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  • richardmitnick 7:51 pm on December 4, 2014 Permalink | Reply
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    From SLAC: “Rattled Atoms Mimic High-temperature Superconductivity” 


    SLAC Lab

    December 4, 2014

    X-ray Laser Experiment Provides First Look at Changes in Atomic Structure that Support Superconductivity

    An experiment at the Department of Energy’s SLAC National Accelerator Laboratory provided the first fleeting glimpse of the atomic structure of a material as it entered a state resembling room-temperature superconductivity – a long-sought phenomenon in which materials might conduct electricity with 100 percent efficiency under everyday conditions.

    a
    In a high-temperature superconducting material known as YBCO, light from a laser causes oxygen atoms (red) to vibrate between layers of copper oxide that are just two molecules thick. (The copper atoms are shown in blue.) This jars atoms in those layers out of their normal positions in a way that likely favors superconductivity. In this short-lived state, the distance between copper oxide planes within a layer increases, while the distance between the layers decreases. (Jörg Harms/Max Planck Institute for the Structure and Dynamics of Matter)

    Researchers used a specific wavelength of laser light to rattle the atomic structure of a material called yttrium barium copper oxide, or YBCO. Then they probed the resulting changes in the structure with an X-ray laser beam from the Linac Coherent Light Source (LCLS), a DOE Office of Science User Facility.

    SLAC LCLS
    SLAC LCLS Inside
    LCLS at SLAC

    They discovered that the initial exposure to laser light triggered specific shifts in copper and oxygen atoms that squeezed and stretched the distances between them, creating a temporary alignment that exhibited signs of superconductivity for a few trillionths of a second at well above room temperature – up to 60 degrees Celsius (140 degrees Fahrenheit). The scientists coupled data from the experiment with theory to show how these changes in atomic positions allow a transfer of electrons that drives the superconductivity.

    New Views of Atoms in Motion

    “This is a highly interesting state, even though it only exists for a short period of time,” said Roman Mankowsky of the Max Planck Institute for the Structure and Dynamics of Matter in Hamburg, Germany, who was lead author of a report on the experiment in the Dec. 4 print issue of Nature. “When the laser excites the material, it shifts the atoms and changes the structure. We hope these results will ultimately help in the design of new materials to enhance superconductivity.”

    Sustaining such a state at room temperature would revolutionize many fields, making the electrical grid more efficient and enabling more powerful and compact computers. Traditional superconductors operate only at temperatures close to absolute zero. YBCO is one of a handful of materials discovered since 1986 that superconduct at somewhat higher temperatures; but they still have to be chilled to at least minus 135 degrees Celsius in order to sustain superconductivity, and scientists still don’t know what allows these so-called high-temperature superconductors to carry electricity with zero resistance.

    A Powerful Tool for Exploring Superconductivity

    Josh Turner, a SLAC staff scientist who has led other studies of YBCO at the LCLS, said powerful tools such as X-ray lasers have excited new interest in superconductor research by allowing researchers to isolate a specific property that they want to learn more about. This is important because high-temperature superconductors can exhibit a tangle of magnetic, electronic and structural properties that may compete or cooperate as the material moves toward a superconducting state. For example, another recently published LCLS study found that exciting YBCO with the same optical laser light disrupts an electronic order that competes with superconductivity.

    “What LCLS is now showing us is how these different properties change over short times,” Turner said. “We can actually see how the electrons or atoms are moving.”

    Mankowsky said future experiments at LCLS could try to sustain the superconducting state for longer periods, use a combination of experimental techniques to study how other properties evolve in the transition into the superconducting state and explore whether the same structural changes are at work in other high-temperature superconductors.

    Researchers from the National Center for Scientific Research in France, Paul Scherrer Institute in Switzerland, Max Planck Institute for Solid State Research in Germany, Swiss Federal Institute of Technology, College of France, University of Geneva, Oxford University in the United Kingdom, the Center for Free-Electron Laser Science in Germany, and University of Hamburg in Germany also participated in the study. The work was supported by the European Research Council, German Science Foundation, Swiss National Superconducting Center and Swiss National Science Foundation.

    See the full article here.

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  • richardmitnick 4:24 pm on December 4, 2014 Permalink | Reply
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    From SLAC: “X-ray Laser Reveals How Bacterial Protein Morphs in Response to Light” 


    SLAC Lab

    December 4, 2014

    A Series of Super-Sharp Snapshots Demonstrates a New Tool for Tracking Life’s Chemistry

    Human biology is a massive collection of chemical reactions, from the intricate signaling network that powers our brain activity to the body’s immune response to viruses and the way our eyes adjust to sunlight. All involve proteins, known as the molecules of life; and scientists have been steadily moving toward their ultimate goal of following these life-essential reactions step by step in real time, at the scale of atoms and electrons.

    Now, researchers have captured the highest-resolution snapshots ever taken with an X-ray laser that show changes in a protein’s structure over time, revealing how a key protein in a photosynthetic bacterium changes shape when hit by light. They achieved a resolution of 1.6 angstroms, equivalent to the radius of a single tin atom.

    m
    This illustration depicts an experiment at SLAC that revealed how a protein from photosynthetic bacteria changes shape in response to light. Samples of the crystallized protein (right), called photoactive yellow protein or PYP, were jetted into the path of SLAC’s LCLS X-ray laser beam (fiery beam from bottom left). The crystallized proteins had been exposed to blue light (coming from left) to trigger shape changes. Diffraction patterns created when the X-ray laser hit the crystals allowed scientists to recreate the 3-D structure of the protein (center) and determine how light exposure changes its shape. (SLAC National Accelerator Laboratory)

    “These results establish that we can use this same method with all kinds of biological molecules, including medically and pharmaceutically important proteins,” said Marius Schmidt, a biophysicist at the University of Wisconsin-Milwaukee who led the experiment at the Department of Energy’s SLAC National Accelerator Laboratory. There is particular interest in exploring the fastest steps of chemical reactions driven by enzymes — proteins that act as the body’s natural catalysts, he said: “We are on the verge of opening up a whole new unexplored territory in biology, where we can study small but important reactions at ultrafast timescales.”

    The results, detailed in a report published online Dec. 4 in Science, have exciting implications for research on some of the most pressing challenges in life sciences, which include understanding biology at its smallest scale and making movies that show biological molecules in motion.

    A New Way to Study Shape-shifting Proteins

    The experiment took place at SLAC’s Linac Coherent Light Source (LCLS), a DOE Office of Science User Facility. LCLS’s X-ray laser pulses, which are about a billion times brighter than X-rays from synchrotrons, allowed researchers to see atomic-scale details of how the bacterial protein changes within millionths of a second after it’s exposed to light.

    SLAC LCLS
    SLAC LCLS Inside
    LCLS at SLAC

    “This experiment marks the first time LCLS has been used to directly observe a protein’s structural change as it happens. It opens the door to reaching even faster time scales,” said Sébastien Boutet, a SLAC staff scientist who oversees the experimental station used in the study. LCLS’s pulses, measured in quadrillionths of a second, work like a super-speed camera to record ultrafast changes, and snapshots taken at different points in time can be compiled into detailed movies.

    The protein the researchers studied, found in purple bacteria and known as PYP for “photoactive yellow protein,” functions much like a bacterial eye in sensing blue light. The mechanism is very similar to that of other receptors in biology, including receptors in the human eye. “Though the chemicals are different, it’s the same kind of reaction,” said Schmidt, who has studied PYP since 2001. Proving the technique works with a well-studied protein like PYP sets the stage to study more complex and biologically important molecules at LCLS, he said.

    Chemistry on the Fly

    In the LCLS experiment, researchers prepared crystallized samples of the protein, and exposed the crystals, each about 2 millionths of a meter long, to blue laser light before jetting them into the LCLS X-ray beam.

    The X-rays produced patterns as they struck the crystals, which were used to reconstruct the 3-D structures of the proteins. Researchers compared the structures of the proteins that had been exposed to light to those that had not to identify light-induced structural changes.

    “In the future we plan to study all sorts of enzymes and other proteins using this same technique,” Schmidt said. “This study shows that the molecular details of life’s chemistry can be followed using X-ray laser crystallography, which puts some of biology’s most sought-after goals within reach.”

    Researchers from the University of Wisconsin-Milwaukee and SLAC were joined by researchers from Arizona State University; Lawrence Livermore National Laboratory; University of Hamburg and DESY in Hamburg, Germany; State University of New York, Buffalo; University of Chicago; and Imperial College in London. The work was supported by the National Science Foundation, National Institutes of Health and Lawrence Livermore National Laboratory.

    See the full article here.

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  • richardmitnick 8:22 pm on December 3, 2014 Permalink | Reply
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    From SLAC: “SLAC, RadiaBeam Build New Tool to Tweak Rainbows of X-ray Laser Light” 


    SLAC Lab

    December 3, 2014

    ‘Dechirper’ Will Give Scientists More Control Over ‘Color Spectrum’ of LCLS X-ray Pulses

    The Department of Energy’s SLAC National Accelerator Laboratory has teamed up with Santa Monica-based RadiaBeam Systems to develop a device known as a dechirper, which will provide a new way of adjusting the range of energies within single pulses from SLAC’s X-ray laser.

    d
    Design drawing of the outer structure of a dechirper that will be used to tweak the “color range” of light pulses from SLAC’s X-ray laser, LCLS. Two dechirpers will be lined up in front of the LCLS undulator—a magnetic structure that generates ultrabright, ultrafast X-rays from bunches of electrons. (RadiaBeam Systems)

    i
    The inside of the dechirper consists of two parallel, 2-meter-long, flat aluminum rails. Electron bunches will travel through a variable gap between the rails at nearly the speed of light. (RadiaBeam Systems)

    r
    The aluminum rails have comb-like grooves that are half a millimeter deep and a quarter millimeter wide. The electron bunches “sense” the grooves, leading to a change in the energy spread of the X-rays they produce. (RadiaBeam Systems)

    “For many experiments it is important to use a specific X-ray energy so that we can study specific chemical elements in our samples,” says LCLS scientist William Schlotter. “The narrower the energy bandwidth, the more precisely we can study those elements.”

    Tweaking the ‘Color Spectrum’ of X-ray Pulses

    LCLS generates ultrabright and ultrashort X-ray pulses from packets of electrons that travel through a magnetic structure, called an undulator, at almost the speed of light. The properties of the electron bunches determine the characteristics of the X-ray light that they produce.

    un
    Working of the undulator. 1: magnets, 2: electron beam entering from the upper left, 3: synchrotron radiation exiting to the lower right

    Many experiments demand X-ray pulses that last only a few quadrillionths of a second, but it is difficult to make electron bunches this short. Therefore, scientists have turned to nature and adopted a solution reminiscent of a bird’s chirp. They create a spread of energies in the electron bunch, with the tail having more energy than the head. When electron bunches pass through another magnetic device known as a chicane, this so-called “energy chirp” allows lagging electrons in the tail to catch up with the ones in the head, creating shorter electron bunches, and thus shorter X-ray pulses.

    However, since the chirp consists of a spectrum of energies, the X-rays also have multiple energies—a rainbow of X-ray “colors” known as the energy bandwidth. Depending on the type of experiment, this can be an advantage or disadvantage, and researchers would like to have new tools to adjust the energy bandwidth to match their needs.

    As the name suggests, the dechirper’s primary task will be to minimize the chirp, i.e. to make pulses with a smaller spread in X-ray energies. Additionally, the dechirper can do the opposite and make X-ray pulses with a broader energy spectrum. In fact, many users have had a desire for a wider bandwidth since LCLS started operations in 2009, as LCLS scientist Sébastien Boutet points out.

    Precision Tool to Manipulate Electron Bunches

    SLAC scientists first proposed the idea for a dechirper in 2012 and, together with researchers from Lawrence Berkeley National Laboratory, demonstrated its feasibility in a test experiment at the Pohang Accelerator Laboratory in South Korea.

    The LCLS device, whose final design review will take place on Dec. 4, will consist of two flat, parallel aluminum rails, each 2 meters long, with comb-like grooves that are half a millimeter deep and a quarter millimeter wide. Two of these devices will be lined up in front of the undulator, with the electron beam traveling through the gap between the rails.

    Even though the electron bunches will not touch the rails, they will “sense” the grooves. These “bumps” along the electrons’ flight path will create a wake at the tail of the bunch, similar to the wake behind a boat gliding over water. “In this process, the tail loses energy while the front stays the same,” explains accelerator physicist Richard Iverson, the project lead at SLAC, where the technical requirements for the dechirper were specified.

    Varying the gap between the rails changes the effect on the electrons, allowing scientists to adjust the chirp of the electron bunches and, consequently, the energy bandwidth of the X-ray pulses generated in the undulator.

    What may sound like a relatively simple setup poses significant challenges for the manufacturing process. “The dechirper’s grooves are only as wide as three or four human hairs,” says project manager Marcos Ruelas at RadiaBeam, where the device is being designed and constructed. “Moreover, the rails must be very flat and smooth. Over the entire length of 4 meters, their height can only differ by 50 micrometers.” To meet these requirements, each 2-meter rail will be manufactured in four smaller blocks.

    The new device is expected to be installed at SLAC in August 2015. It will not only start providing LCLS users with more flexibility for their experiments, but will also become the test bed for dechirpers at SLAC’s next-generation LCLS-II facility and other X-ray lasers worldwide.

    Other key personnel of the project include Karl Bane, Paul Emma, Timothy Maxwell, Zhirong Huang, Gennady Stupakov and Zhen Zhang from SLAC’s Accelerator Directorate, as well as RadiaBeam’s Pedro Frigola, Mark Harrison and David Martin.

    See the full article here.

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  • richardmitnick 4:40 pm on November 21, 2014 Permalink | Reply
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    From SLAC: “Robotics Meet X-ray Lasers in Cutting-edge Biology Studies” 


    SLAC Lab

    November 21, 2014

    Platform Brings Speed, Precision in Determining 3-D Structure of Challenging Biological Molecules

    Scientists at the Department of Energy’s SLAC National Accelerator Laboratory are combining the speed and precision of robots with one of the brightest X-ray lasers on the planet for pioneering studies of proteins important to biology and drug discovery.

    The new system uses robotics and other automated components to precisely maneuver delicate samples for study with the X-ray laser pulses at SLAC’s Linac Coherent Light Source (LCLS). This will speed efforts to map the 3-D structures of nanoscale crystallized proteins, which are important for designing targeted drugs and synthesizing natural systems and processes.

    s
    This illustration shows an experimental setup used in crystallography experiments at SLAC’s Linac Coherent Light Source X-ray laser. The drum-shaped container at left stores supercooled crystal samples that are fetched by a robotic arm and delivered to another device, called a goniometer. The goniometer moves individual crystals through the X-ray beam, which travels from the pipe at upper left toward the lower right. A detector, right, captures X-ray diffraction patterns produced as the X-rays pass through the crystal samples. (SLAC National Accelerator Laboratory)

    i
    Equipment used in a highly automated X-ray crystallography system at SLAC’s Linac Coherent Light Source X-ray laser. The metal drum at lower left contains liquid nitrogen for cooling crystallized samples studied with LCLS’s intense X-ray pulses. (SLAC National Accelerator Laboratory)

    SLAC LCLS
    SLAC LCLS

    A New Way to Study Biology

    “This is an efficient, highly reliable and automated way to obtain high-resolution 3-D structural information from small sizes and volumes of samples, and from samples that are too delicate to study using other X-ray sources and techniques,” said Aina Cohen, who oversaw the development of the platform in collaboration with staff at LCLS and at SLAC’s Stanford Synchrotron Radiation Lightsource (SSRL), both DOE Office of Science User Facilities.

    SLAC SSRL
    SLAC SSRL

    She is co-leader of the Macromolecular Crystallography group in the Structural Molecular Biology (SMB) program at SSRL, which has used robotic sample-handling systems to run remote-controlled experiments for a decade.

    The new setup at LCLS is described in the Oct. 31 edition of Proceedings of the National Academy of Sciences. It includes a modified version of a “goniometer,” a sample-handling device in use at SSRL and many other synchrotrons, as well as a custom version of an SSRL-designed software package that pinpoints the position of crystals in arrays of samples.

    LCLS, with X-ray pulses a billion times brighter than more conventional sources, has already allowed scientists to explore biological samples too small or fragile to study in detail with other tools. The new system provides added flexibility in the type of samples and sample-holders that can be used in experiments.

    Rather than injecting millions of tiny, randomly tumbling crystallized samples into the path of the pulses in a thin liquid stream – common in biology experiments at LCLS – the goniometer-based system places crystals one at a time into the X-ray pulses. This greatly reduces the number of crystals needed for structural studies on rare and important samples that require a more controlled approach.

    Early Successes

    “This system adapts common synchrotron techniques for use at LCLS, which is very important,” said Henrik Lemke, staff scientist at LCLS. “There is a large community of scientists who are familiar with the goniometer technique.”

    The system has already been used to provide a complete picture of a protein’s structure in about 30 minutes using only five crystallized samples of an enzyme, moved one at a time into the X-rays for a sequence of atomic-scale “snapshots.”

    It has also helped to determine the atomic-scale structures of an oxygen-binding protein found in muscles, and another protein that regulates heart and other muscle and organ functions.

    “We have shown that this system works, and we can further automate it,” Cohen said. “Our goal is to make it easy for everyone to use.”

    Many biological experiments at LCLS are conducted in air-tight chambers. The new setup is designed to work in the open air and can also be used to study room-temperature samples, although most of the samples used in the system so far have been deeply chilled to preserve their structure. One goal is to speed up the system so it delivers samples and measures the resulting diffraction patterns as fast as possible, ideally as fast as LCLS delivers pulses: 120 times a second.

    The goniometer setup is the latest addition to a large toolkit of systems that deliver a variety of samples to the LCLS beam, and a new experimental station called MFX that is planned at LCLS will incorporate a permanent version.

    Team Effort

    Developed through a collaboration of SSRL’s Structural Molecular Biology program and the Stanford University School of Medicine, the LCLS goniometer system reflects increasing cooperation in the science of SSRL and LCLS, Cohen said, drawing upon key areas of expertise for SSRL and the unique capabilities of LCLS. “The combined effort of staff at both experimental facilities was key in this success,” she said.

    In addition to staff at SLAC’s SSRL and LCLS and at Stanford University’s School of Medicine, researchers from SLAC’s Photon Science Directorate, the University of Pittsburgh School of Medicine, Howard Hughes Medical Institute, Montana State University, Lawrence Berkeley National Laboratory and the University of California, San Francisco also participated in this effort.

    The work was supported by the Department of Energy Office of Basic Energy Sciences, the SSRL Structural Molecular Biology Program via the DOE Office of Biological and Environmental Research, and the Biomedical Technology Research Resources program at the National Institute of General Medical Sciences, National Institutes of Health.

    See the full article here.

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  • richardmitnick 7:25 pm on November 17, 2014 Permalink | Reply
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    From SLAC: “SLAC X-ray Laser Brings Key Cell Structures into Focus” 


    SLAC Lab

    November 17, 2014

    Experiment is Important Step Toward Atomic-Scale Imaging of Intact Biological Particles

    Scientists have made high-resolution X-ray laser images of an intact cellular structure much faster and more efficiently than ever possible before. The results are an important step toward atomic-scale imaging of intact biological particles, including viruses and bacteria.

    The technique was demonstrated at the Linac Coherent Light Source (LCLS) at the Department of Energy’s SLAC National Accelerator Laboratory and reported in the Nov. 17 issue of Nature Photonics.

    art
    A 20-sided structure from a bacterial cell, called a carboxysome, is struck by an X-ray pulse (purple) at SLAC’s Linac Coherent Light Source. (SLAC National Accelerator Laboratory)

    An international team of scientists used LCLS, a DOE Office of Science User Facility, to produce tens of thousands of high-resolution images of the tiniest individual biological particles yet studied there – 20-sided structures called carboxysomes that are found in some bacterial cells and play a major role in Earth’s life-sustaining carbon cycle. Although these structures have been studied for years, much remains unknown about their inner workings.

    New Views of Bacteria’s Carbon-conversion Engines

    “In an experiment lasting only 12 minutes, we collected many high-quality images using a very small amount of sample,” said Janos Hajdu, a professor of biophysics at Uppsala University in Sweden, which led the research. “In the future you could conceivably get results within minutes that used to take five days for certain types of samples. We showed that with the right type of instruments and detectors, you can increase the throughput of X-ray lasers by a huge amount.”

    The results bolster the aims of the LCLS Single-Particle Imaging initiative, formally launched at SLAC in October in cooperation with the international scientific community, said Christoph Bostedt, a SLAC senior staff scientist who leads the initiative with staff scientist Andy Aquila. The initiative is working toward atomic-scale imaging for many types of biological samples by identifying and addressing technical challenges at LCLS.

    “As this work demonstrates, we are already achieving imaging of single particles today, and we are working to improve upon these capabilities,” Aquila said.

    Bostedt added, “We will tackle these hurdles by working with the community. LCLS managers have committed to support this effort with dedicated experimental time.”

    Biology ‘On the Fly’

    Carboxysomes are microscopic workhorses inside cyanobacteria, which carry out photosynthesis. They pull in carbon dioxide from their surroundings and use an enzyme to convert it to forms that other living things can use. An estimated 40 percent of the organic carbon on Earth was made in these cell structures. “A better understanding of the structure and function of these cell organelles could benefit carbon-cycle research,” said Dirk Hasse of Uppsala University, one of the paper’s lead authors.

    Because they vary in size from about 90 to 140 nanometers, or billionths of a meter, in diameter, it is difficult to crystallize these tiny structures for conventional X-ray studies of their structure.

    A 2011 study by members of the same international team had studied samples of a giant virus, called Mimivirus, using a similar experimental technique that jets samples in a finely focused aerosol spray into the path of the X-ray pulses.

    In the latest study they were able to achieve better resolution, showing features as small as 18 nanometers.

    The scientists said a new design for the “aerosol injector” that shot the samples in a thin stream toward the X-ray pulses was among the key improvements that allowed them to achieve higher-resolution images. They also improved data-analysis tools that automatically sorted the 70,000 images they collected and assembled them into distinct groups. These advances lay the foundation for accurate, high-throughput structure determination for individual biological samples and other types of samples.

    The resolution achieved in this first experiment was not high enough to reveal the interior of the carboxysomes, though the team said that upgrades to higher intensity and a narrower focus of LCLS X-rays could allow far more detailed explorations of many biological samples in this size range, including small viruses. “We haven’t yet reached the limits,” said Filipe Maia of Uppsala University, who participated in the study.

    Pushing the Limits

    Max Hantke of Uppsala University, a lead author of the study, said the ultrashort pulses of X-ray lasers offer important advantages over instruments like electron microscopes that are used to study biological samples.

    For example, the X-ray laser can be used to track ultrafast processes, such as how biological samples respond to pulses of light over time. “These types of experiments are not possible with other methods,” Hantke said.

    In addition to scientists from Uppsala University and SLAC, other researchers who participated in the study were from Lawrence Berkeley National Laboratory; Kansas State University; the National University of Singapore; the University of Melbourne in Australia; University of Rome in Italy; and DESY laboratory, PNSensor, Max Planck Institute for Extraterrestrial Physics and European XFEL, all in Germany.

    This work was supported by the Swedish Research Council, the Knut and Alice Wallenberg Foundation, the European Research Council, the Röntgen-Ångström Cluster, and Stiftelsen Olle Engkvist Byggmästare. The CAMP instrument used in the experiment was funded by the Max Planck Society.

    See the full article here.

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  • richardmitnick 1:22 pm on October 7, 2014 Permalink | Reply
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    From SLAC: “Five Years of Scientific Discoveries with SLAC’s LCLS” 


    SLAC Lab

    October 7, 2014

    From ‘Hollow’ Atoms to Structures Inside Living Cells, SLAC’s Laser Continues to Explore Science at the Extremes

    Five years ago, on the eve of the first X-ray laser experiment at the Department of Energy’s SLAC National Accelerator Laboratory, Linda Young summed up her role in leading this inaugural exploration: “Wow … Quite an honor, quite a responsibility.”

    SLAC LCLS
    SLAC LCLS Inside
    LCLS at SLAC

    Young, who studies interactions of light and matter at the scale of atoms and molecules, is director of the X-ray Science Division at Argonne National Laboratory. She chronicled her team’s pioneering experiment at the Linac Coherent Light Source (LCLS), a DOE Office of Science User Facility, in a series of blog posts in October 2009.

    pulse
    This illustration shows how the first experiment at SLAC’s Linac Coherent Light Source X-ray laser, conducted in October 2009, stripped away electrons from neon atoms. (SLAC National Accelerator Laboratory)

    That first group of scientists studied what happens when intense X-ray pulses from LCLS, a billion times brighter than previous X-ray sources used for research, hit neon atoms. The researchers learned how to precisely tune the pulses to peel away atoms’ outer electrons or carve out their inner electrons, creating temporarily “hollow” atoms. This process had never been explored in such detail.

    team
    Some members of the first experimental team at SLAC’s LCLS X-ray laser: (standing, left to right) Elliot Kanter, Robin Santra, Phay Ho, Stephen Pratt, Stefan Pabst and Anne-Marie March; (sitting, left to right) Linda Young, Stephen Southworth, Bertold Kraessig. (Argonne National Laboratory)

    see
    Scientists in a control room monitor the first experiment at SLAC’s Linac Coherent Light Source. (Argonne National Laboratory)

    poster

    These and other results from early experiments provided a basic understanding of the extent and speed at which LCLS X-rays can damage or destroy samples – knowledge that is especially critical for producing accurate 3-D images of complex molecular structures.

    “We’ve found out not only the basic processes that happen in atoms in response to LCLS pulses, but some of the subtleties that go along with it,” Young said, reflecting on the progress made possible by experiments at LCLS.

    Since that first experiment, the number of LCLS experimental stations has multiplied from one to six, and thousands more scientists have probed previously unreachable realms in fields from biology and chemistry to materials science and astrophysics. LCLS experiments have generated hundreds of articles in peer-reviewed scientific journals, with almost one-third of them appearing in prominent journals like Science and Nature.

    LCLS has already achieved important milestones in several fields, mapping the structure of an enzyme relevant to a disease called African sleeping sickness and a crystallized protein embedded in living bacterial cells, detailing quantum phenomena in microscopic droplets of helium, and learning how DNA guards against damage from ultraviolet light.

    Young has returned to LCLS several times, most recently last spring. It seems there is always a steady supply of new instruments and techniques to try out at LCLS, she said: “The machine scientists keep coming up with new configurations that allow us to delve a little deeper.”

    Importantly, the sensitivity of the X-ray detectors has increased, she noted, and her team is now studying more complex molecules. Young said improvements in computer-based modeling should also help scientists prepare for LCLS experiments and interpret LCLS-generated data.

    She added, “Science at LCLS is still rapidly evolving – I don’t think it has lost its flavor of being very exploratory. We’re just starting to scratch the surface.”

    See the full article here.

    Coming soon: LCLS-II
    SLAC LCLSII

    SLAC Campus
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  • richardmitnick 8:14 am on September 12, 2014 Permalink | Reply
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    From SLAC: “SLAC Scientists Win Prizes for X-ray Laser Work” 


    SLAC Lab

    September 11, 2014

    Three scientists at the Department of Energy’s SLAC National Accelerator Laboratory received international prizes for their achievements in free-electron laser science, a field that has rapidly accelerated since the launch of SLAC’s X-ray laser five years ago.

    The annual prizes were awarded Aug. 27 during FEL 2014, the 36th International Free Electron Laser Conference, in Basel, Switzerland. The SLAC winners are:

    Zhirong Huang, a SLAC associate professor of photon science and PPA who has participated in pioneering projects related to the design and improvement of SLAC’s Linac Coherent Light Source (LCLS) X-ray laser, a Department of Energy Office of Science User Facility. He is a co-recipient of the 2014 FEL Prize, which recognizes significant contributions to the field.
    William Fawley, formerly of Lawrence Berkeley National Laboratory who now supports X-ray FEL R&D at SLAC, shares this year’s FEL Prize with Huang for his work in developing early FEL simulation codes, among other contributions. Fawley collaborates with the SLAC FEL theory group led by Huang, and has been working on a separate FEL project, FERMI@Elettra, in Trieste, Italy.
    Erik Hemsing, an associate staff scientist at SLAC, received the Young FEL Scientist Award for finding a new way to create beams of spiraling light, or “twisted light.”

    three
    From left, SLAC’s Erik Hemsing, Zhirong Huang and William Fawley accept awards during the 36th International Free Electron Laser Conference in Basel, Switzerland. At right is SLAC’s Paul Emma, who served as this year’s FEL Prize committee chairman. (Paul Scherrer Institute)

    “A lot of the people who have won the prize before me are my mentors and collaborators,” said Huang, who worked on X-ray FEL theory and an FEL test facility at Argonne National Laboratory before joining SLAC in 2002. “It’s a really great honor to join them.”

    Huang helped to build a “laser heater” that suppresses instability in SLAC’s linear accelerator in order for the electron bunches to emit intense X-ray light at LCLS, and he was part of the team that started up LCLS five years ago.

    More recently, he helped lead an effort to produce more intense X-ray pulses in a narrower band of wavelengths at LCLS, a process known as “self-seeding.” Huang also oversaw construction of a device that measures the duration of LCLS pulses.

    Fawley said of his award, “It is certainly a nice honor, but for me the real enjoyment is the recognition of all the work done with my collaborators” over the past several decades. He said he is probably best known in the FEL community for co-creating FEL simulation codes that supported high-power FEL research led by Lawrence Livermore National Laboratory in the 1980s and was later used to help investigate the properties of FEL designs like the LCLS. Recently, Fawley and Huang collaborated on a paper that characterizes the enhanced performance of a seeded FEL using the laser heater.

    Hemsing said, “I feel lucky to have the privilege to work alongside many of those who have made significant contributions to the FEL field over the last few decades.”

    Besides his study of twisted light, which has applications ranging from astronomy to fiber optics, Hemsing also has worked on a technique for tuning an electron beam with a laser to produce very short pulses of light with more predictable properties.

    Several new XFELs are under construction around the globe, including projects in Korea, Switzerland and Germany, adding to the XFELs already operating at SLAC and at labs in Germany and Japan.

    “I am surprised at the versatility of these machines, and at the speed at which good, new ideas are brought to reality,” Hemsing said. “It’s still a wide-open field.”

    See the full article here.

    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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  • richardmitnick 7:17 pm on September 10, 2014 Permalink | Reply
    Tags: , , SLAC LCLS,   

    From SLAC- “Plastics in Motion: Exploring the World of Polymers” 


    SLAC Lab

    September 10, 2014

    Experiment Shows Potential of X-ray Laser to Study Complex, Poorly Understood Materials

    Plastics are made of polymers, which are a challenge for scientists to study. Their chainlike strands of thousands of atoms are tangled up in a spaghetti-like jumble, their motion can be measured at many time scales and they are essentially invisible to some common X-ray study techniques.

    poly
    Illustration of a polystrene molecular chain and Styrofoam cups, which are made of polystyrene. (@iStockphoto/Devonyu, Martin McCarthy)

    gel
    This photograph shows a polymer in a molten, gel-like state. (@iStockphoto/Steve Bjorklund)

    A better understanding of polymers at the molecular scale, particularly as they are cooled from a molten state to a more solid form, could lead to improved manufacturing techniques and the creation of new, customizable materials.

    In an experiment at the Department of Energy’s SLAC National Accelerator Laboratory using SLAC’s Linac Coherent Light Source (LCLS) X-ray laser, a DOE Office of Science User Facility, scientists unraveled the complex behavior of polystyrene, a popular polymer found in packing foams and plastic cups, with a sequence of ultrabright X-ray laser pulses. Their work is detailed in the Aug. 11 edition of Scientific Reports.

    SLAC LCLS
    SLAC LCLS

    They measured natural motion in polystyrene samples heated to a gel-like middle ground between their melting point and solid state. This was the first demonstration that LCLS could be used for studying polymers and a whole range of other complex materials using a technique called X-ray photon correlation spectroscopy (XPCS),

    Hyunjung Kim of Sogang University in Korea, who led this research, said, “It was unknown whether the sample would survive the exposure to the ultrabright X-ray laser pulses. However, the X-ray damage effects on the sample were weaker than expected.”

    SLAC staff scientist Aymeric Robert said, “To see how you get from something that was completely moving to something completely static is very poorly understood. Observations of how polymers move in response to temperature changes and other effects can be compared with theoretical models to predict their behavior.” Robert oversees the experimental station at LCLS that is specially designed for this X-ray technique.

    “LCLS should allow scientists to measure motion in these materials in even more detail than possible using conventional X-ray tools,” he added.

    To study motion in the heated samples, researchers embedded a matrix of nanoscale gold spheres into the polymer. Then, they recorded sequences of up to about 150 X-ray images on different sections of the sample, with the delay between images ranging from as little as seven seconds to as much as 17 minutes.

    The XPCS technique measures successive “speckle” patterns that revealed subtle changes in the position of the gold spheres relative to one another – a measure of motion within the overall sample.

    While many experiments at LCLS capture X-ray data in the instant before samples are destroyed by the intense light, this technique allows some materials to survive the effects of many X-ray pulses, which is useful for studying longer-lived properties spanning from milliseconds to minutes.

    “We showed that we could study the complex dynamics in the polymer sample even at slow time scales,” Kim said. While this experiment proved that LCLS can be used to measure the long-duration motions across the entire sample, Kim said future experiments could vary the arrangement and size of the implanted gold spheres to better gauge motion at the scale of the molecular chains. Also, faster repetition of the X-ray laser pulses could help to study motion on a shorter time scale.

    In addition to Sogang University and SLAC’s LCLS, other participating researchers were from University of California, San Diego, Argonne National Laboratory; DESY lab, The Hamburg Center for Ultrafast Imaging and the University of Siegen, in Germany; Northern Illinois University; University of Massachusetts, Amherst; and Pohang Accelerator Laboratory (PAL) in Korea. The research was supported by the National Research Foundation funded by the Ministry of Science, ICT & Future Planning of Korea, and PAL in Korea, and the Department of Energy Office of Basic Energy Sciences.

    rig
    A view of the X-ray Correlation Spectroscopy experimental station at SLAC’s Linac Coherent Light Source (LCLS) X-ray laser. This station is designed to explore polymers and other hard-to-study materials. (SLAC National Accelerator Laboratory)

    graph
    This image (a) shows the experimental setup for an X-ray photon correlation spectroscopy experiment using polymer samples at SLAC’s Linac Coherent Light Source X-ray laser. (b) This transmission electron microscopy image shows nanoscale gold spheres that were embedded in a molten polymer to help study its motion. (c) This speckle pattern was produced as X-rays struck the polymer sample. A succession of these patterns show the changing positions of the gold spheres in the polymer sample, which provides a measure of the polymer’s motion. (10.1038/srep06017)

    image
    A computerized rendering of the X-ray Correlation Spectroscopy station at SLAC’s Linac Coherent Light Source X-ray laser, which was used to study motion in polymer samples. (SLAC National Accelerator Laboratory)

    See the full article here.

    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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  • richardmitnick 1:14 pm on September 4, 2014 Permalink | Reply
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    From SLAC: “Scientists Map Protein in Living Bacterial Cells” 


    SLAC Lab

    September 3, 2014

    Experiment at SLAC’s X-ray Laser Opens Door to Exploring Cell Interiors

    Scientists have for the first time mapped the atomic structure of a protein within a living cell. The technique, which peered into cells with an X-ray laser, could allow scientists to explore some components of living cells as never before.

    The research, published Aug. 18 in Proceedings of the National Academy of Sciences, was conducted at the Department of Energy’s SLAC National Accelerator Laboratory.

    “This is a new way to look inside cells,” said David S. Eisenberg, a biochemistry professor at University of California, Los Angeles, and Howard Hughes Medical Institute investigator.

    “There are a lot of semi-ordered materials in cells where an X-ray laser could provide powerful information,” Eisenberg added. They include arrays in white blood cells that help to fight parasites and infections, insulin-containing structures in the pancreas and structures that break fatty acids and other molecules into smaller units to release energy.

    In the experiment at SLAC’s Linac Coherent Light Source X-ray laser, a DOE Office of Science User Facility, researchers probed a soil-dwelling bacterium, Bacillus thuringiensis or Bt, that is commonly used as a natural insecticide. Strains of this bacterium produce microscopic protein crystals and spores that kill insects. Normally scientists need to find ways to crystallize proteins in order to get their structures – typically a time-consuming, hit-and-miss process – but these naturally occurring crystals eliminated that step.

    SLAC LCLS Inside
    Inside the SLAC LCLS

    A liquid solution containing the living cells was jetted into the path of the ultrabright LCLS X-ray laser pulses. When a laser pulse struck a crystal, it created a pattern of diffracted X-ray light. More than 30,000 of these patterns were combined and analyzed by sophisticated software to reproduce the detailed 3-D structure of the protein.

    Many of the bacterial cells likely ruptured and spewed their crystal contents as they flew at high speed toward the X-rays. But because it took just thousandths of a second for the cells to reach the X-ray pulses, it’s very likely that many of the X-ray images showed protein crystals that were still inside the cells, the researchers concluded.

    three
    Three scenarios suggesting how the integrity of Bacillus thuringiensis (Bt) cells studied at the Linac Coherent Light Source X-ray laser might vary at the moment they are struck by X-rays. The horizontal arrow depicts the flow of the cell samples from a liquid jet to waste collection. The left, middle, and right columns depict three different time points along the liquid jet’s stream. Depending on the rate of cell rupture and the flow rate of the jet, the crystals may arrive at the interaction point either (1) inside intact cells, (2) inside ruptured (“lysed”) cells, or (3) outside of ruptured cells. (10.1073/pnas.1413456111)

    Importantly, Eisenberg said, “The rest of the cell contents don’t obscure the results.”

    In addition, the 3-D structure of proteins obtained from the crystals in living bacteria cells was essentially identical to that obtained through other methods. Earlier studies had already shown that LCLS can be used to study smaller, easier-to-produce crystals than traditional X-ray sources require, although it typically requires a far larger volume of crystals to achieve atomic-scale resolution.

    In an LCLS study published in 2012, a separate team of researchers used protein crystals grown inside live insect cells to study a potential weak spot in a parasite responsible for a disease called African sleeping sickness. But in that experiment they extracted the crystals rather than attempting to study them inside cells.

    Eisenberg said possible next steps include improving the technique by developing new sample-delivery methods that are gentler to the cells’ structure, and producing faster X-ray pulse rates that capture more images and yield even better results.

    “I think this whole area of science is going to continue growing,” he said.

    In addition to UCLA and LCLS, other researchers participating in the study were from Lawrence Berkeley National Laboratory; Arizona State University; University of California, Riverside; the Institute of Structural Biology in France; and the Max Planck Institute for Medical Research in Germany. The research was supported by the U.S. Department of Energy Office of Science, Howard Hughes Medical Institute, Max Planck Society, the National Institutes of Health, the Keck Foundation and the National Science Foundation.

    See the full article here.

    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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  • richardmitnick 1:23 pm on August 26, 2014 Permalink | Reply
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    From SLAC: “X-ray Laser Probes Tiny Quantum Tornadoes in Superfluid Droplets” 


    SLAC Lab

    August 21, 2014

    An experiment at the Department of Energy’s SLAC National Accelerator Laboratory revealed a well-organized 3-D grid of quantum “tornadoes” inside microscopic droplets of supercooled liquid helium – the first time this formation has been seen at such a tiny scale.

    image
    In this illustration, a patterned 3-D grid of tiny whirlpools, called quantum vortices, populates a nanoscale droplet of superfluid helium. Researchers found that in a micron-sized droplet, the density of vortices was 100,000 times greater than in any previous experiment on superfluids. An artistic rendering of a wheel-shaped droplet can be seen in the distance. (SLAC National Accelerator Laboratory)

    The findings by an international research team provide new insight on the strange nanoscale traits of a so-called “superfluid” state of liquid helium. When chilled to extremes, liquid helium behaves according to the rules of quantum mechanics that apply to matter at the smallest scales and defy the laws of classical physics. This superfluid state is one of just a few examples of quantum behavior on a large scale that makes the behavior easier to see and study.

    The results, detailed in the Aug. 22 issue of Science, could help shed light on similar quantum states, such as those in superconducting materials that conduct electricity with 100 percent efficiency or the strange collectives of particles, dubbed Bose-Einstein condensates, which act as a single unit.

    “What we found in this experiment was really surprising. We did not expect the beauty and clarity of the results,” said Christoph Bostedt, a co-leader of the experiment and a senior scientist at SLAC’s Linac Coherent Light Source (LCLS), the DOE Office of Science User Facility where the experiment was conducted.

    machine
    This instrument, called CAMP, was used for the helium nanodroplets experiment at the Linac Coherent Light Source’s Atomic, Molecular and Optical Science (AMO) experimental station. (SLAC National Accelerator Laboratory)

    “We were able to see a manifestation of the quantum world on a macroscopic scale,” said Ken Ferguson, a PhD student from Stanford University working at LCLS.

    While tiny tornadoes had been seen before in chilled helium, they hadn’t been seen in such tiny droplets, where they were packed 100,000 times more densely than in any previous experiment on superfluids, Ferguson said.

    Studying the Quantum Traits of a Superfluid

    Helium can be cooled to the point where it becomes a frictionless substance that remains liquid well below the freezing point of most fluids. The light, weakly attracting atoms have an endless wobble – a quantum state of perpetual motion that prevents them from freezing. The unique properties of superfluid helium, which have been the subject of several Nobel prizes, allow it to coat and climb the sides of a container, and to seep through molecule-wide holes that would have held in the same liquid at higher temperatures.

    In the LCLS experiment, researchers jetted a thin stream of helium droplets, like a nanoscale string of pearls, into a vacuum. Each droplet acquired a spin as it flew out of the jet, rotating up to 2 million turns per second, and cooled to a temperature colder than outer space. The X-ray laser took snapshots of individual droplets, revealing dozens of tiny twisters, called “quantum vortices,” with swirling cores that are the width of an atom.

    The fast rotation of the chilled helium nanodroplets caused a regularly spaced, dense 3-D pattern of vortices to form. This exotic formation, which resembles the ordered structure of a solid crystal and provides proof of the droplets’ quantum state, is far different than the lone whirlpool that would form in a regular liquid, such as briskly stirred cup of coffee.

    More Surprises in Store

    Researchers also discovered surprising shapes in some superfluid droplets. In a normal liquid, droplets can form peanut shapes when rotated swiftly, but the superfluid droplets took a very different form. About 1 percent of them formed unexpected wheel-like shapes and reached rotation speeds never before observed for their classical counterparts.

    Oliver Gessner, a senior scientist at Lawrence Berkeley Laboratory and a co-leader in the experiment, said, “Now that we have shown that we can detect and characterize quantum rotation in helium nanodroplets, it will be important to understand its origin and, ultimately, to try to control it.”

    Andrey Vilesov of the University of Southern California, the third experiment co-leader, added, “The experiment has exceeded our best expectations. Attaining proof of the vortices, their configurations in the droplets and the shapes of the rotating droplets was only possible with LCLS imaging.”

    He said further analysis of the LCLS data should yield more detailed information on the shape and arrangement of the vortices: “There will definitely be more surprises to come.”

    Other research collaborators were from the Stanford PULSE Institute; University of California, Berkeley; the Max Planck Society; Center for Free-Electron Laser Science at DESY; PNSensor GmbH; Chinese University of Hong Kong; and Kansas State University. This work was supported by the National Science Foundation, the U.S. Department of Energy Office of Science and the Max Planck Society.

    See the full article here.

    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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