transitions into a fluid state, they will gain new insights about its component particles of matter and their properties, and about the universe’s formative stages.

    But exacting measurements of these properties – the so-called “equation of state” involved as matter changes from one phase to another in these collisions – have proven challenging. The initial conditions in the experiments can influence the outcome, so it’s challenging to extract equation-of-state measurements that are independent of these conditions.

    “In the nuclear physics community, the holy grail is to see phase transitions in these high-energy interactions, and then determine the equation of state from the experimental data,” Wang said. “This is the most important property of the quark-gluon plasma we have yet to learn from experiments.”

    Researchers also seek insight about the fundamental forces that govern the interactions between quarks and gluons, what physicists refer to as quantum chromodynamics.

    Long-Gang Pang, the lead author of the latest study and a Berkeley Lab-affiliated postdoctoral researcher at UC Berkeley, said that in 2016, while he was a postdoctoral fellow at the Frankfurt Institute for Advanced Studies, he became interested in the potential for artificial intelligence (AI) to help solve challenging science problems.

    He saw that one form of AI, known as a deep convolutional neural network – with architecture inspired by the image-handling processes in animal brains – appeared to be a good fit for analyzing science-related images.

    “These networks can recognize patterns and evaluate board positions and selected movements in the game of Go,” Pang said. “We thought, ‘If we have some visual scientific data, maybe we can get an abstract concept or valuable physical information from this.’”

    Wang added, “With this type of machine learning, we are trying to identify a certain pattern or correlation of patterns that is a unique signature of the equation of state.” So after training, the network can pinpoint on its own the portions of and correlations in an image, if any exist, that are most relevant to the problem scientists are trying to solve.

    Accumulation of data needed for the analysis can be very computationally intensive, Pang said, and in some cases it took about a full day of computing time to create just one image. When researchers employed an array of GPUs that work in parallel – GPUs are graphics processing units that were first created to enhance video game effects and have since exploded into a variety of uses – they cut that time down to about 20 minutes per image.

    They used computing resources at Berkeley Lab’s National Energy Research Scientific Computing Center (NERSC) in their study, with most of the computing work focused at GPU clusters at GSI in Germany and Central China Normal University in China.

    NERSC Cray XC40 Cori II supercomputer

    LBL NERSC Cray XC30 Edison supercomputer


    The Genepool system is a cluster dedicated to the DOE Joint Genome Institute’s computing needs. Denovo is a smaller test system for Genepool that is primarily used by NERSC staff to test new system configurations and software.

    NERSC PDSF


    PDSF is a networked distributed computing cluster designed primarily to meet the detector simulation and data analysis requirements of physics, astrophysics and nuclear science collaborations.

    A benefit of using sophisticated neural networks, the researchers noted, is that they can identify features that weren’t even sought in the initial experiment, like finding a needle in a haystack when you weren’t even looking for it. And they can extract useful details even from fuzzy images.

    “Even if you have low resolution, you can still get some important information,” Pang said.

    Discussions are already underway to apply the machine learning tools to data from actual heavy-ion collision experiments, and the simulated results should be helpful in training neural networks to interpret the real data.

    “There will be many applications for this in high-energy particle physics,” Wang said, beyond particle-collider experiments.

    Also participating in the study were Kai Zhou, Nan Su, Hannah Petersen, and Horst Stocker from the following institutions: Frankfurt Institute for Advanced Studies, Goethe University, GSI Helmholtzzentrum für Schwerionenforschung (GSI), and Central China Normal University. The work was supported by the U.S Department of Energy’s Office of Science, the National Science Foundation, the Helmholtz Association, GSI, SAMSON AG, Goethe University, the National Natural Science Foundation of China, the Major State Basic Research Development Program in China, and the Helmholtz International Center for the Facility for Antiproton and Ion Research.

    NERSC is DOE Office of Science user facility.

    See the full article here .

    Please help promote STEM in your local schools.

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  • richardmitnick 9:06 am on January 23, 2018 Permalink | Reply
    Tags: , , LBNL, , ,   

    From LBNL- “It All Starts With a ‘Spark’: Berkeley Lab Delivers Injector That Will Drive X-Ray Laser Upgrade” 

    Berkeley Logo

    Berkeley Lab

    January 22, 2018
    Glenn Roberts, Jr.
    geroberts@lbl.gov
    (510) 486-5582

    Unique device will create bunches of electrons to stimulate million-per-second X-ray pulses.

    1
    Joe Wallig, left, a mechanical engineering associate, and Brian Reynolds, a mechanical technician, work on the final assembly of the LCLS-II injector gun in a specially designed clean room at Berkeley Lab in August. (Credit: Marilyn Chung/Berkeley Lab)

    Every powerful X-ray pulse produced for experiments at a next-generation laser project, now under construction, will start with a “spark” – a burst of electrons emitted when a pulse of ultraviolet light strikes a 1-millimeter-wide spot on a specially coated surface.

    A team at the U.S. Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) designed and built a unique version of a device, called an injector gun, that can produce a steady stream of these electron bunches that will ultimately be used to produce brilliant X-ray laser pulses at a rapid-fire rate of up to 1 million per second.

    The injector arrived Jan. 22 at SLAC National Accelerator Laboratory (SLAC) in Menlo Park, California, the site of the Linac Coherent Light Source II (LCLS-II), an X-ray free-electron laser project.


    Stanford/SLAC Campus


    SLAC/LCLS II projected view

    2
    An electron beam travels through a niobium cavity, a key component of a future LCLS-II X-ray laser, in this illustration. Kept at minus 456 degrees Fahrenheit, these cavities will power a highly energetic electron beam that will create up to 1 million X-ray flashes per second. (Credit: SLAC National Accelerator Laboratory)

    Getting up to speed

    The injector will be one of the first operating pieces of the new X-ray laser. Initial testing of the injector will begin shortly after its installation.

    The injector will feed electron bunches into a superconducting particle accelerator that must be supercooled to extremely low temperatures to conduct electricity with nearly zero loss. The accelerated electron bunches will then be used to produce X-ray laser pulses.

    Scientists will employ the X-ray pulses to explore the interaction of light and matter in new ways, producing sequences of snapshots that can create atomic- and molecular-scale “movies,” for example, to illuminate chemical changes, magnetic effects, and other phenomena that occur in just quadrillionths (million-billionths) of a second.

    This new laser will complement experiments at SLAC’s existing X-ray laser, which launched in 2009 and fires up to 120 X-ray pulses per second. That laser will also be upgraded as a part of the LCLS-II project.

    SLAC/LCLS

    3
    A rendering of the completed injector gun and related beam line equipment. (Credit: Greg Stewart/SLAC National Accelerator Laboratory)

    The injector gun project teamed scientists from Berkeley Lab’s Accelerator Technology and Applied Physics Division with engineers and technologists from the Engineering Division in what Engineering Division Director Henrik von der Lippe described as “yet another success story from our longstanding partnership – (this was) a very challenging device to design and build.”

    “The completion of the LCLS-II injector project is the culmination of more than three years of effort,” added Steve Virostek, a Berkeley Lab senior engineer who led the gun construction. The Berkeley Lab team included mechanical engineers, physicists, radio-frequency engineers, mechanical designers, fabrication shop personnel, and assembly technicians.

    “Virtually everyone in the Lab’s main fabrication shop made vital contributions,” he added, in the areas of machining, welding, brazing, ultrahigh-vacuum cleaning, and precision measurements.

    The injector source is one of Berkeley Lab’s major contributions to the LCLS-II project, and builds upon its expertise in similar electron gun designs, including the completion of a prototype gun. Almost a decade ago, Berkeley Lab researchers began building a prototype for the injector system in a beam-testing area at the Lab’s Advanced Light Source.

    LBNL/ALS

    That successful effort, dubbed APEX (Advanced Photoinjector Experiment), produced a working injector that has since been repurposed for experiments that use its electron beam to study ultrafast processes at the atomic scale.

    7
    The APEX electron gun and test beamline at the ALS Beam Test Facility. APEX team members include (from left) Daniele Filippetto, Fernando Sannibale, and John Staples of the Accelerator and Fusion Research Division and Russell Wells of the Engineering Division. (Photo by Roy Kaltschmidt, Lawrence Berkeley National Laboratory)

    4
    Daniele Filippetto, a Berkeley Lab scientist, works on the High-Repetition-rate Electron Scattering apparatus (HiRES), which will function like an ultrafast electron camera. HiRES is a new capability that builds on the Advanced Photo-injector Experiment (APEX), a prototype electron source for advanced X-ray lasers. (Roy Kaltschmidt/Berkeley Lab)

    Fernando Sannibale, Head of Accelerator Physics at the ALS, led the development of the prototype injector gun.

    5
    Krista Williams, a mechanical technician, works on the final assembly of LCLS-II injector components on Jan. 11. (Credit: Marilyn Chung/Berkeley Lab)

    “This is a ringing affirmation of the importance of basic technology R&D,” said Wim Leemans, director of Berkeley Lab’s Accelerator Technology and Applied Physics Division. “We knew that the users at next-generation light sources would need photon beams with exquisite characteristics, which led to highly demanding electron-beam requirements. As LCLS-II was being defined, we had an excellent team already working on a source that could meet those requirements.”

    The lessons learned with APEX inspired several design changes that are incorporated in the LCLS-II injector, such as an improved cooling system to prevent overheating and metal deformations, as well as innovative cleaning processes.

    “We’re looking forward to continued collaboration with Berkeley Lab during commissioning of the gun,” said SLAC’s John Galayda, LCLS-II project director. “Though I am sure we will learn a lot during its first operation at SLAC, Berkeley Lab’s operating experience with APEX has put LCLS-II miles ahead on its way to achieving its performance and reliability objectives.”

    Mike Dunne, LCLS director at SLAC, added, “The performance of the injector gun is a critical component that drives the overall operation of our X-ray laser facility, so we greatly look forward to seeing this system in operation at SLAC. The leap from 120 pulses per second to 1 million per second will be truly transformational for our science program.”

    How it works

    Like a battery, the injector has components called an anode and cathode. These components form a vacuum-sealed central copper chamber known as a radio-frequency accelerating cavity that sends out the electron bunches in a carefully controlled way.

    The cavity is precisely tuned to operate at very high frequencies and is ringed with an array of channels that allow it to be water-cooled, preventing overheating from the radio-frequency currents interacting with copper in the injector’s central cavity.

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    A copper cone structure inside the injector gun’s central cavity. (Credit: Marilyn Chung/Berkeley Lab)

    A copper cone structure within its central cavity is tipped with a specially coated and polished slug of molybdenum known as a photocathode. Light from an infrared laser is converted to an ultraviolet (UV) frequency laser, and this UV light is steered by mirrors onto a small spot on the cathode that is coated with cesium telluride (Cs2Te), exciting the electrons.

    These electrons are are formed into bunches and accelerated by the cavity, which will, in turn, connect to the superconducting accelerator. After this electron beam is accelerated to nearly the speed of light, it will be wiggled within a series of powerful magnetic structures called undulator segments, stimulating the electrons to emit X-ray light that is delivered to experiments.

    Precision engineering and spotless cleaning

    Besides the precision engineering that was essential for the injector, Berkeley Lab researchers also developed processes for eliminating contaminants from components through a painstaking polishing process and by blasting them with dry ice pellets.

    The final cleaning and assembly of the injector’s most critical components was performed in filtered-air clean rooms by employees wearing full-body protective clothing to further reduce contaminants – the highest-purity clean room used in the final assembly is actually housed within a larger clean room at Berkeley Lab.

    “The superconducting linear accelerator is extremely sensitive to particulates,” such as dust and other types of tiny particles, Virostek said. “Its accelerating cells can become non-usable, so we had to go through quite a few iterations of planning to clean and assemble our system with as few particulates as possible.”

    8
    Joe Wallig, a mechanical engineering associate, prepares a metal ring component of the injector gun for installation using a jet of high-purity dry ice in a clean room. (Credit: Marilyn Chung/Berkeley Lab)

    The dry ice-based cleaning processes function like sandblasting, creating tiny explosions that cleanse the surface of components by ejecting contaminants. In one form of this cleaning process, Berkeley Lab technicians enlisted a specialized nozzle to jet a very thin stream of high-purity dry ice.

    After assembly, the injector was vacuum-sealed and filled with nitrogen gas to stabilize it for shipment. The injector’s cathodes degrade over time, and the injector is equipped with a “suitcase” of cathodes, also under vacuum, that allows cathodes to be swapped out without the need to open up the device.

    “Every time you open it up you risk contamination,” Virostek explained. Once all of the cathodes in a suitcase are used up, the suitcase must be replaced with a fresh set of cathodes.

    The overall operation and tuning of the injector gun will be remotely controlled, and there is a variety of diagnostic equipment built into the injector to help ensure smooth running.

    Even before the new injector is installed, Berkeley Lab has proposed to undertake a design study for a new injector that could generate electron bunches with more than double the output energy. This would enable higher-resolution X-ray-based images for certain types of experiments.

    Berkeley Lab Contributions to LCLS-II

    John Corlett, Berkeley Lab’s senior team leader, worked closely with the LCLS-II project managers at SLAC and with Berkeley Lab managers to bring the injector project to fruition.

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    Steve Virostek, a senior engineer who led the injector gun’s construction, inspects the mounted injector prior to shipment. (Credit: Marilyn Chung/Berkeley Lab)

    “In addition to the injector source, Berkeley Lab is also responsible for the undulator segments for both of the LCLS-II X-ray free-electron laser beamlines, for the accelerator physics modeling that will optimize their performance, and for technical leadership in the low-level radio-frequency controls systems that stabilize the superconducting linear accelerator fields,” Corlett noted.

    James Symons, Berkeley Lab’s associate director for physical sciences, said, “The LCLS-II project has provided a tremendous example of how multiple laboratories can bring together their complementary strengths to benefit the broader scientific community. The capabilities of LCLS-II will lead to transformational understanding of chemical reactions, and I’m proud of our ability to contribute to this important national project.”

    LCLS-II is being built at SLAC with major technical contributions from Argonne National Laboratory, Fermilab, Jefferson Lab, Berkeley Lab, and Cornell University. Construction of LCLS-II is supported by DOE’s Office of Science.

    10
    Members of the LCLS-II injector gun team at Berkeley Lab. (Credit: Marilyn Chung/Berkeley Lab)

    View more photos of the injector gun and related equipment: here and here.

    See the full article here .

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  • richardmitnick 5:36 pm on January 10, 2018 Permalink | Reply
    Tags: , , , , , , LBNL, , , Organic chemistry, STXM-scanning transmission X-ray microscope, We’re looking at the organic ingredients that can lead to the origin of life” including the amino acids needed to form proteins,   

    From LBNL: “Ingredients for Life Revealed in Meteorites That Fell to Earth” 

    Berkeley Logo

    Berkeley Lab

    January 10, 2018
    Glenn Roberts Jr.
    geroberts@lbl.gov
    (510) 486-5582

    1
    A blue crystal recovered from a meteorite that fell near Morocco in 1998. The scale bar represents 200 microns (millionths of a meter). (Credit: Queenie Chan/The Open University, U.K.)

    Two wayward space rocks, which separately crashed to Earth in 1998 after circulating in our solar system’s asteroid belt for billions of years, share something else in common: the ingredients for life. They are the first meteorites found to contain both liquid water and a mix of complex organic compounds such as hydrocarbons and amino acids.

    A detailed study of the chemical makeup within tiny blue and purple salt crystals sampled from these meteorites, which included results from X-ray experiments at the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab), also found evidence for the pair’s past intermingling and likely parents. These include Ceres, a brown dwarf planet that is the largest object in the asteroid belt, and the asteroid Hebe, a major source of meteorites that fall on Earth.

    The study, published Jan. 10 in the journal Science Advances, provides the first comprehensive chemical exploration of organic matter and liquid water in salt crystals found in Earth-impacting meteorites. The study treads new ground in the narrative of our solar system’s early history and asteroid geology while surfacing exciting possibilities for the existence of life elsewhere in Earth’s neighborhood.

    “It’s like a fly in amber,” said David Kilcoyne, a scientist at Berkeley Lab’s Advanced Light Source (ALS), which provided X-rays that were used to scan the samples’ organic chemical components, including carbon, oxygen, and nitrogen.

    LBNL/ALS

    Kilcoyne was part of the international research team that prepared the study.

    While the rich deposits of organic remnants recovered from the meteorites don’t provide any proof of life outside of Earth, Kilcoyne said the meteorites’ encapsulation of rich chemistry is analogous to the preservation of prehistoric insects in solidified sap droplets.

    Queenie Chan, a planetary scientist and postdoctoral research associate at The Open University in the U.K. who was the study’s lead author, said, “This is really the first time we have found abundant organic matter also associated with liquid water that is really crucial to the origin of life and the origin of complex organic compounds in space.”

    She added, “We’re looking at the organic ingredients that can lead to the origin of life,” including the amino acids needed to form proteins.

    If life did exist in some form in the early solar system, the study notes that these salt crystal-containing meteorites raise the “possibility of trapping life and/or biomolecules” within their salt crystals. The crystals carried microscopic traces of water that is believed to date back to the infancy of our solar system – about 4.5 billion years ago.

    Chan said the similarity of the crystals found in the meteorites – one of which smashed into the ground near a children’s basketball game in Texas in March 1998 and the other which hit near Morocco in August 1998 – suggest that their asteroid hosts may have crossed paths and mixed materials.

    There are also structural clues of an impact – perhaps by a small asteroid fragment impacting a larger asteroid, Chan said.

    This opens up many possibilities for how organic matter may be passed from one host to another in space, and scientists may need to rethink the processes that led to the complex suite of organic compounds on these meteorites.

    “Things are not as simple as we thought they were,” Chan said.

    There are also clues, based on the organic chemistry and space observations, that the crystals may have originally been seeded by ice- or water-spewing volcanic activity on Ceres, she said.

    “Everything leads to the conclusion that the origin of life is really possible elsewhere,” Chan said. “There is a great range of organic compounds within these meteorites, including a very primitive type of organics that likely represent the early solar system’s organic composition.”

    Chan said the two meteorites that yielded the 2-millimeter-sized salt crystals were carefully preserved at NASA’s Johnson Space Center in Texas, and the tiny crystals containing organic solids and water traces measure just a fraction of the width of a human hair. Chan meticulously collected these crystals in a dust-controlled room, splitting off tiny sample fragments with metal instruments resembling dental picks.

    2
    These ALS X-ray images show organic matter (magenta, bottom) sampled from a meteorite, and carbon (top). (Credit: Berkeley Lab)

    “What makes our analysis so special is that we combined a lot of different state-of-the-art techniques to comprehensively study the organic components of these tiny salt crystals,” Chan said.

    Yoko Kebukawa, an associate professor of engineering at Yokohama National University in Japan, carried out experiments for the study at Berkeley Lab’s ALS in May 2016 with Aiko Nakato, a postdoctoral researcher at Kyoto University in Japan. Kilcoyne helped to train the researchers to use the ALS X-ray beamline and microscope.

    The beamline equipped with this X-ray microscope (a scanning transmission X-ray microscope, or STXM) is used in combination with a technique known as XANES (X-ray absorption near edge structure spectroscopy) to measure the presence of specific elements with a precision of tens of nanometers (tens of billionths of a meter).

    “We revealed that the organic matter was somewhat similar to that found in primitive meteorites, but contained more oxygen-bearing chemistry,” Kebukawa said. “Combined with other evidence, the results support the idea that the organic matter originated from a water-rich, or previously water-rich parent body – an ocean world in the early solar system, possibly Ceres.”

    Kebukawa also used the same STXM technique to study samples at the Photon Factory, a research site in Japan. And the research team enlisted a variety of other chemical experimental techniques to explore the samples’ makeup in different ways and at different scales.

    Chan noted that there are some other well-preserved crystals from the meteorites that haven’t yet been studied, and there are plans for follow-up studies to identify if any of those crystals may also contain water and complex organic molecules.

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    Ceres, a dwarf planet in the asteroid belt pictured here in this false-color image, may be the source of organic matter found in two meteorites that crashed to Earth in 1998. (Credit: NASA)

    Kebukawa said she looks forward to continuing studies of these samples at the ALS and other sites: “We may find more variations in organic chemistry.”

    The Advanced Light Source is a DOE Office of Science User Facility.

    Scientists at NASA Johnson Space Center, Kochi Institute for Core Sample Research in Japan, Carnegie Institution of Washington, Hiroshima University, The University of Tokyo, the High-Energy Accelerator Research Organization (KEK) in Japan, and The Graduate University for Advanced Studies (SOKENDAI) in Japan also participated in the study. The work was supported by the U.S. DOE Office of Science, the Universities Space Research Association, NASA, the National Institutes of Natural Sciences in Japan, Japan Society for the Promotion of Science, and The Mitsubishi Foundation.

    See the full article here .

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  • richardmitnick 2:24 pm on January 4, 2018 Permalink | Reply
    Tags: , Biocrusts, , , , LBNL, LC-MS-Liquid chromatography-mass spectrometry, M. vaginatus, Metabolites, Real World Native Biocrusts: Microbial Metabolism, Soil microbiomes   

    From LBNL: “Real World Native Biocrusts: Microbial Metabolism” 

    Berkeley Logo

    Berkeley Lab

    January 4, 2018
    Dan Krotz
    dakrotz@lbl.gov

    1
    Biocrust amongst one of its many natural habitats, taken about 20 miles from the sampling site (near the Corona Arch, Moab, UT). Credit: Tami Swenson

    Arid lands, which cover some 40 percent of the Earth’s terrestrial surface, are too dry to sustain much in the way of vegetation. But far from being barren, they are home to diverse communities of microorganisms—including fungi, bacteria, and archaea—that dwell together within the uppermost millimeters of soil. These biological soil crusts, or biocrusts, can exist for extended periods in a desiccated, dormant state. When it does rain, the microbes become metabolically active, setting in motion a cascade of activity that dramatically alters both the community structure and the soil chemistry.

    “These biocrusts and other soil microbiomes contain a tremendous diversity of both microbes and small molecules (‘metabolites’). However, the connection between the chemical diversity of soil and microbial diversity is poorly understood,” said Trent Northen, a senior scientist at Lawrence Berkeley National Laboratory (Berkeley Lab).

    In a paper published January 2, 2018, in Nature Communications, Berkeley Lab researchers led by the Northen lab report that specific compounds are transformed by and strongly associated with specific bacteria in native biological soil crust (biocrust) using a suite of tools Northen calls “exometabolomics.” Understanding how microbial communities in the biocrusts adapt to their harsh environments could provide important clues to help shed light on the roles of soil microbes in the global carbon cycle.

    The work follows a 2015 study [Nature Communications] that examined how specific small molecule compounds called “metabolites” were transformed in a mixture of bacterial isolates from biocrust samples cultured in a milieu of metabolites from the same soil. “We found that the microbes we investigated were ‘picky’ eaters,” Northen said. “We thought we could use this information to link what’s being consumed to the abundance of the microbes in the intact community, thereby linking the biology to the chemistry.”

    In the new study, the investigators set out to determine whether the microbe-metabolite relationships observed in the simplified test-tube system could be reproduced in a more complex soil environment.

    Biocrusts from the same source – representing four successive stages of maturation – were wet, and the soil water was sampled at five time points. The samples were analyzed by liquid chromatography-mass spectrometry (LC-MS) to characterize the metabolite composition (“metabolomics”), and biocrust DNA was extracted for shotgun sequencing to measure single copy gene markers for the dominant microbe species (“metagenomics”).

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    Biocrust is held together primarily by exopolysaccharides produced by the filamentous Cyanobacterium, M. vaginatus. Samples from the field were collected in petri dishes. In the lab, they were removed from the dishes, cut and placed into multi-well plates before adding water. Credit: Tami Swenson.

    “When we compare the patterns of metabolite uptake and production for isolated bacteria that are related to the most abundant microbes found in the biocrusts, we find that, excitingly, these patterns are maintained,” said Northen. That is, increased abundance of a given microbe is negatively correlated with the metabolites that they consume and positively correlated with metabolites that they release.

    When active, biocrusts take up atmospheric carbon dioxide and fix nitrogen, contributing to the ecosystem’s primary productivity. They also process organic matter in soil, modifying key properties related to soil fertility and water availability.

    “This study suggests that laboratory studies of microbial metabolite processing can help understand the role of these microbes in carbon cycling in the environment. This study gets us closer to understanding the complex food webs that are vital in nutrient dynamics and overall soil fertility,” said study first author Tami Swenson, a scientific engineering associate in Northen’s group within the Berkeley Lab Biosciences Area’s Environmental Genomics and Systems Biology (EGSB) Division.

    Northen’s group is currently working on expanding these studies to capture a greater fraction of microbial diversity. Ultimately, this may enable the prediction of nutrient cycling in terrestrial microbial ecosystems, and perhaps even manipulation by adding specific metabolites.

    The following Berkeley Lab researchers also contributed to the study: Benjamin Bowen, a member of Northen’s lab in EGSB and at the Joint Genome Institute, a DOE Office of Science User Facility, helped analyze metabolomics data; Ulas Karaoz in the Earth and Environmental Sciences Area (EESA) analyzed metagenomics data; and Joel Swenson, a former postdoctoral researcher in Biosciences’ Biological Systems and Engineering Division, helped conduct correlation and statistical analyses.

    This work was supported under a DOE Office of Science Early Career Research Program award. DNA was sequenced using the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley, supported by a National Institutes of Health Instrumentation Grant.

    5
    Regular water was added to mimic a rainfall event. The microbes in biocrust become metabolically active immediately upon wetting. As seen here, M. vaginatus turns green and releases oxygen. Credit: Tami Swenson.

    See the full article here .

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  • richardmitnick 11:07 am on January 3, 2018 Permalink | Reply
    Tags: Compact Accelerator System for Performing Astrophysical Research (CASPAR) collaboration, Facebook visit - watch the included video, , Lab Director looks back at 2017, LBNL, LBNL’s Enhanced Geothermal Systems Collaboration (EGS Collab), Long-Baseline Neutrino Facility and Deep Underground Neutrino Experiment (LBNF/DUNE) project, , Majorana Demonstrator collaboration, Ross Shaft rehabilitation project,   

    From SURF: “Lab Director looks back at 2017” A Gigantic and Important Laboratory in The U.S. 

    SURF logo
    Sanford Underground levels

    Sanford Underground Research facility

    1.3.18
    Executive Director Mike Headley

    1

    2017 has been an exciting year at Sanford Lab. We’ve seen tremendous progress on current and future experiments, including dark matter and neutrino research; the ongoing efforts of the Black Hills Underground Campus; Education and Outreach; and the Ross Shaft rehabilitation project, which reached the 4850 Level in October. Underpinning the success of our projects is our continued commitment to safety at Sanford Lab. I am so proud of our staff, researchers and contractors for their focus on safety every day.

    The success of 2017 is directly related to our strong partnerships with many organizations, including the various science collaborations at Sanford Lab; Fermilab, which has oversight responsibilities for our operations activities for the Department of Energy and is the lead DOE laboratory for the Long-Baseline Neutrino Facility and Deep Underground Neutrino Experiment (LBNF/DUNE) project; and Lawrence Berkeley National Laboratory. I also want to thank the State of South Dakota and the SDSTA Board of Directors for their strong support of the world-leading underground science at Sanford Lab.

    2
    LBNF/DUNE Groundbreaking

    On July 21, we celebrated the groundbreaking of the Long-Baseline Neutrino Facility, which officially kicked off a new era in particle physics. We’re proud to be one of the sites hosting this international mega-science project, which will be the largest in the United States, and to be working alongside Fermilab and the DUNE collaboration. LBNF/DUNE has the potential to unlock the mysteries of neutrinos, which could explain more about how the universe works and why matter exists at all. At its peak, construction of LBNF is expected to create almost 2,000 jobs throughout South Dakota and a similar number of jobs in Illinois. The experiment will take approximately 10 years to build and will operate for about 20 years.

    Read more

    3
    International support

    The LBNF/DUNE project garnered support from CERN in 2016, marking the first time the European-based science facility supported a major project outside of Europe. In another first, the United Kingdom signed an umbrella agreement with the United States on September 20 that commits $88 million toward the LBNF/DUNE project along with accelerator advancements at Fermilab. The $88 million in funding makes the UK the largest country investor in the project outside of the United States.

    Read more

    CM/GC selected: On Aug. 9, a new team officially signed on to help prepare for the excavation and construction of LBNF. Fermi Research Alliance LLC, which operates Fermilab, awarded Kiewit/Alberici Joint Venture (KAJV) a contract to begin laying the groundwork for the excavation for LBNF, the facility that will support DUNE. KAJV will help finalize design and excavation plans for LBNF and oversee the excavation and removal of more than 800,000 tons of rock, as well as the outfitting of the DUNE caverns.

    Read more

    4
    Dark Matter

    For several years, we hosted LUX, one of the world’s most sensitive dark matter experiments. Now, we’re gearing up for the next-generation experiment, LUX-ZEPLIN (LZ). The collaboration had a positive directors’ progress review in November and will begin surface assembly activities in early 2018. We are proud to have made major contributions to LZ, including investing in 80 percent of the xenon, which is being purified at SLAC National Accelerator Laboratory. We’ve also updated the Surface Lab cleanroom (pictured above) and built a radon reduction facility. The experiment is expected to begin operations in 2020 and run for five years.

    Read more

    5
    LUX on display

    Visitors to the Sanford Lab Homestake Visitor Center can now view the decommissioned Large Underground Xenon (LUX) experiment on display as an interactive exhibit. On July 18, researchers unveiled the new exhibit, which features a window that allows visitors to view the inside of the detector: copper grids, white Teflon plates and a depiction of the wire grids that were vital to the success of the experiment. Additionally, an interactive kiosk explains the history of the LUX detector and all of the associated parts that are shown in the exhibit, and an actual PMT, one of 120 used in the experiment.

    Read more

    6

    CASPAR Ribbon Cutting

    In a major step forward, the Compact Accelerator System for Performing Astrophysical Research (CASPAR) collaboration achieved first beam and celebrated with a ribbon-cutting ceremony on July 12. CASPAR’s 50-foot long accelerator uses radio-frequency energy to produce a beam of protons or alpha particles from hydrogen or helium gas. The ions enter the accelerating tube, which is kept at high vacuum, then are directed down the beamline using magnets. The particles crash into a target, releasing the same neutrons that fuel the nuclear reactions in stars and produce a large amount of the heavy elements. The collaboration will begin full operations this year.

    Read more

    7
    Majorana reports results

    After years of planning and building its experiment, the Majorana Demonstrator collaboration announced its initial physics results. The team is looking for a rare type of radioactive decay called neutrinoless double-beta decay, which could answer fundamental questions about the universe, including why there is an imbalance of matter and antimatter in the universe and why we even exist. The Majorana Demonstrator collaboration needed to show it could achieve the low backgrounds required to see this rare physics event. And the team surpassed its goals, reducing backgrounds to a level that shows promise for a next-generation experiment that will be much larger.

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    8
    SIGMA-V

    We’re excited to have a new geology collaboration at Sanford Lab: LBNL’s Enhanced Geothermal Systems Collaboration (EGS Collab), which is studying geothermal systems, a clean-energy technology that could power up to 100 million American homes. The SIGMA-V (Stimulation Investigations for Geothermal Modeling and Analysis) team has been collecting data that will inform better predictive and geomechanic models of the subsurface of the earth by drilling several 60-meter long boreholes on the 4850 Level. The data will be applied toward the Frontier Observatory for Research in Geothermal Energy (FORGE), a flagship DOE geothermal project.

    Read more

    9
    Community outreach

    Interest in what’s happening at Sanford Lab continues to grow. This year more than 2,000 people attended events hosted by Sanford Lab. During Neutrino Day 2017: Discovery, visitors to Lead participated in a practice eclipse balloon launch, hands-on education activities, video conferences from a mile underground and Fermilab, hoistroom tours and “wild science” and geology demonstrations, and learned all about 2017’s Nobel-winning physics experiment, LIGO, which discovered gravitational waves. We also hosted an Eclipse party and several Deep Talks presentations.

    10
    Facebook visit

    Everywhere we go lately, we get asked about Mark Zuckerberg’s July 12 visit to Sanford Lab. The Facebook founder visited South Dakota, where he had lunch with ranchers in Piedmont, discussed net neutrality in Sturgis and stopped by the Sanford Underground Research Facility—all in a single day. In a live-stream video from the 4850 Level, Mr. Zuckerberg talked with Sanford Lab’s Dan Regan and Jaret Heise, and Cabot-Ann Christofferson, a member of the Majorana Collabortion to learn more about the community of Lead and the world-leading science taking place nearly a mile below the earth’s surface. So far, more than 4 million people have viewed the video. We were honored to host him and his team and appreciate his efforts to help Facebook users better understand who we are.

    Watch the live post

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    About us.
    The Sanford Underground Research Facility in Lead, South Dakota, advances our understanding of the universe by providing laboratory space deep underground, where sensitive physics experiments can be shielded from cosmic radiation. Researchers at the Sanford Lab explore some of the most challenging questions facing 21st century physics, such as the origin of matter, the nature of dark matter and the properties of neutrinos. The facility also hosts experiments in other disciplines—including geology, biology and engineering.

    The Sanford Lab is located at the former Homestake gold mine, which was a physics landmark long before being converted into a dedicated science facility. Nuclear chemist Ray Davis earned a share of the Nobel Prize for Physics in 2002 for a solar neutrino experiment he installed 4,850 feet underground in the mine.

    Homestake closed in 2003, but the company donated the property to South Dakota in 2006 for use as an underground laboratory. That same year, philanthropist T. Denny Sanford donated $70 million to the project. The South Dakota Legislature also created the South Dakota Science and Technology Authority to operate the lab. The state Legislature has committed more than $40 million in state funds to the project, and South Dakota also obtained a $10 million Community Development Block Grant to help rehabilitate the facility.

    In 2007, after the National Science Foundation named Homestake as the preferred site for a proposed national Deep Underground Science and Engineering Laboratory (DUSEL), the South Dakota Science and Technology Authority (SDSTA) began reopening the former gold mine.

    In December 2010, the National Science Board decided not to fund further design of DUSEL. However, in 2011 the Department of Energy, through the Lawrence Berkeley National Laboratory, agreed to support ongoing science operations at Sanford Lab, while investigating how to use the underground research facility for other longer-term experiments. The SDSTA, which owns Sanford Lab, continues to operate the facility under that agreement with Berkeley Lab.

    The first two major physics experiments at the Sanford Lab are 4,850 feet underground in an area called the Davis Campus, named for the late Ray Davis. The Large Underground Xenon (LUX) experiment is housed in the same cavern excavated for Ray Davis’s experiment in the 1960s.
    LUX/Dark matter experiment at SURFLUX/Dark matter experiment at SURF

    In October 2013, after an initial run of 80 days, LUX was determined to be the most sensitive detector yet to search for dark matter—a mysterious, yet-to-be-detected substance thought to be the most prevalent matter in the universe. The Majorana Demonstrator experiment, also on the 4850 Level, is searching for a rare phenomenon called “neutrinoless double-beta decay” that could reveal whether subatomic particles called neutrinos can be their own antiparticle. Detection of neutrinoless double-beta decay could help determine why matter prevailed over antimatter. The Majorana Demonstrator experiment is adjacent to the original Davis cavern.

    Another major experiment, the Long Baseline Neutrino Experiment (LBNE)—a collaboration with Fermi National Accelerator Laboratory (Fermilab) and Sanford Lab, is in the preliminary design stages. The project got a major boost last year when Congress approved and the president signed an Omnibus Appropriations bill that will fund LBNE operations through FY 2014. Called the “next frontier of particle physics,” LBNE will follow neutrinos as they travel 800 miles through the earth, from FermiLab in Batavia, Ill., to Sanford Lab.

    Fermilab LBNE
    LBNE

     
  • richardmitnick 12:27 pm on December 14, 2017 Permalink | Reply
    Tags: , , , Bright Galaxy Survey, , Dark matter mock-ups, DESI-Dark Energy Spectroscopic Instrument, Jülich Supercomputer Center in Germany, LBNL, Mock galaxies catalog,   

    From LBNL: “Creating a World of Make-Believe to Better Understand the Real Universe” 

    Berkeley Logo

    Berkeley Lab

    December 14, 2017
    Glenn Roberts Jr.
    geroberts@lbl.gov
    (510) 486-5582

    1
    This plot shows a thin slice through a mock galaxies catalog. The blue and green points are “bright” and “faint” galaxies simulated for the Dark Energy Spectroscopic Instrument’s Bright Galaxy Survey, and the red points show galaxies that are brighter than the magnitude limit of the Sloan Digital Sky Survey, a predecessor sky survey. (Credit: Alex Smith/Durham University)

    SDSS Telescope at Apache Point Observatory, NM, USA, Altitude 2,788 meters (9,147 ft)

    Seeing is believing, or so the saying goes.

    And in some cases, a world of make-believe can help you realize what you’re actually seeing, too.

    Scientists are creating simulated universes, for example – complete with dark matter mock-ups, computer-generated galaxies, quasi quasars, and pseudo supernovae ­– to better understand real-world observations.

    Their aim is to envision how new Earth-based and space-based sky surveys will see the universe, and to help analyze and interpret the vast treasure troves of data that these surveys will amass.

    “We want to be able to hit the ground running once we get real data,” said Stephen Bailey, a physicist at the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) who is the technical lead and manager of data systems for a 3-D sky-mapping project known as the Dark Energy Spectroscopic Instrument, or DESI, that is slated to begin observing in 2019.

    LBNL/DESI spectroscopic instrument on the Mayall 4-meter telescope at Kitt Peak National Observatory starting in 2018

    Several DESI teams are building out separate simulations populated with the many types of objects DESI will encounter. “What is this going to look like for DESI?” Bailey asked. “What is the actual spectra, or light signature, that DESI is going to observe? We have to make sure the mock objects have the right colors and chemical abundances.”

    John Moustakas, an assistant professor of physics at Siena College in New York who is also working on the simulations for DESI, added, “And that’s challenging because nothing like DESI exists.”

    The computerized models are informed by observations from previous surveys and by large-scale simulations of the universe that account for complex physics including dark matter, an unknown form of matter that, together with dark energy, makes up about 95 percent of the total mass and energy in the universe.

    “To the greatest extent possible, the simulations are based on models of real objects – from pulling out all of these pieces from other surveys,” Moustakas said. “Perhaps in a perfect world these would be purely theoretical models, but we don’t understand galaxies well enough to be able to do that.”

    And even though there is data from previous surveys, DESI will see the sky in a different way. “You have to extract out all the instrument parts of all these other surveys to get to: ‘This is what other galaxies look like, intrinsically,’” he said. Next, he said, scientists must figure out how DESI’s unique set of instruments will see them.

    The simulated objects and universes created and refined using powerful supercomputers, including Berkeley Lab’s National Energy Research Scientific Computing Center (NERSC), must ultimately take into account the Earth’s atmospheric noise, and weather and lighting conditions including the phases of the moon, which all affect observations.

    NERSC Cray XC40 Cori II supercomputer

    LBL NERSC Cray XC30 Edison supercomputer


    The Genepool system is a cluster dedicated to the DOE Joint Genome Institute’s computing needs. Denovo is a smaller test system for Genepool that is primarily used by NERSC staff to test new system configurations and software.

    NERSC PDSF


    PDSF is a networked distributed computing cluster designed primarily to meet the detector simulation and data analysis requirements of physics, astrophysics and nuclear science collaborations.

    DESI will operate from the Nicholas U. Mayall 4-Meter Telescope at Kitt Peak National Observatory in Arizona. It will measure the light from tens of millions of galaxies and other objects with a carefully choreographed array of 5,000 swiveling robots – each pointing a fiber-optic cable at a targeted space object. The robotic array will cycle through a sequence of objects, peering up to 11 billion years back in the history of our universe.

    The light captured by DESI will provide precise measurements that will help scientists to retrace the evolution of the universe and learn more about dark energy, which is responsible for the universe’s mysterious, accelerating expansion. Berkeley Lab is the lead lab for the DESI project, and the collaboration now involves about 200 scientists at 40 institutions.

    Alex Smith, a graduate student at Durham University in England and a DESI collaboration member, worked with a team to develop a mock catalog of galaxies for DESI that taps into a powerful simulation of how the universe’s matter has evolved over the past 13 billion years.

    Carried out at the Jülich Supercomputer Center in Germany, this Millennium-XXL simulation used 12,000 computer cores – the equivalent to about 300 years’ worth of computer processing time.

    Jülich Supercomputing Centre in Jülich, Germany

    It generated about 100 terabytes of data, which is nearly as much data as the Hubble Space Telescope transmitted in space images during its first 24 years of operation.

    The mock galaxy catalog that Smith’s team developed focused on the same one-third of the sky that DESI will survey. The catalog shows how galaxies’ clustering and ‘redshift’ – the color based on their distance and movement away from us – changes over time and will likely appear to DESI.

    Due to cosmic expansion, very distant objects appear redder and fainter. Earlier mock catalogs had not accounted for these changes in redshift, Smith said.

    “It’s important to have mock catalogs that have realistic properties – that look similar to how we think the actual survey is going to look,” he added.

    5
    The predicted galaxy distribution in the Millennium XXL simulation. (Click image for larger view.) Each galaxy is represented by a sphere whose intensity and size are related to the expected total mass in stars and the size of its cold gas disk. (Credit: Max-Planck-Institute for Astrophysics)

    His team’s survey used a method known as halo occupation distribution, or HOD, to model the average number of galaxies and their brightness based on the Millennium-XXL survey’s detailed simulations of the distribution of dark matter. In dark matter models, matter forms within clumps of dark matter known as halos, and galaxies are enveloped by these halos.

    Smith noted that the distribution of galaxies within these halos, and other properties incorporated in the latest catalog, are taken from data collected in past surveys, including the Sloan Digital Sky Survey and the Galaxy and Mass Assembly Survey.

    The galaxies in the catalog are simplified to their brightness, as it will appear in one of the wavelength bands that DESI will be scanning. The mock catalog is also intended to simulate the type of galaxies that will be targeted during sky conditions that favor brighter objects, such as those that exist around the times of sunrises and sunsets, or when the moon is brighter in the sky, for example. Separate simulations will account for darker viewing conditions.

    “The mock catalog I created assumes you can observe everything with perfect precision,” Smith noted, so additional properties will need to be added to simulate weather and other effects. The DESI collaboration has access to a decade of weather statistics collected at the Kitt Peak National Observatory, Bailey said.

    Even after the start of DESI’s survey, collaboration scientists will continue to adapt and improve the models.

    6
    A view of some candidate targets for DESI obervations is shown here, along with overlay images showing mock spectra, or light signatures, generated in the planning stages for DESI. (Credit: legacysurvey.org, John Moustakas, DESI collaboration)

    “There is a learning component to it,” Moustakas said. “As we start to observe things, we will then use those targeted objects to build better models of what those objects are.”

    Relying too much on simulations can also be a problem, DESI scientists noted, so observations will provide a needed reality check. For example, superbright objects called quasars, which are among the targets for DESI, have been particularly difficult to simulate.

    “You don’t want to believe your simulations too much, because nature is much harsher,” Moustakas said.

    Bailey added, “We are currently bootstrapping off other experiments; then we’ll be bootstrapping off ourselves.”

    Smith noted that to prepare for ever-larger surveys, there will be a need for more detailed and accurate models to home in on the nature of dark energy and gravity, for example.

    “To be able to make cosmological measurements at the required high precision to be able to tell all of these viable models apart, it’s really important to have more and more realistic mock catalogs,” he said.

    NERSC is a DOE Office of Science User Facility.

    DESI is supported by the U.S. Department of Energy’s Office of High Energy Physics; the U.S. National Science Foundation, Division of Astronomical Sciences under contract to the National Optical Astronomy Observatory; the Science and Technologies Facilities Council of the United Kingdom; the Gordon and Betty Moore Foundation; the Heising-Simons Foundation; the National Council of Science and Technology of Mexico; the Ministry of Economy of Spain; and DESI member institutions. The DESI scientists are honored to be permitted to conduct astronomical research on Iolkam Du’ag (Kitt Peak), a mountain with particular significance to the Tohono O’odham Nation.

    Current DESI Member Institutions include: Aix-Marseille University; Argonne National Laboratory; Barcelona-Madrid Regional Participation Group; Brookhaven National Laboratory; Boston University; Carnegie Mellon University; CEA-IRFU, Saclay; China Participation Group; Cornell University; Durham University; École Polytechnique Fédérale de Lausanne; Eidgenössische Technische Hochschule, Zürich; Fermi National Accelerator Laboratory; Granada-Madrid-Tenerife Regional Participation Group; Harvard University; Korea Astronomy and Space Science Institute; Korea Institute for Advanced Study; Institute of Cosmological Sciences, University of Barcelona; Lawrence Berkeley National Laboratory; Laboratoire de Physique Nucléaire et de Hautes Energies; Mexico Regional Participation Group; National Optical Astronomy Observatory; Siena College; SLAC National Accelerator Laboratory; Southern Methodist University; Swinburne University; The Ohio State University; Universidad de los Andes; University of Arizona; University of California, Berkeley; University of California, Irvine; University of California, Santa Cruz; University College London; University of Michigan at Ann Arbor; University of Pennsylvania; University of Pittsburgh; University of Portsmouth; University of Queensland; University of Rochester; University of Toronto; University of Utah; University of Zurich; UK Regional Participation Group; Yale University. For more information, visit desi.lbl.gov.

    The National Optical Astronomy Observatory (NOAO) is the national center for ground-based nighttime astronomy in the United States (www.noao.edu) and is operated by the Association of Universities for Research in Astronomy (AURA) under a cooperative agreement with the National Science Foundation Division of Astronomical Sciences.

    Established in 2007 by Mark Heising and Elizabeth Simons, the Heising-Simons Foundation (www.heisingsimons.org) is dedicated to advancing sustainable solutions in the environment, supporting groundbreaking research in science, and enhancing the education of children.

    The Gordon and Betty Moore Foundation, established in 2000, seeks to advance environmental conservation, patient care and scientific research. The Foundation’s Science Program aims to make a significant impact on the development of provocative, transformative scientific research, and increase knowledge in emerging fields. For more information, visit http://www.moore.org.

    The Science and Technology Facilities Council (STFC) of the United Kingdom coordinates research on some of the most significant challenges facing society, such as future energy needs, monitoring and understanding climate change, and global security. It offers grants and support in particle physics, astronomy and nuclear physics, visit http://www.stfc.ac.uk.

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    A U.S. Department of Energy National Laboratory Operated by the University of California

    University of California Seal

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  • richardmitnick 12:33 pm on December 5, 2017 Permalink | Reply
    Tags: , Dark fiber refers to unused fiber-optic cable of which there is a glut, Dark Fiber- Using Sensors Beneath Our Feet to Tell Us About Earthquakes Water and Other Geophysical Phenomenon, DAS-Distributed acoustic sensing, Distributed acoustic sensing (DAS) is a novel technology that measures seismic wavefields by shooting short laser pulses across the length of the fiber, , LBNL, , There are now dense corridors of dark fiber crisscrossing the entire country, Using fiber for quake detection   

    From LBNL: “Dark Fiber: Using Sensors Beneath Our Feet to Tell Us About Earthquakes, Water, and Other Geophysical Phenomenon” 

    Berkeley Logo

    Berkeley Lab

    December 5, 2017
    Julie Chao
    JHChao@lbl.gov
    (510) 486-6491

    Berkeley Lab researchers successfully use distributed acoustic sensing for seismic monitoring.

    1
    (from left) Shan Dou, Jonathan Ajo-Franklin, and Nate Lindsey were on a Berkeley Lab team that used fiber optic cables for detecting earthquakes and other subsurface activity. (Credit: Marilyn Chung/Berkeley Lab)

    Scientists at the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) have shown for the first time that dark fiber – the vast network of unused fiber-optic cables installed throughout the country and the world – can be used as sensors for detecting earthquakes, the presence of groundwater, changes in permafrost conditions, and a variety of other subsurface activity.

    In a pair of recently published papers, a team led by Berkeley Lab researcher Jonathan Ajo-Franklin announced they had successfully combined a technology called “distributed acoustic sensing,” which measures seismic waves using fiber-optic cables, with novel processing techniques to allow reliable seismic monitoring, achieving results comparable to what conventional seismometers can measure.

    “This has huge potential because you can just imagine long stretches of fibers being turned into a massive seismic network,” said Shan Dou, a Berkeley Lab postdoctoral fellow. “The idea is that by using fiber that can be buried underground for a long time, we can transform traffic noise or other ambient vibrations into usable seismic signals that can help us to monitor near-surface changes such as permafrost thaw and groundwater-level fluctuations.”

    Dou is the lead author of Distributed Acoustic Sensing for Seismic Monitoring of the Near Surface: A Traffic-Noise Interferometry Case Study, which was published in September in Nature’s Scientific Reports and verified the technique for monitoring the Earth’s near surface. More recently, Ajo-Franklin’s group published a follow-up study led by UC Berkeley graduate student Nate Lindsey, Fiber-Optic Network Observations of Earthquake Wavefields, in Geophysical Research Letters (GRL), which demonstrates the viability of using fiber-optic cables for earthquake detection.

    What is dark fiber?

    Dark fiber refers to unused fiber-optic cable, of which there is a glut thanks to a huge rush to install the cable in the early 1990s by telecommunications companies. Just as the cables were buried underground, the technology for transmitting data improved significantly so that fewer cables were needed. There are now dense corridors of dark fiber crisscrossing the entire country.

    Distributed acoustic sensing (DAS) is a novel technology that measures seismic wavefields by shooting short laser pulses across the length of the fiber. “The basic idea is, the laser light gets scattered by tiny impurities in the fiber,” said Ajo-Franklin. “When fiber is deformed, we will see distortions in the backscattered light, and from these distortions, we can measure how the fiber itself is being squeezed or pulled.”

    3
    Jonathan Ajo-Franklin (left) installing an experimental fiber optic test array at the Richmond Field Station. (Courtesy Jonathan Ajo-Franklin)

    Using a test array they installed in Richmond, California – with fiber-optic cable placed in a shallow L-shaped trench, one leg of about 100 meters parallel to the road and another perpendicular – the researchers verified that they could use seismic waves generated by urban traffic, such as cars and trains, to image and monitor the mechanical properties of shallow soil layers.

    The measurements give information on how “squishy” the soil is at any given point, making it possible to infer a great deal of information about the soil properties, such as its water content or texture. “Imagine a slinky – it can compress or wiggle,” Ajo-Franklin said. “Those correspond to different ways you can squeeze the soil, and how much energy it takes to reduce its volume or shear it.”

    He added: “The neat thing about it is that you’re making measurements across each little unit of fiber. All the reflections come back to you. By knowing all of them and knowing how long it takes for a laser light to travel back and forth on the fiber you can back out what’s happening at each location. So it’s a truly distributed measurement.”

    Having proven the concept under controlled conditions, the team said they expect the technique to work on a variety of existing telecommunications networks, and they are currently conducting follow-up experiments across California to demonstrate this. Ongoing research in Alaska is also exploring the same technique for monitoring the stability of Arctic permafrost.

    Added Dou: “We can monitor the near surface really well by using nothing but traffic noise. It could be fluctuations in groundwater levels, or changes that could provide early warnings for a variety of geohazards such as permafrost thaw, sinkhole formation, and landslides.”

    Using fiber for quake detection

    3
    Nate Lindsey trims cable at the Richmond Field Station (Courtesy Jonathan Ajo-Franklin)

    Building on five years of Berkeley Lab-led research exploring the use of DAS for subsurface monitoring using non-earthquake seismic sources, Ajo-Franklin’s group has now pushed the envelope and has shown that DAS is a powerful tool for earthquake monitoring as well.

    In the GRL study led by Lindsey in collaboration with Stanford graduate student Eileen Martin, the research team took measurements using the DAS technique on fiber-optic arrays in three locations – two in California and one in Alaska. In all cases, DAS proved to be comparably sensitive to earthquakes as conventional seismometers, despite its higher noise levels. Using the DAS arrays, they assembled a catalog of local, regional, and distant earthquakes and showed that processing techniques could take advantage of DAS’ many channels to help understand where earthquakes originate from.

    Ajo-Franklin said that dark fiber has the advantage of being nearly ubiquitous, whereas traditional seismometers, because they are expensive, are sparsely installed, and subsea installations are particularly scarce. Additionally, fiber allows for dense spatial sampling, meaning data points are only meters apart, whereas seismometers typically are separated by many kilometers.

    Lindsey added: “Fiber has a lot of implications for earthquake detection, location, and early warning. Fiber goes out in the ocean, and it’s all over the land, so this technology increases the likelihood that a sensor is near the rupture when an earthquake happens, which translates into finding small events, improved earthquake locations, and extra time for early warning.”

    The GRL paper notes other potential applications of using the dark fiber, including urban seismic hazard analysis, global seismic imaging, offshore submarine volcano detection, nuclear explosion monitoring, and microearthquake characterization.

    The research was funded by the Department of Defense through the Strategic Environmental Research and Development Program as well as by Laboratory Directed Research and Development funding.

    Other co-authors on the GRL paper are Barry Freifeld of Berkeley Lab, Douglas Dreger of UC Berkeley, Martin and Biondo Biondi of Stanford University, Steve Cole of OptaSense Inc., and Stephanie James of Sandia National Laboratories. Lindsey is supported by a National Science Foundation Graduate Research Fellowship. Other co-authors of the Scientific Reports paper are Freifeld, Thomas Daley, Michelle Robertson, John Peterson, and Craig Ulrich of Berkeley Lab; Anna Wagner of the U.S. Army Cold Regions Research & Engineering Laboratory; and Martin.

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    A U.S. Department of Energy National Laboratory Operated by the University of California

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