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  • richardmitnick 3:55 pm on July 27, 2015 Permalink | Reply
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    From SLAC: “New ‘Molecular Movie’ Reveals Ultrafast Chemistry in Motion” 

    SLAC Lab

    June 22, 2015

    This video describes how the Linac Coherent Light Source, an X-ray free-electron laser at SLAC National Accelerator Laboratory, provided the first direct measurements of how a ring-shaped gas molecule unravels in the millionths of a billionth of a second after it is split open by light. The measurements were compiled in sequence to form the basis for computer animations showing molecular motion. (SLAC National Accelerator Laboratory)

    Scientists for the first time tracked ultrafast structural changes, captured in quadrillionths-of-a-second steps, as ring-shaped gas molecules burst open and unraveled. Ring-shaped molecules are abundant in biochemistry and also form the basis for many drug compounds. The study points the way to a wide range of real-time X-ray studies of gas-based chemical reactions that are vital to biological processes.

    This illustration shows shape changes that occur in quadrillionths-of-a-second intervals in a ring-shaped molecule that was broken open by light. The molecular motion was measured using SLAC’s Linac Coherent Light Source X-ray laser. The colored chart shows a theoretical model of molecular changes that syncs well with the actual results. The squares in the background represent panels in an LCLS X-ray detector. (SLAC National Accelerator Laboratory)

    Researchers working at the Department of Energy’s SLAC National Accelerator Laboratory compiled the full sequence of steps in this basic ring-opening reaction into computerized animations that provide a “molecular movie” of the structural changes.

    Conducted at SLAC’s Linac Coherent Light Source, a DOE Office of Science User Facility, the pioneering study marks an important milestone in precisely tracking how gas-phase molecules transform during chemical reactions on the scale of femtoseconds. A femtosecond is a millionth of a billionth of a second.

    “This fulfills a promise of LCLS: Before your eyes, a chemical reaction is occurring that has never been seen before in this way,” said Mike Minitti, a SLAC scientist who led the experiment in collaboration with Peter Weber at Brown University. The results are featured in the June 22 edition of Physical Review Letters.

    “LCLS is a game-changer in giving us the ability to probe this and other reactions in record-fast timescales,” Minitti said, “down to the motion of individual atoms.” The same method can be used to study more complex molecules and chemistry.

    The free-floating molecules in a gas, when studied with the uniquely bright X-rays at LCLS, can provide a very clear view of structural changes because gas molecules are less likely to be tangled up with one another or otherwise obstructed, he added. “Until now, learning anything meaningful about such rapid molecular changes in a gas using other X-ray sources was very limited, at best.”

    New Views of Chemistry in Action

    The study focused on the gas form of 1,3-cyclohexadiene (CHD), a small, ring-shaped organic molecule derived from pine oil. Ring-shaped molecules play key roles in many biological and chemical processes that are driven by the formation and breaking of chemical bonds. The experiment tracked how the ringed molecule unfurls after a bond between two of its atoms is broken, transforming into a nearly linear molecule called hexatriene.

    “There had been a long-standing question of how this molecule actually opens up,” Minitti said. “The atoms can take different paths and directions. Tracking this ultimately shows how chemical reactions are truly progressing, and will likely lead to improvements in theories and models.”

    The Making of a Molecular Movie

    In the experiment, researchers excited CHD vapor with ultrafast ultraviolet laser pulses to begin the ring-opening reaction. Then they fired LCLS X-ray laser pulses at different time intervals to measure how the molecules changed their shape.

    Researchers compiled and sorted over 100,000 strobe-like measurements of scattered X-rays. Then, they matched these measurements to computer simulations that show the most likely ways the molecule unravels in the first 200 quadrillionths of a second after it opens. The simulations, performed by team member Adam Kirrander at the University of Edinburgh, show the changing motion and position of its atoms.

    Each interval in the animations represents 25 quadrillionths of a second ­– about 1.3 trillion times faster than the typical 30-frames-per-second rate used to display TV shows.

    “It is a remarkable achievement to watch molecular motions with such incredible time resolution,” Weber said.

    A gas sample was considered ideal for this study because interference from any neighboring CHD molecules would be minimized, making it easier to identify and track the transformation of individual molecules. The LCLS X-ray pulses were like cue balls in a game of billiards, scattering off the electrons of the molecules and onto a position-sensitive detector that projected the locations of the atoms within the molecules.

    A Successful Test Case for More Complex Studies

    “This study can serve as a benchmark and springboard for larger molecules that can help us explore and understand even more complex and important chemistry,” Minitti said.

    Additional contributors included scientists at Brown and Stanford universities in the U.S. and the University of Edinburgh in the U.K. The work was supported by the DOE Office of Basic Energy Sciences.

    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.

  • richardmitnick 1:36 pm on July 22, 2015 Permalink | Reply
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    From Rockefeller: “Atomic view of cellular pump reveals how bacteria send out proteins” 

    Rockefeller U bloc

    Rockefeller University

    July 22, 2015
    Wynne Parry | 212-327-7789

    A watery passage: The pump, a single-molecule machine, (yellow coils) carries proteins through the cell membrane (pink and dark blue). Within the pump, the researchers found a strikingly large water-filled channel (light blue), a natural environment for hydrophilic proteins. No image credit

    Bacteria have plenty of things to send out into world beyond their own boundaries: coordinating signals to other members of their species, poisons for their enemies, and devious instructions to manipulate host cells they have infected. Before any of this can occur, however, they must first get the shipments past their own cell membranes, and many bacteria have evolved specialized structures and systems for launching the proteins that do these jobs.

    Researchers at The Rockefeller University have determined the structure of a simple but previously unexamined pump that controls the passage of proteins through a bacterial cell membrane, an achievement that offers new insight into the mechanics that allow bacteria to manipulate their environments. The results were published in Nature on July 23.

    “This pump, called PCAT for peptidase-containing ATP-binding cassette transporter, is composed of a single protein, a sort of all-in-one machine capable of recognizing its cargo, processing it, then burning chemical fuel to pump that cargo out of the cell,” says study author Jue Chen, William E. Ford Professor and head of the Laboratory of Membrane Biology and Biophysics. “This new atomic-level structure explains for the first time the links between these three functions.”

    Of the many types of molecules cells need to move into and out of their membranes, proteins are the largest. PCATs specialize in pumping proteins out of the cell, and, because they are single-molecule machines that work alone, or with two partner proteins in some bacteria, they are the simplest such systems.

    Each PCAT molecule has three domains, each in duplicate: one recognizes the cargo by a tag it carries, and cuts off that tag; another binds to and burns ATP, a molecule that contains energy stored within its atomic bonds; and the third forms a channel that spans the cells membrane. Previous work had examined the structure of the first two domains, but the structure of the third, had remained a mystery, along with the details of how the components function together.

    “At this point, we have no idea how many PCATs exist, although we expect they are numerous, because each specializes in a specific type of cargo. For this study, we focused on one we called PCAT1, which transports a small protein of unknown function,” says first author David Yin-wei Lin, a postdoc in the lab. “To get a sense of how PCAT1 changes shape when powered by energy from ATP, we examined the structure in two states, both with and without ATP.”

    The team, which also included Shuo Huang, a research technician who is now a graduate student at Georgia Institute of Technology, purified and crystalized the PCAT1 protein from the heat-loving bacterium Clostridium thermocellum. To determine the structure of the crystals, they used a technique called X-ray diffraction analysis, in which a pattern produced by X-rays bounced off the crystallized protein can be used to infer the structure of the molecule.

    The first structure, determined without ATP, revealed a striking feature: a large, water-filled central channel, a natural environment for a water-loving, or hydrophilic, protein. Two side openings into this channel were guarded by the cargo-recognizing domain, acting as a sort of ticket taker. Sites on this domain would recognize and clip off the cargo’s tag, before ushering the protein into the channel.

    When ATP is present, they found that the side entrances close, freeing the cargo-recognizing domain to move from its station outside of them. In addition, the ATP-binding domains at the bottom of the channel inside the cell come together. The researchers also saw the water channel shrink, leading them to hypothesize that energy from ATP allows PCAT1 to change conformation in such a way that it pushes its cargo out. This suggests that PCAT1 uses a strategy commonly seen in transport proteins known as alternate access, in which one end of the channel is open while the other closes. However, they qualify that PCATs that transport much larger proteins may function differently.

    “By visualizing the structure of this pump, we have been able to determine the details of a transport pathway that, in its simplicity, is fundamentally different from the more complex systems that have been closely studied before. This new information adds to the understanding of how cells send out proteins in order to interact with their environment,” Chen says.

    See the full article here.

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    The Rockefeller University is a world-renowned center for research and graduate education in the biomedical sciences, chemistry, bioinformatics and physics. The university’s 76 laboratories conduct both clinical and basic research and study a diverse range of biological and biomedical problems with the mission of improving the understanding of life for the benefit of humanity.

    Founded in 1901 by John D. Rockefeller, the Rockefeller Institute for Medical Research was the country’s first institution devoted exclusively to biomedical research. The Rockefeller University Hospital was founded in 1910 as the first hospital devoted exclusively to clinical research. In the 1950s, the institute expanded its mission to include graduate education and began training new generations of scientists to become research leaders around the world. In 1965, it was renamed The Rockefeller University.

  • richardmitnick 1:19 pm on July 22, 2015 Permalink | Reply
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    From SLAC: “Long-sought Discovery Fills in Missing Details of Cell ‘Switchboard'” 

    SLAC Lab

    July 22, 2015

    SLAC’s X-ray Laser Lends New Insight into Key Target for Drug Development

    A biomedical breakthrough, published today in the journal Nature, reveals never-before-seen details of the human body’s cellular switchboard that regulates sensory and hormonal responses. The work is based on an X-ray laser experiment at the Department of Energy’s SLAC National Accelerator Laboratory.

    The much-anticipated discovery, a decade in the making, could have broad impacts on development of more highly targeted and effective drugs with fewer side effects to treat conditions including high blood pressure, diabetes, depression and even some types of cancer.

    This video shows a 3-D rendering of a tiny signaling switch found in cells that involves arrestin (magenta), an important signaling protein, while docked with rhodopsin (green), a light-sensitive protein that is a type of G protein-coupled receptor (GPCR) found in the retina of our eyes. The cyan structure at the top is a protein called lysozyme that scientists added to more easily preserve and study the arrestin and rhodopsin structures. An experiment at SLAC’s Linac Coherent Light Source, an X-ray laser, provided this first-ever atomic-scale map of arrestin coupled to a GPCR. (SLAC National Accelerator Laboratory)

    The study has been hailed by researchers familiar with the work as one of the most important scientific results to date using SLAC’s Linac Coherent Light Source (LCLS), a DOE Office of Science User Facility that is one of the brightest sources of X-rays on the planet. The LCLS X-rays are a billion times brighter than those from synchrotrons and produce higher-resolution images while allowing scientists to use smaller samples.

    In crystallography experiments at the Coherent X-ray Imaging experimental station at LCLS, a liquid jet delivers nanoscale crystals into this chamber, where X-ray laser pulses strike them. (SLAC National Accelerator Laboratory)

    This illustration shows arrestin (yellow), an important type of signaling protein, while docked with rhodopsin (orange), a G protein-coupled receptor. GPCRs are embedded in cell membranes and serve an important role in a cellular signaling network. An experiment conducted at SLAC’s Linac Coherent Light Source X-ray laser provided an atomic-scale 3-D map of this joined structure. (SLAC National Accelerator Laboratory)

    These ultrabright X-rays enabled the research team to complete the first 3-D atomic-scale map of a key signaling protein called arrestin while it was docked with a cell receptor involved in vision. The receptor is a well-studied example from a family of hundreds of G protein-coupled receptors, or GPCRs, which are targeted by about 40 percent of drugs on the market. Its structure while coupled with arrestin provides new insight into the on/off signaling pathways of GPCRs.

    The research, led by scientists at the Van Andel Research Institute in Michigan in collaboration with dozens of other scientists from around the globe, represents a major milestone in GPCR structural studies, said Dr. Jeffrey L. Benovic, a biochemistry and molecular biology professor at Thomas Jefferson University in Philadelphia who specializes in such research but was not a part of this study.

    “This work has tremendous therapeutic implications,” Benovic said. “The study is a critical first step and provides key insight into the structural interactions in these protein complexes.”

    Decoding the Body’s Cellular ‘Switchboard’

    Arrestins and another class of specialized signaling proteins called G proteins take turns docking with GPCRs. Both play critical roles in the body’s communications “switchboard,” sending signals that the receptors translate into cell instructions. These instructions are responsible for a range of physiological functions.

    Until now, only a G protein had been seen joined to a receptor at this scale, one of the discoveries recognized with the 2012 Nobel Prize in Chemistry. Before the study at SLAC, little was known about how arrestins – which serve a critical role as the “off” switch in cell signaling, opposite the “on” switch of G proteins – dock with GPCRs, and how this differs from G protein docking. The latest research helps scientists understand how a docked arrestin can block a G protein from docking at the same time, and vice versa.

    Many of the available drugs that activate or deactivate GPCRs block both G proteins and arrestins from docking.

    “The new paradigm in drug discovery is that you want to find this selective pathway – how to activate either the arrestin pathway or the G-protein pathway but not both — for a better effect,” said Eric Xu, a scientist at the Van Andel Research Institute in Michigan who led the experiment. The study notes that a wide range of drugs would likely be more effective and have fewer side effects with this selective activation.

    X-ray Laser Best Tool for Tiny Samples

    Xu said he first learned about the benefits of using SLAC’s X-ray laser for protein studies in 2012. The microscopic arrestin-GPCR crystals, which his team had painstakingly produced over years, proved too difficult to study at even the most advanced type of synchrotron, a more conventional X-ray source.

    In the LCLS experiments, Xu’s team used samples of a form of human rhodopsin – a GPCR found in the retina whose dysfunction can cause night blindness – fused to a type of mouse arrestin that is nearly identical to human arrestin. Measuring just thousandths of a millimeter, the crystals – which had been formed in a toothpaste-like solution – were oozed into the X-ray pulses at LCLS, producing patterns that when combined and analyzed allowed researchers to reconstruct a complete 3-D map of the protein complex

    “While this particular sample serves a specific function in the body, people may start to use this research as a model for how GPCRs, in general, can interact with signaling proteins,” Xu said. His team had been working toward this result since 2005.

    SLAC Director Chi-Chang Kao said of the research milestone, “This important work is a prime example of how SLAC’s unique combination of cutting-edge scientific capabilities, including its expertise in X-ray science and structural biology, are playing key roles in high-impact scientific discoveries.”

    Data Analysis Helps Fill in Missing Piece

    Qingping Xu, a scientist in the Joint Center for Structural Genomics at SLAC’s Stanford Synchrotron Radiation Lightsource who helped to solve the 3-D structure, said it took many hours of computer modeling and data analysis to help understand and refine its details.

    “This structure is especially important because it fills in a missing piece about protein-binding pathways for GPCRs,” he said. Even so, he noted that much work remains in determining the unique structures and docking mechanisms across the whole spectrum of GPCRs and associated signaling proteins.

    Eric Xu said his group hopes to conduct follow-up studies at LCLS with samples of GPCRs bound to different types of signaling proteins.

    In addition to scientists from SLAC, including LCLS and SSRL’s Joint Center for Structural Genomics, and the Van Andel Research Institute, the study also included researchers from: Arizona State University, University of Southern California, DESY lab’s Center for Free Electron Laser Science in Germany, National University of Singapore, New York Structural Biology Center, The Scripps Research Institute, University of California, Los Angeles, University of Toronto, Vanderbilt University, Beijing Computational Science Research Center in China, the University of Wisconsin-Milwaukee, Chinese Academy of Sciences, Paul Scherrer Institute in Switzerland, Trinity College in Ireland, University of Chicago, University of Konstanz in Germany, Chinese Academy of Sciences, Center for Ultrafast Imaging in Germany, and University of Toronto.

    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.

  • richardmitnick 2:51 pm on July 20, 2015 Permalink | Reply
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    From Caltech: “Freezing a Bullet (+)” 

    Caltech Logo

    July 20, 2015
    Kimm Fesenmaier

    Crystal structure of the assembly chaperone of ribosomal protein L4 (Acl4) that picks up a newly synthesized ribosomal protein when it emerges from the ribosome in the cytoplasm, protects it from the degradation machinery, and delivers it to the assembly site of new ribosomes in the nucleus. Credit: Ferdinand Huber/Caltech

    X-Ray Vision, an article in our Spring 2015 issue, examined the central role Caltech has played in developing a powerful technique for revealing the molecular machinery of life. In May, chemist André Hoeltz, who was featured in the article, published a new paper describing how he used the technique to reveal how protein-synthesizing cellular machines are built.

    Ribosomes are vital to the function of all living cells. Using the genetic information from RNA, these large molecular complexes build proteins by linking amino acids together in a specific order. Scientists have known for more than half a century that these cellular machines are themselves made up of about 80 different proteins, called ribosomal proteins, along with several RNA molecules and that these components are added in a particular sequence to construct new ribosomes, but no one has known the mechanism that controls that process.

    Now researchers from Caltech and Heidelberg University have combined their expertise to track a ribosomal protein in yeast all the way from its synthesis in the cytoplasm, the cellular compartment surrounding the nucleus of a cell, to its incorporation into a developing ribosome within the nucleus. In so doing, they have identified a new chaperone protein, known as Acl4, that ushers a specific ribosomal protein through the construction process and a new regulatory mechanism that likely occurs in all eukaryotic cells.

    The results, described in a paper that appears online in the journal Molecular Cell, also suggest an approach for making new antifungal agents.

    The work was completed in the labs of André Hoelz, assistant professor of chemistry at Caltech, and Ed Hurt, director of the Heidelberg University Biochemistry Center (BZH).

    “We now understand how this chaperone, Acl4, works with its ribosomal protein with great precision,” says Hoelz. “Seeing that is kind of like being able to freeze a bullet whizzing through the air and turn it around and analyze it in all dimensions to see exactly what it looks like.”

    That is because the entire ribosome assembly process—including the synthesis of new ribosomal proteins by ribosomes in the cytoplasm, the transfer of those proteins into the nucleus, their incorporation into a developing ribosome, and the completed ribosome’s export back out of the nucleus into the cytoplasm—happens in the tens of minutes timescale. So quickly that more than a million ribosomes are produced per day in mammalian cells to allow for turnover and cell division. Therefore, being able to follow a ribosomal protein through that process is not a simple task.

    Hurt and his team in Germany have developed a new technique to capture the state of a ribosomal protein shortly after it is synthesized. When they “stopped” this particular flying bullet, an important ribosomal protein known as L4, they found that its was bound to Acl4.

    Hoelz’s group at Caltech then used X-ray crystallography to obtain an atomic snapshot of Acl4 and further biochemical interaction studies to establish how Acl4 recognizes and protects L4. They found that Acl4 attaches to L4 (having a high affinity for only that ribosomal protein) as it emerges from the ribosome that produced it, akin to a hand gripping a baseball. Thereby the chaperone ensures that the ribosomal protein is protected from machinery in the cell that would otherwise destroy it and ushers the L4 molecule through the sole gateway between the nucleus and cytoplasm, called the nuclear pore complex, to the site in the nucleus where new ribosomes are constructed.

    “The ribosomal protein together with its chaperone basically travel through the nucleus and screen their surroundings until they find an assembling ribosome that is at exactly the right stage for the ribosomal protein to be incorporated,” explains Ferdinand Huber, a graduate student in Hoelz’s group and one of the first authors on the paper. “Once found, the chaperone lets the ribosomal protein go and gets recycled to go pick up another protein.”

    The researchers say that Acl4 is just one example from a whole family of chaperone proteins that likely work in this same fashion.

    Hoelz adds that if this process does not work properly, ribosomes and proteins cannot be made. Some diseases (including aggressive leukemia subtypes) are associated with malfunctions in this process.

    “It is likely that human cells also contain a dedicated assembly chaperone for L4. However, we are certain that it has a distinct atomic structure, which might allow us to develop new antifungal agents,” Hoelz says. “By preventing the chaperone from interacting with its partner, you could keep the cell from making new ribosomes. You could potentially weaken the organism to the point where the immune system could then clear the infection. This is a completely new approach.”

    Co-first authors on the paper, Coordinated Ribosomal L4 Protein Assembly into the Pre-Ribosome Is Regulated by Its Eukaryote-Specific Extension, are Huber and Philipp Stelter of Heidelberg University. Additional authors include Ruth Kunze and Dirk Flemming also from Heidelberg University. The work was supported by the Boehringer Ingelheim Fonds, the V Foundation for Cancer Research, the Edward Mallinckrodt, Jr. Foundation, the Sidney Kimmel Foundation for Cancer Research, and the German Research Foundation (DFG).

    See the full article here.

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    The California Institute of Technology (commonly referred to as Caltech) is a private research university located in Pasadena, California, United States. Caltech has six academic divisions with strong emphases on science and engineering. Its 124-acre (50 ha) primary campus is located approximately 11 mi (18 km) northeast of downtown Los Angeles. “The mission of the California Institute of Technology is to expand human knowledge and benefit society through research integrated with education. We investigate the most challenging, fundamental problems in science and technology in a singularly collegial, interdisciplinary atmosphere, while educating outstanding students to become creative members of society.”
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  • richardmitnick 1:26 pm on July 7, 2015 Permalink | Reply
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    From SLAC: “Scientists Drive Tiny Shock Waves Through Diamond” 

    SLAC Lab

    July 6, 2015

    X-ray Laser Brings the Physics of Exploding Stars into the Lab

    Researchers prepare for an experiment in the Matter in Extreme Conditions station’s chamber at SLAC’s Linac Coherent Light Source X-ray laser. (SLAC National Accelerator Laboratory)

    Researchers have used an X-ray laser to record, in detail never possible before, the microscopic motion and effects of shock waves rippling across diamond.

    The technique, developed at the Department of Energy’s SLAC National Accelerator Laboratory, allows scientists to precisely explore the complex physics driving massive star explosions, which are critical for understanding fusion energy, and to improve scientific models used to study these phenomena.

    “What is really exciting is that we can capture images of what happens on microscopic scales,” said Bob Nagler, a staff scientist at the Linac Coherent Light Source (LCLS) X-ray laser, a DOE Office of Science User Facility. “People have used X-rays to produce images of shock waves, but never on the tiny scale that LCLS makes possible.” The results were published June 18 in Scientific Reports.

    The ability to measure shock wave properties so clearly at this scale, down to one-thousandth of a meter, can be useful to understanding the fundamental physics at work on far larger scales, too, he said.

    Using X-rays to ‘Freeze’ Shock Waves

    In the experiment, researchers used a powerful optical laser pulse to trigger shock waves in thin, inch-long slivers of diamond. Then they hit the diamond samples with LCLS X-ray pulses at time intervals of hundreds of trillionths of a second, or hundreds of picoseconds. The optical laser destroyed the diamond samples, so new samples were required for each image.

    This sequence of phase-contrast images (a-d) shows a shock wave passing through diamond. The time delay after the start of the shock wave is displayed in nanoseconds (“ns”) for each image. Images e-h are enhanced to more clearly reveal the shock wave features. The dotted box in Figure f shows the area used to measure the compression of the diamond sample caused by the light-triggered shock wave. (DESY)

    This movie shows a shock wave passing through thin diamond. The movie uses a sequence of images that were collected at different time points using SLAC’s Linac Coherent Light source X-ray laser. The movie slows down a process that spanned just 3 nanoseconds, or billionths of a second, and is measured in tens of microns, or hundredths of millimeters. (DESY)

    Researchers compiled the resulting X-ray images into an ultra-slow-motion “movie” about 3 billionths of a second long that shows how a shock wave whips through the diamond faster than the speed of sound.

    “LCLS’ pulses, just 50 quadrillionths of a second long, ‘freeze’ the motion of this elastic wave as it’s propagating through the material,” said Andreas Schropp, the lead author of the study, who is a staff scientist at Germany’s DESY lab.

    The researchers used an X-ray technique called magnified phase-contrast imaging to translate density changes in diamond into vivid, high-resolution shock wave images.

    The experiment yielded information about the compression of the diamond’s structure and the pressure changes caused by the shock wave.

    Upgrades Provide a View Inside Shocked Materials

    The experiment was one of the first using a specialized Matter in Extreme Conditions experimental station at LCLS that is designed to explore extreme states, including those never before directly measured and observed, using powerful X-rays.

    The optical lasers have since been upgraded to reach higher powers, and scientists now have the ability to couple shock wave imaging with another X-ray technique, called wide-angle X-ray scattering, that allows them to explore changes to the atomic structure of the material during a shock wave.

    “This allows us to see how materials behave when they melt, to see the dynamics of materials as they change from one structure to the next,” Nagler said. “This has implications for geoscience, such as understanding the physics of matter deep inside the interior of large planets.”

    Nagler said SLAC scientists have also just completed a new standardized platform that will make it far easier to set up and conduct a wide range of shock wave experiments using different materials and laser configurations.

    Researchers participating in the study were from SLAC’s LCLS; Lawrence Livermore National Laboratory; DESY lab and Dresden University of Technology in Germany; Swinburne University of Technology in Australia; and University of Oxford in the U.K. This work was supported by the DOE Office of Science, Fusion Energy Science; DOE Office of Basic Energy Sciences; Volkswagen Foundation; and the German Ministry of Education and Research.

    See the full article here.

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  • richardmitnick 11:06 am on May 6, 2015 Permalink | Reply
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    From SLAC: “Compact Light Source Improves CT Scans” 

    SLAC Lab

    May 5, 2015

    New Technology May Advance Preclinical Studies of Cancer and Other Diseases

    A new study shows that the recently developed Compact Light Source (CLS) – a commercial X-ray source with roots in research and development efforts at the Department of Energy’s SLAC National Accelerator Laboratory – enables computer tomography scans that reveal more detail than routine scans performed at hospitals today. The new technology could soon be used in preclinical studies and help researchers better understand cancer and other diseases.

    With its ability to image cross sections of the human body, X-ray computer tomography (CT) has become an important diagnostic tool in medicine. Conventional CT scans are very detailed when it comes to bones and other dense body parts that strongly absorb X-rays. However, the technique struggles with the visualization and distinction of “soft tissues” such as organs, which are more transparent to X-rays.

    “Our work demonstrates that we can achieve better results with the Compact Light Source,” says Professor for Biomedical Physics Franz Pfeiffer of the Technical University of Munich in Germany, who led the new study published April 20 in the Proceedings of the National Academy of Sciences. “The CLS allows us to do multimodal tomography scans – a more advanced approach to X-ray imaging.”

    More than One Kind of Contrast

    The amount of detail in a CT scan depends on the difference in brightness, or contrast, which makes one type of tissue distinguishable from another. The absorption of X-rays – the basis for standard CT – is only one way to create contrast.

    Alternatively, contrast can be generated from differences in how tissues change the direction of incoming X-rays, either through bending or scattering X-ray light. These techniques are known as phase-contrast and dark-field CT, respectively.

    “Organs and other soft tissues don’t have a large absorption contrast, but they become visible in phase-contrast tomography,” says the study’s lead author, Elena Eggl, a researcher at the Technical University of Munich. “The dark-field method, on the other hand, is particularly sensitive to structures like vertebrae and the lung’s alveoli.”

    The Compact Light Source by Palo Alto-based Lyncean Technologies Inc. generates X-rays suitable for advanced tomography. The car-sized device is a miniature version of football-field-sized X-ray generators known as synchrotrons and it emerged from basic research at SLAC in the late 1990s and early 2000s. (Lyncean Technologies Inc.)

    X-ray images of a variety of mammography test objects using absorption (left), phase-contrast (center) and dark-field (right) imaging modes. Different objects appear more clearly in one or another image, depending on the object’s properties. (Franz Pfeiffer/Technical University of Munich)

    Shrinking the Synchrotron

    However, these methods require X-ray light with a well-defined wavelength aligned in a particular way – properties that conventional CT scanners in hospitals do not deliver sufficiently.

    For high-quality phase-contrast and dark-field imaging, researchers can use synchrotrons – dedicated facilities where electrons run laps in football-stadium-sized storage rings to produce the desired radiation – but these are large and expensive machines that cannot simply be implemented at every research institute and clinic.

    Conversely, the CLS is a miniature version of a synchrotron that produces suitable X-rays by colliding laser light with electrons circulating in a desk-sized storage ring. Due to its small footprint and lower cost, it could be operated in almost any location.

    “The Large Hadron Collider at CERN is the world’s largest colliding beam storage ring, and the CLS is the smallest,” says SLAC scientist Ronald Ruth, one of the study’s co-authors. Ruth is also chairman of the board of directors and co-founder of Palo Alto-based Lyncean Technologies Inc., which developed the X-ray source based on earlier fundamental research at SLAC. “It turns out that the properties of the CLS are perfect for applications like tomography.”

    See the full article here.

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    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 7:04 am on April 23, 2015 Permalink | Reply
    Tags: , , , X-ray Technology   

    From DESY: “Scientists X-ray anti-inflammatory drug candidates” 


    No Writer Credit

    Structure of the Spiegelmer NOX-E36 bound to its target protein CCL2. Credit: Dominik Oberthür/CFEL

    Using DESY’s ultra bright X-ray source PETRA III, scientists have decoded the molecular and three-dimensional structure of two promising drug candidates from the new group of Spiegelmers for the first time.

    DESY Petra III
    DESY Petra III interior

    The results provide a deeper understanding of the mode of action of these substances that have already entered clinical trials. The researchers from the Universities of Hamburg and Aarhus (Denmark) together with colleagues from the biotech company NOXXON in Berlin present their work in the journal Nature Communications.

    Spiegelmers are a young group of promising pharmaceutical substances. They rely on the same building blocks as the nucleic acids RNA and DNA that fulfil various tasks in the organism – from storing genetic information and messaging to the regulation of genes. Artificial RNA or DNA molecules called aptamers can be tailored to bind to certain proteins with high specificity, blocking their function. Aptamers are well tolerated in the organism as they consist of natural building blocks. For these reasons, aptamers are seen as promising drug candidates. Since 2006, an aptamer for the treatment of age-related macular degeneration [AMD], an eye condition that can lead to blindness, is approved and on the market.

    Usually, RNA and DNA molecules are quickly degraded by enzymes within the body. This severely limits their application as pharmaceutical drugs. However, most biomolecules come in two mirror-image variants, the L-form and the D-form. Natural nucleic acids always exist in the D-form, while proteins are always build in their L-form in the body. Artificial aptamers that are constructed in the naturally not occurring L-form are not degraded by the organism. These mirror-image variants of aptamers are called Spiegelmers. “An advantage of Spiegelmers is that they are not targeted by the body’s enzymes,” explains Prof. Christian Betzel from the University of Hamburg.

    “Spiegelmers can be identified and optimised in the lab through a sophisticated evolutionary procedure. However, exact structure data of Spiegelmers have not been available until now,” says first author Dr. Dominik Oberthür from the Center for Free-Electron Laser Science CFEL, a cooperation of DESY, Max Planck Society and the University of Hamburg. If the exact structure of a Spiegelmer and its binding site at the target protein is known, its mode of action can be decoded and its structure could be further fine-tuned, if necessary.

    The team around Betzel used PETRA III’s bright X-rays to analyse the Spiegelmer NOX-E36 from NOXXON. It blocks the protein CCL2 that is involved in many inflammatory processes in the body. “If you target an inflammatory protein with a Spiegelmer, you have a good chance to tone down the inflammation in the body,” notes Betzel. NOX-E36 has already been successfully tested in a phase IIa clinical trial with patients.

    In order to analyse the structure of the drug candidate, the scientists first had to grow crystals of the Spiegelmer bound to its target protein CCL2. “Growing these crystals was quite a challenge,” recalls Betzel. Because it contradicts their natural function, most biomolecules are notoriously hard to crystallise.

    The crystals were analysed at the PETRA III measuring station P13, run by the European Molecular Biology Laboratory EMBL. Crystals diffract X-ray light, producing a characteristic pattern on the detector. From this diffraction pattern the structure of the crystal’s building blocks can be calculated – in this case the Spiegelmer’s structure, bound to its target protein. In the same manner, a group around Laure Yatime from the University of Aarhus solved the structure of another Spiegelmer: NOX-D20 binds to the protein C5a that is involved into many inflammatory processes, too. The group also reports the structure in Nature Communications.

    The analyses reveal the structure of both Spiegelmers with a spatial resolution of 0.2 nanometres (millionths of a millimetre) – that’s on the order of individual atoms. “I am delighted to finally have a high resolution visualization of the remarkable shapes of two Spiegelmer drug candidates,” comments Dr. Sven Klussmann, founder and chief scientific officer of NOXXON, and also co-author on both articles. “The structural data not only provide the first look at the unusual interaction of a mirror-image oligonucleotide with a natural protein but also deepens our understanding of the two molecules’ mode of action.”

    Crystal structure of a mirror-image L-RNA aptamer (Spiegelmer) in complex with the natural L-protein target CCL2; Dominik Oberthür, John Achenbach, Azat Gabdulkhakov, Klaus Buchner, Christian Maasch, Sven Falke, Dirk Rehders, Sven Klussmann & Christian Betzel; „Nature Communications“, 2015; DOI: 10.1038/ncomms7923

    Structural basis for the targeting of complement anaphylatoxin C5a using a mixed L-RNA/L-DNA aptamer; Laure Yatime, Christian Maasch, Kai Hoehlig, Sven Klussmann, Gregers R. Andersen & Axel Vater; „Nature Communications“, 2015; DOI: 10.1038/ncomms7481

    See the full article here.

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    Stem Education Coalition


    DESY is one of the world’s leading accelerator centres. Researchers use the large-scale facilities at DESY to explore the microcosm in all its variety – from the interactions of tiny elementary particles and the behaviour of new types of nanomaterials to biomolecular processes that are essential to life. The accelerators and detectors that DESY develops and builds are unique research tools. The facilities generate the world’s most intense X-ray light, accelerate particles to record energies and open completely new windows onto the universe. 
That makes DESY not only a magnet for more than 3000 guest researchers from over 40 countries every year, but also a coveted partner for national and international cooperations. Committed young researchers find an exciting interdisciplinary setting at DESY. The research centre offers specialized training for a large number of professions. DESY cooperates with industry and business to promote new technologies that will benefit society and encourage innovations. This also benefits the metropolitan regions of the two DESY locations, Hamburg and Zeuthen near Berlin.

  • richardmitnick 12:27 pm on April 9, 2015 Permalink | Reply
    Tags: , , , X-ray Technology   

    From BNL: “First NSLS-II X-Ray Images Hint at Science to Come” 

    Brookhaven Lab

    April 9, 2015
    Laura Mgrdichian


    In another “first” at the National Synchrotron Light Source II (NSLS-II) at Brookhaven National Laboratory, a group working at the Hard X-Ray Nanoprobe has taken the facility’s inaugural x-ray images. Their striking renderings of a monarch butterfly specimen demonstrate the synchrotron’s ability to generate extremely detailed images and foretell a future of exciting research.

    An X-ray image of the butterfly antennae (A), the mouth (B), and one of claws (C). The imaged regions are indicated in the optical microgram in the center.

    “The staff scientists at the HXN beamline immensely enjoyed producing these amazingly sharp images,” said HXN group leader Yong Chu. “Even non-scientists can appreciate their superb quality, particularly when comparing them with a typical x-ray taken at a hospital. Their spectacular sharpness is due to the world-leading brightness of NSLS-II.”

    He continued, “This is a first step toward our ultimate goal of achieving x-ray images with details at the one-nanometer level and serves as a preview of the many exciting scientific results that will soon be discovered at HXN and NSLS-II’s many other beamlines.”

    The images were taken as part of a system check of the HXN beamline at NSLS-II, a U.S. Department of Energy Office of Science User Facility. After the beamline components and optics were aligned, monochromatic x-rays were sent from the first optical enclosure to the experimental station. At that point, the images were taken using a high-resolution charge-coupled device (CCD) camera with an optically coupled scintillation screen, which is a typical setup for x-ray imaging. During the test, the HXN group used an imaging resolution of 1.5 microns (millionths of a meter) per pixel.

    The test images were produced using x-rays that were only one-thousandth of the maximum power of NSLS-II. The butterfly sample was positioned 63 meters away from the x-ray source, and the CCD camera was placed 160 millimeters away from the sample. This camera-to-sample distance was chosen to yield images with the optimal contrast using a method called in-line phase-contrast imaging. Because the butterfly was much larger than the field of view of the camera, different parts of the specimen were imaged separately. Those images were then stitched together to construct a broader view.

    “The images show amazing contrast, as if they were hand-drawn by an artist,” said Hanfei Yan, one of the HXN beamline scientists.

    “Even at this modest imaging resolution of 1.5 microns, the collected images exhibit many interesting features of the insect that are not obvious to the public, such as the internal structure of the butterfly’s mouth, or proboscis,” said Sebastian Kalbfleisch, a member of the HXN beamline team. “The images also show elaborate semi-periodic joint structure in the antenna, which allow a butterfly to move its feelers freely in all directions.”

    Wah-Keat Lee, who is leading development of the NSLS-II Full-Field X-ray Imaging (FXI) beamline, added, “These superb images speak for themselves as to why NSLS-II is an ideal synchrotron for x-ray imaging.”

    Each image took five seconds to generate because only one-thousandth of the full power of NSLS-II was used. This means that, at the maximum storage-ring current of 500 milliamps, scientists will be able to perform monochromatic beam x-ray imaging with a five-millisecond exposure time.

    This month, Chu said, the HXN team will commission a one-of-kind x-ray microscope, equipped with novel x-ray lenses called multilayer Laue lenses, both of which are developed at NSLS-II. This unique instrument will produce images with a resolution equivalent to ten thousand times smaller than a human hair, and they will help him and his group reveal structural details in their samples, including elemental composition, crystalline ordering, and chemical states.

    See the full article here.

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    BNL Campus

    One of ten national laboratories overseen and primarily funded by the Office of Science of the U.S. Department of Energy (DOE), Brookhaven National Laboratory conducts research in the physical, biomedical, and environmental sciences, as well as in energy technologies and national security. Brookhaven Lab also builds and operates major scientific facilities available to university, industry and government researchers. The Laboratory’s almost 3,000 scientists, engineers, and support staff are joined each year by more than 5,000 visiting researchers from around the world.Brookhaven is operated and managed for DOE’s Office of Science by Brookhaven Science Associates, a limited-liability company founded by Stony Brook University, the largest academic user of Laboratory facilities, and Battelle, a nonprofit, applied science and technology organization.

  • richardmitnick 8:58 am on April 9, 2015 Permalink | Reply
    Tags: , , , , X-ray Technology   

    From XFEL: “European XFEL scientists look deep into the atom” 

    XFEL bloc

    European XFEL

    09 April 2015
    No Writer Credit

    Digging into the “Giant Resonance”, scientists find hints of new quantum physics

    A cooperation between theoretical and experimental physicists has uncovered previously unknown quantum states inside atoms. The results, described in a paper published today in the journal Nature Communications, allow a better understanding of some aspects of electron behaviour in atoms, which in turn could lead to better insights into technologically relevant materials.

    In this study, scientists from European XFEL and the Center for Free Electron Laser Science (CFEL) at DESY examined the unknown quantum states in atoms of the noble gas xenon using DESY’s X-ray laser FLASH.

    XFEL Campus


    The bright X-ray light of free-electron lasers such as FLASH and the European XFEL allowed the scientists to observe these states for the first time. (CFEL is a joint venture between DESY, the University of Hamburg, and the Max Planck Society.)

    Atoms can develop an electrical charge by losing or gaining one or more electrons. This process, called ionization, was thought to be fairly simple. As an electron departs, it can briefly “hang” between the different locations of electrons in the atom, also called “shells”. In the world of quantum mechanics, this brief pause—lasting less than a femtosecond, or a quadrillionth of a second—is enough to be measured as what is called a “resonance”.

    “In a resonance, the electrons are ‘talking’ to each other”, says Michael Meyer, a leading scientist at European XFEL. This conversation of sorts can be picked up on a spectrograph, and, in most atoms, it shows up in a very narrow energy range.

    Yet for the past half century, scientists also have noted a strange resonance in atoms of the noble gas xenon and some rare earth elements. In contrast to other resonances, it covers a very broad energy range. This became known as the “giant dipole resonance”. “There were no good tools to investigate the giant dipole resonance more deeply”, says Meyer. “But extreme-ultraviolet and X-ray FELs present an opportunity to re-examine xenon’s strange property.” Such facilities have the possibility of studying nonlinear processes, or phenomena that are not a direct result of a single interaction—in the case of photoionization the disappearance of one photon, with its energy being transferred to the electron that can thus escape the atom. The extraordinary intensity of FELs makes non-linear processes observable—in this case, a process whereby two photons disappear, simultaneously transferring their energy to the escaping electron.

    Graphical representation of a 4d electron orbital in atomic xenon. Antonia Karamatskou / DESY

    This has become evident when Tommaso Mazza, a scientist in Meyer’s group at European XFEL, and others investigated the ionization of xenon atoms under intense FEL radiation at DESY’s FLASH. In parallel, DESY scientist Robin Santra, the leader of the CFEL theory group, and a student in his group, Antonia Karamatskou, thought there was something more to the giant dipole resonance. They worked off of a forty-year old suggestion that had been largely ignored: that xenon actually had not one but two resonances, and that earlier spectrographic techniques could not distinguish between them. In contrast, X-ray FELs can target very specific energies in the electronic structure of the atom using just two individual particles of light, enabling scientists to see both resonances more clearly.

    Santra and Karamatskou made calculations describing the energies of the resonances. The data from the experiments performed at FLASH by Tommaso Mazza and others match Santra’s and Karamatskou’s predictions. This is the first evidence of the giant dipole resonance being composed of two other resonances.

    Both Santra and Meyer think that there is far more to the behaviour of electrons within atoms in general than has been previously understood. The result point to not yet fully understood aspects of how atoms function.

    “We don’t even yet understand why there might be a second resonance”, Santra says. “Many people think simple atomic physics is figured out, but as this collaboration has shown, there is a lot of hidden stuff out there!”

    Also, the experiment has shown that FELs can be highly sophisticated tools for studying quantum physics. Santra says he expects the European XFEL, which is due to open to users in 2017, to expand these possibilities even further.

    The research collaboration between Meyer and Santra was initiated and supported by the Collaborative Research Center at the University of Hamburg, SFB 925.

    “Sensitivity of nonlinear photoionization to resonance substructure in collective excitation”; T. Mazza, A. Karamatskou, M. Ilchen, S. Bakhtiarzadeh, A.J. Rafipoor, P. O’Keeffe, T.J. Kelly, N. Walsh, J.T. Costello, M. Meyer & R. Santra; Nature Communications, 2015; DOI: 10.1038/ncomms7799

    See the full article here.

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    XFEL Campus

    The Hamburg area will soon boast a research facility of superlatives: The European XFEL will generate ultrashort X-ray flashes—27 000 times per second and with a brilliance that is a billion times higher than that of the best conventional X-ray radiation sources.

    The outstanding characteristics of the facility are unique worldwide. Starting in 2017, it will open up completely new research opportunities for scientists and industrial users.

  • richardmitnick 8:49 am on April 2, 2015 Permalink | Reply
    Tags: , , , X-ray Technology   

    From SLAC: “Scientists Track Ultrafast Creation of a Catalyst with X-ray Laser” 

    SLAC Lab

    April 1, 2015

    Chemical Transformations Driven by Light Provide Key Insight to Steps in Solar-energy Conversion

    This artistic rendering shows an iron-centered molecule that is severed by laser light (upper left). Within hundreds of femtoseconds, or quadrillionths of a second, a molecule of ethanol from a solvent rushes in (bottom right) to bond with the iron-centered molecule. (SLAC National Accelerator Laboratory)

    An international team has for the first time precisely tracked the surprisingly rapid process by which light rearranges the outermost electrons of a metal compound and turns it into an active catalyst – a substance that promotes chemical reactions.

    The results, published April 1 in Nature, could help in the effort to develop novel catalysts to efficiently produce fuel using sunlight. The research was performed with an X-ray laser at the Department of Energy’s SLAC National Accelerator Laboratory.

    “We were able to determine how light rearranges the outermost electrons of the compound on timescales down to a few hundred femtoseconds, or quadrillionths of a second,” said Philippe Wernet, a scientist at Helmholtz-Zentrum Berlin for Materials and Energy who led the experiment.

    Researchers hope that learning these details will allow them to develop rules for predicting and controlling the short-lived early steps in important reactions, including the ones plants use to turn sunlight and water into fuel during photosynthesis. Scientists are seeking to replicate these natural processes to produce hydrogen fuel from sunlight and water, for example, and to master the chemistry required to produce other renewable fuels.

    “The eventual goal is to design chemical reactions that behave exactly the way you want them to,” Wernet said.

    In the experiment at SLAC’s Linac Coherent Light Source, a DOE Office of Science User Facility, the scientists studied a yellowish fluid called iron pentacarbonyl, which consists of carbon monoxide “spurs” surrounding a central iron atom. It is a basic building block for more complex compounds and also provides a simple model for studying light-induced chemical reactions.

    SLAC LCLS Inside

    Researchers had known that exposing this iron compound to light can cleave off one of the five carbon monoxide spurs, causing the molecule’s remaining electrons to rearrange. The arrangement of the outermost electrons determines the molecule’s reactivity – including whether it might make a good catalyst – and also informs how reactions unfold.

    What wasn’t well understood was just how quickly this light-triggered transformation occurs and which short-lived intermediate states the molecule goes through on its way to becoming a stable product.

    At LCLS, the scientists struck a thin stream of the iron compound, which was mixed into an ethanol solvent, with pulses of optical laser light to break up the iron-centered molecules. Just hundreds of femtoseconds later, an ultrabright X-ray pulse probed the molecules’ transformation, which was recorded with sensitive detectors.

    By varying the arrival time of the X-ray pulses, they tracked the rearrangements of the outermost electrons during the molecular transformations.

    Roughly half of the severed molecules enter a chemically reactive state in which their outermost electrons are prone to binding other molecules. As a consequence, they either reconnect with the severed part or bond with an ethanol molecule to form a new compound. In other cases the outermost electrons in the molecule stabilize themselves in a configuration that makes the molecule non-reactive. All of these changes were observed within the time it takes light to travel a few thousandths of an inch.

    “To see this happen so quickly was extremely surprising,” Wernet said.

    Several years’ worth of data analysis and theoretical work were integral to the study, he said. The next step is to move on from model compounds to LCLS studies of the actual molecules used to make solar fuels.

    “This was a really exciting experiment, as it was the first time we used the LCLS to study chemistry in a liquid compound,” said Josh Turner, a SLAC staff scientist who participated in the experiment. “The LCLS is unique in the world in its ability to resolve these types of ultrafast processes in the right energy range for this compound.”

    SLAC’s Kelly Gaffney, a chemist who contributed expertise in how the changing arrangement of electrons steered the chemical reactions, said, “This work helps set the stage for future studies at LCLS and shows how cooperation across different research areas at SLAC enables broader and better science.”

    In addition to researchers from Helmholtz-Zentrum Berlin for Materials and Energy and LCLS, other scientists who assisted in the study were from: SLAC’s Stanford Synchrotron Radiation Lightsource; the SLAC and Stanford PULSE Institute; University of Potsdam, Max Planck Institute for Biophysical Chemistry, Goettingen University and DESY lab in Germany; Stockholm University and MAX-lab in in Sweden; Utrecht University in the Netherlands; Paul Scherrer Institute in Switzerland; and the University of Pennsylvania.

    This work was supported by the Volkswagen Foundation, the Swedish Research Council, the Carl Tryggers Foundation, the Magnus Bergvall Foundation, Collaborative Research Centers of the German Science Foundation and the Helmholtz Virtual Institute “Dynamic Pathways in Multidimensional Landscapes,” and the U.S. Department of Energy Office of Science.

    See the full article here.

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    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.

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