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  • richardmitnick 8:22 am on June 23, 2017 Permalink | Reply
    Tags: , , , How a Single Chemical Bond Balances Cells Between Life and Death, Protein cytochrome c, SLAC LCLS, , ,   

    From SLAC: “How a Single Chemical Bond Balances Cells Between Life and Death” 


    SLAC Lab

    June 22, 2017
    Amanda Solliday

    1
    An optical laser (green) excites the iron-containing active site of the protein cytochrome c, and then an X-ray laser (white) probes the iron a few femtoseconds to picoseconds later. The critical iron-sulfur bond is broken as the optical laser heats the protein, and rebinds as the system cools. (Greg Stewart/SLAC National Accelerator Laboratory)

    Slight changes in the machinery of a cell determine whether it lives or begins a natural process known as programmed cell death. In many forms of life—from bacteria to humans—a single chemical bond in a protein called cytochrome c can make this call. As long as the bond is intact, the protein transfers electrons needed to produce energy through respiration. When the bond breaks, the protein switches gear and triggers the breakdown of mitochondria, the structures that power the cell’s activities.

    For the first time, scientists have measured exactly how much energy cytochrome c puts into maintaining that bond in a state where it’s strong enough to endure, but easy enough to break when the cell’s life span is ending.

    They used intense X-rays from two facilities, the Linac Coherent Light Source (LCLS) X-ray free-electron laser and the Stanford Synchrotron Radiation Lightsource (SSRL) at the Department of Energy’s SLAC National Accelerator Laboratory.

    SLAC/LCLS

    SLAC/SSRL

    The collaboration, led by Edward Solomon, professor of chemistry at Stanford University and of photon science at SLAC, published their results today in Science.

    “This is a very general yet extremely important process in biochemistry, and with an X-ray laser we now have insight into how this regulation works,” says Roberto Alonso-Mori, LCLS staff scientist and a co-author of the study. “These are processes that are going on a million-fold in our bodies and everywhere there is life.”

    The study marks the first time that anyone has been able to experimentally quantify how the rigid structure of the cytochrome c molecule supports this crucial bond between iron and sulfur atoms in what’s known as an entatic state, where the protein maintains a bond that is just strong enough to perform both of its jobs, says Michael Mara, lead author of the study and a former postdoctoral researcher at Stanford University, now at University of California, Berkeley.

    “This was important because we had shown the bond is weak and shouldn’t be present at room temperature in the absence of the protein constraints,” says Solomon. “But the protein is able to contribute energy to keep this bond intact for electron transfer. In this LCLS experiment, we determined exactly how much energy the rest of the protein contributes to maintaining the bond: about 4 kcal/mol that is derived from an adjacent hydrogen bond network.”

    “We were able to show how nature tunes this system to change the properties on a fundamental level and perform two very different functions,” Mara says. “The energy contribution by cytochrome c is really at a sweet spot. It makes me wonder what sort of similar effects you might see in other protein systems, and it makes us realize that there is exciting new science on the horizon.”

    Ultrafast Changes

    Cytochrome c is present in a wide range of life forms and contributes to both cellular respiration and programmed cell death, the pathway to the natural end of a cell’s life cycle. How exactly the state of the bond relates to these two functions had not yet been demonstrated or quantified.

    Scientists knew from earlier studies that a particular iron-sulfur bond is key. When iron in the protein binds to sulfur contained in one of the protein’s amino-acid building blocks, cytochrome c participates in electron transfer. By transferring electrons, the protein helps generate energy needed for biological processes that maintain life.

    But when cytochrome c encounters cardiolipin, a lipid present in the membrane of the cell’s mitochondria, the iron-sulfur bond breaks, and the protein becomes an enzyme that creates holes in the mitochondria’s outer membrane – the first step in programmed cell death.

    These changes occur incredibly fast, in less than 20 picoseconds, so the experiment required ultrafast pulses of X-rays generated by LCLS to take snapshots of the process.

    “We photoexcited the iron atoms in the protein’s active site—which contains an iron-rich compound known as heme—with an ultrafast laser before probing it with the LCLS X-ray pulses at different time delays,” says Alonso-Mori.

    Each 50-femtosecond laser pulse heated the heme by a couple of hundred degrees. X-ray pulses from LCLS took images of what happened as the heat traveled from the iron to other parts of the protein. After 100 femtoseconds, the iron-sulfur bond would break, only to form again once the sample cooled. Watching this process allowed the scientists to measure energy fluctuations in real time and better understand how this critical bond forms and breaks.

    “The entatic state concept is really interesting, but you have to come up with creative ways to demonstrate and quantify it,” says Ryan Hadt, a former Stanford University doctoral student on an Enrico Fermi Fellowship at Argonne National Laboratory who together with his advisor, Professor Solomon, came up with the idea for the experiment and co-wrote the initial proposal around the time LCLS first came online in 2009.

    “Our research group was excited about this new instrument and wanted to use it to do a definitive experiment,” Hadt adds.

    A Question Raised by Earlier Work

    This experiment builds on an earlier study [JACS] conducted at SSRL that found that the iron-sulfur bond was quite weak, says Thomas Kroll, staff scientist at SSRL and lead author of this prior study.

    In the latest study, spectroscopy at SSRL also built the framework for the LCLS pump-probe experiment. It allowed the scientists to compare what the molecule originally looked like to how it changed when the temperature rose.

    “It’s important to understand how these proteins actually work,” Kroll says. “Because if you don’t understand how they work, how can we create better medicines in an informed and controlled way?”

    Knowledge of cytochrome c’s function is also valuable to the fields of bioenergy and environmental science, since it is a critically important protein in bacteria and plants.

    The DOE Office of Science and the National Institute of General Medical Sciences of the National Institutes of Health supported this research. The Structural Molecular Biology program at SSRL is funded by DOE Office of Science and the National Institutes of Health, National Institute of General Medical Sciences. LCLS and SSRL are DOE Office of Science User Facilities.

    See the full article here .

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    SLAC is a multi-program laboratory exploring frontier questions in photon science, astrophysics, particle physics and accelerator research. Located in Menlo Park, California, SLAC is operated by Stanford University for the DOE’s Office of Science.
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  • richardmitnick 8:06 am on June 23, 2017 Permalink | Reply
    Tags: A Single Electron’s Tiny Leap Sets Off ‘Molecular Sunscreen’ Response, , , , , , SLAC LCLS,   

    From SLAC: “A Single Electron’s Tiny Leap Sets Off ‘Molecular Sunscreen’ Response” 


    SLAC Lab

    June 22, 2017
    Glennda Chui

    1
    Thymine – the molecule illustrated in the foreground – is one of the four basic building blocks that make up the double helix of DNA. It’s such a strong absorber of ultraviolet light that the UV in sunlight should deactivate it, yet this does not happen. Researchers used an X-ray laser at SLAC National Accelerator Laboratory to observe the infinitesimal leap of a single electron that sets off a protective response in thymine molecules, allowing them to shake off UV damage. (Greg Stewart/SLAC National Accelerator Laboratory)

    In experiments at the Department of Energy’s SLAC National Accelerator Laboratory, scientists were able to see the first step of a process that protects a DNA building block called thymine from sun damage: When it’s hit with ultraviolet light, a single electron jumps into a slightly higher orbit around the nucleus of a single oxygen atom.

    This infinitesimal leap sets off a response that stretches one of thymine’s chemical bonds and snaps it back into place, creating vibrations that harmlessly dissipate the energy of incoming ultraviolet light so it doesn’t cause mutations.

    The technique used to observe this tiny switch-flip at SLAC’s Linac Coherent Light Source (LCLS) X-ray free-electron laser can be applied to almost any organic molecule that responds to light – whether that light is a good thing, as in photosynthesis or human vision, or a bad thing, as in skin cancer, the scientists said. They described the study in Nature Communications today.

    SLAC/LCLS

    “All of these light-sensitive organic molecules tend to absorb light in the ultraviolet. That’s not only why you get sunburn, but it’s also why your plastic eyeglass lenses offer some UV protection,” said Phil Bucksbaum, a professor at SLAC and Stanford University and director of the Stanford PULSE Institute at SLAC. “You can even see these effects in plastic lawn furniture – after a couple of seasons it can become brittle and discolored simply due to the fact that the plastic was absorbing ultraviolet light all the time, and the way it absorbs sun results in damage to its chemical bonds.”

    Catching Electrons in Action

    Thymine and the other three DNA building blocks also strongly absorb ultraviolet light, which can trigger mutations and skin cancer, yet these molecules seem to get by with minimal damage. In 2014, a team led by Markus Guehr ­– then a SLAC senior staff scientist and now on the faculty of the University of Potsdam in Germany – reported that they had found the answer: The stretch-snap of a single bond and resulting energy-dissipating vibrations, which took place within 200 femtoseconds, or millionths of a billionth of a second after UV light exposure.

    But what made the bond stretch? The team knew the answer had to involve electrons, which are responsible for forming, changing and breaking bonds between atoms. So they devised an ingenious way to catch the specific electron movements that trigger the protective response.

    It relied on the fact that electrons don’t orbit an atom’s nucleus in neat concentric circles, like planets orbiting a sun, but rather in fuzzy clouds that take a different shape depending on how far they are from the nucleus. Some of these orbitals are in fact like a fuzzy sphere; others look a little like barbells or the start of a balloon animal. You can see examples here.

    2
    No image caption or credit, but there is a comment,
    “I see the distribution in different orbitals. So if for example I take the S orbitals, they are all just a sphere. So wont the 2S orbital overlap with the 1S overlap, making the electrons in each orbital “meet” at some point? Or have I misunderstood something?”

    Strong Signal Could Solve Long-Standing Debate

    For this new experiment, the scientists hit thymine molecules with a pulse of UV laser light and tuned the energy of the LCLS X-ray laser pulses so they would home in on the response of the oxygen atom that’s at one end of the stretching, snapping bond.

    The energy from the UV light excited one of the atom’s electrons to jump into a higher orbital. This left the atom in a sort of tippy state where just a little more energy would boost a second electron into a higher orbital; and that second jump is what sets off the protective response, changing the shape of the molecule just enough to stretch the bond.

    The first jump, which was previously known to happen, is difficult to detect because the electron winds up in a rather diffuse orbital cloud, Guehr said. But the second, which had never been observed before, was much easier to spot because that electron ended up in an orbital with a distinctive shape that gave off a big signal.

    “Although this was a very tiny electron movement, the signal kind of jumped out at us in the experiment,” Guehr said. “I always had a feeling this would be a strong transition, just intuitively, but when we saw this come in it was a special moment, one of the best moments an experimentalist can have.”

    Settling a Longstanding Debate

    Study lead author Thomas Wolf, an associate staff scientist at SLAC, said the results should settle a longstanding debate about how long after UV exposure the protective response kicks in: It happens 60 femtoseconds after UV light hits. This time span is important, he said, because the longer the atom spends in the tippy state between the first jump and the second, the more likely it is to undergo some sort of reaction that could damage the molecule.

    Henrik Koch, a theorist at NTNU in Norway who was a guest professor at Stanford at the time, led the study with Guehr. He led the effort to model, understand and interpret what happened in the experiment, and he participated in it to an unusual extent, Guehr said.

    “He is extremely experienced in applying theory to methodology development, and he had this curiosity to bring this to our experiment,” Guehr said. “He was so fascinated by this research that he did something completely untypical of a theorist – he came to LCLS, into the control room, and he wanted to see the data coming in. I found that completely amazing and very motivating. It turned out that some of my previous thinking was completely right but other aspects were completely wrong, and Henrik did the right theory at the right level so we could learn from it.”

    See the full article here .

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    SLAC is a multi-program laboratory exploring frontier questions in photon science, astrophysics, particle physics and accelerator research. Located in Menlo Park, California, SLAC is operated by Stanford University for the DOE’s Office of Science.
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  • richardmitnick 5:09 pm on June 20, 2017 Permalink | Reply
    Tags: , , In order to use the limited beam time and the precious sample material more efficiently the team developed a new method., Micro-patterned chip containing thousands of tiny pores to hold the protein crystals, SLAC LCLS, Speed up protein analysis, Structural biology, , X-ray free-electron laser,   

    From SLAC: “SLAC Experiment is First to Decipher Atomic Structure of an Intact Virus with an X-ray Laser” 


    SLAC Lab

    June 20, 2017

    1
    Surface structure of the bovine enterovirus 2. The three virus proteins are color-coded. (Jingshan Ren/University of Oxford)

    A ground-breaking experimental method developed by an international research team will substantially speed up protein analysis.

    An international team of scientists has for the first time used an X-ray free-electron laser to unravel the structure of an intact virus particle on the atomic level. The method dramatically reduces the amount of virus material required, while also allowing the investigations to be carried out several times faster than before. This opens up entirely new research opportunities, as the research team led by Alke Meents, a scientist at Germany’s DESY lab, reports in the journal Nature Methods.

    The researchers tested their method with the Linac Coherent Light Source (LCLS) X-ray free-electron laser at the Department of Energy’s SLAC National Accelerator Laboratory. Now they are working to increase the capacity and speed of the technique in anticipation of future experiments at the European XFEL X-ray free-electron laser, which is just going into operation near Hamburg, Germany.

    SLAC/LCLS

    European XFEL

    “This is a much-welcome and important technological development that will greatly optimize data collection at LCLS and other X-ray free-electron lasers for certain classes of challenging experiments,” says co-author Roberto Alonso Mori, a staff scientist in the LCLS hard X-ray group. “The same technology could be used not only for biological science but could also help data collection in other areas.”

    2
    Micrograph of the microstructured chip, loaded with crystals for the investigation. Each square is a tiny crystal. (Philip Roedig/DESY)

    A Well-Rounded View of Life

    In the field known as structural biology, scientists examine the three-dimensional structure of biological molecules in order to work out how they function. This knowledge enhances our understanding of fundamental biological processes, such as the way substances are transported in and out of a cell, and can also inform drug development.

    “Knowing the three-dimensional structure of a molecule like a protein gives great insight into its biological behaviour,” explains co-author David Stuart, director of life sciences at the Diamond Light Source synchrotron facility in the United Kingdom and a professor at the University of Oxford. “One example is how understanding the structure of a protein that a virus uses to ‘hook’ onto a cell could mean that we’re able to design a defense for the cell to make the virus incapable of attacking it.”

    X-ray crystallography is by far the most prolific tool used by structural biologists and has already been used to determine the structure of thousands of biological molecules. Tiny crystals of the protein of interest are grown, and then illuminated using high-energy X-rays. The crystals diffract the X-rays in characteristic ways so that the resulting diffraction patterns can be used to deduce the spatial structure of the crystal – and hence of its components – on the atomic scale. However, protein crystals are nowhere near as stable and sturdy as salt crystals, for example. They are difficult to grow, often remaining tiny, and are easily damaged by the X-rays.

    “X-ray lasers have opened up a new path to protein crystallography, because their extremely intense pulses can be used to analyse even extremely tiny crystals that would not produce a sufficiently bright diffraction image using other X-ray sources,” says co-author Armin Wagner from Diamond Light Source. However, each of these microcrystals can only produce a single diffraction image before it evaporates as a result of the X-ray pulse. To perform the structural analysis, though, hundreds or even thousands of diffraction images are needed. In such experiments, scientists therefore inject a fine liquid jet of protein crystals through an X-ray laser beam that pulses in a rapid sequence of extremely short bursts. Each time an X-ray pulse happens to strike a microcrystal, a diffraction image is produced and recorded.

    This method is very successful and has already been used to determine the structure of more than 80 biomolecules, the researchers point out in their paper. However, most of the sample material is wasted. “The hit rate is typically less than 2 percent of pulses, so most of the precious microcrystals end up unused in the collection container,” says Meents, who is based at the Center for Free-Electron Laser Science (CFEL) in Hamburg, a cooperation of DESY, the University of Hamburg and the German Max Planck Society. The standard method therefore typically requires several hours of beam time and significant amounts of sample material.

    Protein Crystals on a Chip

    In order to use the limited beam time and the precious sample material more efficiently, the team developed a new method. The scientists use a micro-patterned chip containing thousands of tiny pores to hold the protein crystals. The X-ray laser then scans the chip line by line, and ideally this allows a diffraction image to be recorded for each pulse of the laser.

    The research team tested its method on two virus samples using SLAC’s LCLS X-ray laser, which produces 120 pulses per second. They loaded their sample holder with a small amount of microcrystals of the bovine enterovirus 2 (BEV2), a virus that causes miscarriages, stillbirths and infertility in cattle, and which is very difficult to crystallise.

    In this experiment, the scientists achieved a hit rate – where the X-ray laser successfully targeted the crystal – of up to 9 percent, five times the hit rate of the previous method. Within just 14 minutes they had collected enough data to determine the correct structure of the virus – which was already known from other experiments – down to a scale of 2.3 angstroms.

    “To the best of our knowledge, this is the first time the atomic structure of an intact virus particle has been determined using an X-ray laser,” Meents says. “Whereas earlier methods at other X-ray light sources required crystals with a total volume of 3.5 nanoliters, or billionths of a liter, we managed using crystals that were more than 10 times smaller, having a total volume of just 0.23 nanoliters.”

    This experiment was conducted at room temperature; while rapidly cooling the protein crystals would protect them to some extent from radiation damage, this is not generally feasible when working with extremely sensitive virus crystals. Crystals of isolated virus proteins can, however, be frozen and in a second test, the researchers studied a viral protein called polyhedrin that makes up a viral occlusion body — a container used by certain virus species to protect up to several thousand virus particles at a time against environmental influences so they can remain intact much longer.

    From Room Temperature to a Deep Chill

    For the second test, the scientist loaded their chip with polyhedrin crystals and examined them using the X-ray laser while keeping the chip at temperatures below minus 180 degrees Celsius. Here, the scientists achieved a hit rate of up to 90 percent. In just 10 minutes they recorded more than enough diffraction images to determine the protein structure to within 2.4 angstroms.

    “For the structure of polyhedrin, we only had to scan a single chip that was loaded with four micrograms of protein crystals; that is orders of magnitude less than the amount that would normally be needed,” explains Meents.

    “Our approach not only reduces the data collection time and the quantity of the sample needed, it also opens up the opportunity of analysing entire viruses using X-ray lasers,” Meents sums up. The scientists now want to increase the capacity of their chip by a factor of ten, from 22,500 to some 200,000 micropores, and further increase the scanning speed to up to one thousand samples per second. This would better exploit the potential of the European XFEL, which will be able to produce up to 27,000 X-ray laser pulses per second, as well as an upgraded LCLS that is scheduled to come on line in the early 2020s and produce up to a million pulses per second. Furthermore, the next generation of chips will expose only those micropores that are targeted for analysis, to prevent the remaining crystals from being damaged by scattered radiation from the X-ray laser.

    Diamond scientists have collaborated with the team at DESY, with much of the development and testing of the micro-patterned chip being on Diamond’s I02 and I24 beamlines. Researchers from the University of Oxford, the University of Eastern Finland, the Swiss Paul Scherrer Institute, Lawrence Berkeley National Laboratory and SLAC were also involved in the research. LCLS is a DOE Office of Science User Facility.

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    SLAC Campus
    SLAC is a multi-program laboratory exploring frontier questions in photon science, astrophysics, particle physics and accelerator research. Located in Menlo Park, California, SLAC is operated by Stanford University for the DOE’s Office of Science.
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  • richardmitnick 12:01 pm on June 19, 2017 Permalink | Reply
    Tags: , , , , First atomic structure of an intact virus deciphered with an X-ray laser, SLAC LCLS,   

    From DESY: “First atomic structure of an intact virus deciphered with an X-ray laser” 

    DESY
    DESY

    2017/06/19

    Groundbreaking experimental method will speed up protein analysis substantially.

    1
    Surface structure of the bovine enterovirus 2, the three virus proteins are colour coded. Credit: Jingshan Ren, University of Oxford

    An international team of scientists has for the first time used an X-ray free-electron laser to unravel the structure of an intact virus particle on the atomic level. The method used dramatically reduces the amount of virus material required, while also allowing the investigations to be carried out several times faster than before. This opens up entirely new research opportunities, as the research team lead by DESY scientist Alke Meents reports in the journal Nature Methods.

    In the field known as structural biology, scientists examine the three-dimensional structure of biological molecules in order to work out how they function. This knowledge enhances our understanding of the fundamental biological processes taking place inside organisms, such as the way in which substances are transported in and out of a cell, and can also be used to develop new drugs.

    “Knowing the three-dimensional structure of a molecule like a protein gives great insight into its biological behaviour,” explains co-author David Stuart, Director of Life Sciences at the synchrotron facility Diamond Light Source in the UK and a professor at the University of Oxford. “One example is how understanding the structure of a protein that a virus uses to ‘hook’ onto a cell could mean that we’re able to design a defence for the cell to make the virus incapable of attacking it.”

    X-ray crystallography is by far the most prolific tool used by structural biologists and has already revealed the structures of thousands of biological molecules. Tiny crystals of the protein of interest are grown, and then illuminated using high-energy X-rays. The crystals diffract the X-rays in characteristic ways so that the resulting diffraction patterns can be used to deduce the spatial structure of the crystal – and hence of its components – on the atomic scale. However, protein crystals are nowhere near as stable and sturdy as salt crystals, for example. They are difficult to grow, often remaining tiny, and are easily damaged by the X-rays.

    “X-ray lasers have opened up a new path to protein crystallography, because their extremely intense pulses can be used to analyse even extremely tiny crystals that would not produce a sufficiently bright diffraction image using other X-ray sources,” adds co-author Armin Wagner from Diamond Light Source. However, each of these microcrystals can only produce a single diffraction image before it evaporates as a result of the X-ray pulse. To perform the structural analysis, though, hundreds or even thousands of diffraction images are needed. In such experiments, scientists therefore inject a fine liquid jet of protein crystals through a pulsed X-ray laser, which releases a rapid sequence of extremely short bursts. Each time an X-ray pulse happens to strike a microcrystal, a diffraction image is produced and recorded.

    This method is very successful and has already been used to determine the structure of more than 80 biomolecules. However, most of the sample material is wasted. “The hit rate is typically less than two per cent of pulses, so most of the precious microcrystals end up unused in the collection container,” says Meents, who is based at the Center for Free-Electron Laser Science (CFEL) in Hamburg, a cooperation of DESY, the University of Hamburg and the German Max Planck Society. The standard method therefore typically requires several hours of beamtime and significant amounts of sample material.

    3
    Micrograph of the microstructured chip, loaded with crystals for the investigation. Each square is a tiny crystal. Credit: Philip Roedig, DESY

    n order to use the limited beamtime and the precious sample material more efficiently, the team developed a new method. The scientists use a micro-patterned chip containing thousands of tiny pores to hold the protein crystals. The X-ray laser then scans the chip line by line, and ideally this allows a diffraction image to be recorded for each pulse of the laser.

    The research team tested its method on two different virus samples using the LCLS X-ray laser at the SLAC National Accelerator Laboratory in the US, which produces 120 pulses per second.

    SLAC/LCLS

    They loaded their sample holder with a small amount of microcrystals of the bovine enterovirus 2 (BEV2), a virus that can cause miscarriages, stillbirths, and infertility in cattle, and which is very difficult to crystallise.

    In this experiment, the scientists achieved a hit rate – where the X-ray laser successfully targeted the crystal – of up to nine per cent. Within just 14 minutes they had collected enough data to determine the correct structure of the virus – which was already known from experiments at other X-ray light sources – down to a scale of 0.23 nanometres (millionths of a millimetre).

    “To the best of our knowledge, this is the first time the atomic structure of an intact virus particle has been determined using an X-ray laser,” Meents points out. “Whereas earlier methods at other X-ray light sources required crystals with a total volume of 3.5 nanolitres, we managed using crystals that were more than ten times smaller, having a total volume of just 0.23 nanolitres.”

    This experiment was conducted at room temperature. While cooling the protein crystals would protect them to some extent from radiation damage, this is not generally feasible when working with extremely sensitive virus crystals. Crystals of isolated virus proteins can, however, be frozen, and in a second test, the researchers studied the viral protein polyhedrin that makes up a viral occlusion body for up to several thousands of virus particles of certain species. The virus particles use these containers to protect themselves against environmental influences and are therefore able to remain intact for much longer times.

    4
    Schematic of the experimental set-up: The chip loaded with nanocrystals is scanned by the fine X-ray beam (green) pore by pore. Ideally, each crystal produces a distinctive diffraction pattern. Credit: Philip Roedig, DESY

    For the second test, the scientist loaded their chip with polyhedrin crystals and examined them using the X-ray laser while keeping the chip at temperatures below minus 180 degrees Celsius. Here, the scientists achieved a hit rate of up to 90 per cent. In just ten minutes they had recorded more than enough diffraction images to determine the protein structure to within 0.24 nanometres. “For the structure of polyhedrin, we only had to scan a single chip which was loaded with four micrograms of protein crystals; that is orders of magnitude less than the amount that would normally be needed,” explains Meents.

    “Our approach not only reduces the data collection time and the quantity of the sample needed, it also opens up the opportunity of analysing entire viruses using X-ray lasers,” Meents sums up. The scientists now want to increase the capacity of their chip by a factor of ten, from 22,500 to some 200,000 micropores, and further increase the scanning speed to up to one thousand samples per second. This would better exploit the potential of the new X-ray free-electron laser European XFEL, which is just going into operation in the Hamburg region and which will be able to produce up to 27,000 pulses per second.

    European XFEL

    Furthermore, the next generation of chips will only expose those micropores that are currently being analysed, to prevent the remaining crystals from being damaged by scattered radiation from the X-ray laser.

    Researchers from the University of Oxford, the University of Eastern Finland, the Swiss Paul Scherrer Institute, the Lawrence Berkeley National Laboratory in the US and SLAC were also involved in the research. Diamond scientists have collaborated with the team at DESY, with much of the development and testing of the micro-patterned chip being done on Diamond’s I02 and I24 beamlines.

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    desi

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

     
  • richardmitnick 1:44 pm on May 31, 2017 Permalink | Reply
    Tags: , , , SLAC LCLS,   

    From SLAC: “The World’s Most Powerful X-ray Laser Beam Creates ‘Molecular Black Hole’” 


    SLAC Lab

    May 31, 2017
    Andrew Gordon
    agordon@slac.stanford.edu
    (650) 926-2282

    When the X-rays blast electrons out of one atom, stripping it from the inside out, it steals more from its neighbors – a new insight that could help advance high-res imaging of whole viruses, bacteria and complex materials.

    1
    In this illustration, an ultra-intense X-ray laser pulse from SLAC’s Linac Coherent Light Source knocks so many electrons out of a molecule’s iodine atom (right) that the iodine starts pulling in electrons from the rest of the molecule (lower left), like an electromagnetic version of a black hole. Many of the stolen electrons are also knocked out by the laser pulse; then the molecule explodes. (DESY/Science Communication Lab)

    When scientists at the Department of Energy’s SLAC National Accelerator Laboratory focused the full intensity of the world’s most powerful X-ray laser on a small molecule, they got a surprise: A single laser pulse stripped all but a few electrons out of the molecule’s biggest atom from the inside out, leaving a void that started pulling in electrons from the rest of the molecule, like a black hole gobbling a spiraling disk of matter.

    Within 30 femtoseconds – millionths of a billionth of a second – the molecule lost more than 50 electrons, far more than scientists anticipated based on earlier experiments using less intense beams or isolated atoms. Then it blew up.

    The results, published today in Nature, give scientists fundamental insights they need to better plan and interpret experiments using the most intense and energetic X-ray pulses from SLAC’s Linac Coherent Light Source (LCLS) X-ray free-electron laser.

    SLAC/LCLS

    Experiments that require these ultrahigh intensities include attempts to image individual biological objects, such as viruses and bacteria, at high resolution. They are also used to study the behavior of matter under extreme conditions, and to better understand charge dynamics in complex molecules for advanced technological applications.

    “For any type of experiment you do that focuses intense X-rays on a sample, you want to understand how it reacts to the X-rays,” said Daniel Rolles of Kansas State University. “This paper shows that we can understand and model the radiation damage in small molecules, so now we can predict what damage we will get in other systems.”

    Like Focusing the Sun Onto a Thumbnail

    The experiment, led by Rolles and Artem Rudenko of Kansas State, took place at LCLS’s Coherent X-ray Imaging instrument (CXI). It delivers X-rays with the highest possible energies achievable at LCLS, known as hard X-rays, and records data from samples in the instant before the laser pulse destroys them.

    How intense are those X-ray pulses?

    “They are about a hundred times more intense than what you would get if you focused all the sunlight that hits the Earth’s surface onto a thumbnail,” said LCLS staff scientist and co-author Sebastien Boutet.

    For this study, researchers used special mirrors to focus the X-ray beam into a spot just over 100 nanometers in diameter – about a hundredth the size of the one used in most CXI experiments, and a thousand times smaller than the width of a human hair. They looked at three types of samples: individual xenon atoms, which have 54 electrons each, and two types of molecules that each contain a single iodine atom, which has 53 electrons.

    Heavy atoms around this size are important in biochemical reactions, and researchers sometimes add them to biological samples to enhance contrast for imaging and crystallography applications. But until now, no one had investigated how the ultra-intense CXI beam affects molecules with atoms this heavy.

    X-rays Trigger Electron Cascades

    The team tuned the energy of the CXI pulses so they would selectively strip the innermost electrons from the xenon or iodine atoms, creating “hollow atoms.” Based on earlier studies with less energetic X-rays, they thought cascades of electrons from the outer parts of the atom would drop down to fill the vacancies, only to be kicked out themselves by subsequent X-rays. That would leave just a few of the most tightly bound electrons. And, in fact, that’s what happened in both the freestanding xenon atoms and the iodine atoms in the molecules.

    But in the molecules, the process didn’t stop there. The iodine atom, which had a strong positive charge after losing most of its electrons, continued to suck in electrons from neighboring carbon and hydrogen atoms, and those electrons were also ejected, one by one.

    Rather than losing 47 electrons, as would be the case for an isolated iodine atom, the iodine in the smaller molecule lost 54, including the ones it grabbed from its neighbors – a level of damage and disruption that’s not only higher than would normally be expected, but significantly different in nature.

    Results Feed Into Theory to Improve Experiments

    “We think the effect was even more important in the larger molecule than in the smaller one, but we don’t know how to quantify it yet,” Rudenko said. “We estimate that more than 60 electrons were kicked out, but we don’t actually know where it stopped because we could not detect all the fragments that flew off as the molecule fell apart to see how many electrons were missing. This is one of the open questions we need to study.”

    For the data analyzed to date, the theoretical model provided excellent agreement with the observed behavior, providing confidence that more complex systems can now be studied, said LCLS Director Mike Dunne. “This has important benefits for scientists wishing to achieve the highest-resolution images of biological molecules to inform the development of better pharmaceuticals, for example,” he said. “These experiments will also guide the development of a next-generation instrument for the LCLS-II upgrade project, which will provide a major leap in capability due to the increase in repetition rate from 120 pulses per second to 1 million.”

    SLAC LCLS-II

    The theory work for the study was led by Robin Santra of the Center for Free-Electron Laser Science at DESY and the University of Hamburg in Germany. Other research institutions contributing to the study were Tohoku University in Japan; Max Planck Institute for Nuclear Physics, Max Planck Institute for Medical Research, Hamburg Center for Ultrafast Imaging and the National Metrology Institute (PTB) in Germany; the University of Science and Technology in Beijing; Aarhus University in Denmark; Sorbonne University in France; the DOE’s Argonne National Laboratory and Brookhaven National Laboratory; the University of Chicago; and Northwestern University. Funding for the research came from the DOE Office of Science and from the German Research Foundation (DFG).

    See the full article here .

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  • richardmitnick 1:45 pm on April 18, 2017 Permalink | Reply
    Tags: , , , Gabriella Carini, How do you catch femtosecond light?, , , , SLAC LCLS, ,   

    From SLAC: “How do you catch femtosecond light?” 


    SLAC Lab

    1
    Gabriella Carini
    Staff Scientist
    Joined SLAC: 2011
    Specialty: Developing detectors that capture light from X-ray sources
    Interviewed by: Amanda Solliday

    Gabriella Carini enjoys those little moments—after hours and hours of testing in clean rooms, labs and at X-ray beamlines—when she first sees an instrument work.

    She earned her PhD in electronic engineering at the University of Palermo in Italy and now heads the detectors department at the Linac Coherent Light Source (LCLS), the X-ray free-electron laser at SLAC.

    SLAC/LCLS

    Scientists from around the world use the laser to probe natural processes that occur in tiny slivers of time. To see on this timescale, they need a way to collect the light and convert it into data that can be examined and interpreted.

    It’s Carini’s job to make sure LCLS has the right detector equipment at hand to catch the “precious”, very intense laser pulses, which may last only a few femtoseconds.

    When the research heads in new directions, as it constantly does, this requires her to look for fresh technology and turn these ideas into reality.

    When did you begin working with detectors?

    I moved to the United States as a doctoral student. My professor at the time suggested I join a collaboration at Brookhaven National Laboratory, where I started developing gamma ray detectors to catch radioactive materials.

    Radioactive materials give off gamma rays as they decay, and gamma rays are the most energetic photons, or particles of light. The detectors I worked on were made from cadmium zinc telluride, which has very good stopping power for highly energetic photons. These detectors can identify radioactive isotopes for security—such as the movement of nuclear materials—and contamination control, but also gamma rays for medical and astrophysical observations.

    We had some medical projects going on at the time, too, with detectors that scan for radioactive tracers used to map tissues and organs with positron emission tomography.

    From gamma ray detectors, I then moved to X-rays, and I began working on the earliest detectors for LCLS.

    How do you explain your job to someone outside the X-ray science community?

    I say, “There are three ingredients for an experiment—the source, the sample and the detector.”

    You need a source of light that illuminates your sample, which is the problem you want to solve or investigate. To understand what is happening, you have to be able to see the signal produced by the light as it interacts with the sample. That’s where the detector comes in. For us, the detector is like the “eyes” of the experimental set-up.

    What do you like most about your work?

    2

    There’s always a way we can help researchers optimize their experiments, tweak some settings, do more analysis and correction.

    This is important because scientists are going to encounter a lot of different types of detectors if they work at various X-ray facilities.

    I like to have input from people who are running the experiments. Because I did experiments myself as a graduate student, I’m very sensitive to whether a system is user-friendly. If you don’t make something that researchers can take the best advantage of, then you didn’t do your job fully.

    And detectors are never perfect, no matter which one you buy or build.

    There are a lot of people who have to come together to make a detector system. It’s not one person’s work. It’s many, many people with lots of different expertise. You need to have lots of good interpersonal skills.

    What are some of the challenges of creating detectors for femtosecond science?

    In more traditional X-ray sources the photons arrive distributed over time, one after the other, but when you work with ultrafast laser pulses like the ones from LCLS, all your information about a sample arrives in a few femtoseconds. Your detector has to digest this entire signal at once, process the information and send it out before another pulse comes. This requires deep understanding of the detector physics and needs careful engineering. You need to optimize the whole signal chain from the sensor to the readout electronics to the data transmission.

    We also have mechanical challenges because we have to operate in very unusual conditions: intense optical lasers, injectors with gas and liquids, etc. In many cases we need to use special filters to protect the detectors from these sources of contamination.

    4
    And often, you work in vacuum. With “soft” or low-energy X-rays, they are absorbed very quickly in air. Your entire system has to be vacuum-compatible. With many of our substantial electronics, this requires some care.

    So there are lots of things to take into account. Those are just a few examples. It’s very complicated and can vary quite a bit from experiment to experiment.

    Is there a new project you are really excited about?

    All of LCLS-II—this fills my life! We’re coming up with new ideas and new technologies for SLAC’s next X-ray laser, which will have a higher firing rate—up to a million pulses per second. For me, this is a multidimensional puzzle. Every science case and every instrument has its own needs and we have to find a route through the many options and often-competing parameters to achieve our goals.

    X-ray free-electron lasers are a big driver for detector development. Ten years ago, no one would have talked about X-ray cameras delivering 10,000 pictures per second. The new X-ray lasers are really a game-changer in developing detectors for photon science, because they require detectors that are just not readily available.

    LCLS-II will be challenging, but it’s exciting. For me, it’s thinking about what we can do now for the very first day of operation. And while doing that, we need to keep pushing the limits of what we have to do next to take full advantage of our new machine.

    6

    SLAC LCLS-II

    See the full article here .

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  • richardmitnick 7:10 am on April 18, 2017 Permalink | Reply
    Tags: Agostino Marinelli, , , SLAC LCLS   

    From SLAC: “Seeing the World in Femtoseconds” 


    SLAC Lab

    Q&A series with SLAC scientists

    4.17.17
    Kathryn Jepsen

    1
    Agostino Marinelli
    Accelerator Physicist

    Joined SLAC: 2012

    Specialty: Improving the capabilities of the Linac Coherent Light Source

    SLAC/LCLS

    Agostino “Ago” Marinelli first met pioneering accelerator physicist Claudio Pellegrini as an undergraduate student at the University of Rome. It was 2007, a couple of years before the Linac Coherent Light Source (LCLS) came online at SLAC, and people were abuzz about free-electron laser physics.

    Caught up in the excitement, Marinelli pursued a PhD in accelerator physics at the University of California, Los Angeles under Jamie Rosenzweig’s mentorship. Today he is involved in research and development related to femtosecond science at LCLS.

    Marinelli focuses on research at the femtosecond timescale because, he says, “it’s the fastest we can reach now with X-rays, and as an accelerator physicist, I get excited about technical things like that.”

    Why did you get involved in X-ray science?

    2
    Claudio Pellegrini

    Part of it was Claudio—he’s a very charismatic character. He’s an inspiring character. The field was very interesting. I thought it was a good way to spend my PhD.
    LCLS was promising so much innovation: a laser 10 billion times brighter than we had then. That sounds like something that somebody who is 24 would love to get involved in. It just sounded like something that would change science in a positive way, and I wanted to be a part of it.

    What is a free-electron laser?
    Free-electron lasers were invented by John Madey at Stanford in 1971; later on in the ’90s Claudio Pellegrini and collaborators proposed to extend free-electron lasers to the X-ray regime. They were the next step after synchrotron light sources.

    Synchrotrons send electrons around in a circle. That gives you radiation you can use in experiments. The difference between a synchrotron and the free-electron laser is the same difference between this light [points to a ceiling light] and a laser. It’s the difference between a bunch of kids making noise and a choir.

    In a synchrotron, the electrons are all doing the same thing, going around in a circle, but they are unaware of each other. They are all emitting X-rays in a random way. What makes a free-electron laser a laser is that all the electrons are emitting radiation in a coherent way. They are all synchronized.

    Also, since in an FEL you are using very intense and short electron bunches, the X-ray pulses will also be very short, down to the femtosecond level.

    What do you do with the free-electron laser?

    We talk to the users—they’re researchers that have some science they want to study with the machine. Then we “shape” the X-rays—set up the machine in a way that’s ideal for that experiment. The LCLS accelerator is very flexible. You can do all sorts of tricks with it—like arbitrarily changing the pulse duration, varying the X-ray polarization or making multiple pulses of different colors.

    Speaking of which, in 2014 the European Physical Society awarded you the Frank Sacherer Prize for your work using “two-color” beams with LCLS. What is that about?

    Normally LCLS shoots 120 X-ray pulses a second. But you can also make it send two pulses of different energies, separated by a few to 100 femtoseconds. You excite your sample with the first one and probe it with the second. You have to observe it within femtoseconds after you excite it because reactions happen that fast.

    3
    Normally you would excite the sample with an external optical laser; that’s how pump-probe is done. But in molecular dynamics, if you can excite a molecule with X-rays instead of an optical laser, you can get atom specificity—you can target a specific atom in the molecule.

    Each atom has a core energy level. If you know that, you can shoot the X-ray and hit only the oxygen in a molecule; oxygen is the only thing that is going to react. With two pulses at separate energies, you can target different atoms in a molecule to see which one triggers a certain reaction.

    What kinds of things do you study on the femtosecond scale?

    A femtosecond is close to the fundamental scale of atomic and molecular physics—so, things like chemistry.

    A chemical reaction is essentially two molecules or atoms interacting in some way and sharing charge and giving away energy. Ultimately to understand that, you have to understand how charge and energy flow in a molecule. You have to understand the very fundamental motion of electrons and ions in the molecule. On the femtosecond scale, you can see the positions of the atoms rearranging as it happens.

    Chemical reactions are a dynamic process. They start with something. They end with something. We want to know what happens in between.

    Why?

    If you want the reaction to end with something else, if you want it to end with something slightly different, you want to understand how it happens so you can make changes on purpose.

    What are you most excited about now?

    I’m really excited about what I’m about to do, which is this sub-femtosecond project called XLEAP. We will shape the LCLS electron beam with a high-power infrared laser and use it to generate pulses that are shorter than a femtosecond! What we will be looking at is energy and electrons moving around a molecule, which happens even faster than the atoms rearranging.

    Right now we’re really blind to all of this. To me, the way I understand it is, going to that timescale, you’re peeking into the very fundamental, quantum nature of the electrons in the molecule.

    If you ask me, “What is the ultimate problem it will solve for us?”—the answer is: I don’t know. In general when you’re blind to some fundamental process in nature and suddenly you can see it, my guess is something good is going to come of it.

    See the full article here .

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  • richardmitnick 3:55 pm on April 17, 2017 Permalink | Reply
    Tags: , , , , , SLAC LCLS, , ,   

    From SLAC: “SLAC’s X-ray Laser Glimpses How Electrons Dance with Atomic Nuclei in Materials” 


    SLAC Lab

    September 22, 2016

    Studies Could Help Design and Control Materials with Intriguing Properties, Including Novel Electronics, Solar Cells and Superconductors.

    From hard to malleable, from transparent to opaque, from channeling electricity to blocking it: Materials come in all types. A number of their intriguing properties originate in the way a material’s electrons “dance” with its lattice of atomic nuclei, which is also in constant motion due to vibrations known as phonons.

    This coupling between electrons and phonons determines how efficiently solar cells convert sunlight into electricity. It also plays key roles in superconductors that transfer electricity without losses, topological insulators that conduct electricity only on their surfaces, materials that drastically change their electrical resistance when exposed to a magnetic field, and more.

    At the Department of Energy’s SLAC National Accelerator Laboratory, scientists can study these coupled motions in unprecedented detail with the world’s most powerful X-ray laser, the Linac Coherent Light Source (LCLS). LCLS is a DOE Office of Science User Facility.

    SLAC/LCLS

    1
    An illustration shows how laser light excites electrons (white spheres) in a solid material, creating vibrations in its lattice of atomic nuclei (black and blue spheres). SLAC’s LCLS X-ray laser reveals the ultrafast “dance” between electrons and vibrations that accounts for many important properties of materials. (SLAC National Accelerator Laboratory)

    “It has been a long-standing goal to understand, initiate and control these unusual behaviors,” says LCLS Director Mike Dunne. “With LCLS we are now able to see what happens in these materials and to model complex electron-phonon interactions. This ability is central to the lab’s mission of developing new materials for next-generation electronics and energy solutions.”

    LCLS works like an extraordinary strobe light: Its ultrabright X-rays take snapshots of materials with atomic resolution and capture motions as fast as a few femtoseconds, or millionths of a billionth of a second. For comparison, one femtosecond is to a second what seven minutes is to the age of the universe.

    Two recent studies made use of these capabilities to study electron-phonon interactions in lead telluride, a material that excels at converting heat into electricity, and chromium, which at low temperatures has peculiar properties similar to those of high-temperature superconductors.

    Turning Heat into Electricity and Vice Versa

    Lead telluride, a compound of the chemical elements lead and tellurium, is of interest because it is a good thermoelectric: It generates an electrical voltage when two opposite sides of the material have different temperatures.

    “This property is used to power NASA space missions like the Mars rover Curiosity and to convert waste heat into electricity in high-end cars,” says Mariano Trigo, a staff scientist at the Stanford PULSE Institute and the Stanford Institute for Materials and Energy Sciences (SIMES), both joint institutes of Stanford University and SLAC. “The effect also works in the opposite direction: An electrical voltage applied across the material creates a temperature difference, which can be exploited in thermoelectric cooling devices.”

    Mason Jiang, a recent graduate student at Stanford, PULSE and SIMES, says, “Lead telluride is exceptionally good at this. It has two important qualities: It’s a bad thermal conductor, so it keeps heat from flowing from one side to the other, and it’s also a good electrical conductor, so it can turn the temperature difference into an electric current. The coupling between lattice vibrations, caused by heat, and electron motions is therefore very important in this system. With our study at LCLS, we wanted to understand what’s naturally going on in this material.”

    In their experiment, the researchers excited electrons in a lead telluride sample with a brief pulse of infrared laser light, and then used LCLS’s X-rays to determine how this burst of energy stimulated lattice vibrations.

    2
    This illustration shows the arrangement of lead and tellurium atoms in lead telluride, an excellent thermoelectric that efficiently converts heat into electricity and vice versa. In its normal state (left), lead telluride’s structure is distorted and has a relatively large degree of lattice vibrations (blurring). When scientists hit the sample with a laser pulse, the structure became more ordered (right). The results elucidate how electrons couple with these distortions – an interaction that is crucial for lead telluride’s thermoelectric properties. (SLAC National Accelerator Laboratory)

    “Lead telluride sits at the precipice of a coupled electronic and structural transformation,” says principal investigator David Reis from PULSE, SIMES and Stanford. “It has a tendency to distort without fully transforming – an instability that is thought to play an important role in its thermoelectric behavior. With our method we can study the forces involved and literally watch them change in response to the infrared laser pulse.”

    The scientists found that the light pulse excites particular electronic states that are responsible for this instability through electron-phonon coupling. The excited electrons stabilize the material by weakening certain long-range forces that were previously associated with the material’s low thermal conductivity.

    “The light pulse actually walks the material back from the brink of instability, making it a worse thermoelectric,” Reis says. “This implies that the reverse is also true – that stronger long-range forces lead to better thermoelectric behavior.”

    The researchers hope their results, published July 22 in Nature Communications, will help them find other thermoelectric materials that are more abundant and less toxic than lead telluride.

    Controlling Materials by Stimulating Charged Waves

    The second study looked at charge density waves – alternating areas of high and low electron density across the nuclear lattice – that occur in materials that abruptly change their behavior at a certain threshold. This includes transitions from insulator to conductor, normal conductor to superconductor, and from one magnetic state to another.

    These waves don’t actually travel through the material; they are stationary, like icy waves near the shoreline of a frozen lake.

    “Charge density waves have been observed in a number of interesting materials, and establishing their connection to material properties is a very hot research topic,” says Andrej Singer, a postdoctoral fellow in Oleg Shpyrko’s lab at the University of California, San Diego. “We’ve now shown that there is a way to enhance charge density waves in crystals of chromium using laser light, and this method could potentially also be used to tweak the properties of other materials.”

    This could mean, for example, that scientists might be able to switch a material from a normal conductor to a superconductor with a single flash of light. Singer and his colleagues reported their results on July 25 in Physical Review Letters.

    The research team used the chemical element chromium as a simple model system to study charge density waves, which form when the crystal is cooled to about minus 280 degrees Fahrenheit. They stimulated the chilled crystal with pulses of optical laser light and then used LCLS X-ray pulses to observe how this stimulation changed the amplitude, or height, of the charge density waves.

    “We found that the amplitude increased by up to 30 percent immediately after the laser pulse,” Singer says. “The amplitude then oscillated, becoming smaller and larger over a period of 450 femtoseconds, and it kept going when we kept hitting the sample with laser pulses. LCLS provides unique opportunities to study such process because it allows us to take ultrafast movies of the related structural changes in the lattice.”

    Based on their results, the researchers suggested a mechanism for the amplitude enhancement: The light pulse interrupts the electron-phonon interactions in the material, causing the lattice to vibrate. Shortly after the pulse, these interactions form again, which boosts the amplitude of the vibrations, like a pendulum that swings farther out when it receives an extra push.

    A Bright Future for Studies of the Electron-Phonon Dance

    Studies like these have a high priority in solid-state physics and materials science because they could pave the way for new materials and provide new ways to control material properties.

    With its 120 ultrabright X-ray pulses per second, LCLS reveals the electron-phonon dance with unprecedented detail. More breakthroughs in the field are on the horizon with LCLS-II – a next-generation X-ray laser under construction at SLAC that will fire up to a million X-ray flashes per second and will be 10,000 times brighter than LCLS.

    “LCLS-II will drastically increase our chances of capturing these processes,” Dunne says. “Since it will also reveal subtle electron-phonon signals with much higher resolution, we’ll be able to study these interactions in much greater detail than we can now.”

    Other research institutions involved in the studies were University College Cork, Ireland; Imperial College London, UK; Duke University; Oak Ridge National Laboratory; RIKEN Spring-8 Center, Japan; University of Tokyo, Japan; University of Michigan; and University of Kiel, Germany. Funding sources included DOE Office of Science; Science Foundation Ireland; Volkswagen Foundation, Germany; and Federal Ministry of Education and Research, Germany. Preliminary X-ray studies on lead telluride were performed at SLAC’s Stanford Synchrotron Radiation Lightsource (SSRL), a DOE Office of Science User Facility, and at the Spring-8 Angstrom Compact Free-electron Laser (SACLA), Japan.

    SLAC/SSRL

    SACLA Free-Electron Laser Riken Japan


    his movie introduces LCLS-II, a future light source at SLAC. It will generate over 8,000 times more light pulses per second than today’s most powerful X-ray laser, LCLS, and produce an almost continuous X-ray beam that on average will be 10,000 times brighter. (SLAC National Accelerator Laboratory)

    See the full article here .

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  • richardmitnick 7:48 am on November 4, 2016 Permalink | Reply
    Tags: , , , SLAC LCLS, ,   

    From SLAC: SLAC, Berkeley Lab Researchers Prepare for Scientific Computing on the Exascale” 


    SLAC Lab

    November 3, 2016

    1
    NERSC CRAY Cori supercomputer
    Development and testing of future exascale computing tools for X-ray laser data analysis and the simulation of plasma wakefield accelerators will be done on the Cori supercomputer at NERSC, the National Energy Research Scientific Computing Center at Lawrence Berkeley National Laboratory. (NERSC)

    Researchers at the Department of Energy’s SLAC National Accelerator Laboratory are playing key roles in two recently funded computing projects with the goal of developing cutting-edge scientific applications for future exascale supercomputers that can perform at least a billion billion computing operations per second – 50 to 100 times more than the most powerful supercomputers in the world today.

    The first project, led by SLAC, will develop computational tools to quickly sift through enormous piles of data produced by powerful X-ray lasers. The second project, led by DOE’s Lawrence Berkeley National Laboratory (Berkeley Lab), will reengineer simulation software for a potentially transformational new particle accelerator technology, called plasma wakefield acceleration.

    The projects, which will each receive $10 million over four years, are among 15 fully-funded application development proposals and seven proposals selected for seed funding by the DOE’s Exascale Computing Project (ECP). The ECP is part of President Obama’s National Strategic Computing Initiative and intends to maximize the benefits of high-performance computing for U.S. economic competiveness, national security and scientific discovery.

    “Many of our modern experiments generate enormous quantities of data,” says Alex Aiken, professor of computer science at Stanford University and director of the newly formed SLAC Computer Science division, who is involved in the X-ray laser project. “Exascale computing will create the capabilities to handle unprecedented data volumes and, at the same time, will allow us to solve new, more complex simulation problems.”

    Analyzing ‘Big Data’ from X-ray Lasers in Real Time

    X-ray lasers, such as SLAC’s Linac Coherent Light Source (LCLS) have been proven to be extremely powerful “microscopes” that are capable of glimpsing some of nature’s fastest and most fundamental processes on the atomic level.

    SLAC/LCLS
    SLAC/LCLS

    Researchers use LCLS, a DOE Office of Science User Facility, to create molecular movies, watch chemical bonds form and break, follow the path of electrons in materials and take 3-D snapshots of biological molecules that support the development of new drugs.

    At the same time X-ray lasers also generate giant amounts of data. A typical experiment at LCLS, which fires 120 flashes per second, fills up hundreds of thousands of gigabytes of disk space. Analyzing such a data volume in a short amount of time is already very challenging. And this situation is set to become dramatically harder: The next-generation LCLS-II X-ray laser will deliver 8,000 times more X-ray pulses per second, resulting in a similar increase in data volumes and data rates.

    SLAC/LCLS II schematic
    SLAC/LCLS II schematic

    Estimates are that the data flow will greatly exceed a trillion data ‘bits’ per second, and require hundreds of petabytes of online disk storage.

    As a result of the data flood even at today’s levels, researchers collecting data at X-ray lasers such as LCLS presently receive only very limited feedback regarding the quality of their data.

    “This is a real problem because you might only find out days or weeks after your experiment that you should have made certain changes,” says Berkeley Lab’s Peter Zwart, one of the collaborators on the exascale project, who will develop computer algorithms for X-ray imaging of single particles. “If we were able to look at our data on the fly, we could often do much better experiments.”

    Amedeo Perazzo, director of the LCLS Controls & Data Systems Division and principal investigator for this “ExaFEL” project, says, “We want to provide our users at LCLS, and in the future LCLS-II, with very fast feedback on their data so that can make important experimental decisions in almost real time. The idea is to send the data from LCLS via DOE’s broadband science network ESnet to NERSC, the National Energy Research Scientific Computing Center, where supercomputers will analyze the data and send the results back to us – all of that within just a few minutes.” NERSC and ESnet are DOE Office of Science User Facilities at Berkeley Lab.

    LBL NERSC Cray XC30 Edison supercomputer
    LBL NERSC Cray XC30 Edison supercomputer

    lcls-ii-image
    LCLS II

    X-ray data processing and analysis is quite an unusual task for supercomputers. “Traditionally these high-performance machines have mostly been used for complex simulations, such as climate modeling, rather than processing real-time data” Perazzo says. “So we’re breaking completely new ground with our project, and foresee a number of important future applications of the data processing techniques being developed.”

    This project is enabled by the investments underway at SLAC to prepare for LCLS-II, with the installation of new infrastructure capable of handling these enormous amounts of data.

    A number of partners will make additional crucial contributions.

    “At Berkeley Lab, we’ll be heavily involved in developing algorithms for specific use cases,” says James Sethian, a professor of mathematics at the University of California, Berkeley, and head of Berkeley Lab’s Mathematics Group and the Center for Advanced Mathematics for Energy Research Applications (CAMERA). “This includes work on two different sets of algorithms. The first set, developed by a team led by Nick Sauter, consists of well-established analysis programs that we’ll reconfigure for exascale computer architectures, whose larger computer power will allow us to do better, more complex physics. The other set is brand new software for emerging technologies such as single-particle imaging, which is being designed to allow scientists to study the atomic structure of single bacteria or viruses in their living state.”

    The “ExaFEL” project led by Perazzo will take advantage of Aiken’s newly formed Stanford/SLAC team, and will collaborate with researchers at Los Alamos National Laboratory to develop systems software that operates in a manner that optimizes its use of the architecture of the new exascale computers.

    “Supercomputers are very complicated, with millions of processors running in parallel,” Aiken says. “It’s a real computer science challenge to figure out how to use these new architectures most efficiently.”

    Finally, ESnet will provide the necessary networking capabilities to transfer data between the LCLS and supercomputing resources. Until exascale systems become available in the mid-2020s, the project will use NERSC’s Cori supercomputer for its developments and tests.

    esnet-map
    ESnet

    See the full article here .

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  • richardmitnick 7:40 am on October 12, 2016 Permalink | Reply
    Tags: , , , SLAC LCLS,   

    From SLAC: “X-rays Reveal New Path In Battle Against Mosquito-borne Illness” 


    SLAC Lab

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    The mosquito larvicide BinAB is composed of two proteins, BinA (yellow) and BinB (blue). Inside bacterial cells, BinAB naturally forms nanocrystals. Using these crystals and the intense X-ray pulses produced by SLAC’s Linac Coherent Light Source, scientists shed light on the three-dimensional structure of BinAB and its mode of action. (SLAC National Accelerator Laboratory)

    September 28, 2016

    SLAC’s X-ray Laser Provides Clues to Engineering a New Protein to Kill Mosquitos Carrying Dengue, Zika

    Structural biology research conducted at the U.S. Department of Energy’s SLAC National Accelerator Laboratory has uncovered how small insecticidal protein crystals that are naturally produced by bacteria might be tailored to combat dengue fever and the Zika virus.

    SLAC’s X-ray free-electron laser – the Linac Coherent Light Source (LCLS), a DOE Office of Science User Facility – offered unprecedented views of the toxin BinAB, used as a larvicide in public health efforts against mosquito-borne diseases such as malaria, West Nile virus and viral encephalitis.

    SLAC/LCLS
    SLAC/LCLS

    The larvicide is currently ineffective against the Aedes mosquitos that transmit Zika and dengue fever, and therefore not used to combat these species of mosquitos at this time. The new information provides clues to how scientists could design a composite toxin that would work against a broader range of mosquito species, including Aedes.

    Today, Nature published the study.

    “A more detailed look at the proteins’ structure provides information fundamental to understanding how the crystals kill mosquito larvae,” said Jacques-Philippe Colletier, a scientist at the Institut de Biologie Structurale in Grenoble, France and lead author on the paper. “This is a prerequisite for modifying the toxin to adapt it to our needs.”

    Selective Mosquito Control, Courtesy of Bacteria

    The BinAB crystals are produced by Lysinibacillus sphaericus bacteria, which release the crystals along with spores at the end of their life cycle. Mosquito larvae eat the crystals along with the spores, and then die.

    BinAB is inactive in the crystalline state and does not work on contact. For the crystals to dissolve, they must be exposed to alkaline conditions, such as those in a mosquito larva’s gut. The binary protein is then activated, recognized by a specific receptor at the surface of cells and internalized.

    Because Aedes larvae can evade one of these steps of intoxication, they are resistant to BinAB. These larvae do not express the correct receptors at the surface of their intestinal cells. Many other insect species, small crustaceans and humans also lack these receptors, as well as alkaline digestive systems.

    “Part of the appeal is that the larvicide’s safe because it’s so specific, but that’s also part of its limitation,” said Michael Sawaya, a scientist at the University of California, Los Angeles-DOE Molecular Biology Institute and co-author on the paper.

    For public health officials who want to prevent mosquito-borne disease, BinAB could also offer an alternative for controlling certain species of mosquitos that have begun to show resistance to other forms of chemical control.

    Creating a Tailored Insecticide

    The research team already knew the larvicide is composed of a pair of proteins, BinA and BinB, that pair together in crystals and are later activated by larval digestive enzymes.

    In the LCLS experiments, they learned the molecular basis for how the two proteins paired with each other – each performing an important, unique function. Previous research had determined that BinA is the toxic part of the complex, while BinB is responsible for binding the toxin to the mosquito’s intestine. BinB ushers BinA into the cells; once inside, BinA kills the cell.

    The scientists also identified four “hot spots” on the proteins that are activated by the alkaline conditions in the larval gut. All together, they trigger a change from a nontoxic form of the protein to a version that is lethal to mosquito larvae.

    Using the information gathered during the crystallography study, the research team has already begun to engineer a form of the BinAB proteins that will work against more species of mosquitos. This is ongoing work at Institut de Biologie Structurale, UCLA, University of California, Riverside and SLAC.

    Solving the Structure

    Only coarse details were known about the unique three-dimensional structure and biological behavior of BinAB prior to the experiment at LCLS.

    “We chose to look at the BinAB larvicide because it is so widely used, yet the structural details were a mystery,” said Brian Federici, professor of entomology at UC Riverside.

    The small size of the crystals made them difficult to study at conventional X-ray sources. So the research team used genetic engineering techniques to increase the size of the crystals, and the bright, fast pulses of light at LCLS allowed the scientists to collect detailed structural data from the tiny crystals before X-rays damaged their samples.

    The researchers used a crystallography technique called de novo phasing. This involves tagging the crystals with heavy metal markers, collecting tens of thousands of X-ray diffraction patterns, and combining the information collected to obtain a three-dimensional map of the electron density of the protein.

    “This is the first time we’ve used de novo phasing on a crystal of great interest at an X-ray free-electron laser,” said Sebastien Boutet, SLAC scientist.

    The technique had so far only been used on test samples where the structure was already known, in order to prove that it would work.

    “The most immediate need is to now expand the spectrum of action of the BinAB toxin to counter the progression of Zika, in particular,” said Colletier. “BinAB is already effective against Culex [carrier of West Nile encephalitis] and Anopheles [carrier of malaria] mosquitos. With the results of the study, we now feel more confident that we can design the protein to target Aedes mosquitos.”

    Additional contributors to the research include scientists from the Howard Hughes Medical Institutes at UCLA, Lawrence Berkeley National Laboratory, and Stanford University. The Institut de Biologie Structurale is a research center for integrated structural biology funded by the Commissariat à l’Énergie Atomique, the Centre National de la Recherche Scientifique and the Université Grenoble Alpes. The Collaborative Innovation Award program of Howard Hughes Medical Institute (HCIA-HHMI), W.M Keck Foundation, National Institutes of Health, National Science Foundation, France Alzheimer Foundation, Agence Nationale de la Recherche, and DOE Office of Science supported the research.

    See the full article here .

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