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  • richardmitnick 11:32 pm on February 12, 2020 Permalink | Reply
    Tags: , , Biophysical chemistry, Chromophores, Macromolecular crystallography, , Photoisomerization, , , SLAC National Accelerator Laboratory   

    From SLAC National Accelerator Lab: “Researchers show how electric fields affect a molecular twist within light-sensitive proteins” 

    From SLAC National Accelerator Lab

    February 12, 2020
    By Ali Sundermier

    A better understanding of this phenomenon, which is crucial to many processes that occur in biological systems and materials, could enable researchers to develop light-sensitive proteins for areas such as biological imaging and optogenetics.

    A team of scientists from the Department of Energy’s SLAC National Accelerator Laboratory and Stanford University has gained insight into how electric fields affect the way energy from light drives molecular motion and transformation in a protein commonly used in biological imaging. A better understanding of this phenomenon, which is crucial to many processes that occur in biological systems and materials, could enable researchers to finely tune a system’s properties to harness these effects, for instance using light to control neurons in the brain. Their findings were published in Science in January.

    Twist and shout

    Human vision, photosynthesis and other natural processes harvest light with proteins that contain molecules known as chromophores, many of which twist when light hits them. The hallmark of this twisting motion, called photoisomerization, is that part of the molecule rotates around a particular chemical bond.

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    When light hits certain chromophores in proteins, it causes them to twist and change shape. This atomic reconfiguration, known as photoisomerization, changes the molecule’s chemical and physical properties. The hallmark of this process is a rotation that occurs around a chemical bond in the molecule. New research shows that the electric fields within a protein play a large role in determining which bond this rotation occurs around. (Chi-Yun Lin/Stanford University)

    “Something about the protein environment is steering this very specific and important process,” says Steven Boxer, a biophysical chemist and Stanford professor who oversaw the research. “One possibility is that the distribution of atoms in the molecular space blocks or allows rotation about each chemical bond, known as the steric effect. An alternative has to do with the idea that when molecules with double bonds are excited, there is a separation of charge, and so the surrounding electric fields might favor the rotation of one bond over another. This is called the electrostatic effect.”

    A different tune

    To find out more about this process, the researchers looked at green fluorescent protein, a protein frequently used in biological imaging whose chromophore can respond to light in a number of ways that are sensitive to its local environment within the protein, producing fluorescent light of various colors and intensities.

    Stanford graduate students Matt Romei and Chi-Yun Lin, who led the study, tuned the electronic properties of the chromophore within the protein by introducing chemical groups that systematically added or subtracted electrons from the chromophore to engineer an electric field effect. Then they measured how this affected the chromophore’s twisting motion.

    With the help of coauthor Irimpan Mathews, a scientist at SLAC’s Stanford Synchrotron Radiation Lightsource (SSRL), the researchers used an X-ray technique called macromolecular crystallography at SSRL beamlines 7-1, 12-2 and 14-1 to map the structures of these tuned proteins to show that these changes had little effect on the atomic structure of the chromophore and surrounding protein.

    SLAC/SSRL

    Then, using a combination of techniques, they were able to measure how changes to the chromophore’s electron distribution affected where rotation occurred when it was hit by light.

    “Until now, most of the research on photoisomerization in this particular protein has been either theoretical or focused on the steric effect,” Romei says. “This research is one of the first to investigate the phenomenon experimentally and show the importance of the electrostatic effect. Once we plotted the data, we saw these really nice trends that suggest that tuning the chromophore’s electronic properties has a huge impact on its bond isomerization properties.”

    Honing tools

    These results also suggest ways to design light-sensitive proteins by manipulating the environment around the chromophore. Lin adds that this same experimental approach could be used to study and control the electrostatic effect in many other systems.

    “We’re trying to figure out the principle that controls this process,” Lin says. “Using what we learn, we hope to apply these concepts to develop better tools in fields such as optogenetics, where you can selectively manipulate nerves to lead to certain functions in the brain.”

    Boxer adds that the idea that the organized electric fields within proteins are important for many biological functions is an emerging concept that could be of interest to a broad audience.

    “Much of the work in our lab focuses on developing methods to measure these fields and connect them with function such as enzymatic catalysis,” he says, “and we now see that photoisomerization fits into this framework.”

    This work was funded in part by the National Institutes of Health (NIH). SSRL is a DOE Office of Science user facility. The SSRL Structural Molecular Biology Program is supported by the NIH and the DOE Office of Biological and Environmental Research. Part of this work was performed at the Stanford Nano Shared Facilities and supported by the National Science Foundation.

    See the full article here .


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    Please help promote STEM in your local schools.

    Stem Education Coalition

    SLAC/LCLS


    SLAC/LCLS II projected view


    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.

    SSRL and LCLS are DOE Office of Science user facilities.

     
  • richardmitnick 12:14 pm on February 12, 2020 Permalink | Reply
    Tags: Atom or noise?, , , , , , SLAC National Accelerator Laboratory, Stanford’s Department of Bioengineering   

    From SLAC National Accelerator Lab: “Atom or noise? New method helps cryo-EM researchers tell the difference” 

    From SLAC National Accelerator Lab

    February 11, 2020
    Nathan Collins

    Cryogenic electron microscopy can in principle make out individual atoms in a molecule, but distinguishing the crisp from the blurry parts of an image can be a challenge. A new mathematical method may help.

    Cryogenic electron microscopy, or cryo-EM, has reached the point where researchers could in principle image individual atoms in a 3D reconstruction of a molecule – but just because they could see those details doesn’t always mean they do. Now, researchers at the Department of Energy’s SLAC National Accelerator Laboratory and Stanford University have proposed a new way to quantify how accurate such reconstructions are and, in the process, how confident they can be in their molecular interpretations. The study was published February 10 in Nature Methods.

    Cryo-EM works by freezing biological molecules which can contain thousands of atoms so they can be imaged under an electron microscope. By aligning and combining many two-dimensional images, researchers can compute three-dimensional maps of an entire molecule, and this technique has been used to study everything from battery failure to the way viruses invade cells. However, an issue that has been hard to solve is how to accurately assess the true level of detail or resolution at every point in such maps and in turn determine what atomic features are truly visible or not.

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    A cryo-EM map of the molecule apoferritin (left) and a detail of the map showing the atomic model researchers use to construct Q-scores. (Image courtesy Greg Pintilie)

    Wah Chiu, a professor at SLAC and Stanford, Grigore Pintilie, a computational scientist in Chiu’s group, and colleagues devised the new measures, known as Q-scores, to address that issue. To compute Q-scores, scientists start by building and adjusting an atomic model until it best matches the corresponding cryo-EM derived 3D map. Then, they compare the map to an idealized version in which each atom is well-resolved, revealing to what degree the map truly resolves the atoms in the atomic model.

    The researchers validated their approach on large molecules, including a protein called apoferritin that they studied in the Stanford-SLAC Cryo-EM Facilities. Kaiming Zhang, another research scientist in Chiu’s group, produced 3D maps close to the highest resolution reached to date – up to 1.75 angstrom, less than a fifth of a nanometer. Using such maps, they showed how Q-scores varied in predictable ways based on overall resolution and on which parts of a molecule they were studying. Pintilie and Chiu say they hope Q-scores will help biologists and others using cryo-EM better understand and interpret the 3D maps and resulting atomic models.

    The study was performed in collaboration with researchers from Stanford’s Department of Bioengineering. Molecular graphics and analysis were performed using the University of California, San Francisco’s Chimera software package. The project was funded by the National Institutes of Health.

    See the full article here .


    five-ways-keep-your-child-safe-school-shootings
    Please help promote STEM in your local schools.

    Stem Education Coalition

    SLAC/LCLS


    SLAC/LCLS II projected view


    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.

    SSRL and LCLS are DOE Office of Science user facilities.

     
  • richardmitnick 9:54 am on February 6, 2020 Permalink | Reply
    Tags: "Could the next generation of particle accelerators come out of the 3D printer?", , , , Consortium on the Properties of Additive-Manufactured Copper, , , , SLAC National Accelerator Laboratory   

    From SLAC National Accelerator Lab: “Could the next generation of particle accelerators come out of the 3D printer?” 

    From SLAC National Accelerator Lab

    February 5, 2020
    Jennifer Huber

    SLAC scientists and collaborators are developing 3D copper printing techniques to build accelerator components.

    Imagine being able to manufacture complex devices whenever you want and wherever you are. It would create unforeseen possibilities even in the most remote locations, such as building spare parts or new components on board a spacecraft. 3D printing, or additive manufacturing, could be a way of doing just that. All you would need is the materials the device will be made of, a printer and a computer that controls the process.

    Diana Gamzina, a staff scientist at the Department of Energy’s SLAC National Accelerator Laboratory; Timothy Horn, an assistant professor of mechanical and aerospace engineering at North Carolina State University; and researchers at RadiaBeam Technologies dream of developing the technique to print particle accelerators and vacuum electronic devices for applications in medical imaging and treatment, the electrical grid, satellite communications, defense systems and more.

    1
    Examples of 3D-printed copper components that could be used in a particle accelerator: X-band klystron output cavity with micro-cooling channels (at left) and a set of coupled accelerator cavities. (Christopher Ledford/North Carolina State University)

    In fact, the researchers are closer to making this a reality than you might think.

    “We’re trying to print a particle accelerator, which is really ambitious,” Gamzina said. “We’ve been developing the process over the past few years, and we can already print particle accelerator components today. The whole point of 3D printing is to make stuff no matter where you are without a lot of infrastructure. So you can print your particle accelerator on a naval ship, in a small university lab or somewhere very remote.”

    3D printing can be done with liquids and powders of numerous materials, but there aren’t any well-established processes for 3D printing ultra-high-purity copper and its alloys – the materials Gamzina, Horn and their colleagues want to use. Their research focuses on developing the method.

    Indispensable copper

    Accelerators boost the energy of particle beams, and vacuum electronic devices are used in amplifiers and generators. Both rely on components that can be easily shaped and conduct heat and electricity extremely well. Copper has all of these qualities and is therefore widely used.

    Traditionally, each copper component is machined individually and bonded with others using heat to form complex geometries. This manufacturing technique is incredibly common, but it has its disadvantages.

    “Brazing together multiple parts and components takes a great deal of time, precision and care,” Horn said. “And any time you have a joint between two materials, you add a potential failure point. So, there is a need to reduce or eliminate those assembly processes.”

    Potential of 3D copper printing

    3D printing of copper components could offer a solution.

    It works by layering thin sheets of materials on top of one another and slowly building up specific shapes and objects. In Gamzina’s and Horn’s work, the material used is extremely pure copper powder.

    The process starts with a 3D design, or “construction manual,” for the object. Controlled by a computer, the printer spreads a few-micron-thick layer of copper powder on a platform. It then moves the platform about 50 microns – half the thickness of a human hair – and spreads a second copper layer on top of the first, heats it with an electron beam to about 2,000 degrees Fahrenheit and welds it with the first layer. This process repeats over and over until the entire object has been built.


    3D printing of copper devices
    3D printing of a layer of a device known as a traveling wave tube using copper powder. (Christopher Ledford/North Carolina State University)

    The amazing part: no specific tooling, fixtures or molds are needed for the procedure. As a result, 3D printing eliminates design constraints inherent in traditional fabrication processes and allows the construction of objects that are uniquely complex.

    “The shape doesn’t really matter for 3D printing,” said SLAC staff scientist Chris Nantista, who designs and tests 3D-printed samples for Gamzina and Horn. “You just program it in, start your system and it can build up almost anything you want. It opens up a new space of potential shapes.”

    The team took advantage of that, for example, when building part of a klystron – a specialized vacuum tube that amplifies radiofrequency signals – with internal cooling channels at NCSU. Building it in one piece improved the device’s heat transfer and performance.

    Compared to traditional manufacturing, 3D printing is also less time consuming and could translate into cost savings of up to 70%, Gamzina said.

    A challenging technique

    But printing copper devices has its own challenges, as Horn, who began developing the technique with collaborators from RadiaBeam years ago, knows. One issue is finding the right balance between the thermal and electrical properties and strengths of the printed objects. But the biggest hurdle for manufacturing accelerators and vacuum electronics, though, is that these high-vacuum devices require extremely high quality and pure materials to avoid part failures, such as cracking or vacuum leaks.

    The research team tackled these challenges by first improving the material’s surface quality, using finer copper powder and varying the way they fused layers together. However, using finer copper powder led to the next challenge. It allowed more oxygen to attach to the copper powder, increasing the oxide in each layer and making the printed objects less pure.

    So, Gamzina and Horn had to find a way to reduce the oxygen content in their copper powders. The method they came up with, which they recently reported in Applied Sciences, relies on hydrogen gas to bind oxygen into water vapor and drive it out of the powder.

    Using this method is somewhat surprising, Horn said. In a traditionally manufactured copper object, the formation of water vapor would create high-pressure steam bubbles inside the material, and the material would blister and fail. In the additive process, on the other hand, the water vapor escapes layer by layer, which releases the water vapor more effectively.

    Although the technique has shown great promise, the scientists still have a ways to go to reduce the oxygen content enough to print an actual particle accelerator. But they have already succeeded in printing a few components, such as the klystron output cavity with internal cooling channels and a string of coupled cavities that could be used for particle acceleration.

    Planning to team up with industry partners

    The next phase of the project will be driven by the newly-formed Consortium on the Properties of Additive-Manufactured Copper, which is led by Horn. The consortium currently has four active industry members – Siemens, GE Additive, RadiaBeam and Calabazas Creek Research – with more on the way.

    “This would be a nice example of collaboration between an academic institution, a national lab and small and large businesses,” Gamzina said. “It would allow us to figure out this problem together. Our work has already allowed us to go from ‘just imagine, this is crazy’ to ‘we can do it’ in less than two years.”

    This work was primarily funded by the Naval Sea Systems Command, as a Small Business Technology Transfer Program with Radiabeam, SLAC, and NCSU. Other SLAC contributors include Chris Pearson, Andy Nguyen, Arianna Gleason, Apurva Mehta, Kevin Stone, Chris Tassone and Johanna Weker. Additional contributions came from Christopher Ledford and Christopher Rock at NCSU and Pedro Frigola, Paul Carriere, Alexander Laurich, James Penney and Matt Heintz at RadiaBeam.

    See the full article here .


    five-ways-keep-your-child-safe-school-shootings
    Please help promote STEM in your local schools.

    Stem Education Coalition

    SLAC/LCLS


    SLAC/LCLS II projected view


    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.

    SSRL and LCLS are DOE Office of Science user facilities.

     
  • richardmitnick 10:02 am on January 31, 2020 Permalink | Reply
    Tags: "First detailed electronic study of new nickelate superconductor", , , , , SLAC National Accelerator Laboratory,   

    From SLAC National Accelerator Lab and Stanford University: “First detailed electronic study of new nickelate superconductor” 

    Stanford University Name
    From Stanford University

    and

    SLAC National Accelerator Lab

    January 20, 2020 [Just showed up in social media.]
    Glennda Chui

    Discovered at SLAC and Stanford, this new class of unconventional superconductors is starting to give up its secrets – including a surprising 3D metallic state.

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    A SLAC/Stanford study found that a recently discovered family of nickelate superconductors differs in surprising ways from a related family, the cuprates. Both come in 2D oxide planes (red, green, and grey spheres representing copper, nickel and oxygen ions, respectively) separated by layers of a rare earth material (gold spheres). Cuprates are inherently insulators, and even when they’re doped to add free-flowing electrons (blue spheres), as shown here, their electrons rarely leave to interact with other layers of material. But these nickelates are inherently metals. Even in the non-doped state depicted here, their electrons mix with electrons from the rare-earth layers in a way that creates a 3D metallic state. (Greg Stewart/SLAC National Accelerator Laboratory)

    The discovery last year of the first nickel oxide material that shows clear signs of superconductivity set off a race by scientists around the world to find out more. The crystal structure of the material is similar to copper oxides, or cuprates, which hold the world record for conducting electricity with no loss at relatively high temperatures and normal pressures. But do its electrons behave in the same way?

    The answers could help advance the synthesis of new unconventional superconductors and their use for power transmission, transportation and other applications, and also shed light on how the cuprates operate – which is still a mystery after more than 30 years of research.

    In a paper published today in Nature Materials, a team led by scientists at the Department of Energy’s SLAC National Accelerator Laboratory and Stanford University report the first detailed investigation of the electronic structure of superconducting nickel oxides, or nickelates. The scientists used two techniques, resonant inelastic X-ray scattering (RIXS) and X-ray absorption spectroscopy (XAS), to get the first complete picture of the nickelates’ electronic structure – basically the arrangement and behavior of their electrons, which determine a material’s properties.

    Both cuprates and nickelates come in thin, two-dimensional sheets that are layered with other elements, such as rare-earth ions. These thin sheets become superconducting when they’re cooled below a certain temperature and the density of their free-flowing electrons is adjusted in a process known as “doping.”

    Cuprates are insulators in their pre-doped “ground” states, meaning that their electrons are not mobile. After doping the electrons can move freely but they are mostly confined to the cuprate layers, rarely traveling through the intervening rare-earth layers to reach their cuprate neighbors.

    But in the nickelates, the team discovered, this is not the case. The undoped compound is a metal with freely flowing electrons. Furthermore, the intervening layers actually contribute electrons to the nickelate sheets, creating a three-dimensional metallic state that is quite different from what’s seen in the cuprates.

    This is an entirely new type of ground state for transition metal oxides such as cuprates and nickelates, the researchers said. It opens new directions for experiments and theoretical studies of how superconductivity arises and how it can be optimized in this system and possibly in other compounds.

    The study was funded by the DOE Office of Science through the Stanford Institute for Materials and Energy Sciences (SIMES) at SLAC. The lead authors of the study were SIMES researchers Matthias Hepting (now at Max Planck Institute in Stuttgart, Germany), Wei-Sheng Lee and Chunjing Jia. The team also included SIMES researcher Danfeng Li, who led the experiments [see above link] that discovered the new superconducting nickelates, as well as theorists at SIMES and at Leiden University in The Netherlands.

    XAS and RIXS measurements were carried out at the Swiss Light Source in Switzerland, the Diamond Light Source in the United Kingdom, NSRRC in Taiwan and Lawrence Berkeley National Laboratory’s Advanced Light Source, which is a DOE Office of Science user facility.

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    Swiss Light Source. https://lightsources.org/lightsources-of-the-world/europe/swiss-light-source-sls/

    Diamond Light Source, located at the Harwell Science and Innovation Campus in Oxfordshire U.K.

    4
    National Synchrotron Radiation Research Center. East, Hsinchu City, Taiwan. Ministry of Science and Technology (Taiwan)

    LBNL ALS

    Stanford University campus. No image credit

    See the full article here .


    five-ways-keep-your-child-safe-school-shootings
    Please help promote STEM in your local schools.

    Stem Education Coalition

    SLAC/LCLS


    SLAC/LCLS II projected view


    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.
    The scientists used special software, designed by van den Bedem, that is highly sensitive to identifying protein movement from X-ray crystallography data to interpret the results, revealing never-before-seen motions that play a key role in catalyzing complex reactions, such as breaking down antibiotics. Next, the researchers hope to use LCLS to obtain room temperature structures of other enzymes to get a better look at how the motions occurring within them help move along reactions.
    SSRL and LCLS are DOE Office of Science user facilities. This work was funded by the DOE Office of Science and the National Institutes of Health, among other sources.

    Stanford University

    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.

     
  • richardmitnick 9:53 am on January 22, 2020 Permalink | Reply
    Tags: "A new strategy for directly detecting light particle dark matter", , , , , , SLAC National Accelerator Laboratory   

    From SLAC National Accelerator Lab via phys.org: “A new strategy for directly detecting light particle dark matter” 

    From SLAC National Accelerator Lab

    via


    phys.org

    January 21, 2020
    Ingrid Fadelli

    1
    A schematic figure of the potential experiment proposed in the paper. Credit: Berlin et al.

    For almost a century, astronomers have hypothesized that the universe contains more matter than what can be observed by the human eye. It is now believed that approximately 80 percent of the universe’s mass is made up of a type of matter that does not emit light or energy and that scientists are still unable to observe directly, referred to as Dark Matter.

    Fritz Zwicky discovered Dark Matter when observing the movement of the Coma Cluster., Vera Rubin a Woman in STEM denied the Nobel, did most of the work on Dark Matter.

    Fritz Zwicky from http:// palomarskies.blogspot.com

    Coma cluster via NASA/ESA Hubble

    Astronomer Vera Rubin at the Lowell Observatory in 1965, worked on Dark Matter (The Carnegie Institution for Science)


    Vera Rubin measuring spectra, worked on Dark Matter (Emilio Segre Visual Archives AIP SPL)


    Vera Rubin, with Department of Terrestrial Magnetism (DTM) image tube spectrograph attached to the Kitt Peak 84-inch telescope, 1970. https://home.dtm.ciw.edu

    The LSST, or Large Synoptic Survey Telescope is to be named the Vera C. Rubin Observatory by an act of the U.S. Congress.

    LSST telescope, The Vera Rubin Survey Telescope currently under construction on the El Peñón peak at Cerro Pachón Chile, a 2,682-meter-high mountain in Coquimbo Region, in northern Chile, alongside the existing Gemini South and Southern Astrophysical Research Telescopes.

    LSST Data Journey, Illustration by Sandbox Studio, Chicago with Ana Kova

    Dark Matter Research

    Universe map Sloan Digital Sky Survey (SDSS) 2dF Galaxy Redshift Survey

    Scientists studying the cosmic microwave background [CMB]hope to learn about more than just how the universe grew—it could also offer insight into dark matter, dark energy and the mass of the neutrino.

    [caption id="attachment_73741" align="alignnone" width="632"] CMB per ESA/Planck

    Dark matter cosmic web and the large-scale structure it forms The Millenium Simulation, V. Springel et al

    Dark Matter Particle Explorer China

    DEAP Dark Matter detector, The DEAP-3600, suspended in the SNOLAB deep in Sudbury’s Creighton Mine

    LBNL LZ Dark Matter project at SURF, Lead, SD, USA


    Inside the ADMX experiment hall at the University of Washington Credit Mark Stone U. of Washington. Axion Dark Matter Experiment

    While there are now countless studies and theories about dark matter, there is still no direct experimental evidence supporting its existence. Several physicists have tried to devise methods to detect dark matter in the universe, yet all of these have so far been unsuccessful.

    Over the past few decades, researchers have started to wonder how dark matter could possibly be detected, especially considering that it consists of particles that are much lighter than protons. A model that has gained substantial attention is one that considers dark matter as a particle that has a very small charge under normal electromagnetism.

    Drawing inspiration from this model, researchers at the SLAC National Accelerator Laboratory in California have recently devised a new strategy that could directly detect light particle dark matter that has long-ranged interactions with ordinary matter. The strategy they came up with, presented in a paper published in Physical Review Letters, entails distorting the local flow of dark matter with time-varying fields and measuring these distortions using shielded resonant detectors.

    “So far, most ideas of how to detect dark matter particles have relied on trying to detect small energy depositions from dark matter scattering in a very sensitive detector,” Asher Berlin, one of the researchers who carried out the study, told Phys.org. “My collaborators and I recently realized that an alternative detection mechanism exists: Instead of waiting for dark matter to deposit some small amount of energy in a detector via scattering, it is possible to directly manipulate the trajectories of individual dark matter particles, setting up disturbances that can then be measured with very sensitive resonant detectors, similar to everyday radios.”

    In contrast with most strategies for detecting dark matter introduced in previous studies, the new strategy proposed by Berlin and his colleagues takes advantage of the “collective” effect that many individual dark matter particles could produce, rather than the effect derived from a single dark matter particle. As a result, their detection method benefits from the small mass/momentum of light dark matter, particularly if compared with techniques that try to measure dark matter scattering within a detector, which is typically far more challenging if the dark matter particles are very light.

    “We have identified a potentially promising alternative to detecting sub-MeV particle-like dark matter without relying on energy deposition from scattering,” Berlin explained. “At this point, any new idea, including ours, may open up the possibility toward successfully discovering dark matter particles.”

    In their paper, Berlin and his colleagues theoretically applied their newly devised detection scheme to sub-MeV dark matter particles with very small electric charges or that are coupled to a light vector mediator. Their analyses suggest that their approach can probe dark matter masses ranging between 10MeV and below one meV, thus potentially reaching beyond what previous theories and detection efforts have achieved.

    While the strategy devised by the researchers seems promising, it is still merely theoretical. In the coming years, however, their work could inform the development of new tools for detecting dark matter particles, which would ultimately help to determine the validity and possible limitations of their approach.

    “In the future, we plan on teaming up with experimentalists who are interested in actually building such a detector,” Berlin said. “We also plan on investigating related detection ideas for other possible dark matter particles that possess different kinds of interactions with normal matter.”

    See the full article here .


    five-ways-keep-your-child-safe-school-shootings
    Please help promote STEM in your local schools.

    Stem Education Coalition

    SLAC/LCLS


    SLAC/LCLS II projected view


    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.
    The scientists used special software, designed by van den Bedem, that is highly sensitive to identifying protein movement from X-ray crystallography data to interpret the results, revealing never-before-seen motions that play a key role in catalyzing complex reactions, such as breaking down antibiotics. Next, the researchers hope to use LCLS to obtain room temperature structures of other enzymes to get a better look at how the motions occurring within them help move along reactions.
    SSRL and LCLS are DOE Office of Science user facilities. This work was funded by the DOE Office of Science and the National Institutes of Health, among other sources.

     
  • richardmitnick 9:17 pm on January 13, 2020 Permalink | Reply
    Tags: "Connecting the dots in the sky could shed new light on dark matter", , , , , , , SLAC National Accelerator Laboratory   

    From SLAC National Accelerator Lab: “Connecting the dots in the sky could shed new light on dark matter” 

    From SLAC National Accelerator Lab

    January 13, 2020
    Manuel Gnida

    Matching up maps of matter and light from the Dark Energy Survey and Fermi Gamma-ray Space Telescope may help astrophysicists understand what causes a faint cosmic gamma-ray glow.

    Dark Energy Survey


    Dark Energy Camera [DECam], built at FNAL


    NOAO/CTIO Victor M Blanco 4m Telescope which houses the DECam at Cerro Tololo, Chile, housing DECam at an altitude of 7200 feet

    Timeline of the Inflationary Universe WMAP

    The Dark Energy Survey (DES) is an international, collaborative effort to map hundreds of millions of galaxies, detect thousands of supernovae, and find patterns of cosmic structure that will reveal the nature of the mysterious dark energy that is accelerating the expansion of our Universe. DES began searching the Southern skies on August 31, 2013.

    According to Einstein’s theory of General Relativity, gravity should lead to a slowing of the cosmic expansion. Yet, in 1998, two teams of astronomers studying distant supernovae made the remarkable discovery that the expansion of the universe is speeding up. To explain cosmic acceleration, cosmologists are faced with two possibilities: either 70% of the universe exists in an exotic form, now called dark energy, that exhibits a gravitational force opposite to the attractive gravity of ordinary matter, or General Relativity must be replaced by a new theory of gravity on cosmic scales.

    DES is designed to probe the origin of the accelerating universe and help uncover the nature of dark energy by measuring the 14-billion-year history of cosmic expansion with high precision. More than 400 scientists from over 25 institutions in the United States, Spain, the United Kingdom, Brazil, Germany, Switzerland, and Australia are working on the project. The collaboration built and is using an extremely sensitive 570-Megapixel digital camera, DECam, mounted on the Blanco 4-meter telescope at Cerro Tololo Inter-American Observatory, high in the Chilean Andes, to carry out the project.

    Over six years (2013-2019), the DES collaboration used 758 nights of observation to carry out a deep, wide-area survey to record information from 300 million galaxies that are billions of light-years from Earth. The survey imaged 5000 square degrees of the southern sky in five optical filters to obtain detailed information about each galaxy. A fraction of the survey time is used to observe smaller patches of sky roughly once a week to discover and study thousands of supernovae and other astrophysical transients.

    NASA/Fermi LAT

    NASA/Fermi Gamma Ray Space Telescope

    Astrophysicists have come a step closer to understanding the origin of a faint glow of gamma rays covering the night sky. They found that this light is brighter in regions that contain a lot of matter and dimmer where matter is sparser – a correlation that could help them narrow down the properties of exotic astrophysical objects and invisible dark matter.

    The glow, known as unresolved gamma-ray background, stems from sources that are so faint and far away that researchers can’t identify them individually. Yet, the fact that the locations where these gamma rays originate match up with where mass is found in the distant universe could be a key puzzle piece in identifying those sources.

    2
    In a new study, astrophysicists have found a certain gamma-ray glow in the sky, known as unresolved gamma-ray background (yellow), to coincide with cosmic regions that contain a lot of matter (red). The correlation could lead to a better understanding of highly energetic astrophysical objects and dark matter. The gamma-ray map was created with nine years of data from the Fermi spacecraft, and the map showing the density of matter is based on one year of data from the Dark Energy Survey (DES). (Daniel Gruen/SLAC/Stanford, Chihway Chang/University of Chicago, Alex Drlica-Wagner/Fermilab)

    The background is the sum of a lot of things ‘out there’ that produce gamma rays. Having been able to measure for the first time its correlation with gravitational lensing – tiny distortions of images of far galaxies produced by the distribution of matter – helps us disentangle them,” said Simone Ammazzalorso from the University of Turin and the National Institute for Nuclear Physics (INFN) in Italy, who co-led the analysis.

    The study used one year of data from the Dark Energy Survey (DES), which takes optical images of the sky, and nine years of data from the Fermi Gamma-ray Space Telescope, which observes cosmic gamma rays while it orbits the Earth.

    “What’s really intriguing is that the correlation we measured doesn’t completely match our expectations,” said Panofsky fellow Daniel Gruen from the Kavli Institute for Particle Astrophysics and Cosmology (KIPAC) at the Department of Energy’s SLAC National Accelerator Laboratory and Stanford University, who led the analysis for the DES collaboration. “This could mean that we either need to adjust our existing models for objects that emit gamma rays, or it could hint at other sources, such as dark matter.”

    The study was accepted today for publication in Physical Review Letters.

    Two sensitive ‘eyes’ on the sky

    Gamma radiation, the most energetic form of light, is produced in a wide range of cosmic phenomena – often extremely violent ones, such as exploding stars, dense neutron stars rotating at high speeds and powerful beams of particles shooting out of active galaxies whose central supermassive black holes gobble up matter.

    Another potential source is invisible dark matter, which is believed to make up 85 percent of all matter in the universe. It could produce gamma rays when dark matter particles meet and destroy each other in space.

    The Large Area Telescope (LAT) on board the Fermi spacecraft is a highly sensitive “eye” for gamma radiation, and its data provide a detailed map of gamma-ray sources in the sky.

    But when scientists subtract all the sources they already know, their map is far from empty; it still contains a gamma-ray background whose brightness varies from region to region.

    “Unfortunately gamma rays don’t have a label that would tell us where they came from,” Gruen said. “That’s why we need additional information to unravel their origin.”

    That’s where DES comes in. With its 570-megapixel Dark Energy Camera, mounted on the Victor M. Blanco 4-meter Telescope at the Cerro Tololo Inter-American Observatory in Chile, it snaps images of hundreds of millions of galaxies.

    Cerro Tololo Inter-American Observatory on Cerro Tololo in the Coquimbo Region of northern Chile Altitude 2,207 m (7,241 ft)

    Their exact shapes tell researchers how the gravitational pull of matter bends light in the universe – an effect that shows itself as tiny distortions in galaxy images, known as weak gravitational lensing. Based on these data, the DES researchers create the most detailed maps yet of matter in the cosmos.

    In the new study, the scientists superimposed the Fermi and DES maps, which revealed that the two aren’t independent. The unresolved gamma-ray background is more intense in regions with more matter and less intense in regions with less matter.

    “The result itself is not surprising. We expect that there are more gamma ray producing processes in regions that contain more matter, and we’ve been predicting this correlation for a while,” said Nicolao Fornengo, one of Ammazzalorso’s supervisors in Turin. “But now we’ve succeeded in actually detecting this correlation for the first time, and we can use it to understand what causes the gamma ray background.”

    Potential hint at dark matter.

    Fritz Zwicky discovered Dark Matter when observing the movement of the Coma Cluster., Vera Rubin a Woman in STEM denied the Nobel, did most of the work on Dark Matter.

    Fritz Zwicky from http:// palomarskies.blogspot.com

    Coma cluster via NASA/ESA Hubble

    Astronomer Vera Rubin at the Lowell Observatory in 1965, worked on Dark Matter (The Carnegie Institution for Science)


    Vera Rubin measuring spectra, worked on Dark Matter (Emilio Segre Visual Archives AIP SPL)


    Vera Rubin, with Department of Terrestrial Magnetism (DTM) image tube spectrograph attached to the Kitt Peak 84-inch telescope, 1970. https://home.dtm.ciw.edu

    The LSST, or Large Synoptic Survey Telescope is to be named the Vera C. Rubin Observatory by an act of the U.S. Congress.

    LSST telescope, The Vera Rubin Survey Telescope currently under construction on the El Peñón peak at Cerro Pachón Chile, a 2,682-meter-high mountain in Coquimbo Region, in northern Chile, alongside the existing Gemini South and Southern Astrophysical Research Telescopes.

    Dark Matter Research

    Universe map Sloan Digital Sky Survey (SDSS) 2dF Galaxy Redshift Survey

    Scientists studying the cosmic microwave background [CMB]hope to learn about more than just how the universe grew—it could also offer insight into dark matter, dark energy and the mass of the neutrino.

    [caption id="attachment_73741" align="alignnone" width="632"] CMB per ESA/Planck

    Dark matter cosmic web and the large-scale structure it forms The Millenium Simulation, V. Springel et al

    Dark Matter Particle Explorer China

    DEAP Dark Matter detector, The DEAP-3600, suspended in the SNOLAB deep in Sudbury’s Creighton Mine

    LBNL LZ Dark Matter project at SURF, Lead, SD, USA


    Inside the ADMX experiment hall at the University of Washington Credit Mark Stone U. of Washington. Axion Dark Matter Experiment

    One of the most likely sources for the gamma-ray glow is very distant blazars – active galaxies with supermassive black holes at their centers. As the black holes swallow surrounding matter, they spew high-speed jets of plasma and gamma rays that, if the jets point at us, are detected by the Fermi spacecraft.

    Blazars would be the simplest assumption, but the new data suggest that a simple population of blazars might not be enough to explain the observed correlation between gamma rays and mass distribution, the researchers said.

    5
    By now iconic illustration of a blazar, a powerful object that produces beams of gamma rays when material spirals into a massive black hole. Blazars are the most common extraterrestrial sources of high-energy gamma rays detected by the Fermi Gamma-ray Space Telescope. (M. Weiss/CfA)

    In fact, our models for emissions from blazars can fairly well explain the low-energy part of the correlation, but we see deviations for high-energy gamma rays,” Gruen said. “This can mean several things: It could indicate that we need to improve our models for blazars or that the gamma rays could come from other sources.”

    One of these other sources could be dark matter. A leading theory predicts the mysterious stuff is made of weakly interacting massive particles, or WIMPs, which could annihilate each other in a flash of gamma rays when they collide. Gamma rays from certain matter-rich cosmic regions could therefore stem from these particle interactions.

    The idea to look for gamma-ray signatures of annihilating WIMPs is not a new one. Over the past years, scientists have searched for them in various locations believed to contain a lot of dark matter, including the center of the Milky Way and the Milky Way’s companion galaxies. However, these searches haven’t produced identifiable dark matter signals yet. The new results could be used for additional searches that test the WIMP hypothesis.

    Planning next steps

    Although the probability that the measured correlation is just a random effect is only about one in a thousand, the researchers need more data for a conclusive analysis.

    “These results, connecting for the first time our maps of gamma rays and matter, are very interesting and have a lot of potential, but at the moment the connection is still relatively weak, and one has to interpret the data carefully,” said KIPAC Director Risa Wechsler, who was not involved in the study.

    One of the main limitations of the current analysis is the amount of available lensing data, Gruen said. “With data from 40 million galaxies, DES has already pushed this to a new level, and that’s why we were able to do the analysis in the first place. But we need even better measurements,” he said.

    With its next data release, DES will provide lensing data for 100 million galaxies, and the future Legacy Survey of Space and Time (LSST) at the Vera Rubin Observatory will look at billions of galaxies in a much larger region of the sky.

    “Our study demonstrates with actual data that we can use the correlation between the distributions of matter and gamma rays to learn more about what causes the gamma-ray background,” Fornengo said. “With more DES data, LSST coming online and other projects like the Euclid space telescope on the horizon, we’ll be able to go much deeper in our understanding of the potential sources.”

    ESA/Euclid spacecraft depiction

    Then, the scientists might be able to tell if some of that gamma-ray glow stems from dark matter’s self-destruction.

    DES is an international project with over 400 scientists from 25 institutions in 7 countries, who have come together to carry out the survey. Parts of the project were funded by DOE’s Office of Science and the National Science Foundation. NASA’s Fermi Gamma-ray Space Telescope is an international and multi-agency space observatory. The analysis used Fermi-LAT data that were publicly released by the international LAT collaboration.

    See the full article here .


    five-ways-keep-your-child-safe-school-shootings
    Please help promote STEM in your local schools.

    Stem Education Coalition

    SLAC/LCLS


    SLAC/LCLS II projected view


    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.

     
  • richardmitnick 2:28 pm on January 4, 2020 Permalink | Reply
    Tags: A particle accelerator that fits on a chip, SLAC National Accelerator Laboratory,   

    From Stanford University: “Stanford researchers build a particle accelerator that fits on a chip, miniaturizing a technology that can now find new applications in research and medicine” 

    Stanford University Name
    From Stanford University

    January 2, 2020
    Tom Abate
    tabate@stanford.edu
    (650) 815-1602 (mobile)

    Just as engineers once compressed some of the power of room-sized mainframes into desktop PCs, so too have Stanford researchers shown how to pack some of the punch delivered by today’s ginormous particle accelerators onto a tiny silicon chip.

    1
    This image, magnified 25,000 times, shows a section of an accelerator-on-a-chip. The gray structures focus infrared laser light (shown in yellow and purple) on electrons flowing through the center channel. By packing 1,000 channels onto an inch-sized chip, Stanford researchers hope to accelerate electrons to 94 percent of the speed of light. (Image credit: Courtesy Neil Sapra)

    On a hillside above Stanford University, the SLAC National Accelerator Laboratory operates a scientific instrument nearly 2 miles long.

    SLAC Campus

    In this giant accelerator, a stream of electrons flows through a vacuum pipe, as bursts of microwave radiation nudge the particles ever-faster forward until their velocity approaches the speed of light, creating a powerful beam that scientists from around the world use to probe the atomic and molecular structures of inorganic and biological materials.

    Now, for the first time, scientists at Stanford and SLAC have created a silicon chip that can accelerate electrons – albeit at a fraction of the velocity of that massive instrument – using an infrared laser to deliver, in less than a hair’s width, the sort of energy boost that takes microwaves many feet.

    Writing in the Jan. 3 issue of Science, a team led by electrical engineer Jelena Vuckovic explained how they carved a nanoscale channel out of silicon, sealed it in a vacuum and sent electrons through this cavity while pulses of infrared light – to which silicon is as transparent as glass is to visible light – were transmitted by the channel walls to speed the electrons along.

    The accelerator-on-a-chip demonstrated in Science is just a prototype, but Vuckovic said its design and fabrication techniques can be scaled up to deliver particle beams accelerated enough to perform cutting-edge experiments in chemistry, materials science and biological discovery that don’t require the power of a massive accelerator.

    “The largest accelerators are like powerful telescopes. There are only a few in the world and scientists must come to places like SLAC to use them,” Vuckovic said. “We want to miniaturize accelerator technology in a way that makes it a more accessible research tool.”

    Team members liken their approach to the way that computing evolved from the mainframe to the smaller but still useful PC. Accelerator-on-a-chip technology could also lead to new cancer radiation therapies, said physicist Robert Byer, a co-author of the Science paper. Again, it’s a matter of size. Today, medical X-ray machines fill a room and deliver a beam of radiation that’s tough to focus on tumors, requiring patients to wear lead shields to minimize collateral damage.

    “In this paper we begin to show how it might be possible to deliver electron beam radiation directly to a tumor, leaving healthy tissue unaffected,” said Byer, who leads the Accelerator on a Chip International Program, or ACHIP, a broader effort of which this current research is a part.

    Inverse design

    In their paper, Vuckovic and graduate student Neil Sapra, the first author, explain how the team built a chip that fires pulses of infrared light through silicon to hit electrons at just the right moment, and just the right angle, to move them forward just a bit faster than before.

    To accomplish this, they turned the design process upside down. In a traditional accelerator, like the one at SLAC, engineers generally draft a basic design, then run simulations to physically arrange the microwave bursts to deliver the greatest possible acceleration. But microwaves measure 4 inches from peak to trough, while infrared light has a wavelength one-tenth the width of a human hair. That difference explains why infrared light can accelerate electrons in such short distances compared to microwaves. But this also means that the chip’s physical features must be 100,000 times smaller than the copper structures in a traditional accelerator. This demands a new approach to engineering based on silicon integrated photonics and lithography.

    Vuckovic’s team solved the problem using inverse design algorithms that her lab has developed. These algorithms allowed the researchers to work backward, by specifying how much light energy they wanted the chip to deliver, and tasking the software with suggesting how to build the right nanoscale structures required to bring the photons into proper contact with the flow of electrons.

    “Sometimes, inverse designs can produce solutions that a human engineer might not have thought of,” said R. Joel England, a SLAC staff scientist and co-author on the Science paper.

    The design algorithm came up with a chip layout that seems almost otherworldly. Imagine nanoscale mesas, separated by a channel, etched out of silicon. Electrons flowing through the channel run a gantlet of silicon wires, poking through the canyon wall at strategic locations. Each time the laser pulses – which it does 100,000 times a second – a burst of photons hits a bunch of electrons, accelerating them forward. All of this occurs in less than a hair’s width, on the surface of a vacuum-sealed silicon chip, made by team members at Stanford.

    The researchers want to accelerate electrons to 94 percent of the speed of light, or 1 million electron volts (1MeV), to create a particle flow powerful enough for research or medical purposes. This prototype chip provides only a single stage of acceleration, and the electron flow would have to pass through around 1,000 of these stages to achieve 1MeV. But that’s not as daunting at it may seem, said Vuckovic, because this prototype accelerator-on-a-chip is a fully integrated circuit. That means all of the critical functions needed to create acceleration are built right into the chip, and increasing its capabilities should be reasonably straightforward.

    The researchers plan to pack a thousand stages of acceleration into roughly an inch of chip space by the end of 2020 to reach their 1MeV target. Although that would be an important milestone, such a device would still pale in power alongside the capabilities of the SLAC research accelerator, which can generate energy levels 30,000 times greater than 1MeV. But Byer believes that, just as transistors eventually replaced vacuum tubes in electronics, light-based devices will one day challenge the capabilities of microwave-driven accelerators.

    Meanwhile, in anticipation of developing a 1MeV accelerator on a chip, electrical engineer Olav Solgaard, a co-author on the paper, has already begun work on a possible cancer-fighting application. Today, highly energized electrons aren’t used for radiation therapy because they would burn the skin. Solgaard is working on a way to channel high-energy electrons from a chip-sized accelerator through a catheter-like vacuum tube that could be inserted below the skin, right alongside a tumor, using the particle beam to administer radiation therapy surgically.

    “We can derive medical benefits from the miniaturization of accelerator technology in addition to the research applications,” Solgaard said.

    See the full article here .


    five-ways-keep-your-child-safe-school-shootings
    Please help promote STEM in your local schools.

    Stem Education Coalition

    Stanford University campus. No image credit

    Stanford University

    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

    Stanford University Seal

     
  • richardmitnick 10:30 pm on December 17, 2019 Permalink | Reply
    Tags: "Scientists discover how proteins form crystals that tile a microbe’s shell", , , , , , SLAC National Accelerator Laboratory,   

    From SLAC National Accelerator Lab: “Scientists discover how proteins form crystals that tile a microbe’s shell” 

    From SLAC National Accelerator Lab

    December 17, 2019
    Glennda Chui

    1
    In this illustration, protein crystals join six-sided ’tiles’ forming at top left and far right, part of a protective shell worn by many microbes. A new study zooms in on the first steps of crystal formation and helps explain how microbial shells assemble themselves so quickly. Credit: Greg Stewart/SLAC National Accelerator Laboratory

    A new understanding of the nucleation process could shed light on how the shells help microbes interact with their environments, and help people design self-assembling nanostructures for various tasks.

    Many microbes wear beautifully patterned crystalline shells, which protect them from a harsh world and can even help them reel in food. Studies at the Department of Energy’s SLAC National Accelerator Laboratory and Stanford University have revealed this food-reeling process and shown how shells assemble themselves from protein building blocks.

    Now the same team has zoomed in on the very first step in microbial shell-building: nucleation, where squiggly proteins crystallize into sturdy building blocks, much like rock candy crystallizes around a string dipped into sugar syrup.

    The results, published today in the Proceedings of the National Academy of Sciences, could shed light on how the shells help microbes interact with other organisms and with their environments, and also help scientists design self-assembling nanostructures for various tasks.

    2

    Jonathan Herrmann, a graduate student in Professor Soichi Wakatsuki’s group at SLAC and Stanford, collaborated with the structural molecular biology team at SLAC’s Stanford Synchrotron Radiation Lightsource (SSRL) on the study.

    SLAC/SSRL

    They scattered a powerful beam of X-rays off protein molecules that were floating in a solution to see how the atomic structures of the molecules changed as they nucleated into crystals. Meanwhile, other researchers made a series of cryogenic electron microscope (cryo-EM) images at various points in the nucleation process to show what happened over time.

    They found out that crystal formation takes place in two steps: One end of the protein molecule nucleates into crystal while the other end, called the N-terminus, continues to wiggle around. Then the N-terminus joins in, and the crystallization is complete. Far from being a laggard, the N-terminus actually speeds up the initial nucleation step ­– although exactly how it does this is still unknown, the researchers said – and this helps explain why microbial shells can form so quickly and efficiently.

    Some of the X-ray data was collected at Lawrence Berkeley National Laboratory’s Advanced Light Source, which like SSRL is a DOE Office of Science user facility.

    LBNL ALS

    Researchers from the University of British Columbia and from Professor Lucy Shapiro’s laboratory at Stanford also contributed to this work, funded in part by the National Institute of General Medical Sciences and the Chan Zuckerberg Biohub. Work in Wakatsuki’s labs at SLAC and Stanford was funded by a Laboratory Directed Research and Development grant from SLAC, the DOE Office of Science’s Office of Biological and Environmental Research, and Stanford’s Precourt Institute for Energy.

    See the full article here .


    five-ways-keep-your-child-safe-school-shootings
    Please help promote STEM in your local schools.

    Stem Education Coalition

    SLAC/LCLS


    SLAC/LCLS II projected view


    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.
    The scientists used special software, designed by van den Bedem, that is highly sensitive to identifying protein movement from X-ray crystallography data to interpret the results, revealing never-before-seen motions that play a key role in catalyzing complex reactions, such as breaking down antibiotics. Next, the researchers hope to use LCLS to obtain room temperature structures of other enzymes to get a better look at how the motions occurring within them help move along reactions.
    SSRL and LCLS are DOE Office of Science user facilities. This work was funded by the DOE Office of Science and the National Institutes of Health, among other sources.

     
  • richardmitnick 8:16 am on December 17, 2019 Permalink | Reply
    Tags: "Researchers reveal how enzyme motions catalyze reactions", , , , Enzymes, SLAC National Accelerator Laboratory, ,   

    From SLAC National Accelerator Lab: “Researchers reveal how enzyme motions catalyze reactions” 

    From SLAC National Accelerator Lab

    December 16, 2019
    Ali Sundermier

    What they learned could lead to a better understanding of how antibiotics are broken down in the body, potentially leading to the development of more effective drugs.

    1
    This illustration shows how an enzyme moves and changes as it catalyzes complex reactions and breaks down organic compounds. (10.1073/pnas.1901864116)

    In a time-resolved X-ray experiment, researchers uncovered, at atomic resolution and in real time, the previously unknown way that a microbial enzyme breaks down organic compounds.

    The team, led by Mark Wilson at the University of Nebraska Lincoln (UNL) and Henry van den Bedem at the Department of Energy’s SLAC National Accelerator Laboratory (now at Atomwise Inc.), published their findings last week in the Proceedings of the National Academy of Sciences. What they learned about this enzyme, whose structure is similar to one that is implicated in neurodegenerative diseases such as Parkinson’s, could lead to a better understanding of how antibiotics are broken down by microbes and to the development of more effective drugs.

    Previously, the researchers used SLAC’s Stanford Synchrotron Radiation Lightsource (SSRL) to obtain the structure of the enzyme at very low temperatures using X-ray crystallography.

    SLAC/SSRL

    In this study, Medhanjali Dasgupta, a UNL graduate student who was the study’s first author, used the Linac Coherent Light Source (LCLS), SLAC’s X-ray laser, to watch the enzyme and its substrate within the crystal move and change as it went through a full catalytic cycle at room temperature.

    SLAC/LCLS

    The scientists used special software, designed by van den Bedem, that is highly sensitive to identifying protein movement from X-ray crystallography data to interpret the results, revealing never-before-seen motions that play a key role in catalyzing complex reactions, such as breaking down antibiotics. Next, the researchers hope to use LCLS to obtain room temperature structures of other enzymes to get a better look at how the motions occurring within them help move along reactions.

    SSRL and LCLS are DOE Office of Science user facilities. This work was funded by the DOE Office of Science and the National Institutes of Health, among other sources.

    See the full article here .


    five-ways-keep-your-child-safe-school-shootings
    Please help promote STEM in your local schools.

    Stem Education Coalition

    SLAC/LCLS


    SLAC/LCLS II projected view


    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.


     
  • richardmitnick 10:44 am on December 4, 2019 Permalink | Reply
    Tags: "Study sheds light on the really peculiar ‘normal’ phase of high-temperature superconductors", , Quantum critical point theory, SLAC National Accelerator Laboratory, The study was carried out on a compound called Bi2212   

    From SLAC National Accelerator Lab: “Study sheds light on the really peculiar ‘normal’ phase of high-temperature superconductors” 

    From SLAC National Accelerator Lab

    December 3, 2019
    Glennda Chui

    It reveals an abrupt transition in cuprates where particles give up their individuality. The results flip a popular theory on its head.

    Every character has a back story, and so do high-temperature superconductors, which conduct electricity with no loss at much higher temperatures than scientists once thought possible. To figure out how they work, researchers need to understand their “normal” state, which gives rise to superconductivity when the material is cooled below a critical transition temperature and the density of free-flowing electrons is tweaked in a process known as “doping.”

    Even in their normal state, these materials are pretty peculiar. Now, an experiment at the Department of Energy’s SLAC National Accelerator Laboratory has probed the normal state more accurately than ever before, and discovered an abrupt shift in the behavior of electrons in which they suddenly give up their individuality and behave like an electron soup.

    A research team from SLAC and Stanford University described the results in Science.

    “The abnormality of this normal state is suspected to be the reason why these superconductors are such good superconductors,” says Dirk Van Der Marel, a researcher at the University of Geneva who was not involved in the study.

    “This study has essentially overthrown a very popular and hotly debated theory, called quantum critical point theory, that is thought to underlie superconductivity not only in this material, but in other materials as well. This is a disruptive finding, but it’s a step forward, because it frees our minds to explore other ideas.”

    1
    An illustration shows how the normal state of a superconducting cuprate abruptly changes when the density of free-flowing electrons is tweaked in a process known as doping. Particle-like excitations that are characteristic of a conventional metal (right) disappear as the ‘strange metallic’ state (left) takes over. (Greg Stewart/SLAC National Accelerator Laboratory)

    Exploring a well-known cuprate

    The study was carried out on a compound called Bi2212, one of the most thoroughly studied high-temperature superconductors. As a copper oxide, or cuprate, it’s part of a family of compounds where high-temperature superconductivity was first discovered more than 30 years ago.

    Scientists across the world have been working ever since to understand how these materials function, with a goal of finding superconductors that operate at close to room temperature for applications like perfectly efficient power lines.

    One of the most important tools for studying these materials is angle-resolved photoemission spectroscopy (ARPES). It uses light – in this case a beam of ultraviolet light from SLAC’s Stanford Synchrotron Radiation Lightsource (SSRL) – to kick electrons out of the material and measure their energy and momentum. This reveals how the electrons inside the material behave, which in turn determines its properties.

    In superconductivity, for instance, electrons overcome their mutual repulsion and form a sort of collective soup in which they can pair up and flow past obstacles without losing any of their energy.

    Frustrated electrons

    Earlier generations of so-called conventional superconductors, which operate only at extremely low temperatures, are conventional metals in their normal state, where their electrons act independently, as they do in most materials.

    But in cuprates the picture is very different. Even in their normal, non-superconducting state, electrons seem to recognize each other and act collectively, as if they were dragging each other around, in what’s known as “strange metal” and even “incoherent strange metal” behavior.

    “In a way you can think about these electrons as being frustrated,” said Zhi-Xun Shen, a professor at Stanford and SLAC and investigator with the Stanford Institute for Materials and Energy Sciences (SIMES) at SLAC who led the study. “In other words, the electrons have sort of lost their individual identity and become part of the soup. This is a really interesting, challenging state to describe in theoretical ways.”

    It’s been hard to explore these fascinating normal states at the warm temperatures where they occur, said Su-Di Chen, a Stanford graduate student who performed the experiments with SLAC postdoctoral researcher Yu He, Stanford postdoc Jun-Feng He and SSRL scientist Makoto Hashimoto. The theoretical part of the study at SLAC was led by SIMES Director Thomas Devereaux.

    A surprisingly sharp boundary

    In ARPES experiments, samples are usually placed in a cold environment inside a vacuum chamber to minimize contamination of the surface, Chen said: “But even if you put them in an ultra-high vacuum, residual gas molecules can still attach to the sample surface and affect the quality of our measurement. This problem gets worse when you warm the environment around the sample to the temperatures where the normal states exist.”

    To get around this, Hashimoto said, the team found a way to warm the sample, which is about the size of the tip of a ballpoint pen, by warming just the part of the setup that holds it while keeping everything else cold. This allowed them to examine the electrons’ behavior across a range of temperatures and doping levels.

    “What we saw was that as you increase the level of doping, there’s a very sharp boundary,” Hashimoto said. “On one side the electrons are jammed, or frustrated. Then, as more electrons are added, they suddenly start moving smoothly, an indication that the material is now a conventional metal. This transition was known to happen, but the fact that it was so sharp was a real surprise.”

    A challenge for theory

    The results pose a challenge for theorists who still struggle to explain how high-temperature superconductors work, said paper co-author Jan Zaanen, a theoretical physicist at the University of Leiden in The Netherlands.

    Current theory predicts that because changes in the nature of Bi2212 are gradual at very low, superconducting temperatures, they should also be gradual at the higher temperatures where the material is in a normal state, he said. Instead the high-temperature changes are abrupt, like what happens when a pot of water starts to boil: You can see either water or bubbles of steam in the roiling pot, but nothing in between.

    “There are quite a number of reasons to believe that the strange metal in the normal state may be an example of densely entangled matter,” Zaanen said. “Entanglement is the property of the quantum world that sharply distinguishes it from anything classical. We have no theoretical machines, be it classical computers or the available mathematics, that can describe it!

    “But quantum computers are designed to handle such densely entangled stuff,” he said. “My dream is that these results will eventually land on the top of the list of benchmark problems for the quantum computing community to solve.”

    SSRL is a DOE Office of Science user facility. Samples for the study were grown by Hiroshi Eisaki of the National Institute of Advanced Industrial Science and Technology in Japan. The work was funded by the DOE Office of Science.

    See the full article here .


    five-ways-keep-your-child-safe-school-shootings
    Please help promote STEM in your local schools.

    Stem Education Coalition

    SLAC/LCLS


    SLAC/LCLS II projected view


    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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