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  • richardmitnick 9:03 am on February 23, 2019 Permalink | Reply
    Tags: "Faculty Senate hears presentation on SLAC and votes on resolution to affirm diversity, , , free expression and civility", SLAC Labs,   

    From Stanford University and SLAC Lab: “Faculty Senate hears presentation on SLAC and votes on resolution to affirm diversity, free expression and civility” 

    SLAC National Accelerator Lab

    Stanford University Name
    From Stanford University

    February 22, 2019
    Chris Bliss

    1
    SLAC Director Chi-Chang Kao speaking to the Faculty Senate on Thursday. (Image credit: L.A. Cicero)

    The partnership of SLAC National Accelerator Laboratory and Stanford University allows both organizations to leverage their resources and expertise to advance scientific discovery, SLAC Director Chi-Chang Kao said in his report to the Faculty Senate on Thursday. His presentation touched on the laboratory’s storied 57-year history, the partnership with Stanford, its current focus and its aspirations for the future.

    At the meeting, the senate also approved a motion endorsing need-blind admissions for international undergraduate students and passed a resolution to affirm diversity, free expression and civility. In other business, the senate voted to establish the charge of a new ad hoc Committee on the Professoriate, which will look at the recommendations from the Provost’s Task Force on Lecturers.

    Report from SLAC

    Founded in 1962, SLAC National Accelerator Laboratory is a U.S. Department of Energy (DOE) national laboratory managed by Stanford.

    Kao said that SLAC’s unique partnership with Stanford distinguishes the lab from other DOE sites and enables SLAC to increase its scientific impact.

    Last year, DOE funding at SLAC supported the work of nearly 50 Stanford researchers and 400 graduate students and postdoctoral scholars, and a growing number of Stanford researchers from across the campus – more than 500 in 2018 – use the state-of-the-art facilities.

    Kao said SLAC’s partnership with Stanford is “very important” and envisions more opportunities to collaborate with the university. Looking to the future, SLAC aspires to solve the big science questions – from the origin of the universe to the laws of physics, and Stanford researchers will be integral to this work. “These big questions need research at scale both in terms of the size of the teams, the cost and the complexity. A national laboratory is exactly the place to do that,” Kao said.

    Today, SLAC designs, constructs and operates large-scale instruments to explore the universe using satellites, telescopes, underground detectors and instrumentation capabilities, Kao said. Two instruments are currently under construction: the LCLS-II, an upgrade to the LCLS (Linac Coherent Light Source), which creates X-rays a billion times brighter than available before, and FACET-II (Facility for Advanced Accelerator Experimental Tests), which will drive new research in accelerator technology.


    SLAC LCLS-II

    SLAC FACET-II upgrading its Facility for Advanced Accelerator Experimental Tests (FACET) – a test bed for new technologies that could revolutionize the way we build particle accelerators

    Developing new technologies is a central focus at SLAC and the lab has broadened its mission into new areas like national security, cancer treatment, neuroscience, telecommunications and advanced electronics for autonomous vehicles.

    In response to a question about how SLAC negotiates with the government about the projects it undertakes, Kao responded that in recent years the government has exerted more influence; however, “the more engagement campus faculty have with SLAC, that will help us be the leader in influencing the policy of the future.”

    International undergraduate admissions and financial aid

    The Faculty Senate approved a motion from the Committee on Undergraduate Admission and Financial Aid (C-UAFA) endorsing need-blind admissions for international students. Stanford currently has a need-blind admission process for U.S. domestic students and meets the full demonstrated financial need of all students who are admitted to Stanford and are eligible for aid.

    C-UAFA chair David Lobell, professor of Earth system science, introduced the motion regarding need-blind international admissions, which stated, in part, “As a global leader in higher education, Stanford University should be accessible to the best students in the world regardless of their socio-economic background.”

    President Marc Tessier-Lavigne applauded the work of C-UAFA in bring the issue forward. He noted that last spring the university made the commitment to go down the path to becoming need-blind for international undergraduate students. “We all recognize that it requires tremendous resources and it can’t happen overnight, but unless we prioritize it, it won’t get done,” he said.

    Resolution on diversity, free expression and civility

    The senate also voted to approve a resolution to reaffirm the university’s commitment to diversity, the observance of mutual respect and civility in discussion of controversial subjects and adherence to the university’s Fundamental Standard of student conduct. Developed by the Steering Committee of the Faculty Senate, this resolution is the result of several conversations the senate has had this academic year about this issue, including an entire meeting devoted to free speech and academic freedom. The document was conceived out of concern about the damages to the larger democracy incurred by hate speech and disinformation and the importance of academic freedom to the university’s educational mission.

    Prior to the vote, there was much discussion about the wording of the resolution, particularly on a passage that directly quotes from the Fundamental Standard: “Students are expected to show both within and without the university such respect for order, morality, personal honor and the rights of others as is demanded of good citizens.”

    Acknowledging that the Fundamental Standard, adopted in 1896, was a product of its time, several senate members argued that some of the language in the resolution should be changed to better reflect current thinking about standards of conduct. However, two amendments proposing alterations to the language in the resolution failed to pass.

    The resolution charges the Planning and Policy Board to develop recommendations for “promoting a culture of civility in the service of diversity, academic freedom and educative discourse at Stanford University.”

    Committee on the Professoriate

    In other business, the senate voted to establish the charge of a new ad hoc Committee on the Professoriate. The committee will consider recommendations made last fall by the Provost’s Task Force on Lecturers, specifically about adding, changing and eliminating some titles for teaching faculty and clarifying the criteria for the ranks of senior fellow and center fellow.

    The new committee is charged with providing the senate with a final report by the end of autumn quarter 2020.

    Provost’s report

    Provost Persis Drell reported on challenges the Budget Group is facing in putting together the 2019-20 budget plan. She said several factors are contributing to what she expects will be a “tight” year, including modest returns on the university’s endowment payout. She noted that the endowment payout has not kept up with inflation for the past four years, and that trend is anticipated to continue.

    She said that implementing the long-range vision is also a priority for the university, and while some initiatives will attract philanthropy, others may require realignment of existing resources in order to fulfill.

    The need to continue to address affordability challenges for all segments of the Stanford community is also a major consideration in budget planning, said Drell. “I believe our community will accept some cost cutting in order to meet the affordability challenges we are all facing, and meeting those is an essential component in ensuring a dynamic future for the university,” she said, adding that cost savings would be best accomplished by letting the leaders of the units figure out how to implement them, rather than a top-down approach.

    “In the Budget Group process, we’ve seen very thoughtful submissions, making it clear that university leadership is looking for ways to protect our core programs and departments while building a framework for our future,” she said.

    The full minutes of the Feb. 21 meeting, including the discussion that followed the presentations, will be posted on the Faculty Senate website. The next senate meeting is scheduled for March 7.

    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 Campus
    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.

    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 8:30 pm on February 21, 2019 Permalink | Reply
    Tags: , , , , Molecular ensemble, , , , PtPOP, SLAC Labs, , ,   

    From SLAC National Accelerator Lab: “Researchers watch molecules in a light-triggered catalyst ring ‘like an ensemble of bells’’ 

    From SLAC National Accelerator Lab

    February 21, 2019
    Ali Sundermier

    1
    Synchronized molecules
    When photocatalyst molecules absorb light, they start vibrating in a coordinated way, like an ensemble of bells. Capturing this response is a critical step towards understanding how to design molecules for the efficient transformation of light energy to high-value chemicals. (Gregory Stewart/SLAC National Accelerator Laboratory)

    A better understanding of these systems will aid in developing next-generation energy technologies.

    Photocatalysts ­– materials that trigger chemical reactions when hit by light – are important in a number of natural and industrial processes, from producing hydrogen for fuel to enabling photosynthesis.

    Now an international team has used an X-ray laser at the Department of Energy’s SLAC National Accelerator Laboratory to get an incredibly detailed look at what happens to the structure of a model photocatalyst when it absorbs light.

    The researchers used extremely fast laser pulses to watch the structure change and see the molecules vibrating, ringing “like an ensemble of bells,” says lead author Kristoffer Haldrup, a senior scientist at Technical University of Denmark (DTU). This study paves the way for deeper investigation into these processes, which could help in the design of better catalysts for splitting water into hydrogen and oxygen for next-generation energy technologies.

    “If we can understand such processes, then we can apply that understanding to developing molecular systems that do tricks like that with very high efficiency,” Haldrup says.

    The results published last week in Physical Review Letters.

    Molecular ensemble

    The platinum-based photocatalyst they studied, called PtPOP, is one of a class of molecules that scissors hydrogen atoms off various hydrocarbon molecules when hit by light, Haldrup says: “It’s a testbed – a playground, if you will – for studying photocatalysis as it happens.”

    At SLAC’S X-ray laser, the Linac Coherent Light Source (LCLS), the researchers used an optical laser to excite the platinum-containing molecules and then used X-rays to see how these molecules changed their structure after absorbing the visible photons.

    SLAC/LCLS

    The extremely short X-ray laser pulses allowed them to watch the structure change, Haldrup says.

    The researchers used a trick to selectively “freeze” some of the molecules in their vibrational motion, and then used the ultrashort X-ray pulses to capture how the entire ensemble of molecules evolved in time after being hit with light. By taking these images at different times they can stitch together the individual frames like a stop-motion movie. This provided them with detailed information about molecules that were not hit by the laser light, offering insight into the ultrafast changes occurring in the molecules when they are at their lowest energy.

    Swimming in harmony

    Even before the light hits the molecules, they are all vibrating but out of sync with one another. Kelly Gaffney, co-author on this paper and director of SLAC’s Stanford Synchrotron Radiation Lightsource, likens this motion to swimmers in a pool, furiously treading water.

    SLAC SSRL Campus


    SLAC/SSRL


    SLAC/SSRL

    When the optical laser hits them, some of the molecules affected by the light begin moving in unison and with greater intensity, switching from that discordant tread to synchronized strokes. Although this phenomenon has been seen before, until now it was difficult to quantify.

    “This research clearly demonstrates the ability of X-rays to quantify how excitation changes the molecules,” Gaffney says. “We can not only say that it’s excited vibrationally, but we can also quantify it and say which atoms are moving and by how much.”

    Predictive chemistry

    To follow up on this study, the researchers are investigating how the structures of PtPOP molecules change when they take part in chemical reactions. They also hope to use the information they gained in this study to directly study how chemical bonds are made and broken in similar molecular systems.

    “We get to investigate the very basics of photochemistry, namely how exciting the electrons in the system leads to some very specific changes in the overall molecular structure,” says Tim Brandt van Driel, a co-author from DTU who is now a scientist at LCLS. “This allows us to study how energy is being stored and released, which is important for understanding processes that are also at the heart of photosynthesis and the visual system.”

    A better understanding of these processes could be key to designing better materials and systems with useful functions.

    “A lot of chemical understanding is rationalized after the fact. It’s not predictive at all,” Gaffney says. “You see it and then you explain why it happened. We’re trying to move the design of useful chemical materials into a more predictive space, and that requires accurate detailed knowledge of what happens in the materials that already work.”

    LCLS and SSRL are DOE Office of Science user facilities. This research was supported by DANSCATT; the Independent Research Fund Denmark; the Icelandic Research Fund; the Villum Foundation; and the AMOS program within the Chemical Sciences, Geosciences and Biosciences Division of the DOE Office of Basic Energy Sciences.

    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 Campus
    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 1:22 pm on August 7, 2018 Permalink | Reply
    Tags: Catching the dance of antibiotics and ribosomes at room temperature, , , , , SLAC Labs, ,   

    From SLAC National Accelerator Lab: “Catching the dance of antibiotics and ribosomes at room temperature” 

    From SLAC National Accelerator Lab

    August 6, 2018
    Ali Sundermier

    1
    Hasan DeMirci refers to ribosomes as the 3D printers of the human body because they synthesize proteins, which are essential to life. (Dawn Harmer/SLAC National Accelerator Laboratory)

    2
    Interns in DeMirci’s lab help grow ribosome crystals. Once grown and suspended in a special chemical solution called “mother liquor,” the crystals are imaged at the LCLS to uncover how they interact with antibiotics. (Dawn Harmer/SLAC National Accelerator Laboratory)

    Antibiotics have been a pillar of modern medicine since the 1940s. Streptomycin, which belongs to a class of antibiotics called aminoglycosides, was the first hint of light in the millennia-long search for a treatment for tuberculosis, which remains one of the deadliest infectious diseases in human history.

    Today, aminoglycosides are the most commonly prescribed antibiotics in the world due to their low cost and high effectiveness in tackling a broad spectrum of bacterial infections. But they also bring along side effects that can have lifelong impacts. Depending on the dosage and the particular antibiotic, an estimated 10 to 20 percent of patients who take aminoglycosides suffer kidney damage and 20 to 60 percent end up with irreversible hearing loss.

    Now researchers at the Department of Energy’s SLAC National Accelerator Laboratory have developed a new imaging technique to better understand the mechanisms that lead to hearing loss when aminoglycosides are introduced to the body. Using the lab’s Linac Coherent Light Source (LCLS) X-ray laser and Stanford Synchrotron Lightsource (SSRL), SLAC researchers, in collaboration with researchers at Stanford University, were able to observe interactions between the drugs and bacterial ribosomes at both extremely low and room temperatures, revealing never-before-seen details.

    SLAC LCLS

    SLAC/SSRL

    They also demonstrated how small modifications to the antibiotics can lead to dramatic changes in ribosome shape that eliminate hearing loss. The research could lead to a better understanding of which parts of a drug molecule cause unwanted reactions in the body, which will enable the development of more effective antibiotics with fewer side effects.

    The group was led by research associate and senior author Hasan DeMirci. Their results were published in Nucleic Acids Research.

    3D printing proteins

    Hasan DeMirci refers to ribosomes – tiny molecular machines made up of tangles of RNA and proteins clumped together and intricately wired like ramen noodles in soup – as “the 3D printers of the human body.” The ribosomes synthesize proteins using the genetic information contained in DNA, “building our bodies from the ground up.”

    3
    Ribosomes (shown here) are tiny molecular machines made up of tangles of RNA and proteins clumped together and intricately wired like ramen noodles in soup. (Hasan DeMirci/SLAC National Accelerator Laboratory)

    “While one subunit of the ribosome, its brain, deciphers and translates the genetic code, the other, its hands, links together amino acids to form proteins,” DeMirci said.

    Unlike viruses, which have to leech off hosts to survive, bacteria have their own ribosomes, which is where antibiotics come into play. Bacterial ribosomes are the targets of many antibiotics. So-called “cidal” antibiotics like aminoglycosides function by attacking the brains of bacterial ribosomes, causing them to make mistakes and fill the cells with protein-like garbage molecules.

    “It’s like a house with a lot of hoarded junk,” DeMirci says. “There’s no going back. From that point the bacteria just die.”

    The problem with this strategy is that human cells contain energy-producing factories called mitochondria that have their very own ribosomes – and since those ribosomes are dangerously similar to those found in bacteria, they’re also vulnerable to antibiotic attack.

    “We’re killing the bacteria, but the same drug gets into our mitochondria and destroys the ribosomes there,” DeMirci says. “Now we cannot produce those enzymes that power us. You take an antibiotic and you start losing your hearing, your kidney fails.”

    Insights into molecular machinery

    DeMirci has a strong interest in aminoglycosides because he can use them to gain insight into the molecular machinery of the ribosome.

    “What I really want to know is what those drugs can teach us about how ribosomes decipher the genetic code,” DeMirci said. “Drugs give us an opportunity to stop that process at different stages to understand how each and every step is catalyzed by the ribosome.”

    To better understand this process, he struck up a collaboration with Anthony Ricci, a biophysicist and professor of medicine at Stanford who focuses on the inner ear. In previous research, Ricci found that aminoglycosides infiltrate specialized channels to target the sensory cells essential to hearing.

    “You can think of it as a roach motel,” Ricci says. “The drugs can get in but they can’t get out. They start to build up, binding to the ribosomes and altering protein synthesis. This puts a huge metabolic load on the sensory cells, which eventually leads to their deaths.”

    A major goal of Ricci’s lab has been to design and develop new aminoglycosides that kill bacteria but cannot squeeze through the channel. In order to do this, the researchers need to understand exactly how the aminoglycosides interact with the ribosomes so they can modify parts of the drug without weakening its bacteria-killing properties.

    Defrosting interactions

    The best way to reach this understanding, researchers have found, is through a technique called X-ray crystallography. In X-ray crystallography, researchers use the patterns formed when a beam of X-rays scatters off a crystal sample to form a 3D model of how its atoms and molecules are arranged. This technique allows researchers to observe how a drug binds to a ribosome.

    While the key interactions in these processes happen at body temperature, around 37 degrees Celsius, X-ray crystallography usually has to be done at extremely low, or cryogenic, temperatures, around minus 180 degrees Celsius. This leads to gaps in the data, obscuring tiny details that could greatly inform future experiments.

    “Our bodies are warm, so the important biology is happening at body temperature,” DeMirci said, “but in crystallography everything is frozen. When you cool these processes down, you miss out on thermal fluctuations, tiny movements that could change your understanding of how the drugs and ribosomes are behaving.”

    In order to design better antibiotics, they need to get as close a view as they can of this interaction happening under physiological conditions. At the LCLS, using a technique called serial femtosecond crystallography, DeMirci is able to catch the intricate waltz of the drugs and ribosomes at room temperature. Rather than freeze the ribosome crystals, the researchers suspend them in ‘mother liquor,’ a special chemical solution they were grown in that keeps them stable, so they are “swimming happily, still wiggling and fluctuating,” he says.

    The crystals travel from a reservoir to the interaction region through a single capillary, like a garden hose. Once in the interaction region, the crystals are zapped with a beam of X-rays from the LCLS, which scatters off of them into a detector and provides the researchers with patterns they can use to build detailed 3D models of the ribosome before and after they’ve bound with the drugs. They then use these models to piece together a simulation of the interaction.

    4
    At LCLS, crystallized ribosomes travel through a capillary into the interaction region, where they are zapped with a beam of X-rays. The X-rays scatter off the crystals into a detector, providing the researchers with patterns they can use to build detailed 3D models of interactions between the drug and ribosome. (Greg Stewart/SLAC National Accelerator Laboratory)

    Uncovering hidden wiggles

    To demonstrate their technique, the researchers imaged modified and unmodified drugs binding to ribosomes at both cryogenic and room temperatures to see if they could catch any differences. They found that the drug molecules were less flexible at cryogenic temperatures: Tiny wiggles essential to a better understanding of their interactions with ribosomes were frozen in place.

    “Despite the fact that we’ve recorded hundreds of thousands of structures of ribosomal interactions, less than a handful of new-generation drugs have been designed based on these cryogenic structures,” DeMirci said. “That’s because every small interaction makes a huge difference, even a single hydrogen bond.”

    With the images taken at room temperature, Ricci’s group identified a site where the drug could be modified without altering its effectiveness.

    “We now have some idea that when the drug binds with the ribosome, a global change occurs in the ribosome that might actually be important for the function of the antibiotic and the sensitivity of the ribosome,” Ricci said.

    Refining the jigsaw pieces

    In the next phase of experiments, DeMirci hopes to design a setup in which the antibiotics aren’t introduced until the last second before the ribosome is imaged so that they can watch as it binds to the ribosome, rather than just taking images before and after.

    Up to this point, Ricci said, his group had been doing drug synthesis with very little information or insight into how the antibiotic interacts with the ribosome.

    “What this paper and overall collaboration allow is a direct investigation of the drug-ribosome interaction,” he said. “It’s like having more defined pieces to the jigsaw puzzle. You don’t have to guess about what’s happening.”

    Developing antibiotics that can fight off drug-resistant bacteria with minimal side effects is essential because the rise of antibiotic resistant strains is currently the biggest threat to modern medicine, DeMirci said.

    “Every year more than a million people die from tuberculosis and nearly half a million are HIV positive,” he said. “People don’t usually die from HIV or cancer, they die because their immune system is suppressed and they can’t fight off bacterial infections. That’s when you need antibiotics. But what if you don’t have one that’s effective against the resistant strains? That’s exactly what’s happening right now. This research can help us make informed decisions when designing the next generation of drugs.”

    The research team included scientists from LCLS; SSRL; SLAC’s Biosciences Division; the Stanford PULSE Institute; and the Stanford School of Medicine.

    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 Campus
    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 6:54 am on August 3, 2018 Permalink | Reply
    Tags: , , , How synthetic diamonds grow, , SLAC Labs   

    From SLAC Lab: “In a first, scientists precisely measure how synthetic diamonds grow” 

    From SLAC Lab

    August 2, 2018
    Glennda Chui

    1
    A SLAC-Stanford study has precisely measured for the first time how synthetic diamonds grow from diamondoid seeds, like the one at left. (Greg Stewart, SLAC National Accelerator Laboratory)

    A SLAC-Stanford study reveals exactly what it takes for diamond to crystallize around a “seed” cluster of atoms. The results apply to industrial processes and to what happens in clouds overhead.

    Natural diamond is forged by tremendous pressures and temperatures deep underground. But synthetic diamond can be grown by nucleation, where tiny bits of diamond “seed” the growth of bigger diamond crystals. The same thing happens in clouds, where particles seed the growth of ice crystals that then melt into raindrops.

    Scientists have now observed for the first time how diamonds grow from seed at an atomic level, and discovered just how big the seeds need to be to kick the crystal growing process into overdrive.

    The results, published this week in Proceedings of the National Academy of Sciences, shed light on how nucleation proceeds not just in diamonds, but in the atmosphere, in silicon crystals used for computer chips and even in proteins that clump together in neurological diseases.

    “Nucleation growth is a core tenet of materials science, and there’s a theory and a formula that describes how this happens in every textbook,” says Nicholas Melosh, a professor at Stanford University and the Department of Energy’s SLAC National Accelerator Laboratory who led the research. “It’s how we describe going from one material phase to another, for example from liquid water to ice.”

    But interestingly, he says, “despite the widespread use of this process everywhere, the theory behind it had never been tested experimentally, because observing how crystal growth starts from atomic-scale seeds is extremely difficult.”

    2
    An illustration shows how diamondoids (left), the tiniest possible specks of diamond, were used to seed the growth of nanosized diamond crystals (right). Trillions of diamondoids were attached to the surface of a silicon wafer, which was then tipped on end and exposed to a hot plasma (purple) containing carbon and hydrogen, the two elements needed to form diamond. A new study found that diamond growth really took off when seeds contained at least 26 carbon atoms. (Greg Stewart/SLAC National Accelerator Laboratory)

    The smallest possible specks

    In fact, scientists have known for a long time that the current theory often overestimates how much energy it takes to kick off the nucleation process, and by quite a bit. They’ve come up with potential ways to reconcile the theory with reality, but until now those ideas have been tested only at a relatively large scale, for instance with protein molecules, rather than at the atomic scale where nucleation begins.

    To see how it works at the smallest scale, Melosh and his team turned to diamondoids, the tiniest possible bits of diamond. The smallest ones contain just 10 carbon atoms. These specks are the focus of a DOE-funded program at SLAC and Stanford where naturally occurring diamondoids are isolated from petroleum fluids, sorted by size and shape and studied. Recent experiments suggest they could be used as Lego-like blocks for assembling nanowires or “molecular anvils” for triggering chemical reactions, among other things.

    The latest round of experiments was led by Stanford postdoctoral researcher Matthew Gebbie. He’s interested in the chemistry of interfaces – places where one phase of matter encounters another, for instance the boundary between air and water. It turns out that interfaces are incredibly important in growing diamonds with a process called CVD, or chemical vapor deposition, that’s widely used to make synthetic diamond for industry and jewelry.

    “What I’m excited about is understanding how size and shape and molecular structure influence the properties of materials that are important for emerging technologies,” Gebbie says. “That includes nanoscale diamonds for use in sensors and in quantum computing. We need to make them reliably and with consistently high quality.”

    Diamond or pencil lead?

    To grow diamond in the lab with CVD, tiny bits of crushed diamond are seeded onto a surface and exposed to a plasma – a cloud of gas heated to such high temperatures that electrons are stripped away from their atoms. The plasma contains hydrogen and carbon, the two elements needed to form a diamond.

    This plasma can either dissolve the seeds or make them grow, Gebbie says, and the competition between the two determines whether bigger crystals form. Since there are many ways to pack carbon atoms into a solid, it all has to be done under just the right conditions; otherwise you can end up with graphite, commonly known as pencil lead, instead of the sparkly stuff you were after.

    Diamondoid seeds give scientists a much finer level of control over this process. Although they’re too small to see directly, even with the most powerful microscopes, they can be precisely sorted according to the number of carbon atoms they contain and then chemically attached to the surface of a silicon wafer so they’re pinned in place while being exposed to plasma. The crystals that grow around the seeds eventually get big enough to count under a microscope, and that’s what the researchers did.

    The magic number is 26

    Although diamondoids had been used to seed the growth of diamonds before, these were the first experiments to test the effects of using seeds of various sizes. The team discovered that crystal growth really took off with seeds that contain at least 26 carbon atoms.

    Even more important, Gebbie says, they were able to directly measure the energy barrier that diamondoid particles have to overcome in order to grow into crystals.

    “It was thought that this barrier must be like a gigantic mountain that the carbon atoms should not be able to cross – and, in fact, for decades there’s been an open question of why we could even make diamonds in the first place,” he says. “What we found was more like a mild hill.”

    Gebbie adds, “This is really fundamental research, but at the end of the day, what we’re really excited about and driving for is a predictable and reliable way to make diamond nanomaterials. Now that we’ve developed the underlying scientific knowledge needed to do that, we’ll be looking for ways to put these diamond nanomaterials to practical use.”

    This research took place at SIMES, the Stanford Institute for Materials and Energy Sciences, with major funding from the DOE Office of Science. In addition to SLAC and Stanford, researchers contributing to this study came from the Institute of Physics of the Czech Academy of Sciences, University Hasselt in Belgium and the Institute of Organic Chemistry at Justus-Liebig University in Germany.

    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 Campus
    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 2:14 pm on July 5, 2018 Permalink | Reply
    Tags: Mapping Energy Landscapes of Chemical Reactions, SLAC Labs, Ultra-High-Speed ‘Electron Camera   

    From SLAC Lab: “SLAC’s Ultra-High-Speed ‘Electron Camera’ Catches Molecules at a Crossroads” 


    From SLAC Lab

    July 5, 2018
    Andrew Gordon
    agordon@slac.stanford.edu
    650) 926-2282

    Manuel Gnida

    1
    Animation of a trifluoroiodomethane molecule (carbon shown in black, fluoride in green, iodine in pink) responding to laser light. The light flash stretches the bond between the carbon and iodine atoms to a point where the bond can either break (at right) or stay intact (at left). Since molecules are quantum systems, they actually exist in both states at once. (Greg Stewart/SLAC National Accelerator Laboratory)

    An extremely fast “electron camera” at the Department of Energy’s SLAC National Accelerator Laboratory has produced the most detailed atomic movie of the decisive point where molecules hit by light can either stay intact or break apart. The results could lead to a better understanding of how molecules respond to light in processes that are crucial for life, like photosynthesis and vision, or that are potentially harmful, such as DNA damage from ultraviolet light.

    In the study, published today in Science, researchers looked at a gas whose molecules have five atoms each. They watched in real time how light stretched the bond between two atoms in the molecules to a “point of no return,” sending the molecules on a path that either further separated the atoms and cleaved the bond or caused the atoms to vibrate while preserving the bond.

    “The starting and end points of a chemical reaction are often obvious, but it’s much more challenging to take snapshots of the rapid reaction steps in between,” said postdoctoral researcher Jie Yang, the study’s lead author from SLAC’s Accelerator Directorate and the Stanford PULSE Institute. “The crossroads where a molecule can do one thing or another are an important factor in determining the outcome of a reaction. Now we’ve been able to observe directly for the first time how the atomic nuclei of a molecule rearrange at such an intersection.”

    Co-author Todd Martinez, a professor at SLAC and Stanford University and an investigator at PULSE, said, “The system we studied is a paradigm for the much more complex light-driven reactions in nature.” For example, the absorption of ultraviolet light can cause damage to DNA, but other mechanisms turn the light’s energy into molecular vibrations and minimize the harmful effect.

    Ultra-High-Speed Snapshots of Atoms in Motion

    The first steps in light-driven reactions are extremely fast. Molecules absorb light almost instantaneously, leading to a rapid rearrangement of their electrons and atomic nuclei. To see what happens in real time, researchers need ultra-high-speed cameras that can “freeze” motions occurring within femtoseconds, or millionths of a billionth of a second.

    The camera used in the study was an instrument for ultrafast electron diffraction (UED), in which a high-energy beam of electrons probes the interior of a sample, generating snapshots of its atomic architecture at different points in time during a chemical reaction. Strung together, these snapshots turn into a movie of the speedy atomic motions.

    3
    With SLAC’s new apparatus for ultrafast electron diffraction – one of the world’s fastest “electron cameras” – researchers can study motions in materials that take place in less than 100 quadrillionths of a second. A pulsed electron beam is created by shining laser pulses on a metal photocathode. The beam gets accelerated by a radiofrequency field and focused by a magnetic lens. Then it travels through a sample and scatters off the sample’s atomic nuclei and electrons, creating a diffraction image on a detector. Changes in these diffraction images over time are used to reconstruct ultrafast motions of the sample’s interior structure. (SLAC National Accelerator Laboratory)

    At SLAC, the researchers flashed laser light into a gas of trifluoroiodomethane molecules and observed over the course of hundreds of femtoseconds how bonds between carbon and iodine atoms elongated to a point at which the bond either broke, splitting off iodine from the molecules, or contracted, setting off vibrations of the atoms along the bond.

    “UED was absolutely crucial to seeing that point during the reaction,” said physicist Xijie Wang, head of SLAC’s UED program and the study’s principal investigator. “Other methods either don’t detect nuclear motions directly or haven’t reached the resolution necessary to make this kind of observation in gases.”

    Mapping Energy Landscapes of Chemical Reactions

    The observation is in agreement with calculations that provide a deeper understanding of what happens during the reaction.

    The laser light “energizes” the molecules, elevating them from a low-energy ground state to a higher-energy excited state (see image below). Molecular states like these can be described by energy landscapes, with mountains of more energy and valleys of less energy. Like a golf ball rolling on a curved putting green, the molecules can follow reaction paths on these surfaces.

    When the landscapes of different molecular states intersect, the reaction can proceed in several directions. Chemists call this point a conical intersection.

    4
    Illustration of the laser-driven response of trifluoroiodomethane molecules (balls and sticks). A laser flash elevates the molecule from a low-energy ground state to an excited state of higher energy (at left). The molecular states are shown as energy landscapes, on which the molecule can follow reaction paths (arrows). At a point where two excited states intersect (conical intersection), the reaction can take two routes: the molecule can either break apart (dissociation) or stay intact and vibrate (vibration). (Greg Stewart/SLAC National Accelerator Laboratory)

    n fact, molecules at conical intersections exist in several states at once – an oddity rooted in the fact that molecules are tiny quantum systems, said co-author Xiaolei Zhu, a postdoctoral researcher at PULSE and Stanford. “We can predict this behavior in computer simulations,” he said. “Now we’ve also directly seen that the molecules behave exactly that way in the experiment.”

    The team is now planning the next steps. “We’re continuing to develop the UED method so that we can look at similar processes in liquids,” Wang said. “This will bring us even closer to understanding light-driven chemical reactions in biological environments.”

    In addition to SLAC and Stanford, the research team included scientists from the Center for Free-Electron Laser Science at the German research center DESY; Max Planck Institute for the Structure and Dynamics of Matter in Germany; University of York in the United Kingdom; University of Potsdam in Germany; and University of Nebraska, Lincoln. Large parts of this project were 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 Campus
    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 11:35 am on July 3, 2018 Permalink | Reply
    Tags: , , SLAC Labs, ,   

    From SLAC Lab: “X-Ray Experiment Confirms Theoretical Model for Making New Materials” 


    From SLAC Lab

    July 2, 2018
    Glennda Chui

    1
    In an experiment at SLAC, scientists loaded ingredients for making a material into a thin glass tube and used X-rays (top left) to observe the phases it went through as it was forming (shown in bubbles). The experiment verified theoretical predictions made by scientists at Berkeley Lab with the help of supercomputers (right). (Greg Stewart/SLAC National Accelerator Laboratory)

    By observing changes in materials as they’re being synthesized, scientists hope to learn how they form and come up with recipes for making the materials they need for next-gen energy technologies.

    Over the last decade, scientists have used supercomputers and advanced simulation software to predict hundreds of new materials with exciting properties for next-generation energy technologies.

    Now they need to figure out how to make them.

    To predict the best recipe for making a material, they first need a better understanding of how it forms, including all the intermediate phases it goes through along the way – some of which may be useful in their own right.

    Now experiments at the Department of Energy’s SLAC National Accelerator Laboratory have confirmed the predictive power of a new computational approach to materials synthesis. Researchers say that this approach, developed at the DOE’s Lawrence Berkeley National Laboratory, could streamline the creation of novel materials for solar cells, batteries and other sustainable technologies.

    “In the last 10 years, computational scientists have gotten really good at predicting the properties of new materials, but not so good at telling experimentalists like me how to make them,” said Michael Toney, a distinguished staff scientist at SLAC. “The theoretical framework developed at Berkeley Lab can help guide us in thinking about ways to synthesize and test these promising materials.”

    This team described their findings June 29 in Nature Communications.

    Metastable Materials

    “Most theoretical approaches are great for predicting the endpoints of a reaction – what chemicals you start with, and what material you get at the end,” said study co-author Laura Schelhas, an associate staff scientist with SLAC’s Applied Energy Program. “But other interesting materials that form along the reaction pathway are often overlooked.”

    These intermediate materials are said to exist in a state of metastability.

    “Materials always want to be in their lowest-energy phase or ground state,” Schelhas explained. “Materials in a metastable state are higher in energy and will eventually transition to the more stable ground state. A diamond, for example, is a metastable state of carbon that will revert to its ground state, graphite, over millions of years.”

    During synthesis, materials can crystallize into a series of metastable phases – some lasting only a few minutes, others persisting for hours. Some of these phases have properties that are potentially useful for technological applications. Others may block the formation of a material you want to make. Scientists want to isolate the useful phases and avoid creating the undesirable ones.

    Co-authors Wenhao Sun and Gerbrand Ceder at Berkeley Lab and Daniil Kitchaev of the Massachusetts Institute of Technology recently developed a theoretical model to predict which metastable phases a material will form during synthesis.

    “The key insight is to consider influences other than temperature and pressure that can affect a material’s formation,” Sun said. “For example, at a very small scale, surface energy is important, and impurities that materials take up from the surrounding environment can stabilize some types of crystalline structures. We developed a theory to quantify how these factors govern the formation of metastable phases, and then worked with SLAC to design an experiment to test it.”

    The experiment, conducted at SLAC’s Stanford Synchrotron Radiation Lightsource (SSRL), focused on manganese oxide, a compound whose formation can involve a variety of metastable crystalline structures. Some of these metastable structures are useful for battery applications or catalysis.

    SLAC/SSRL

    2
    Schematic representation of remnant metastability in a crystallization pathway. a Free-energy of three phases (supersaturated solution (gray), M (green), S (blue)) as a function of the surface-area-to-volume ratio, 1/R (R is a particle radius). The gray line corresponds to the free-energy of a supersaturated solution, green is a metastable phase M that is size-stabilized by a low surface energy (given by the slope), and blue is the bulk equilibrium phase S, with high surface energy. b Phase diagram in the 1/R axis created from the projection of lowest free-energy phases. c A multistage crystallization pathway (red arrow in a ) proceeds downhill in energy, but phase transformations are limited by nucleation. Crystal growth of M prior to the induction of S means M can grow into a size-regime where phase M is metastable. S will then nucleate, and quickly grow by consuming M via dissolution-reprecipitation. The characteristic length scale of size-driven phase transitions lies in the 2 nm–50 nm range. Nature Communications

    “Although manganese oxide has been widely studied, we still don’t have a good understanding of how to make specific metastable phases of the material,” Toney said. “Figuring out why certain recipes favor certain metastable structures will help us predict recipes for synthesizing not just this material, but others as well.”

    Theory vs. Experiment

    Sun and Schelhas designed an experiment to carefully manipulate a single ingredient in a recipe for making manganese oxide and track its effect on the formation of metastable crystals.

    SLAC scientists led by postdoctoral researcher Bor-Rong Chen used powerful X-ray beams at SSRL to observe the chemical reaction as it happened.

    “It’s pretty simple,” Schelhas said. “We load up manganese salts and other reaction materials into a small glass capillary, seal it and heat it. Then we shoot X-rays through the capillary while the reaction is occurring and watch the signal that reflects off the crystals. That signal allows us to determine the atomic structure of each metastable phase as it forms.”

    At first, the metastable phases identified by X-ray diffraction didn’t seem to match the theoretical predictions, Chen said.

    “We worked with the theorists at Berkeley Lab to retool the model,” she said, “and arrived at some explanations for why certain metastable phases might be skipped in a reaction, or why they might persist longer than we anticipated.”

    To continue developing their understanding of synthesis, the researchers plan to conduct experiments on more complicated materials.

    “This work marks only the initial steps in a much longer journey towards a predictive theory of materials synthesis,” Sun said. “Our goal is to build a powerful toolkit to design recipes for making exactly the materials we want.”

    The team also found that they could stop the reaction at the point where a metastable material has formed, which will make it possible to test those materials for desirable properties in future studies, Schelhas said.

    “We’re starting to push science into a new space in terms of understanding how you go about synthesis,” she added. “Predictive models have the potential to profoundly alter the way that materials design is done. That could greatly speed up the adoption of more advanced materials in areas like photovoltaics, batteries, thermoelectrics and a whole host of other sustainable technologies.”

    Other co-authors of the study are from the Colorado School of Mines and the DOE’s National Renewable Energy Laboratory.

    SSRL is a DOE Office of Science user facility. Funding for this work came from the Center for Next Generation of Materials Design, an Energy Frontier Research Center led by DOE’s National Renewable Energy Laboratory and 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 Campus
    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 1:40 pm on June 28, 2018 Permalink | Reply
    Tags: , High-speed ‘electron camera’, , SLAC Labs, UED-ultrafast electron diffraction   

    From SLAC: “Atomic Movie of Melting Gold Could Help Design Materials for Future Fusion Reactors” 


    From SLAC Lab

    June 28, 2018

    Press Office Contact:
    Andrew Gordon,
    agordon@slac.stanford.edu,
    (650) 926-2282

    By Manuel Gnida

    1
    A study using a powerful beam of electrons at SLAC has revealed new atomic details of the melting of gold, potentially benefitting the development of fusion power reactors, steel processing plants, spacecraft and other applications. (Greg Stewart/SLAC National Accelerator Laboratory)

    SLAC’s high-speed ‘electron camera’ shows for the first time the coexistence of solid and liquid in laser-heated gold, providing new clues for designing materials that can withstand extreme conditions.

    Researchers at the Department of Energy’s SLAC National Accelerator Laboratory have recorded the most detailed atomic movie of gold melting after being blasted by laser light. The insights they gained into how metals liquefy have potential to aid the development of fusion power reactors, steel processing plants, spacecraft and other applications where materials have to withstand extreme conditions for long periods of time.


    This video explains how researchers at SLAC are using a method known as ultrafast electron diffraction (UED) to develop an atomic-level understanding of how metals melt, which could help them design materials for applications where materials have to withstand extreme conditions, such as nuclear fusion. (Farrin Abbott/Greg Stewart/SLAC National Accelerator Laboratory)

    Nuclear fusion is the process that powers stars like the sun. Scientists want to copy this process on Earth as a relatively clean and safe way of generating virtually unlimited amounts of energy. But to build a fusion reactor, they need materials that can survive being exposed to temperatures of a few hundred millions of degrees Fahrenheit and intense radiation produced in the fusion reaction.

    “Our study is an important step toward better predictions of the effects extreme conditions have on reactor materials, including heavy metals such as gold,” said SLAC postdoctoral researcher Mianzhen Mo, one of the lead authors of a study published today in Science. “The atomic-level description of the melting process will help us make better models of the short- and long-term damage in those materials, such as crack formation and material failure.”

    The study used SLAC’s high-speed electron camera – an instrument for ultrafast electron diffraction (UED) – which is capable of tracking nuclear motions with a shutter speed of about 100 millionths of a billionth of a second, or 100 femtoseconds.

    Melting in Pockets

    The team discovered that the melting started at the surfaces of nanosized grains within the gold sample – regions in which the gold atoms neatly line up in crystals – and at the boundaries between them.

    “This behavior had been predicted in theoretical studies, but we’ve now actually observed it for the first time,” said Siegfried Glenzer, head of SLAC’s High Energy Density Science Division and the study’s principal investigator. “Our method allows us to examine the behavior of any material in extreme environments in atomic detail, which is key to understanding and predicting material properties and could open up new avenues for the design of future materials.”

    2
    This animation shows the results of a recent study at SLAC, in which researchers used a powerful beam of electrons to watch gold melt extremely rapidly after being heated by a laser pulse. The data reveal that the melting starts at the surfaces of nanosized grains and the boundaries between them, leading to the formation of pockets of liquid that are surrounded by solid. This mix evolves over time until only liquid is left. (Farrin Abbott/Greg Stewart/SLAC National Accelerator Laboratory)

    To study the melting process, the researchers focused the laser beam onto a sample of gold crystals and watched how the atomic nuclei in the crystals responded, using the UED instrument’s electron beam as a probe. By stitching together snapshots of the atomic structure taken at various times after the laser hit, they created a stop-motion movie of the structural changes over time.

    “About 7 to 8 trillionths of a second after the laser flash, we saw the solid begin turning into a liquid,” said SLAC postdoctoral researcher Zhijang Chen, one of the study’s lead authors. “But the solid didn’t liquefy everywhere at the same time. Instead, we observed the formation of pockets of liquid surrounded by solid gold. This mix evolved over time until only liquid was left after about a billionth of a second.”

    Superb ‘Electron Vision’

    To get to this level of detail, the researchers needed a special camera like SLAC’s UED instrument, which is able to see the atomic makeup of materials and is fast enough to track extremely rapid motions of atomic nuclei.

    And because the melting process is destructive, another feature of the instrument was also absolutely crucial.

    “In our experiment, the sample ultimately melted and vaporized,” said accelerator physicist Xijie Wang, head of SLAC’s UED initiative. “But even if we were able to cool it down so that it becomes a solid again, it wouldn’t have the exact same starting structure. So, for every frame of the atomic movie we want to collect all the structural information in a single-shot experiment – a single pass of the electron beam through the sample. We were able to do just that because our instrument uses a very energetic electron beam that produces a strong signal.”

    3

    This movie shows the transition of a gold sample from a solid (dotted pattern) to a liquid (ring pattern) after being heated by a laser pulse. It was taken with SLAC’s ultrafast “electron” camera, an instrument for ultrafast electron diffraction (UED), in which a powerful electron beam scatters off the atoms in the sample. This interaction generates the intensity pattern seen in the movie, which captures the first 40 trillionths of a second after the laser flash. (Mianzhen Mo/SLAC National Accelerator Laboratory)

    The research team included scientists from SLAC; DOE’s Los Alamos National Laboratory; the University of British Columbia and the University of Alberta in Canada; and the University of Rostock and the University of Duisburg-Essen in Germany. The work was supported 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 Campus
    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 12:21 pm on June 15, 2018 Permalink | Reply
    Tags: , , Retinal, SLAC Labs   

    From SLAC Lab: “Scientists Make the First Molecular Movie of One of Nature’s Most Widely Used Light Sensors” 


    From SLAC Lab

    June 14, 2018
    Glennda Chui


    A molecular movie based on experimental data shows the retinal molecule, in green, changing shape along with parts of its surrounding protein pocket, in pink, when hit by light. The changing numbers are distances in angstroms. One angstrom is one ten-billionth of a meter. That’s roughly the diameter of the smallest atoms. (Paul Scherrer Institute, Andy Freeberg/SLAC)

    The X-ray laser movie shows what happens when light hits retinal, a key part of vision in animals and photosynthesis in microbes. The action takes place in a trillionth of an eye blink.

    Scientists have made the first molecular movie of the instant when light hits a sensor that’s widely used in nature for probing the environment and harvesting energy from light. The sensor, a form of vitamin A known as retinal, is central to a number of important light-driven processes in people, animals, microbes and algae, including human vision and some forms of photosynthesis, and the movie shows it changing shape in a trillionth of an eye blink.

    “To my knowledge, nobody has measured changes in a retinal biosensor so quickly and so accurately,” said Jörg Standfuss, a biologist at the Paul Scherrer Institute (PSI) in Switzerland who led the research at the Department of Energy’s SLAC National Accelerator Laboratory. “And the fact that we saw just the opposite of what we intuitively expected was spectacular and surprising to us.”

    The team carried out their experiments at the lab’s Linac Coherent Light Source (LCLS) X-ray laser and reported the results today in Science.

    SLAC/LCLS

    Comming soon (A really bad attempt at lab humor. In fact, it will be a while).

    SLAC/LCLS II projected view

    In the past, scientists had to fill the gaps in their knowledge about retinal’s behavior by making inferences based on theory and computer simulations, said Mark Hunter, a staff scientist at LCLS and paper co-author. But in this study, “LCLS’s super-short pulses allowed us to collect data on where the atoms actually were in space and how that changed over time,” he said, “so it gave us a much more direct visualization of molecules in motion.”

    Colorful Lakes and Arching Cats

    Retinal is so central to human vision – it’s named for the retina at the back of the eye – that scientists have been studying it for nearly a century, steadily building a more detailed picture of how it works. It’s also used in the burgeoning field of optogenetics to turn groups of nerve cells on and off, revealing how the brain works and how things go wrong in conditions like depression, stroke and addiction.

    The retinal studied in this experiment came from salt-loving microbes that use it to harvest energy from the sun. (Fun fact: Purple and orange-red pigments in these microbes give the briny waters they live in, from San Francisco Bay salt ponds to Senegal’s Lake Retba, their incredibly vivid colors.)

    Retinal does its job while snuggled deep into a pocket of specialized proteins in the membrane of the cell. When hit by light, the retinal changes shape – in this case it curves, like a cat arching its back. This creates a signal that’s transmitted by the protein into the cell’s interior, initiating photosynthesis or vision.

    Scientists thought retinal set off the signal by pushing on the protein pocket as it changed shape. But the LCLS experiments found just the opposite: The pocket actually changed shape first, creating space for the retinal to perform its arching-cat maneuver. Nearby water molecules also moved aside and made room, Standfuss said. It all took place within 200 to 500 femtoseconds, or millionths of a billionth of a second. That’s about a trillionth of the blink of an eye, making this one of the fastest chemical reactions known in living things.

    “In retrospect, this makes a lot of sense,” Standfuss said. “We always say seeing is believing in structural biology, and in this case it’s very true. The molecular movie we made makes it so obvious what’s going on that you can immediately grasp it. This solves a very important piece of the puzzle of how retinal works that people have been wondering about.”

    The protein pocket’s initial movements are triggered by small changes in electrical charge that rearrange certain chemical bonds, he said. These movements guide the retinal’s response and make it much more efficient, which is why it requires only a few photons of light and why nature can use that light so effectively.


    In this pair of molecular movies we see the retinal molecule (in the middle of each frame) and parts of its surrounding protein pocket with their shapes defined by their electron clouds (blue lines). The top frame shows the retinal molecule from the side, and the bottom one shows it from the top as it curves in response to light. (Paul Scherrer Institute)

    Catching Molecules in Action

    How can you watch something so small that happens so fast? The X-ray laser was key, Standfuss said. LCLS produces brilliant pulses of X-ray laser light that scatter off the electrons in a sample and reveal how its atoms are arranged. Like a camera with an extreme zoom lens and ultrafast shutter speed, the X-ray laser can also make snapshots of molecules moving, breaking apart and interacting with each other.

    In this case, the researchers looked at samples of retinal snuggled into pockets of bacteriorhodopsin, a purple protein found in simple microbes like those in the salt ponds.

    After years of effort, PSI postdoctoral researcher Przemyslaw Nogly, the lead author of the report, found ways to pack these retinal-protein pairs into thousands and thousands of tiny but well-ordered crystals. One after another, crystals were hit with light from an optical laser – a stand-in for sunlight – followed by X-ray laser pulses to record the response. Then Nogly and the team boiled down data into 20 snapshots and assembled them into stop-action movies that show the retinal moving in sync with its protein pocket.

    Proteins like bacteriorhodopsin that sit in cell membranes are notoriously difficult to study because it’s so hard to form them into crystals for X-ray experiments, Hunter said. But scientists have learned that they crystallize more readily when embedded in a fatty, toothpaste-like sludge that mimics their natural environment, and that’s how these crystals were formed and delivered into the X-ray beam.

    The researchers were also able to detect “protein quakes,” vibrations that release some of the energy deposited by the light flashes. These had been predicted by theory and came off as expected.

    Standfuss said he has spent most of his career studying retinal and its role in vision, which involves slightly different shape changes in the protein-embedded molecule. “I really hope that we can now study the same reaction in many different systems,” he said. “Now that we see for the first time how it works in one particular bacterial protein, I want to understand how it works in the human eye as well.”

    LCLS researchers Sergio Carbajo, Jason Koglin, Matthew Seaberg and Thomas Lane were co-authors of this study. Other contributors came from PSI, the University of Gothenburg in Sweden, the Fritz Haber Center for Molecular Dynamics at the Hebrew University of Jerusalem, the RIKEN SPring-8 Center and Kyoto University in Japan, the Center for Free-Electron Laser Science at DESY in Germany and Arizona State University. Major funding came from the European Horizon 2020 Program, the Swedish Research Council and the Swiss National Science Foundation.

    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 Campus
    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 8:53 pm on May 15, 2018 Permalink | Reply
    Tags: Cryo-EM, , SLAC Labs   

    From SLAC Lab: “SLAC Will Open One of Three NIH National Service Centers for Cryo-Electron Microscopy” 


    From SLAC Lab

    May 15, 2018
    Glennda Chui

    1
    Proton pumps control the balance of acidity in the cell. This cryo-EM image shows a proton pump that’s part of an enzyme found in both yeast and humans. It consists of 15 protein subunits. The pink part rotates to transport protons across the cell’s outer membrane. Mutations in the human version of the pump interfere with the body’s normal cycle of continually replacing old bone with new. (https://www.cell.com/molecular-cell/abstract/S1097-2765%2818%2930104-7 [Molecular Cell])

    The National Institutes of Health center on the SLAC campus will make this revolutionary technology available to scientists nationwide and teach them how to use it to study 3D structures of biological machines and molecules.

    The National Institutes of Health announced today that it will establish a national service and training center for cryogenic electron microscopy research at the Department of Energy’s SLAC National Accelerator Laboratory.

    Professor Wah Chiu and members of the new Stanford-SLAC cryo-EM team stand in front of a cryo-EM instrument as work nears completion on their new facility at SLAC. (Dawn Harmer- SLAC)

    It’s one of three national service and training centers the NIH is setting up to make the Nobel prize-winning technology available to scientists nationwide and teach them how to use it.

    Known as cryo-EM for short, this powerful high-resolution imaging method has become a revolutionary tool for biology over the past few years due to rapid improvements in transmission electron microscopes, detectors and software. Last year the technique earned three of its key developers the 2017 Nobel Prize in chemistry. Cryo-EM allows scientists to make detailed 3D images of DNA, RNA, proteins, viruses, cells and the tiny molecular machines within the cell, revealing how they change shape and interact in complex ways while carrying out life’s functions.

    However, the high cost of buying and operating the high-voltage electron microscopes and a lack of training opportunities have slowed the widespread adoption of the technology.

    The new data collection centers will address this by providing funding for instruments and associated lab equipment and bringing in scientists from across the nation for research and training. In addition to SLAC, centers will be set up at the New York Structural Biology Center and at the Oregon Health & Science University in partnership with DOE’s Pacific Northwest National Laboratory, the NIH announced. The awards are anticipated to total $128 million over six years, pending the availability of funds.

    “Cryo-electron microscopy is allowing us to resolve the three-dimensional structures of important biomolecules involved in disease that were inaccessible using previous technologies,” said National Institute of General Medical Sciences Director Jon R. Lorsch. “NIH wants to ensure as many scientists as possible have access to this crucial technology.”

    The NIH center at SLAC will be known as the SLAC-Stanford Cryo-EM Center (S2C2). It marks the second major step in carrying out the Stanford-SLAC Cryo-EM Initiative, whose goal is to establish one of the world’s foremost hubs for cryo-EM research and training for scientists at the lab, the university and in the broader scientific community around the globe.

    The first step took place earlier this year, when the Stanford-SLAC Cryo-EM Facility opened on the SLAC campus with four state-of-the-art microscopes.

    The new NIH center, which will operate independently but in synergy with the recently established Stanford-SLAC facility, will install several more electron microscopes and associated specimen preparation devices in the lab’s soon-to-open Arrillaga Science Center.

    “This new center complements our existing facilities and capabilities, enhancing an integrated suite of unique tools to advance materials, chemical and biological science discoveries critical to the DOE Office of Science mission,” said SLAC Director Chi-Chang Kao.

    Wah Chiu, a professor at SLAC and Stanford and leader of the cryo-EM program, added, “This is an exciting moment for those in the U.S. scientific community who do not have access to cryo-EM instrumentation in their own institutions, and we are very pleased to share our decades of experience in this research with others.

    “I believe that this NIH initiative will have a great impact on popularizing this powerful imaging tool,” he said, “which will likely lead to many discoveries of 3D structures of biological machines and molecules in both their normal and diseased states and hasten our national efforts to prevent and cure a variety of diseases, including cancer, diabetics, neurodegeneration, cardiovascular diseases and infection.”

    For questions or comments, contact the SLAC Office of Communications at communications@slac.stanford.edu.

    See the full article here .

    Please help promote STEM in your local schools.

    stem

    Stem Education Coalition

    SLAC Campus
    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 9:01 am on May 7, 2018 Permalink | Reply
    Tags: , , Construction Begins on One of the World’s Most Sensitive Dark Matter Experiments, , , , SLAC Labs, , SuperCDMS SNOLAB experiment,   

    From SLAC Lab: “Construction Begins on One of the World’s Most Sensitive Dark Matter Experiments” 


    From SLAC Lab

    May 7, 2018

    Press Office Contact: Andrew Gordon,
    agordon@slac.stanford.edu
    (650) 926-2282

    Written by Manuel Gnida

    1
    The future SuperCDMS SNOLAB experiment will hunt for weakly interacting massive particles (WIMPs), hypothetical components of dark matter. If a WIMP (white trace) strikes an atom inside the experiment’s detector crystals (gray), it will cause the crystal lattice to vibrate (blue). The collision will also send electrons (red) through the crystal that enhance the vibrations. (Greg Stewart/SLAC National Accelerator Laboratory)

    2
    The future SuperCDMS SNOLAB experiment will hunt for weakly interacting massive particles (WIMPs), hypothetical components of dark matter. This photo shows one of the experiment’s detector crystals within its protective copper housing. (Andy Freeberg/SLAC National Accelerator Laboratory)

    3
    SLAC’s Paul Brink handles the SuperCDMS SNOLAB engineering tower. (Chris Smith/SLAC National Accelerator Laboratory)

    4
    A SuperCDMS SNOLAB detector, fabricated at Texas A&M University. (Matt Cherry/SuperCDMS collaboration/SLAC National Accelerator Laboratory)

    5
    Dan Bauer (left) and Mark Ruschman in Fermilab’s Lab G , where the SuperCDMS SNOLAB project is preparing to test the cryogenics system for the new experiment. (Reidar Hahn/Fermi National Accelerator Laboratory)

    6
    Fermilab’s Mark Ruschman tests prototypes for the SuperCDMS SNOLAB cryogenics system. (Reidar Hahn/Fermi National Accelerator Laboratory)

    The SuperCDMS SNOLAB project, a multi-institutional effort led by SLAC, is expanding the hunt for dark matter to particles with properties not accessible to any other experiment.

    SNOLAB, Sudbury, Ontario, Canada.

    The U.S. Department of Energy has approved funding and start of construction for the SuperCDMS SNOLAB experiment, which will begin operations in the early 2020s to hunt for hypothetical dark matter particles called weakly interacting massive particles, or WIMPs. The experiment will be at least 50 times more sensitive than its predecessor, exploring WIMP properties that can’t be probed by other experiments and giving researchers a powerful new tool to understand one of the biggest mysteries of modern physics.

    The DOE’s SLAC National Accelerator Laboratory is managing the construction project for the international SuperCDMS collaboration of 111 members from 26 institutions, which is preparing to do research with the experiment.

    “Understanding dark matter is one of the hottest research topics – at SLAC and around the world,” said JoAnne Hewett, head of SLAC’s Fundamental Physics Directorate and the lab’s chief research officer. “We’re excited to lead the project and work with our partners to build this next-generation dark matter experiment.”

    With the DOE approvals, known as Critical Decisions 2 and 3, the researchers can now build the experiment. The DOE Office of Science will contribute $19 million to the effort, joining forces with the National Science Foundation ($12 million) and the Canada Foundation for Innovation ($3 million).

    “Our experiment will be the world’s most sensitive for relatively light WIMPs – in a mass range from a fraction of the proton mass to about 10 proton masses,” said Richard Partridge, head of the SuperCDMS group at the Kavli Institute for Particle Astrophysics and Cosmology (KIPAC), a joint institute of SLAC and Stanford University. “This unparalleled sensitivity will create exciting opportunities to explore new territory in dark matter research.”

    An Ultracold Search 6,800 Feet Underground

    Scientists know that visible matter in the universe accounts for only 15 percent of all matter. The rest is a mysterious substance, called dark matter. Due to its gravitational pull on regular matter, dark matter is a key driver for the evolution of the universe, affecting the formation of galaxies like our Milky Way. It therefore is fundamental to our very own existence.

    But scientists have yet to find out what dark matter is made of. They believe it could be composed of dark matter particles, and WIMPs are top contenders. If these particles exist, they would barely interact with their environment and fly right through regular matter untouched. However, every so often, they could collide with an atom of our visible world, and dark matter researchers are looking for these rare interactions.

    7
    The centerpiece of the SuperCDMS SNOLAB experiment will be four detector towers (left), each containing six detector packs. The towers will be mounted inside the SNOBOX (right), a vessel in which the detector packs will be cooled to almost absolute zero temperature. (Greg Stewart/SLAC National Accelerator Laboratory)

    In the SuperCDMS SNOLAB experiment, the search will be done using silicon and germanium crystals, in which the collisions would trigger tiny vibrations. However, to measure the atomic jiggles, the crystals need to be cooled to less than minus 459.6 degrees Fahrenheit – a fraction of a degree above absolute zero temperature. These ultracold conditions give the experiment its name: Cryogenic Dark Matter Search, or CDMS. The prefix “Super” indicates an increased sensitivity compared to previous versions of the experiment.

    The collisions would also produce pairs of electrons and electron deficiencies that move through the crystals, triggering additional atomic vibrations that amplify the signal from the dark matter collision. The experiment will be able to measure these “fingerprints” left by dark matter with sophisticated superconducting electronics.

    The experiment will be assembled and operated at the Canadian laboratory SNOLAB – 6,800 feet underground inside a nickel mine near the city of Sudbury. It’s the deepest underground laboratory in North America. There it will be protected from high-energy particles, called cosmic radiation, which can create unwanted background signals.

    8
    The SuperCDMS dark matter experiment will be located at the Canadian laboratory SNOLAB, 2 kilometers (6,800 feet) underground inside a nickel mine near the city of Sudbury. It’s the deepest underground laboratory in North America. There it will be protected from high-energy particles, called cosmic radiation, which can create unwanted background signals. (Greg Stewart/SLAC National Accelerator Laboratory; inset: SNOLAB)

    “SNOLAB is excited to welcome the SuperCDMS SNOLAB collaboration to the underground lab,” said Kerry Loken, SNOLAB project manager. “We look forward to a great partnership and to supporting this world-leading science.”

    Over the past months, a detector prototype has been successfully tested at SLAC. “These tests were an important demonstration that we’re able to build the actual detector with high enough energy resolution, as well as detector electronics with low enough noise to accomplish our research goals,” said KIPAC’s Paul Brink, who oversees the detector fabrication at Stanford.

    Together with seven other collaborating institutions, SLAC will provide the experiment’s centerpiece of four detector towers, each containing six crystals in the shape of oversized hockey pucks. The first tower could be sent to SNOLAB by the end of 2018.

    “The detector towers are the most technologically challenging part of the experiment, pushing the frontiers of our understanding of low-temperature devices and superconducting readout,” said Bernard Sadoulet, a collaborator from the University of California, Berkeley.

    A Strong Collaboration for Extraordinary Science

    In addition to SLAC, two other national labs are involved in the project. Fermi National Accelerator Laboratory is working on the experiment’s intricate shielding and cryogenics infrastructure, and Pacific Northwest National Laboratory is helping understand background signals in the experiment, a major challenge for the detection of faint WIMP signals.

    9
    Slideshow of SuperCDMS SNOLAB photos. For more images, visit the SuperCDMS SNOLAB photostream on Flickr.

    A number of U.S. and Canadian universities also play key roles in the experiment, working on tasks ranging from detector fabrication and testing to data analysis and simulation. The largest international contribution comes from Canada and includes the research infrastructure at SNOLAB.

    “We’re fortunate to have a close-knit network of strong collaboration partners, which is crucial for our success,” said KIPAC’s Blas Cabrera, who directed the project through the CD-2/3 approval milestone. “The same is true for the outstanding support we’re receiving from the funding agencies in the U.S. and Canada.”

    Fermilab’s Dan Bauer, spokesperson of the SuperCDMS collaboration said, “Together we’re now ready to build an experiment that will search for dark matter particles that interact with normal matter in an entirely new region.”

    SuperCDMS SNOLAB will be the latest in a series of increasingly sensitive dark matter experiments. The most recent version, located at the Soudan Mine in Minnesota, completed operations in 2015.

    “The project has incorporated lessons learned from previous CDMS experiments to significantly improve the experimental infrastructure and detector designs for the experiment,” said SLAC’s Ken Fouts, project manager for SuperCDMS SNOLAB. “The combination of design improvements, the deep location and the infrastructure support provided by SNOLAB will allow the experiment to reach its full potential in the search for low-mass dark matter.”

    For more information on the SuperCDMS SNOLAB project and the SuperCDMS collaboration, check out this website:

    SuperCDMS SNOLAB Website

    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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