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  • richardmitnick 1:19 pm on September 13, 2017 Permalink | Reply
    Tags: , , , LBNL, , PHENIX (Python-based Hierarchical ENvironment for Integrated Xtallography), , TFIIH-Transcription factor IIH   

    From LBNL: “Berkeley Lab Scientists Map Key DNA Protein Complex at Near-Atomic Resolution” 

    Berkeley Logo

    Berkeley Lab

    September 13, 2017
    Sarah Yang
    scyang@lbl.gov
    (510) 486-4575

    1
    The cryo-EM structure of Transcription Factor II Human (TFIIH). The atomic coordinate model, colored according to the different TFIIH subunits, is shown inside the semi-transparent cryo-EM map. (Credit: Basil Greber/Berkeley Lab and UC Berkeley)

    Chalking up another success for a new imaging technology that has energized the field of structural biology, researchers at the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) obtained the highest resolution map yet of a large assembly of human proteins that is critical to DNA function.

    The scientists are reporting their achievement today in an advanced online publication of the journal Nature. They used cryo-electron microscopy (cryo-EM) to resolve the 3-D structure of a protein complex called transcription factor IIH (TFIIH) at 4.4 angstroms, or near-atomic resolution. This protein complex is used to unzip the DNA double helix so that genes can be accessed and read during transcription or repair.

    “When TFIIH goes wrong, DNA repair can’t occur, and that malfunction is associated with severe cancer propensity, premature aging, and a variety of other defects,” said study principal investigator Eva Nogales, faculty scientist at Berkeley Lab’s Molecular Biophysics and Integrated Bioimaging Division. “Using this structure, we can now begin to place mutations in context to better understand why they give rise to misbehavior in cells.”

    TFIIH’s critical role in DNA function has made it a prime target for research, but it is considered a difficult protein complex to study, especially in humans.

    ___________________________________________________________________
    How to Capture a Protein
    1
    It takes a large store of patience and persistence to prepare specimens of human transcription factor IIH (TFIIH) for cryo-EM. Because TFIIH exists in such minute amounts in a cell, the researchers had to grow 50 liters of human cells in culture to yield a few micrograms of the purified protein.

    Human TFIIH is particularly fragile and prone to falling apart in the flash-freezing process, so researchers need to use an optimized buffer solution to help protect the protein structure.

    “These compounds that protect the proteins also work as antifreeze agents, but there’s a trade-off between protein stability and the ability to produce a transparent film of ice needed for cryo-EM,” said study lead author Basil Greber.

    Once Greber obtains a usable sample, he settles down for several days at the cryo-electron microscope at UC Berkeley’s Stanley Hall for imaging.

    “Once you have that sample inside the microscope, you keep collecting data as long as you can,” he said. “The process can take four days straight.”
    ___________________________________________________________________

    Mapping complex proteins

    “As organisms get more complex, these proteins do, too, taking on extra bits and pieces needed for regulatory functions at many different levels,” said Eva Nogales, who is also a UC Berkeley professor of molecular and cell biology and a Howard Hughes Medical Institute investigator. “The fact that we resolved this protein structure from human cells makes this even more relevant to disease research. There’s no need to extrapolate the protein’s function based upon how it works in other organisms.”

    Biomolecules such as proteins are typically imaged using X-ray crystallography, but that method requires a large amount of stable sample for the crystallization process to work. The challenge with TFIIH is that it is hard to produce and purify in large quantities, and once obtained, it may not form crystals suitable for X-ray diffraction.

    Enter cryo-EM, which can work even when sample amounts are very small. Electrons are sent through purified samples that have been flash-frozen at ultracold temperatures to prevent crystalline ice from forming.

    Cryo-EM has been around for decades, but major advances over the past five years have led to a quantum leap in the quality of high-resolution images achievable with this technique.

    “When your goal is to get resolutions down to a few angstroms, the problem is that any motion gets magnified,” said study lead author Basil Greber, a UC Berkeley postdoctoral fellow at the California Institute for Quantitative Biosciences (QB3). “At high magnifications, the slight movement of the specimen as electrons move through leads to a blurred image.”

    Making movies

    The researchers credit the explosive growth in cryo-EM to advanced detector technology that Berkeley Lab engineer Peter Denes helped develop. Instead of a single picture taken for each sample, the direct detector camera shoots multiple frames in a process akin to recording a movie. The frames are then put together to create a high-resolution image. This approach resolves the blur from sample movement. The improved images contain higher quality data, and they allow researchers to study the sample in multiple states, as they exist in the cell.

    Since shooting a movie generates far more data than a single frame, and thousands of movies are being collected during a microscopy session, the researchers needed the processing punch of supercomputers at the National Energy Research Scientific Computing Center (NERSC) at Berkeley Lab.

    NERSC Cray Cori II supercomputer

    LBL NERSC Cray XC30 Edison supercomputer

    NERSC Hopper Cray XE6 supercomputer

    The output from these computations was a 3-D map that required further interpretation.

    “When we began the data processing, we had 1.5 million images of individual molecules to sort through,” said Greber. “We needed to select particles that are representative of an intact complex. After 300,000 CPU hours at NERSC, we ended up with 120,000 images of individual particles that were used to compute the 3-D map of the protein.”

    To obtain an atomic model of the protein complex based on this 3-D map, the researchers used PHENIX (Python-based Hierarchical ENvironment for Integrated Xtallography), a software program whose development is led by Paul Adams, director of Berkeley Lab’s Molecular Biophysics and Integrated Bioimaging Division and a co-author of this study.

    Not only does this structure improve basic understanding of DNA repair, the information could be used to help visualize how specific molecules are binding to target proteins in drug development.

    “In studying the physics and chemistry of these biological molecules, we’re often able to determine what they do, but how they do it is unclear,” said Nogales. “This work is a prime example of what structural biologists do. We establish the framework for understanding how the molecules function. And with that information, researchers can develop finely targeted therapies with more predictive power.”

    Other co-authors on this study are Pavel Afonine and Thi Hoang Duong Nguyen, both of whom have joint appointments at Berkeley Lab and UC Berkeley; and Jie Fang, a researcher at the Howard Hughes Medical Institute.

    NERSC is a DOE Office of Science User Facility located at Berkeley Lab. In addition to NERSC, the researchers used the Lawrencium computing cluster at Berkeley Lab. This work was funded by the National Institute of General Medical Sciences and the Swiss National Science Foundation.

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  • richardmitnick 8:33 am on August 28, 2017 Permalink | Reply
    Tags: , , Berkeley Lab’s Molecular Foundry, , Exciton effect, LBNL, Moly sulfide, , New Results Reveal High Tunability of 2-D Material, Photoluminescence excitation (PLE) spectroscopy,   

    From LBNL: “New Results Reveal High Tunability of 2-D Material” 

    Berkeley Logo

    Berkeley Lab

    August 25, 2017
    Glenn Roberts Jr
    geroberts@lbl.gov
    (510) 486-5582

    1
    From left: Kaiyuan Yao, Nick Borys, and P. James Schuck, seen here at Berkeley Lab’s Molecular Foundry, measured a property in a 2-D material that could help realize new applications. (Credit: Marilyn Chung/Berkeley Lab)

    Two-dimensional materials are a sort of a rookie phenom in the scientific community. They are atomically thin and can exhibit radically different electronic and light-based properties than their thicker, more conventional forms, so researchers are flocking to this fledgling field to find ways to tap these exotic traits.

    Applications for 2-D materials range from microchip components to superthin and flexible solar panels and display screens, among a growing list of possible uses. But because their fundamental structure is inherently tiny, they can be tricky to manufacture and measure, and to match with other materials. So while 2-D materials R&D is on the rise, there are still many unknowns about how to isolate, enhance, and manipulate their most desirable qualities.

    Now, a science team at the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) has precisely measured some previously obscured properties of moly sulfide, a 2-D semiconducting material also known as molybdenum disulfide or MoS2. The team also revealed a powerful tuning mechanism and an interrelationship between its electronic and optical, or light-related, properties.

    To best incorporate such monolayer materials into electronic devices, engineers want to know the “band gap,” which is the minimum energy level it takes to jolt electrons away from the atoms they are coupled to, so that they flow freely through the material as electric current flows through a copper wire. Supplying sufficient energy to the electrons by absorbing light, for example, converts the material into an electrically conducting state.

    As reported in the Aug. 25 issue of Physical Review Letters, researchers measured the band gap for a monolayer of moly sulfide, which has proved difficult to accurately predict theoretically, and found it to be about 30 percent higher than expected based on previous experiments. They also quantified how the band gap changes with electron density – a phenomenon known as “band gap renormalization.”

    “The most critical significance of this work was in finding the band gap,” said Kaiyuan Yao, a graduate student researcher at Berkeley Lab and the University of California, Berkeley, who served as the lead author of the research paper.

    2
    This diagram shows a triangular sample of monolayer moly sulfide (dark blue) on silicon-based layers (light blue and green) during an experimental technique known as photoluminescence excitation spectroscopy. (Credit: Berkeley Lab)

    “That provides very important guidance to all of the optoelectronic device engineers. They need to know what the band gap is” in orderly to properly connect the 2-D material with other materials and components in a device, Yao said.

    Obtaining the direct band gap measurement is challenged by the so-called “exciton effect” in 2-D materials that is produced by a strong pairing between electrons and electron “holes” ­– vacant positions around an atom where an electron can exist. The strength of this effect can mask measurements of the band gap.

    Nicholas Borys, a project scientist at Berkeley Lab’s Molecular Foundry who also participated in the study, said the study also resolves how to tune optical and electronic properties in a 2-D material.

    “The real power of our technique, and an important milestone for the physics community, is to discern between these optical and electronic properties,” Borys said.

    The team used several tools at the Molecular Foundry, a facility that is open to the scientific community and specializes in the creation and exploration of nanoscale materials.

    The Molecular Foundry technique that researchers adapted for use in studying monolayer moly sulfide, known as photoluminescence excitation (PLE) spectroscopy, promises to bring new applications for the material within reach, such as ultrasensitive biosensors and tinier transistors, and also shows promise for similarly pinpointing and manipulating properties in other 2-D materials, researchers said.

    The research team measured both the exciton and band gap signals, and then detangled these separate signals. Scientists observed how light was absorbed by electrons in the moly sulfide sample as they adjusted the density of electrons crammed into the sample by changing the electrical voltage on a layer of charged silicon that sat below the moly sulfide monolayer.

    3
    This image shows a slight “bump” (red arrow) in charted experimental data that reveals the band gap measurement in a 2-D material known as moly sulfide. (Credit: Berkeley Lab)

    Researchers noticed a slight “bump” in their measurements that they realized was a direct measurement of the band gap, and through a slew of other experiments used their discovery to study how the band gap was readily tunable by simply adjusting the density of electrons in the material.

    “The large degree of tunability really opens people’s eyes,” said P. James Schuck, who was director of the Imaging and Manipulation of Nanostructures facility at the Molecular Foundry during this study.

    “And because we could see both the band gap’s edge and the excitons simultaneously, we could understand each independently and also understand the relationship between them,” said Schuck, who is now at Columbia University. “It turns out all of these properties are dependent on one another.”

    4
    Kaiyuan Yao works with equipment at Berkeley Lab’s Molecular Foundry that was used to help measure a property in a 2-D material. (Credit: Marilyn Chung/Berkeley Lab)

    Moly sulfide, Schuck also noted, is “extremely sensitive to its local environment,” which makes it a prime candidate for use in a range of sensors. Because it is highly sensitive to both optical and electronic effects, it could translate incoming light into electronic signals and vice versa.

    Schuck said the team hopes to use a suite of techniques at the Molecular Foundry to create other types of monolayer materials and samples of stacked 2-D layers, and to obtain definitive band gap measurements for these, too. “It turns out no one yet knows the band gaps for some of these other materials,” he said.

    The team also has expertise in the use of a nanoscale probe to map the electronic behavior across a given sample.

    Borys added, “We certainly hope this work seeds further studies on other 2-D semiconductor systems.”

    The Molecular Foundry is a DOE Office of Science User Facility that provides free access to state-of-the-art equipment and multidisciplinary expertise in nanoscale science to visiting scientists.

    Researchers from the Kavli Energy NanoSciences Institute at UC Berkeley and Berkeley Lab, and from Arizona State University also participated in this study, which was supported by the National Science Foundation.

    See the full article here .

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  • richardmitnick 12:09 pm on August 14, 2017 Permalink | Reply
    Tags: , , , , LBNL, New 3-D Simulations Show How Galactic Centers Cool Their Jets,   

    From LBNL: “New 3-D Simulations Show How Galactic Centers Cool Their Jets” 

    Berkeley Logo

    Berkeley Lab

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

    1
    This rendering illustrates magnetic kink instability in simulated jets beaming from a galaxy’s center. The jets are believed to be associated with supermassive black holes. The magnetic field line (white) in each jet is twisted as the central object (black hole) rotates. As the jets contact higher-density matter the magnetic fields build up and become unstable. The irregular bends and asymmetries of the magnetic field lines are symptomatic of kink instability. The instability dissipates the magnetic fields into heat with the change in density, leading them to become less tightly wound. (Credit: Berkeley Lab, Purdue University, NASA).

    Some of the most extreme outbursts observed in the universe are the mysterious jets of energy and matter beaming from the center of galaxies at nearly the speed of light. These narrow jets, which typically form in opposing pairs are believed to be associated with supermassive black holes and other exotic objects, though the mechanisms that drive and dissipate them are not well understood.

    Now, a small team of researchers has developed theories supported by 3-D simulations to explain what’s at work.

    Finding common causes for instabilities in space jets

    “These jets are notoriously hard to explain,” said Alexander “Sasha” Tchekhovskoy, a former NASA Einstein fellow who co-led the new study as a member of the Nuclear Science Division at the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab), and the Astronomy and Physics departments and Theoretical Astrophysics Center at UC Berkeley. “Why are they so stable in some galaxies and in others they just fall apart?”

    As much as half of the jets’ energy can escape in the form of X-rays and stronger forms of radiation. The researchers showed how two different mechanisms – both related to the jets’ interaction with surrounding matter, known as the “ambient medium” – serve to reduce about half of the energy of these powerful jets.

    “The exciting part of this research is that we are now coming to understand the full range of dissipation mechanisms that are working in the jet,” no matter the size or type of jet, he said.

    2
    An animation showing magnetic field instabilities in two jets of radiation and matter beaming from a supermassive black hole (center). The magnetic field (white) is twisted by the black hole’s spin. (Credit: Berkeley Lab, Purdue University)

    The study that Tchekhovskoy co-led with Purdue University scientists Rodolfo Barniol Duran and Dimitrios Giannios is published in the Aug. 21 edition of Monthly Notices of the Royal Astronomical Society. The study concludes that the ambient medium itself has a lot to do with how the jets release energy.

    “We were finally able to simulate jets that start from the black hole and propagate to very large distances – where they bump into the ambient medium,” said Duran, formerly a postdoctoral research associate at Purdue University who is now a faculty member at California State University, Sacramento.

    Tchekhovskoy, who has studied these jets for over a decade, said that an effect known as magnetic kink stability, which causes a sudden bend in the direction of some jets, and another effect that triggers a series of shocks within other jets, appear to be the primary mechanisms for energy release. The density of the ambient medium that the jets encounter serves as the key trigger for each type of release mechanism.

    “For a long time, we have speculated that shocks and instabilities trigger the spectacular light displays from jets. Now these ideas and models can be cast on a much firmer theoretical ground,” said Giannios, assistant professor of physics and astronomy at Purdue.

    The length and intensity of the jets can illuminate the properties of their associated black holes, such as their age and size and whether they are actively “feeding” on surrounding matter. The longest jets extend for millions of light years into surrounding space.

    “When we look at black holes, the first things we notice are the central streaks of these jets. You can make images of these streaks and measure their lengths, widths, and speeds to get information from the very center of the black hole,” Tchekhovskoy noted. “Black holes tend to eat in binges of tens and hundreds of millions of years. These jets are like the ‘burps’ of black holes – they are determined by the black holes’ diet and frequency of feeding.”

    3
    This animation shows the propagation of a jet of high-energy radiation and matter from a black hole (at the base of the animation) in a simulation, at four different time points. The frames show what happens as the jet contacts denser matter as it reaches out into surrounding space. (Credit: Berkeley Lab, Purdue University)

    While nothing – not even light – can escape a black hole’s interior, the jets somehow manage to draw their energy from the black hole. The jets are driven by a sort of accounting trick, he explained, like writing a check for a negative amount and having money appear in your account. In the black hole’s case, it’s the laws of physics rather than a banking loophole that allow black holes to spew energy and matter even as they suck in surrounding matter.

    The incredible friction and heating of gases spiraling in toward the black hole cause extreme temperatures and compression in magnetic fields, resulting in an energetic backlash and an outflow of radiation that escapes the black hole’s strong pull.

    A tale of magnetic kinks and sequenced shocks

    Earlier studies had shown how magnetic instabilities (kinks) in the jets can occur when jets run into the ambient medium. This instability is like a magnetic spring. If you squish the spring from both ends between your fingers, the spring will fly sideways out of your hand. Likewise, a jet experiencing this instability can change direction when it rams into matter outside of the black hole’s reach.

    The same type of instability frustrated scientists working on early machines that attempted to create and harness a superhot, charged state of matter known as a plasma in efforts to develop fusion energy, which powers the sun. The space jets, also known as active galactic nuclei (AGN) jets, also are a form of plasma.

    The latest study found that in cases where an earlier jet had “pre-drilled” a hole in the ambient medium surrounding a black hole and the matter impacted by the newly formed jet was less dense, a different process is at work in the form of “recollimation” shocks.

    These shocks form as matter and energy in the jet bounce off the sides of the hole. The jet, while losing energy from every shock, immediately reforms a narrow column until its energy eventually dissipates to the point that the beam loses its tight focus and spills out into a broad area.

    “With these shocks, the jet is like a phoenix. It comes out of the shock every time,” though with gradually lessening energy, Tchekhovskoy said. “This train of shocks cumulatively can dissipate quite a substantial amount of the total energy.”

    The researchers designed the models to smash against different densities of matter in the ambient medium to create instabilities in the jets that mimic astrophysical observations.

    Peering deeper into the source of jets

    New, higher-resolution images of regions in space where supermassive black holes are believed to exist – from the Event Horizon Telescope (EHT), for example – should help to inform and improve models and theories explaining jet behavior, Tchekhovskoy said, and future studies could also include more complexity in the jet models, such as a longer sequence of shocks.

    “It would be really interesting to include gravity into these models,” he said, “and to see the dynamics of buoyant cavities that the jet fills up with hot magnetized plasma as it drills a hole” in the ambient medium.

    4
    Side-by-side comparison of density “snapshots” produced in a 3-D simulation of jets beaming out from a black hole (at the base of images). Red shows higher density and blue shows lower density. The black directional lines show magnetic field streamlines. The perturbed magnetic lines reflect both the emergence of irregular magnetic fields in the jets and the large-scale deviations of the jets out of the image plane, both caused by the 3-D magnetic kink instability. (Credit: Berkeley Lab, Purdue University)

    He added, “Seeing deeper into where the jets come from – we think the jets start at the black hole’s event horizon (a point of no return for matter entering the black hole) – would be really helpful to see in nature these ‘bounces’ in repeating shocks, for example. The EHT could resolve this structure and provide a nice test of our work.”

    This work was supported by NASA through the Astrophysics Theory Program and Einstein Fellowship, the National Science Foundation through an XSEDE supercomputer allocation, the NASA High-End Computing Program through the NASA Advanced Supercomputing Division at Ames Research Center, Purdue University, and UC Berkeley through the Theoretical Astrophysics Center fellowship and access to the Savio supercomputer.

    See the full article here .

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  • richardmitnick 5:22 pm on August 2, 2017 Permalink | Reply
    Tags: LBNL, , New Simulations Could Help in Hunt for Massive Mergers of Neutron Stars and Black Holes,   

    From LBNL: “New Simulations Could Help in Hunt for Massive Mergers of Neutron Stars, Black Holes” 

    Berkeley Logo

    Berkeley Lab

    August 2, 2017
    Glenn Roberts Jr
    geroberts@lbl.gov

    1
    This image, from a computerized simulation, shows the formation of an inner disk of matter and a wide, hot disk of matter 5.5 milliseconds after the merger of a neutron star and a black hole. (Credit: Classical and Quantum Gravity)

    Now that scientists can detect the wiggly distortions in space-time created by the merger of massive black holes, they are setting their sights on the dynamics and aftermath of other cosmic duos that unify in catastrophic collisions.

    Working with an international team, scientists at the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) have developed new computer models to explore what happens when a black hole joins with a neutron star – the superdense remnant of an exploded star.

    Using supercomputers to rip open neutron stars

    The simulations, carried out in part at Berkeley Lab’s National Energy Research Scientific Computing Center (NERSC), are intended to help detectors home in on the gravitational-wave signals.

    NERSC

    NERSC Cray Cori II supercomputer

    LBL NERSC Cray XC30 Edison supercomputer

    NERSC Hopper Cray XE6 supercomputer

    Telescopes, too, can search for the brilliant bursts of gamma-rays and the glow of the radioactive matter that these exotic events can spew into surrounding space.

    In separate papers published in a special edition of the scientific journal Classical and Quantum Gravity, Berkeley Lab and other researchers present the results of detailed simulations.

    One of the studies models the first milliseconds (thousandths of a second) in the merger of a black hole and neutron star, and the other details separate simulations that model the formation of a disk of material formed within seconds of the merger, and of the evolution of matter that is ejected in the merger.

    2
    Early “snapshots” from a simulation of a neutron star-black hole merger. This entire animated sequence occurs within 43 milliseconds (43 thousandths of a second). (Credit: Classical and Quantum Gravity)

    That ejected matter likely includes gold and platinum and a range of radioactive elements that are heavier than iron.

    Any new information scientists can gather about how neutron stars rip apart in these mergers can help to unlock their secrets, as their inner structure and their likely role in seeding the universe with heavy elements are still shrouded in mystery.

    “We are steadily adding more realistic physics to the simulations,” said – Foucart, who served as a lead author for one of the studies as a postdoctoral researcher in Berkeley Lab’s Nuclear Science Division.

    “But we still don’t know what’s happening inside neutron stars. The complicated physics that we need to model make the simulations very computationally intensive.”

    Finding signs of a black hole–neutron star merger

    Foucart, who will soon be an assistant professor at the University of New Hampshire, added, “We are trying to move more toward actually making models of the gravitational-wave signals produced by these mergers,” which create a rippling in space-time that researchers hope can be detected with improvements in the sensitivity of experiments including Advanced LIGO, the Laser Interferometer Gravitational-Wave Observatory.


    Caltech/MIT Advanced aLigo Hanford, WA, USA installation


    Caltech/MIT Advanced aLigo detector installation Livingston, LA, USA

    Cornell SXS, the Simulating eXtreme Spacetimes (SXS) project


    Gravitational waves. Credit: MPI for Gravitational Physics/W.Benger-Zib

    ESA/eLISA the future of gravitational wave research

    In February 2016, LIGO scientists confirmed the first detection of a gravitational wave, believed to be generated by the merger of two black holes, each with masses about 30 times larger than the sun.

    The signals of a neutron star merging with black holes or another neutron star are expected to generate gravitational waves that are slightly weaker but similar to those of black hole–black hole mergers, Foucart said.

    Radioactive ‘waste’ in space

    Daniel Kasen, a scientist in the Nuclear Science Division at Berkeley Lab and associate professor of physics and astronomy at UC Berkeley who participated in the research, said that inside neutron stars “there may be exotic states of matter unlike anything realized anywhere else in the universe.”

    In some computer simulations the neutron stars were swallowed whole by the black hole, while in others there was a fraction of matter coughed up into space. This ejected matter is estimated to range up to about one-tenth of the mass of the sun.

    While much of the matter gets sucked into the larger black hole that forms from the merger, “the material that gets flung out eventually turns into a kind of radioactive ‘waste,’” he said. “You can see the radioactive glow of that material for a period of days or weeks, from more than a hundred million light years away.” Scientists refer to this observable radioactive glow as a “kilonova.”

    The simulations use different sets of calculations to help scientists visualize how matter escapes from these mergers. By modeling the speed, trajectory, amount and type of matter, and even the color of the light it gives off, astrophysicists can learn how to track down actual events.

    The weird world of neutron stars

    The size range of neutron stars is set by the ultimate limit on how densely matter can be compacted, and neutron stars are among the most superdense objects we know about in the universe.

    Neutron stars have been observed to have masses up to at least two times that of our sun but measure only about 12 miles in diameter, on average, while our own sun has a diameter of about 865,000 miles. At large enough masses, perhaps about three times the mass of the sun, scientists expect that neutron stars must collapse to form black holes.

    A cubic inch of matter from a neutron star is estimated to weigh up to 10 billion tons. As their name suggests, neutron stars are thought to be composed largely of the neutrally charged subatomic particles called neutrons, and some models expect them to contain long strands of matter – known as “nuclear pasta” – formed by atomic nuclei that bind together.

    Neutron stars are also expected to be almost perfectly spherical, with a rigid and incredibly smooth crust and an ultrapowerful magnetic field. They can spin at a rate of about 43,000 revolutions per minute (RPMs), or about five times faster than a NASCAR race car engine’s RPMs.

    The aftermath of neutron star mergers

    The researchers’ simulations showed that the radioactive matter that first escapes the black hole mergers may be traveling at speeds of about 20,000 to 60,000 miles per second, or up to about one-third the speed of light, as it is swung away in a long “tidal tail.”

    “This would be strange material that is loaded with neutrons,” Kasen said. “As that expanding material cools and decompresses, the particles may be able to combine to build up into the heaviest elements.” This latest research shows how scientists might find these bright bundles of heavy elements.

    “If we can follow up LIGO detections with telescopes and catch a radioactive glow, we may finally witness the birthplace of the heaviest elements in the universe,” he said. “That would answer one of the longest-standing questions in astrophysics.”

    Most of the matter in a black hole–neutron star merger is expected to be sucked up by the black hole within a millisecond of the merger, and other matter that is not flung away in the merger is likely to form an extremely dense, thin, donut-shaped halo of matter.

    The thin, hot disk of matter that is bound by the black hole is expected to form within about 10 milliseconds of the merger, and to be concentrated within about 15 to 70 miles of it, the simulations showed. This first 10 milliseconds appears to be key in the long-term evolution of these disks.

    Over timescales ranging from tens of milliseconds to several seconds, the hot disk spreads out and launches more matter into space. “A number of physical processes – from magnetic fields to particle interactions and nuclear reactions – combine in complex ways to drive the evolution of the disk,” said Rodrigo Fernández, an assistant professor of physics at the University of Alberta in Canada who led one of the studies.

    Simulations carried out on NERSC’s Edison supercomputer were crucial in understanding how the disk ejects matter and in providing clues for how to observe this matter, said Fernández, a former UC Berkeley postdoctoral researcher.

    What’s next?

    Eventually, it may be possible for astronomers scanning the night sky to find the “needle in a haystack” of radioactive kilonovae from neutron star mergers that had been missed in the LIGO data, Kasen said.

    “With improved models, we are better able to tell the observers exactly which flashes of light are the signals they are looking for,” he said. Kasen is also working to build increasingly sophisticated models of neutron star mergers and supernovae through his involvement in the DOE Exascale Computing Project.

    As the sensitivity of gravitational-wave detectors improves, Foucart said, it may be possible to detect a continuous signal produced by even a tiny bump on the surface of a neutron star, for example, or signals from theorized one-dimensional objects known as cosmic strings.

    “This could also allow us to observe events that we have not even imagined,” he said.

    5

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  • richardmitnick 3:39 pm on August 1, 2017 Permalink | Reply
    Tags: A newly discovered collective rattling effect in a type of crystalline semiconductor blocks most heat transfer while preserving high electrical conductivity, , , LBNL, , , Scanning Electron microscopy   

    From LBNL: “A Semiconductor That Can Beat the Heat” 

    Berkeley Logo

    Berkeley Lab

    July 31, 2017
    Jon Weiner
    jrweiner@lbl.gov
    (510) 486-4014

    A newly discovered collective rattling effect in a type of crystalline semiconductor blocks most heat transfer while preserving high electrical conductivity – a rare pairing that scientists say could reduce heat buildup in electronic devices and turbine engines, among other possible applications.

    A team led by scientists at the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) discovered these exotic traits in a class of materials known as halide perovskites, which are also considered promising candidates for next-generation solar panels, nanoscale lasers, electronic cooling, and electronic displays.

    These interrelated thermal and electrical (or “thermoelectric”) properties were found in nanoscale wires of cesium tin iodide (CsSnI3). The material was observed to have one of the lowest levels of heat conductivity among materials with a continuous crystalline structure.

    1
    Rattling structures of halide perovskites: cesium tin iodide (left) and cesium lead iodide (right). (Credit: Berkeley Lab/UC Berkeley)

    This so-called single-crystal material can also be more easily produced in large quantities than typical thermoelectric materials, such as silicon-germanium, researchers said.

    “Its properties originate from the crystal structure itself. It’s an atomic sort of phenomenon,” said Woochul Lee, a postdoctoral researcher at Berkeley Lab who was the lead author of the study, published the week of July 31 in the Proceedings of the National Academy of Sciences journal. These are the first published results relating to the thermoelectric performance of this single crystal material.

    Researchers earlier thought that the material’s thermal properties were the product of “caged” atoms rattling around within the material’s crystalline structure, as had been observed in some other materials. Such rattling can serve to disrupt heat transfer in a material.

    “We initially thought it was atoms of cesium, a heavy element, moving around in the material,” said Peidong Yang, a senior faculty scientist at Berkeley Lab’s Materials Sciences Division who led the study.

    Jeffrey Grossman, a researcher at the Massachusetts Institute of Technology, then performed some theory work and computerized simulations that helped to explain what the team had observed. Researchers also used Berkeley Lab’s Molecular Foundry, which specializes in nanoscale research, in the study.

    “We believe there is essentially a rattling mechanism, not just with the cesium. It’s the overall structure that’s rattling; it’s a collective rattling,” Yang said. “The rattling mechanism is associated with the crystal structure itself,” and is not the product of a collection of tiny crystal cages. “It is group atomic motion,” he added.

    Within the material’s crystal structure, the distance between atoms is shrinking and growing in a collective way that prevents heat from easily flowing through.

    But because the material is composed of an orderly, single-crystal structure, electrical current can still flow through it despite this collective rattling. Picture its electrical conductivity is like a submarine traveling smoothly in calm underwater currents, while its thermal conductivity is like a sailboat tossed about in heavy seas at the surface.

    Yang said two major applications for thermoelectric materials are in cooling, and in converting heat into electrical current. For this particular cesium tin iodide material, cooling applications such as a coating to help cool electronic camera sensors may be easier to achieve than heat-to-electrical conversion, he said.

    A challenge is that the material is highly reactive to air and water, so it requires a protective coating or encapsulation to function in a device.

    Cesium tin iodide was first discovered as a semiconductor material decades ago, and only in recent years has it been rediscovered for its other unique traits, Yang said. “It turns out to be an amazing gold mine of physical properties,” he noted.

    3
    Scanning electron microscope images of suspended micro-island devices. Individual AIHP NW is suspended between two membranes. (Credit: Berkeley Lab/UC Berkeley).

    To measure the thermal conductivity of the material, researchers bridged two islands of an anchoring material with a cesium tin iodide nanowire. The nanowire was connected at either end to micro-islands that functioned as both a heater and a thermometer. Researchers heated one of the islands and precisely measured how the nanowire transported heat to the other island.

    They also performed scanning electron microscopy to precisely measure the dimensions of the nanowire. They used these dimensions to provide an exacting measure of the material’s thermal conductivity. The team repeated the experiment with several different nanowire materials and multiple nanowire samples to compare thermoelectric properties and verify the thermal conductivity measurements.

    “A next step is to alloy this (cesium tin iodide) material,” Lee said. “This may improve the thermoelectric properties.”

    Also, just as computer chip manufacturers implant a succession of elements into silicon wafers to improve their electronic properties – a process known as “doping” – scientists hope to use similar techniques to more fully exploit the thermoelectric traits of this semiconductor material. This is relatively unexplored territory for this class of materials, Yang said.

    The research team also included other scientists from Berkeley Lab’s Materials Sciences Division and the Molecular Foundry, the Kavli Energy NanoScience Institute at UC Berkeley and Berkeley Lab, and UC Berkeley’s Department of Chemistry.

    The Molecular Foundry is a DOE Office of Science User Facility that provides free access to state-of-the-art equipment and multidisciplinary expertise in nanoscale science to visiting scientists from all over the world.

    This work was supported by the Department of Energy’s Office of Basic Energy Sciences.

    More information about Peidong Yang’s research group: http://nanowires.berkeley.edu/.

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  • richardmitnick 12:42 pm on July 20, 2017 Permalink | Reply
    Tags: , Commercialization of enhanced geothermal systems (EGS), LBNL,   

    From LBNL: “Berkeley Lab to Lead Multimillion-Dollar Geothermal Energy Project” 

    Berkeley Logo

    Berkeley Lab

    July 20, 2017
    Julie Chao
    JHChao@lbl.gov
    (510) 486-6491

    1
    Berkeley Lab scientist Tim Kneafsey demonstrates how he places rock samples, from the Brady Geothermal Field in Nevada, into a stress permeability apparatus, which tests how long a fracture can remain open. (Credit: Marilyn Chung/Berkeley Lab.)

    The Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) will lead a new $9 million project aimed at removing technical barriers to commercialization of enhanced geothermal systems (EGS), a clean energy technology with the potential to power 100 million American homes.

    Berkeley Lab will partner with seven other DOE national labs and six universities to develop field experiments focused on understanding and modeling rock fractures, an essential element of geothermal systems. Scientists will use the Sanford Underground Research Facility (SURF) in South Dakota to create small-scale fracture networks in crystalline rock 1,500 meters below ground.

    “We will be putting instrumentation within tens of meters of the fractures and will be able to detect fracturing at a higher resolution than what has ever been done before,” said Berkeley Lab’s Tim Kneafsey, who leads the project. “The goal is to work towards increasing our understanding of fracturing and fluid flow in EGS, which could provide a significant amount of electricity as a large quantity of accessible hot rock lies untapped across the U.S.”

    In geothermal systems, heat acquired from water circulating in rock fractures deep in the Earth’s crust is extracted for conversion to electricity. Conventional geothermal technology is possible only in locations with particular geological characteristics, either near active volcanic centers or in places with a very high temperature gradient, such as much of Nevada and parts of the western United States. These locations have the three components essential to extracting geothermal energy—heat, fluid, and permeability, a measure of how easily fluid can circulate through the rock’s fractures, picking up heat as it moves.

    With EGS, a fracture network can be enhanced or engineered, thus bypassing the geographic limitations of conventional geothermal energy. EGS could eventually provide more than 100 gigawatts (GW) of economically viable electric generating capacity in the continental United States, a huge increase over the current geothermal capacity of 3.5 GW.

    “Although geothermal energy production is already used effectively, there is a lot we need to learn about how to create and develop an EGS reservoir,” Kneafsey said. “This project will seek to understand the relationship between permeability creation and heat extraction in crystalline rocks under certain stress and temperature conditions.”

    Dubbed EGS Collab, the project has been awarded $9 million for the first year by DOE’s Geothermal Technologies Office. Other national labs partnering in the project include Sandia, Lawrence Livermore, Idaho, Los Alamos, Pacific Northwest, Oak Ridge, and the National Renewable Energy Laboratory.

    Douglas Blankenship, manager of geothermal research at Sandia National Laboratories, is the co-lead with Kneafsey. Additionally, professors from Stanford University, the University of Wisconsin, the South Dakota School of Mines and Technology, the Colorado School of Mines, Penn State University, and the University of Oklahoma will also contribute.

    See the full article here .

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  • richardmitnick 12:58 pm on July 19, 2017 Permalink | Reply
    Tags: , LBNL, New Droplet-on-Tape Method Assists Biochemical Research at X-Ray Lasers, , ,   

    From SLAC: “New Droplet-on-Tape Method Assists Biochemical Research at X-Ray Lasers” 


    SLAC Lab

    February 27, 2017 [Never saw this one before]

    1
    Acoustic droplet ejection allows scientists to deposit nanoliters of sample directly into the X-ray beam, considerably increasing the efficiency of sample consumption. A femtosecond pulse from an X-ray free-electron laser then intersects with a droplet that contains protein crystals. (SLAC National Accelerator Laboratory)

    SLAC/LCLS

    2
    As the drops move forward, they are hit with pulses of visible light or treated with oxygen gas, which triggers different chemical reactions depending on the sample studied. (SLAC National Accelerator Laboratory)

    Biological samples studied with intense X-rays at free-electron lasers are destroyed within nanoseconds after they are exposed. Because of this, the samples need to be continually refreshed to allow the many images needed for an experiment to be obtained. Conventional methods use jets that supply a continuous stream of samples, but this can be very wasteful as the X-rays only interact with a tiny fraction of the injected material.

    To help address this issue, scientists at the Department of Energy’s Lawrence Berkeley National Laboratory, SLAC National Accelerator Laboratory, Brookhaven National Laboratory, and other institutes designed a new assembly-line system that rapidly replaces exposed samples by moving droplets along a miniature conveyor belt, timed to coincide with the arrival of the X-ray pulses.

    The droplet-on-tape system now allows the team to study the biochemical reactions in real-time from microseconds to seconds, revealing the stages of these complex reactions.

    In their approach, protein solution or crystals are precisely deposited in tiny liquid drops, made as ultrasound waves push the liquid onto a moving tape. As the drops move forward, they are hit with pulses of visible light or treated with oxygen gas, which triggers different chemical reactions depending on the sample studied. This allows the study of processes such as photosynthesis, which determines how plants absorb light from the sun and convert it into useable energy.

    Finally, powerful X-ray pulses from SLAC’s X-ray laser, the Linac Coherent Light Source (LCLS), probe the drops. In this study published in Nature Methods, the X-ray light scattered from the sample onto two different detectors simultaneously, one for X-ray crystallography and the other for X-ray emission spectroscopy. These are two complementary methods that provide information about the geometric and electronic structure of the catalytic sites of the proteins and allowed them to watch with atomic precision how the protein structures changed during the reaction.

    Below, see the conveyor belt in action at LCLS, a Department of Energy Office of Science User Facility.

    3
    Droplet-on-tape conveyor belt system delivers samples at the Linac Coherent Light Source (LCLS). (SLAC National Accelerator Laboratory)

    See the full article here .

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    SLAC is a multi-program laboratory exploring frontier questions in photon science, astrophysics, particle physics and accelerator research. Located in Menlo Park, California, SLAC is operated by Stanford University for the DOE’s Office of Science.
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  • richardmitnick 2:36 pm on July 5, 2017 Permalink | Reply
    Tags: A Whole-Genome Sequenced Rice Mutant Resource for the Study of Biofuel Feedstocks, , Fast-neutron irradiation causes different types of mutations, , , Kitaake: a model rice variety with a short life cycle, LBNL   

    From LBNL: “A Whole-Genome Sequenced Rice Mutant Resource for the Study of Biofuel Feedstocks” 

    Berkeley Logo

    Berkeley Lab

    July 5, 2017
    Sarah Yang
    scyang@lbl.gov
    (510) 486-4575

    JBEI researchers create open-access web portal to accelerate functional genetic research in plants.

    1
    Genome-wide distribution of fast-neutron-induced mutations in the Kitaake rice mutant population (green). Even distribution of mutations is important to achieve saturation of the genome. Colored lines (center) represent translocations of DNA fragments from one chromosome to another. (Credit: Guotian Li and Rashmi Jain/Berkeley Lab).

    Rice is a staple food for over half of the world’s population and a model for studies of candidate bioenergy grasses such as sorghum, switchgrass, and Miscanthus. To optimize crops for biofuel production, scientists are seeking to identify genes that control key traits such as yield, resistance to disease, and water use efficiency.

    Populations of mutant plants, each one having one or more genes altered, are an important tool for elucidating gene function. With whole-genome sequencing at the single nucleotide level, researchers can infer the functions of the genes by observing the gain or loss of particular traits. But the utility of existing rice mutant collections has been limited by several factors, including the cultivars’ relatively long six-month life cycle and the lack of sequence information for most of the mutant lines.

    In a paper published in The Plant Cell, a team led by Pamela Ronald, a professor in the Genome Center and the Department of Plant Pathology at UC Davis and director of Grass Genetics at the Department of Energy’s (DOE’s) Joint BioEnergy Institute (JBEI), with collaborators from UC Davis and the DOE Joint Genome Institute (JGI), reported the first whole-genome sequenced fast-neutron induced mutant population of Kitaake, a model rice variety with a short life cycle.

    Kitaake (Oryza sativa L. ssp. japonica) completes its life cycle in just nine weeks and is not sensitive to photoperiod changes. This novel collection will accelerate functional genetic research in rice and other monocots, a type of flowering plant species that includes grasses.

    “Some of the most popular rice varieties people use right now only have two generations per year. Kitaake has up to four, which really speeds up functional genomics work,” said Guotian Li, a project scientist at Lawrence Berkeley National Laboratory (Berkeley Lab) and deputy director of Grass Genetics at JBEI.

    In a previously published pilot study [Molecular Plant], Li, Mawsheng Chern, and Rashmi Jain, co-first authors on The Plant Cell paper, demonstrated that fast-neutron irradiation produced abundant and diverse mutations in Kitaake, including single base substitutions, deletions, insertions, inversions, translocations, and duplications. Other techniques that have been used to generate rice mutant populations, such as the insertion of gene and chromosome segments and the use of gene editing tools like CRISPR-Cas9, generally produce a single type of mutation, Li noted.

    “Fast-neutron irradiation causes different types of mutations and gives different alleles of genes so we really can get something that’s not achievable from other collections,” he said.

    Whole-genome sequencing of this mutant population – 1,504 lines in total with 45-fold coverage – allowed the researchers to pinpoint each mutation at a single-nucleotide resolution. They identified 91,513 mutations affecting 32,307 genes, 58 percent of all genes in the roughly 389-megabase rice genome. A high proportion of these were loss-of-function mutations.

    Using this mutant collection, the Grass Genetics group identified an inversion affecting a single gene as the causative mutation for the short-grain phenotype in one mutant line with a population containing just 50 plants. In contrast, researchers needed more than 16,000 plants to identify the same gene using the conventional approach.

    “This comparison clearly demonstrates the power of the sequenced mutant population for rapid genetic analysis,” said Ronald.

    This high-density, high-resolution catalog of mutations, developed with JGI’s help, provides researchers opportunities to discover novel genes and functional elements controlling diverse biological pathways. To facilitate open access to this resource, the Grass Genetics group has established a web portal called KitBase, which allows users to find information related to the mutant collection, including sequence, mutation and phenotypic data for each rice line. Additional information about the database can be found through JGI.

    Additional Berkeley Lab scientists who contributed to this work include co-first authors Rashmi Jain and Mawsheng Chern; Tong Wei and Deling Ruan, both affiliated with JBEI’s Feedstocks Division and with Berkeley Lab’s Environmental Genomics and Systems Biology Division; Nikki Pham and Kyle Jones of JBEI’s Feedstocks Division; and Joel Martin, Wendy Schackwitz, Anna Lipzen, Diane Bauer, Yi Peng, and Kerrie Barry of the JGI.

    Support for the research at JBEI, a DOE Bioenergy Research Center, and JGI, a DOE Office of Science User Facility, was provided by DOE’s Office of Science. Additional support was provide by the National Institutes of Health and the National Science Foundation.

    See the full article here .

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  • richardmitnick 11:08 am on July 1, 2017 Permalink | Reply
    Tags: , , LBNL,   

    From Stanford Scope: “Researchers discover new mechanism involved in gene silencing” 

    Stanford University Name
    Stanford University

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    Scope blog

    June 30, 2017
    Jennifer Huber

    1
    No image caption or credit.

    Heterochromatin is a key player in gene regulation. This tightly packed complex of nuclear proteins and DNA is usually found in regions where genes are silenced. Unfortunately, how it works is not fully understood.

    Now, researchers from the Lawrence Berkeley National Laboratory have shown that heterochromatin organizes DNA into different physical compartments inside a cell nucleus to promote distinct genome functions. And it does this using liquid-liquid phase separation, the same mechanism that separates mixtures of oil and water, as recently reported in Nature.

    Previously, scientists thought that heterochromatin’s dense packing silenced genes by preventing regulatory proteins from gaining access. The theory was that the tightly wound strands made it difficult for the proteins to get to the genetic material inside. However, this didn’t explain why heterochromatin excludes some small proteins while admitting other large ones.

    The new study, using fruit flies and mouse cells, identified a different mechanism. The Berkeley Lab researchers observed two non-mixing liquids in the cell nucleus: one that contained silenced heterochromatin and another that contained DNA with expressed genes. They found that the heterochromatin droplets fused together like drops of oil in water, indicating that the distinct heterochromatin compartments arise through liquid-liquid phase separation.

    “We are excited about these findings because they explain a mystery that’s existed in the field for a decade,” said lead author Amy Strom, a biology graduate student at the University of California, Berkeley, in a recent news release. “That is, if compaction controls access to silenced sequences, how are other large proteins still able to get in? Chromatin organization by phase separation means that proteins are targeted to one liquid or the other based not on size, but on other physical traits, like charge, flexibility, and interaction partners.”

    The researchers hope a better understanding of how heterochromatin works will ultimately lead to improved gene therapy or other treatments that rely on accurate regulation of gene expression.

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    Scope is an award-winning blog founded in 2009 and produced by the Stanford University School of Medicine. If you’re curious about the latest advances in medicine and health and enjoy compelling, fresh and easily digestible news and features, then we’ve got just the thing. We’ve written quite a bit (7,000 posts and counting!), and we’re quite proud of it — so please enjoy.

    Leland and Jane Stanford founded the University to “promote the public welfare by exercising an influence on behalf of humanity and civilization.” Stanford opened its doors in 1891, and more than a century later, it remains dedicated to finding solutions to the great challenges of the day and to preparing our students for leadership in today’s complex world. Stanford, is an American private research university located in Stanford, California on an 8,180-acre (3,310 ha) campus near Palo Alto. Since 1952, more than 54 Stanford faculty, staff, and alumni have won the Nobel Prize, including 19 current faculty members

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  • richardmitnick 8:35 pm on June 28, 2017 Permalink | Reply
    Tags: , , , Katie Dunne, LBNL, , , ,   

    From LBNL: Women in STEM “Berkeley Lab Intern Finds Her Way in Particle Physics” Katie Dunne 

    Berkeley Logo

    Berkeley Lab

    June 27, 2017
    Theresa Duque
    tnduque@lbl.gov
    (510) 495-2418

    1
    Intern Katherine Dunne with mentor Maurice Garcia-Sciveres. (Credit: Marilyn Chung/Berkeley Lab)

    As a high school student in Birmingham, Alabama, Berkeley Lab Undergraduate Research (BLUR) intern Katie Dunne first dreamed of becoming a physicist after reading Albert Einstein’s biography, but didn’t know anyone who worked in science. “I felt like the people who were good at math and science weren’t my friends,” she said. So when it came time for college, she majored in English, and quickly grew dissatisfied because it wasn’t challenging enough. Eventually, she got to know a few engineers, but none of them were women, she recalled.

    She still kept physics in the back of her mind until she read an article about “The First Lady of Physics,” Chien-Shiung Wu, an experimental physicist who worked on the Manhattan Project, and later designed the “Wu experiment,” which proved that the conservation of parity is violated by weak interactions. “Two male theorists who proposed parity violation won the 1957 Nobel Prize in physics, and Wu did not,” Dunne said. “When I read about her, I decided that that’s what I want to do – design experiments.”

    So she put physics front and center, and about four years ago, transferred as a physics major to the City College of San Francisco. “With Silicon Valley nearby, there are many opportunities here to get work experience in instrumentation and electrical engineering,” Dunne said. In the summers of 2014 and 2015, she landed internships in the Human Factors division at NASA Ames Research Center in Mountain View, where she streamlined the development of a printed circuit board for active infrared illumination.

    But it wasn’t until she took a class in modern physics when she discovered her true passion – particle physics. “When we got to quantum physics, it was great. Working on the problems of quantum physics is exciting,” she said. “It’s so elegant and dovetails with math. It’s the ultimate mystery because we can’t observe quantum behavior.”

    When it came time to apply for her next summer internship in 2016, instead of reapplying for a position at NASA, she googled “ATLAS,” the name of a 7,000-ton detector for the Large Hadron Collider (LHC). Her search drummed up an article about Beate Heinemann, who, at the time, was a researcher with dual appointments at UC Berkeley and Berkeley Lab and was deputy spokesperson of the ATLAS collaboration. (Heinemann is also one of the 20 percent of female physicists working on the ATLAS experiment.)

    CERN/ATLAS detector

    When Dunne contacted Heinemann to ask if she would consider her for an internship, she suggested that she contact Maurice Garcia-Sciveres, a physicist at Berkeley Lab whose research specializes in pixel detectors for ATLAS, and who has mentored many students interested in instrumentation.

    Garcia-Sciveres invited Dunne to a meeting so she could see the kind of work that they do. “I could tell I would get a lot of hands-on experience,” she said. So she applied for her first internship with Garcia-Sciveres through the Community College Internship (CCI) program – which, like the BLUR internship program, is managed by Workforce Development & Education at Berkeley Lab – and started to work with his team on building prototype integrated circuit (IC) test systems for ATLAS as part of the High Luminosity Large Hadron Collider (HL-LHC) Project, an international collaboration headed by CERN to increase the LHC’s luminosity (rate of collisions) by a factor of 10 by 2020.

    3
    A quad module with a printed circuit board (PCB) for power and data interface to four FE-I4B chips. Dunne designed the PCB. (Credit: Katie Dunne/Berkeley Lab)

    “For the ATLAS experiment, we work with the Engineering Division to build custom electronics and integrated circuits for silicon detectors. Our work is focused on improving the operation, testing, and debugging of these ICs,” said Garcia-Sciveres.

    During Dunne’s first internship, she analyzed threshold scans for an IC readout chip, and tested their radiation hardness – or threshold for tolerating increasing radiation doses – at the Lab’s 88-Inch Cyclotron and at SLAC National Accelerator Laboratory. “Berkeley Lab is a unique environment for interns. They throw you in, and you learn on the job. The Lab gives students opportunities to make a difference in the field they’re working in,” she said.

    For Garcia-Sciveres, it didn’t take long for Dunne to prove she could make a difference for his team. Just after her first internship at Berkeley Lab, the results from her threshold analysis made their debut as data supporting his presentation at the 38th International Conference on High Energy Physics (ICHEP) in August 2016. “The results were from her measurements,” he said. “This is grad student-level work she’s been doing. She’s really good.”

    5
    Katie Dunne delivers a poster presentation in spring 2017. (Credit: Marilyn Chung/Berkeley Lab)

    After the conference, Garcia-Sciveres asked Dunne to write the now published proceedings (he and the other authors provided her with comments and suggested wording). And this past January, Dunne presented “Results of FE65-P2 Stability Tests for the High Luminosity LHC Upgrade” during the “HL-LHC, BELLE2, Future Colliders” session of the American Physical Society (APS) Meeting in Washington, D.C.

    This summer, for her third and final internship at the Lab, Dunne is working on designing circuit boards needed for the ATLAS experiment, and assembling and testing prototype multi-chip modules to evaluate system performance. She hopes to continue working on ATLAS when she transfers to UC Santa Cruz as a physics major in the fall, and would like to get a Ph.D. in physics one day. “I love knowing that the work I do matters. My internships and work experience as a research assistant at Berkeley Lab have made me more confident in the work I’m doing, and more passionate about getting things done and sharing my results,” she said.

    Go here for more information about internships hosted by Workforce Development & Education at Berkeley Lab, or contact them at education@lbl.gov.

    See the full article here .

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