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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
    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 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
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    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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  • richardmitnick 4:09 pm on August 21, 2014 Permalink | Reply
    Tags: , , SLAC LCLS,   

    From Berkeley Lab: “Researchers Map Quantum Vortices Inside Superfluid Helium Nanodroplets” 

    Berkeley Logo

    Berkeley Lab

    August 21, 2014
    Kate Greene

    Scientists have, for the first time, characterized so-called quantum vortices that swirl within tiny droplets of liquid helium. The research, led by scientists at the U.S. Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab), the University of Southern California, and SLAC National Accelerator Laboratory, confirms that helium nanodroplets are in fact the smallest possible superfluidic objects and opens new avenues for studying quantum rotation.

    “The observation of quantum vortices is one of the most clear and unique demonstrations of the quantum properties of these microscopic objects,” says Oliver Gessner, senior scientist in the Chemical Sciences Division at Berkeley Lab. Gessner and colleagues, Andrey Vilesov of the University of Southern California and Christoph Bostedt of SLAC National Accelerator Laboratory at Stanford, led the multi-facility and multi-university team that published the work this week in Science.

    Droplet_art_fin3drop
    Illustration of analysis of superfluid helium nanodroplets. Droplets are emitted via a cooled nozzle (upper right) and probed with x-ray from the free-electron laser. The multicolored pattern (upper left) represents a diffraction pattern that reveals the shape of a droplet and the presence of quantum vortices such as those represented in the turquoise circle with swirls (bottom center). Credit: Felix P. Sturm and Daniel S. Slaughter, Berkeley Lab.

    The finding could have implications for other liquid or gas systems that contain vortices, says USC’s Vilesov. “The quest for quantum vortices in superfluid droplets has stretched for decades,” he says. “But this is the first time they have been seen in superfluid droplets.”

    Superfluid helium has long captured scientist’s imagination since its discovery in the 1930s. Unlike normal fluids, superfluids have no viscosity, a feature that leads to strange and sometimes unexpected properties such as crawling up the walls of containers or dripping through barriers that contained the liquid before it transitioned to a superfluid.

    Helium superfluidity can be achieved when helium is cooled to near absolute zero (zero kelvin or about -460 degrees F). At this temperature, the atoms within the liquid no longer vibrate with heat energy and instead settle into a calm state in which all atoms act together in unison, as if they were a single particle.

    For decades, researchers have known that when superfluid helium is rotated–in a little spinning bucket, say–the rotation produces quantum vortices, swirls that are regularly spaced throughout the liquid. But the question remained whether anyone could see this behavior in an isolated, nanoscale droplet. If the swirls were there, it would confirm that helium nanodroplets, which can range in size from tens of nanometers to microns, are indeed superfluid throughout and that the motion of the entire liquid drop is that of a single quantum object rather than a mixture of independent particles.

    But measuring liquid flow in helium nanodroplets has proven to be a serious challenge. “The way these droplets are made is by passing helium through a tiny nozzle that is cryogenically cooled down to below 10 Kelvin,” says Gessner. “Then, the nanoscale droplets shoot through a vacuum chamber at almost 200 meters-per-second. They live once for a few milliseconds while traversing the experimental chamber and then they’re gone. How do you show that these objects, which are all different from one another, have quantum vortices inside?”

    og
    Oliver Gessner, Chemical Sciences Division, Berkeley Lab. Credit: Roy Kaltschmidt

    The researchers turned to a facility at SLAC called the Linac Coherent Light Source (LCLS), a DOE Office of Science user facility that is the world’s first x-ray free-electron laser. This laser produces very short light pulses, lasting just a ten-trillionth of a second, which contain a huge number of high-energy photons. These intense x-ray pulses can effectively take snapshots of single, ultra-fast, ultra-small objects and phenomena.

    slac
    Inside the SLAC LCLS

    “With the new x-ray free electron laser, we can now image phenomenon and look at processes far beyond what we could imagine just a decade ago,” says Bostedt of SLAC. “Looking at the droplets gave us a beautiful glimpse into the quantum world. It really opens the door to fascinating sciences.”

    In the experiment, the researchers blasted a stream of helium nanodroplets across the x-ray laser beam inside a vacuum chamber; a detector caught the pattern that formed when the x-ray light diffracted off the drops.

    The diffraction patterns immediately revealed that the shape of many droplets were not spheres, as was previously assumed. Instead, they were oblate. Just as the Earth’s rotation causes it to bulge at the equator, so too do rotating nanodroplets expand around the middle and flatten at the top and bottom.

    But the vortices themselves are invisible to x-ray diffraction, so the researchers used a trick of adding xenon atoms to the droplets. The xenon atoms get pulled into the vortices and cluster together.

    “It’s similar to pulling the plug in a bathtub and watching the kids’ toys gather in the vortex,” says Gessner. The xenon atoms diffract x-ray light much stronger than the surrounding helium, making the regular arrays of vortices inside the droplet visible. In this way, the researchers confirmed that vortices in nanodroplets behave as those found in larger amounts of rotating superfluid helium.

    Armed with this new information, the researchers were able to determine the rotational speed of the nanodroplets. They were surprised to find that the nanodroplets spin up to 100,000 times faster than any other superfluid helium sample ever studied in a laboratory.

    Moreover, while normal liquid drops will change shape as they spin faster and faster–to resemble a peanut or multi-lobed globule, for instance–the researchers saw no evidence of such shapeshifting in the helium nanodroplets. “Essentially, we’re exploring a new regime of quantum rotation with this matter,” Gessner says.

    “It’s a new kind of matter in a sense because it is a self-contained isolated superfluid,” he adds. “It’s just all by itself, held together by its own surface tension. It’s pretty perfect to study these systems if one wants to understand superfluidity and isolate it as much as possible.”

    This research was supported by the DOE Office of Science, Office of Basic Energy Sciences, Chemical Sciences, Geosciences and Biosciences Division as well as the National Science Foundation.

    See the full article here.

    A U.S. Department of Energy National Laboratory Operated by the University of California

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  • richardmitnick 10:12 am on August 7, 2014 Permalink | Reply
    Tags: , , SLAC LCLS,   

    From Slac Lab: “Catching Chemistry in Motion” 


    SLAC Lab

    August 6, 2014
    Laser-timing Tool Works at the Speed of Electrons

    Researchers at the Department of Energy’s SLAC National Accelerator Laboratory have developed a laser-timing system that could allow scientists to take snapshots of electrons zipping around atoms and molecules. Taking timing to this new extreme of speed and accuracy at the Linac Coherent Light Source X-ray laser, a DOE Office of Science user facility, will make it possible to see the formative stages of chemical reactions.

    “Previously, we could see a chemical bond before it’s broken and after it’s broken,” said Ryan Coffee, an LCLS scientist whose team developed this system. “With this tool, we can watch the bond while it is breaking and ‘freeze-frame’ it.”

    The success of most LCLS experiments relies on precise timing of the X-ray laser with another laser, a technique known as “pump-probe.” Typically, light from an optical laser “pumps” or triggers a specific effect in a sample, and researchers vary the arrival of the X-ray laser pulses, which serve as the “probe” to capture images and other data that allow them to study the effects at different points in time.

    Pump-probe experiments at LCLS are used to study a wide range of processes at the atomic or molecular scale, including studies of biological samples and exotic materials like high-temperature superconductors.

    But LCLS X-ray pulses are tricky to control. They have inherent jitter that causes them to fluctuate in arrival time, energy, position, duration and the wavelength of their light.

    There are several tools and techniques that scientists use to understand and limit the impacts of jitter on experiments, and timing tools counter the arrival-time jitter by offering very precise measurements. These measurements can help scientists to interpret their data by pinpointing the timing of changes they see in samples after they are exposed to the first laser pulse. Some experiments would not be possible without precise timing tools because of the ultrafast scale of the changes they are trying to observe.

    Achieving ‘Attosecond’ Experiments

    tool
    An illustration of the setup used to test an “attosecond” timing tool at SLAC’s Linac Coherent Light Source X-ray laser. The dashed line, produced by an algorithm that analyzes the colorized spectrograph image (bottom) represents the arrival time of the X-ray laser. (Ryan Coffee and Nick Hartmann/SLAC)

    Timing tools now in place at most LCLS experimental stations can measure the arrival time of the optical and X-ray laser pulses to an accuracy within 10 femtoseconds, or quadrillionths of a second. The new pulse-measuring system, which is highlighted in the July 27 edition of Nature Photonics, builds upon the existing tools and pushes timing to attoseconds, which are quintillionths (billion-billionths) of a second.

    anime
    This animation shows a sequence of spectrograph images used to precisely measure arrival time of X-rays relative to optical laser pulses at SLAC’s LCLS. The upper edge of the dark blue pattern represents the arrival time of the X-ray laser pulse. The scale at left measures the relative delay of X-ray and optical laser pulses, and the bottom measures the wavelength of the transmitted optical light. (Nick Hartmann/SLAC)

    Nick Hartmann, an LCLS research associate and doctoral student at the University of Bern in Switzerland who is the lead author of the study detailing the system, said, “An X-ray laser with attosecond timing resolution would open up a new class of experiments on the natural time scale of electron motion.”

    The new system uses a high-resolution spectrograph, a type of camera that records the timing and wavelength of the probe laser pulses. The colorful patterns it displays represent the different wavelengths of light that passed, at slightly different times, through a thin sample of silicon nitride.

    This material experiences a cascading reaction in its electrons when it is struck by an X-ray pulse. This effect leaves a brief imprint in the way light passes through the sample, sort of like a temporary interruption of vision following a camera’s flash.

    This X-ray-caused effect shows up in the way the light from the other laser pulse passes through the silicon nitride – it is seen as a brief dip in the amount of light recorded by the spectrograph, like the after-image of a camera flash. An image-analysis algorithm then precisely calculates, based on the recorded patterns, the relative arrival time of the X-ray pulses.

    The new timing system is designed to avoid distortion effects caused by some other timing tools and to work reliably with a variety of focusing and filtering tools. It can provide real-time readouts of laser arrival times and jitter to benefit experiments in progress, and can be added to existing timing setups at LCLS.

    Hartmann said additional innovations could expand the applications of the new system: “We are putting the parts together to allow attosecond experiments at LCLS and other X-ray lasers like it.”

    three
    hese three panels show different types of jitter, or fluctuations, in the X-ray laser pulses produced at SLAC’s Linac Coherent Light Source. The left panel shows how the X-ray beam fluctuates in its direction. The middle panel shows how the spectrum (wavelength or “color”) of the X-ray laser changes randomly from pulse to pulse. The right panel shows the X-ray-caused dip in the amount of light being recorded. (SLAC)

    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 7:36 pm on July 22, 2014 Permalink | Reply
    Tags: , , SLAC LCLS, , ,   

    From SLAC: “Bringing High-energy X-rays into Better Focus” 


    SLAC Lab

    July 22, 2014
    SLAC-invented Etching Process Builds Custom Nanostructures for X-ray Optics

    Scientists at the Department of Energy’s SLAC National Accelerator Laboratory have invented a customizable chemical etching process that can be used to manufacture high-performance focusing devices for the brightest X-ray sources on the planet, as well as to make other nanoscale structures such as biosensors and battery electrodes.

    “The tools researchers use to manipulate X-rays today are very limited,” said Anne Sakdinawat, an associate staff scientist at SLAC’s Stanford Synchrotron Radiation Lightsource (SSRL) who developed the new “V-MACE” process with Chieh Chang, an SSRL research associate.

    scan
    Scanning electron microscope image of a cleaved spiral zone plate, a type of X-ray optic, created using a chemical etching technique that was developed at SLAC. (Chieh Chang, Anne Sakdinawat)

    “Our new technique for fabricating high performance X-ray optics involves just a few chemicals in a simple, easy-to-implement, one-step technology,” Sakdinawat said. “It offers significant advantages in many far-ranging applications.” The patent-pending technique is detailed in the June 27 edition of Nature Communications.

    Focusing X-rays, particularly higher-energy or “hard” X-rays, is particularly challenging at the nanoscale, though it is key to the success of many scientific studies at two of SLAC’s DOE Office of Science user facilities, SSRL and the Linac Coherent Light Source (LCLS) X-ray laser.

    It is also of great interest for commercial applications such as X-ray microscopy, complex electronics, and biomedical devices and imaging tools.

    Existing tools for focusing hard X-rays, such as specialized mirrors and sequences of concave metal structures that form lenses, are generally limited in how they can shape the X-ray light. Focusing the highest-energy X-rays to produce crisp images remains a challenge, as the focusing tools themselves generally lack nanoscale precision and sap away much of the X-ray energy.

    “It’s been technologically very difficult to fabricate structures that offer both high resolution and high efficiency,” Sakdinawat said, and the effectiveness of the structures, which are examples of X-ray “diffractive optics,” is typically based on the height and precision of their features.

    The new fabrication technique is adapted from a process used to create hairlike silicon wires for research on advanced batteries and electronics. It can fabricate structures up to 100 times as tall as they are wide, with dimensions accurate to billionths of a meter. The technique reduces the need to stack multiple layers to create tall structures.

    The researchers used the etching technique to build tall, precise X-ray diffractive optics, called zone plates, whose thinly spaced lines, symmetric rings or spiral patterns alternately obstruct or phase-shift X-rays and allow them to pass through in a way that separates and refocuses them. This improves the focus and produces higher-quality images.

    zone
    Scanning electron microscope (SEM) image of a zone plate pattern produced using a chemical etching technique invented at SLAC. (Chieh Chang, Anne Sakdinawat)

    zone2
    This scanning electron microscope image shows a cross-sectional view of a zone plate produced using a patent-pending chemical etching technique called “V-MACE” developed at SLAC. (Chieh Chang, Anne Sakdinawat)

    “Basically, this is like an artificial crystal,” Sakdinawat said, diffracting the X-ray light in a predictable pattern, as a crystal would. “You can basically manipulate the light in whatever fashion you want – you can shape the light in different ways,” she said, based on the design of the optics and the needs of the experiment.

    Sakdinawat and Chang tested and imaged a sample zone plate at SSRL, and they hope to construct similar plates for use in experiments at SSRL and LCLS.

    The same technique can be used to build other types of precise silicon and metal-coated nanostructures, such as filtration devices, thermoelectric devices that can create electricity from heat and components for tiny bio-sensors that can be embedded in the body, and researchers are working to tailor the process to suit the needs of government agencies and corporate partners.

    “We’re trying to expand into other fields,” Sakdinawat said. “There are many different applications for this.”

    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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