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  • richardmitnick 1:56 pm on August 17, 2017 Permalink | Reply
    Tags: , , , , MPG Institute for Nuclear Physics, , X-ray Technology   

    From MPG Institute for Nuclear Physics: “Sharp x-ray pulses from the atomic nucleus” 

    Max Planck Gesellschaft Institute for Nuclear Physics

    August 17, 2017
    PD Dr. Jörg Evers
    Research Group Leader
    Max Planck Institute for Nuclear Physics, Heidelberg
    Phone:+49 6221 516-177

    Prof. Dr. Thomas Pfeifer
    Max Planck Institute for Nuclear Physics, Heidelberg
    Phone:+49 6221 516-380Fax:+49 6221 516-802

    Honorary Professor Dr. Christoph H. Keitel
    Max Planck Institute for Nuclear Physics, Heidelberg
    Phone:+49 6221 516-150Fax:+49 6221 516-152

    Using a mechanical trick, scientists have succeeded in narrowing the spectrum of the pulses emitted by x-ray lasers.

    X-rays make the invisible visible: they permit the way materials are structured to be determined all the way down to the level of individual atoms. In the 1950s it was x-rays which revealed the double-helix structure of DNA. With new x-ray sources, such as the XFEL free-electron laser in Hamburg, it is even possible to “film” chemical reactions.


    XFEL map

    The results obtained from studies using these new x-ray sources may be about to become even more precise. A team around Kilian Heeg from the Max Planck Institute for Nuclear Physics in Heidelberg has now found a way to make the spectrum of the x-ray pulses emitted by these sources even narrower. In contrast to standard lasers, which generate light of a single colour and wavelength, x-ray sources generally produce pulses with a broad spectrum of different wavelengths. Sharper pulses could soon drive applications that were previously not feasible. This includes testing physical constants and measuring lengths and times even more precisely than can be achieved at present.

    Upgrading x-ray lasers – a mechanical trick can be used to narrow the spectrum of the pulses emitted by x-ray lasers such as the XFEL free electron laser shown here. This would enable x-ray lasers to be used for experiments which would otherwise not be possible, for example testing whether physical constants are really constant. © DESY, Hamburg

    Researchers use light and other electromagnetic radiation for developing new materials at work in electronics, automobiles, aircraft or power plants, as well as for studies on biomolecules such as protein function. Electromagnetic radiation is also the tool of choice for observing chemical reactions and physical processes in the micro and nano ranges. Different types of spectroscopy use different individual wavelengths to stimulate characteristic oscillations in specific components of a structure. Which wavelengths interact with the structure – physicists use the term resonance – tells us something about their composition and how they are constructed; for example, how atoms within a molecule are arranged in space.

    In contrast to visible light, which has a much lower energy, x-rays can trigger resonance not just in the electron shell of an atom, but also deep in the atomic core, its nucleus. X-ray spectroscopy therefore provides unique knowledge about materials. In addition, the resonances of some atomic nuclei are very sharp, in principle allowing extremely precise measurements.

    X-ray sources generate ultra-short flashes with a broad spectrum

    Modern x-ray sources such as the XFEL free electron laser in Hamburg and the PETRA III (Hamburg), and ESRF (Grenoble) synchrotron sources are prime candidates for carrying out such studies.

    DESI Petra III

    ESRF. Grenoble, France

    Free- electron lasers in particular are optimized for generating very short x-ray flashes, which are primarily used to study very fast processes in the microscopic world of atoms and molecules. Ultra short light pulses, however, in turn have a broad spectrum of wavelengths. Consequently, only a small fraction of the light is at the right wavelength to cause resonance in the sample. The rest passes straight through the sample, making spectroscopy of sharp resonances rather inefficient.

    It is possible to generate a very sharp x-ray spectrum – i.e. x-rays of a single wavelength – using filters; however, since this involves removing unused wavelengths, the resulting resonance signal is still weak.

    The new method developed by the researchers in Heidelberg delivers a three to four-fold increase in the intensity of the resonance signal. Together with scientists from DESY in Hamburg and ESRF in Grenoble, Kilian Heeg and Jörg Evers from Christoph Keitel’s Division and a team around Thomas Pfeifer at the Max Planck Institute for Nuclear Physics in Heidelberg have succeeded in making some of the x-ray radiation that would not normally interact with the sample contribute to the resonance signal. They have successfully tested their method on iron nuclei both at the ESRF in Grenoble and at the PETRA III synchrotron of DESY in Hamburg.

    A tiny jolt amplifies the radiation

    The researchers’ approach to amplifying the x-rays is based on the fact that, when x-rays interact with iron nuclei (or any other nuclei) to produce resonance, they are re-emitted after a short delay. These re-emitted x-rays then lag exactly half a wavelength behind that part of the radiation which has passed straight through. This means that the peaks of one wave coincide exactly with the troughs of the other wave, with the result that they cancel each other out. This destructive interference attenuates the X-ray pulses at the resonant wavelength, which is also the fundamental origin of absorption of light.

    “We utilize the time window of about 100 nanoseconds before the iron nuclei re-emit the x-rays,” explains project leader Jörg Evers. During this time window, the researchers move the iron foil by about 40 billionths of a millimetre (0.4 angstroms). This tiny jolt has the effect of producing constructive interference between the emitted and transmitted light waves. “It’s as if two rivers, the waves on one of which are offset by half a wavelength from the waves on the other, meet,” says Evers, “and you shift one of the rivers by exactly this distance.” This has the effect that, after the rivers meet, the waves on the two rivers move in time with each other. Wave peaks coincide with wave peaks and the waves amplify, rather than attenuating, each other. This trick, however, does not just work on light at the resonance wavelengths, but also has the reverse effect (i.e. attenuation) on a broader range of wavelengths around the resonance wavelength. Kilian Heeg puts it like this. “We squeeze otherwise unused x-ray radiation into the resonance.”

    To enable the physicists to move the iron foil fast enough and precisely enough, it is mounted on a piezoelectric crystal. This crystal expands or contracts in response to an applied electrical voltage. Using a specially developed computer program, the Heidelberg-based researchers were able to adjust the electrical signal that controls the piezoelectric crystal to maximize the amplification of the resonance signal.

    Applications in length measurement and atomic clocks

    The researchers see a wide range of potential applications for their new technique. According to Thomas Pfeifer, the procedure will expand the utility of new high-power x-ray sources for high-resolution x-ray spectroscopy. This will enable more accurate modelling of what happens in atoms and molecules. Pfeifer also stresses the utility of the technique in metrology, in particular for high-precision measurements of lengths and the quantum-mechanical definition of time. “With x-rays, it is possible to measure lengths 10,000 times more accurately than with visible light,” explains Pfeifer. This can be used to study and optimize nanostructures such as computer chips and newly developed batteries. Pfeifer also envisages x-ray atomic clocks which are far more precise than even the most advanced optical atomic clocks nowadays based on visible light.

    Not least, better X-ray spectroscopy could enable us to answer one of physics’ great unanswered questions – whether physical constants really are constant or whether they change slowly with time. If the latter were true, resonance lines would drift slowly over time. Extremely sharp x-ray spectra would make it possible to determine whether this is the case over a relatively short period.

    Evers reckons that, once mature, the technique would be relatively easy to integrate into experiments at DESY and ESRF. “It should be possible to make a shoe-box sized device that could be rapidly installed and, according to our calculations, could enable an approximately 10-fold amplification,” he adds.

    Science paper:
    Spectral narrowing of x-ray pulses for precision spectroscopy with nuclear resonances

    See the full article here .

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    The Max-Planck-Institut für Kernphysik (“MPI for Nuclear Physics” or MPIK for short) is a research institute in Heidelberg, Germany.

    The institute is one of the 80 institutes of the Max-Planck-Gesellschaft (Max Planck Society), an independent, non-profit research organization. The Max Planck Institute for Nuclear Physics was founded in 1958 under the leadership of Wolfgang Gentner. Its precursor was the Institute for Physics at the MPI for Medical Research.

    The Max Planck Society is Germany’s most successful research organization. Since its establishment in 1948, no fewer than 18 Nobel laureates have emerged from the ranks of its scientists, putting it on a par with the best and most prestigious research institutions worldwide. The more than 15,000 publications each year in internationally renowned scientific journals are proof of the outstanding research work conducted at Max Planck Institutes – and many of those articles are among the most-cited publications in the relevant field.

    What is the basis of this success? The scientific attractiveness of the Max Planck Society is based on its understanding of research: Max Planck Institutes are built up solely around the world’s leading researchers. They themselves define their research subjects and are given the best working conditions, as well as free reign in selecting their staff. This is the core of the Harnack principle, which dates back to Adolph von Harnack, the first president of the Kaiser Wilhelm Society, which was established in 1911. This principle has been successfully applied for nearly one hundred years. The Max Planck Society continues the tradition of its predecessor institution with this structural principle of the person-centered research organization.

    The currently 83 Max Planck Institutes and facilities conduct basic research in the service of the general public in the natural sciences, life sciences, social sciences, and the humanities. Max Planck Institutes focus on research fields that are particularly innovative, or that are especially demanding in terms of funding or time requirements. And their research spectrum is continually evolving: new institutes are established to find answers to seminal, forward-looking scientific questions, while others are closed when, for example, their research field has been widely established at universities. This continuous renewal preserves the scope the Max Planck Society needs to react quickly to pioneering scientific developments.

  • richardmitnick 1:10 pm on August 17, 2017 Permalink | Reply
    Tags: , , , New diffractometer, X-ray Technology   

    From BNL: “NSLS-II Welcomes New Tool for Studying the Physics of Materials” 

    Brookhaven Lab

    August 17, 2017
    Kelsey Harper

    Versatile instrument for precisely studying materials’ structural, electronic, magnetic characteristics arrives at Brookhaven Lab.

    Beamline lead scientist Christie Nelson works with a diffractometer located at beamline 4-ID.

    A new instrument for studying the physics of materials using high intensity x-ray beams has arrived at the U.S. Department of Energy’s (DOE) Brookhaven National Laboratory. This new diffractometer, installed at beamline 4-ID at the National Synchrotron Light Source II (NSLS-II), a DOE Office of Science User Facility that produces extremely bright beams of x-rays, will offer researchers greater precision when studying materials with unique structural, electronic, and magnetic characteristics. Understanding these materials’ properties could lead to better electronics, solar cells, or superconductors (materials that carry electricity with almost no energy loss).

    A diffractometer allows researchers to “see” the structure of a material by shooting highly focused x-rays at it and measuring how they diffract, or bounce off. According to Brookhaven physicist Christie Nelson, who worked with Huber X-Ray Diffraction Equipment to design the diffractometer, the new instrument has big advantages compared to one that operated at Brookhaven’s original light source, NSLS. Most significantly, it gives researchers additional ways to control where the beam hits the sample and how the x-rays are detected.

    In all diffractometers, both the sample and x-ray detector can rotate in certain directions to let researchers control where the beam hits the sample and where they measure the x-rays that bounce off. This diffractometer, however, has a uniquely large range of motion. The sample can rotate in four directions with extremely high precision, and in two of those directions it rotates much farther than in most other instruments. With this amount of control, researchers can target the precision of the x-ray beam to within 60 millionths of a meter.

    The instrument also has two detectors. While one allows users to quickly survey the overall structure of a sample, the other gives a zoomed-in view of the material’s subtler details. Since this diffractometer can have both detectors attached at the same time, researchers can quickly switch between these two views.

    “It’s a huge upgrade. There’s only one other like it in the world,” said Nelson, referring to a similar instrument at PETRA-III, an x-ray light source in Germany.

    DESY Petra III interior

    This diffractometer can also hold a cold chamber for looking at samples over a wide range of temperatures, all the way down to two Kelvin, or -271 degrees Celsius.

    “That’s crazy cold,” said Nelson—it’s just two degrees above “absolute zero,” the coldest anything can be.

    This cold chamber lets researchers study materials whose properties change with temperature. A research group from the University of California, Berkeley, has already used it to study superconductors, which need intense cold to function. The diffractometer allowed them to see fundamental changes in the material’s electronic structure as the temperature decreased.

    In the future, Nelson expects scientists will use the tool to examine materials at very high temperatures, under an electric or magnetic field, or in an environment with a custom atmosphere.

    “It’s a very versatile instrument,” said Nelson.

    The newly acquired diffractometer before its installation at NSLS-II.

    The diffractometer additionally allows researchers to study magnetism. Similar to the way polarized sunglasses only let in light oriented in a certain direction, NSLS-II produces ‘polarized’ beams of x-rays that are all lined up the same way. When these x-rays interact with magnetic areas of a sample, their orientation shifts. The diffractometer can detect these subtle changes, allowing researchers to study a material’s different magnetic characteristics.

    A group from the University of Toronto used this feature to study the magnetic properties of “double perovskites.” Although these materials are structurally similar to those used in prototype solar cells, the Toronto group is most interested in their unique magnetic properties and potential applications in quantum computing and information storage.

    Nelson looks forward to welcoming future research teams to use the new instrument at NSLS-II. “It’s yet another tool that enables the cutting-edge discoveries that happen here,” she said.

    NSLS-II is funded by the DOE Office of Science.

    See the full article here .

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

  • richardmitnick 11:03 am on July 31, 2017 Permalink | Reply
    Tags: , Nanocrystals, , , , , Superlattices, X-ray Technology   

    From SLAC: “Scientists Watch ‘Artificial Atoms’ Assemble into Perfect Lattices with Many Uses” 

    SLAC Lab

    July 31, 2017
    Written by Glennda Chui

    Press Office Contact:
    Andrew Gordon
    (650) 926-2282

    An illustration shows nanocrystals assembling into an ordered ‘superlattice’ – a process that a SLAC/Stanford team was able to observe in real time with X-rays from the Stanford Synchrotron Radiation Lightsource (SSRL). They discovered that this assembly takes just a few seconds when carried out in hot solutions. The results open the door for rapid self-assembly of nanocrystal building blocks into complex structures with applications in optoelectronics, solar cells, catalysis and magnetic materials. (Greg Stewart/SLAC National Accelerator Laboratory.)


    Some of the world’s tiniest crystals are known as “artificial atoms” because they can organize themselves into structures that look like molecules, including “superlattices” that are potential building blocks for novel materials.

    Now scientists from the Department of Energy’s SLAC National Accelerator Laboratory and Stanford University have made the first observation of these nanocrystals rapidly forming superlattices while they are themselves still growing. What they learn will help scientists fine-tune the assembly process and adapt it to make new types of materials for things like magnetic storage, solar cells, optoelectronics and catalysts that speed chemical reactions.

    The key to making it work was the serendipitous discovery that superlattices can form superfast – in seconds rather than the usual hours or days – during the routine synthesis of nanocrystals. The scientists used a powerful beam of X-rays at SLAC’s Stanford Synchrotron Radiation Lightsource (SSRL) to observe the growth of nanocrystals and the rapid formation of superlattices in real time.

    A paper describing the research, which was done in collaboration with scientists at the DOE’s Argonne National Laboratory, was published today in Nature.

    A lab in the Stanford Chemical Engineering Department where nanocrystals are grown. Experiments at SLAC’s Stanford Synchrotron Radiation Lightsource (SSRL) were able to observe the simultaneous growth of nanocrystals and superlattices for the first time. (Dawn Harmer/SLAC National Accelerator Laboratory.)

    “The idea is to see if we can get an independent understanding of how these superlattices grow so we can make them more uniform and control their properties,” said Chris Tassone, a staff scientist at SSRL who led the study with Matteo Cargnello, assistant professor of chemical engineering at Stanford.

    Tiny Crystals with Outsized Properties

    Scientists have been making nanocrystals in the lab since the 1980s. Because of their tiny size –they’re billionths of a meter wide and contain just 100 to 10,000 atoms apiece — they are governed by the laws of quantum mechanics, and this gives them interesting properties that can be changed by varying their size, shape and composition. For instance, spherical nanocrystals known as quantum dots, which are made of semiconducting materials, glow in colors that depend on their size; they are used in biological imaging and most recently in high-definition TV displays.

    In the early 1990s, researchers started using nanocrystals to build superlattices, which have the ordered structure of regular crystals, but with small particles in place of individual atoms. These, too, are expected to have unusual properties that are more than the sum of their parts.

    But until now, superlattices have been grown slowly at low temperatures, sometimes in a matter of days.

    That changed in February 2016, when Stanford postdoctoral researcher Liheng Wu serendipitously discovered that the process can occur much faster than scientists had thought.

    The experimental set-up at SLAC’s Stanford Synchrotron Radiation Lightsource (SSRL) where scientists used an X-ray beam to observe superlattices forming during the synthesis of nanocrystals for the first time. The vessel where the reactions took place is at bottom center, wrapped in gold heating tape that boosted the temperature inside to more than 230 degrees Celsius. (Liheng Wu/Stanford University.)

    ‘Something Weird Is Happening’

    He was trying to make nanocrystals of palladium – a silvery metal that’s used to promote chemical reactions in catalytic converters and many industrial processes – by heating a solution containing palladium atoms to more than 230 degrees Celsius. The goal was to understand how these tiny particles form, so their size and other properties could be more easily adjusted.

    The team added small windows to a reaction chamber about the size of a tangerine so they could shine an SSRL X-ray beam through it and watch what was happening in real time.

    “It’s kind of like cooking,” Cargnello explained. “The reaction chamber is like a pan. We add a solvent, which is like the frying oil; the main ingredients for the nanocrystals, such as palladium; and condiments, which in this case are surfactant compounds that tune the reaction conditions so you can control the size and composition of the particles. Once you add everything to the pan, you heat it up and fry your stuff.”

    Wu and Stanford graduate student Joshua Willis expected to see the characteristic pattern made by X-rays scattering off the tiny particles. They saw a completely different pattern instead.

    “So something weird is happening,” they texted their adviser.

    The something weird was that the palladium nanocrystals were assembling into superlattices.

    Members of the nanocrystal research team, from left: Assistant Professor Jian Qin, postdoctoral researcher Liheng Wu and Assistant Professor Matteo Cargnello, all of Stanford; SLAC staff scientist Chris Tassone; and Stanford graduate student Joshua Willis. (Dawn Harmer/SLAC National Accelerator Laboratory)

    A Balance of Forces

    At this point, “The challenge was to understand what brings the particles together and attracts them to each other but not too strongly, so they have room to wiggle around and settle into an ordered position,” said Jian Qin, an assistant professor of chemical engineering at Stanford who performed theoretical calculations to better understand the self-assembly process.

    Once the nanocrystals form, what seems to be happening is that they acquire a sort of hairy coating of surfactant molecules. The nanocrystals glom together, attracted by weak forces between their cores, and then a finely tuned balance of attractive and repulsive forces between the dangling surfactant molecules holds them in just the right configuration for the superlattice to grow.

    To the scientists’ surprise, the individual nanocrystals then kept on growing, along with the superlattices, until all the chemical ingredients in the solution were used up, and this unexpected added growth made the material swell. The researchers said they think this occurs in a wide range of nanocrystal systems, but had never been seen because there was no way to observe it in real time before the team’s experiments at SSRL.

    “Once we understood this system, we realized this process may be more general than we initially thought,” Wu said. “We have demonstrated that it’s not only limited to metals, but it can also be extended to semiconducting materials and very likely to a much larger set of materials.”

    The team has been doing follow-up experiments to find out more about how the superlattices grow and how they can tweak the size, composition and properties of the finished product.

    Ian Salmon McKay, a graduate student in chemical engineering at Stanford, and Benjamin T. Diroll, a postdoctoral researcher at Argonne National Laboratory’s Center for Nanoscale Materials (CNM), also contributed to the work.

    SSRL and CNM are DOE Office of Science User Facilities. The research was funded by the DOE Office of Science and by a Laboratory Directed Research and Development grant from SLAC.

    See the full article here .

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    SLAC is a multi-program laboratory exploring frontier questions in photon science, astrophysics, particle physics and accelerator research. Located in Menlo Park, California, SLAC is operated by Stanford University for the DOE’s Office of Science.

  • richardmitnick 9:24 am on July 13, 2017 Permalink | Reply
    Tags: , extraterrestrial ice can form in just billionths of a second, , , , Stanford scientists discover how dense, , X-ray Technology   

    From Stanford: “Stanford scientists discover how dense, extraterrestrial ice can form in just billionths of a second” 

    Stanford University Name
    Stanford University

    July 12, 2017
    Adam Hadhazy

    At the Linac Coherent Light Source, Stanford scientists used the world’s most powerful X-ray laser to create an extraterrestrial form of ice. (Image credit: Brad Plummer).

    Stanford researchers have for the first time captured the freezing of water, molecule-by-molecule, into a strange, dense form called ice VII (“ice seven”), found naturally in otherworldly environments, such as when icy planetary bodies collide.

    In addition to helping scientists better understand those remote worlds, the findings – published online July 11 in Physical Review Letters – could reveal how water and other substances undergo transitions from liquids to solids. Learning to manipulate those transitions might open the way someday to engineering materials with exotic new properties.

    “These experiments with water are the first of their kind, allowing us to witness a fundamental disorder-to-order transition in one of the most abundant molecules in the universe,” said study lead author Arianna Gleason, a postdoctoral fellow at Los Alamos National Laboratory and a visiting scientist in the Extreme Environments Laboratory of Stanford’s School of Earth, Energy & Environmental Sciences.

    Scientists have long studied how materials undergo phase changes between gas, liquid and solid states. Phase changes can happen rapidly, however, and on the tiny scale of mere atoms. Previous research has struggled to capture the moment-to-moment action of phase transitions, and instead worked backward from stable solids in piecing together the molecular steps taken by predecessor liquids.

    “There have been a tremendous number of studies on ice because everyone wants to understand its behavior,” said study senior author Wendy Mao, an associate professor of geological sciences and a Stanford Institute for Materials and Energy Sciences (SIMES) principal investigator. “What our new study demonstrates, and which hasn’t been done before, is the ability to see the ice structure form in real time.”

    Catching ice in the act

    Those timescales became achievable thanks to the Linac Coherent Light Source, the world’s most powerful X-ray laser located at the nearby SLAC National Accelerator Laboratory. There, the science team beamed an intense, green-colored laser at a small target containing a sample of liquid water. The laser instantly vaporized layers of diamond on one side of the target, generating a rocket-like force that compressed the water to pressures exceeding 50,000 times that of Earth’s atmosphere at sea level.

    As the water compacted, a separate beam from an instrument called the X-ray Free Electron Laser arrived in a series of bright pulses only a femtosecond, or a quadrillionth of a second, long. Akin to camera flashes, this strobing X-ray laser snapped a set of images revealing the progression of molecular changes, flip book–style, while the pressurized water crystallized into ice VII. The phase change took just 6 billionths of a second, or nanoseconds. Surprisingly, during this process, the water molecules bonded into rod shapes, and not spheres as theory predicted.

    The platform developed for this study – combining high pressure with snapshot images – could help researchers probe the myriad ways water freezes, depending on pressure and temperature. Under the conditions on our planet’s surface, water crystallizes in only one way, dubbed ice Ih (“ice one-H”) or simply “hexagonal ice,” whether in glaciers or ice cube trays in the freezer.

    Delving into extraterrestrial ice types, including ice VII, will help scientists model such remote environments as comet impacts, the internal structures of potentially life-supporting, water-filled moons like Jupiter’s Europa, and the dynamics of jumbo, rocky, oceanic exoplanets called super-Earths.

    “Any icy satellite or planetary interior is intimately connected to the object’s surface,” Gleason said. “Learning about these icy interiors will help us understand how the worlds in our solar system formed and how at least one of them, so far as we know, came to have all the necessary characteristics for life.”

    Other co-authors on the study include Cindy Bolme of Los Alamos National Laboratory; Eric Galtier, Hae Ja Lee and Eduardo Granados of the SLAC National Accelerator Laboratory; Dan Dolan, Chris Seagle and Tom Ao of Sandia National Laboratories; and Suzanne Ali, Amy Lazicki, Damian Swift and Peter Celliers of Lawrence Livermore National Laboratory.

    Funding was provided by the National Science Foundation, the Los Alamos National Laboratory, the U.S. Department of Energy Office of Science, Fusion Energy Science and the SLAC National Accelerator Laboratory.

    See the full article here .

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  • richardmitnick 5:34 pm on July 5, 2017 Permalink | Reply
    Tags: , , Getting ready for LCLS-II, , X-ray Technology   

    From SLAC: “SLAC’s Electron Hub Gets New ‘Metro Map’ for World’s Most Powerful X-Ray Laser” 

    SLAC Lab

    July 5, 2017
    Manuel Gnida

    A reconfiguration of SLAC’s historic Beam Switch Yard will include electron transport lines needed for LCLS-II, a major upgrade to the Linac Coherent Light Source (LCLS) X-ray laser. (Greg Stewart/SLAC National Accelerator Laboratory)

    The central hub for powerful electron beams at the Department of Energy’s SLAC National Accelerator Laboratory is getting a makeover to prepare for the installation of LCLS-II – a major upgrade to the Linac Coherent Light Source (LCLS), the world’s first hard X-ray free-electron laser. LCLS-II will deliver the most powerful X-rays ever made in a lab, with beams that are 10,000 times brighter than before, opening up unprecedented research opportunities in chemistry, materials science, biology and energy research.

    Central portion of the BSY before (left) and after the Reconfiguration Project. (Scott DeBarger/SLAC National Accelerator Laboratory)

    A Monumental Clean-up Operation

    To clear the path for LCLS-II, crews first had to remove all unnecessary materials from the BSY – a monumental task considering SLAC’s rich history in accelerator science and the legacy material it created.

    “When experiments end, most of the old equipment is typically left in place,” says SLAC’s Mark Woodley, an optics designer involved in the BSY Reconfiguration Project. “Only the things that are in the way of new experiments are taken out.”

    In its early days in the 1960s, the linac delivered electron beams to three experimental stations. There was one line going straight into the lab’s research yard. Today this line continues to the LCLS undulator. Pulsed magnets in the BSY could divert the beam into End Stations A and B via two beamlines that branched off the central line.

    In 1980, two more branches were added to feed electrons and positrons, the antiparticle siblings of electrons, into the two storage rings of the PEP accelerator (PEP-II from 1999). In 1987, another two branches were needed to deliver beams to the two arms of the Stanford Linear Collider (SLC).

    Most of the old materials left behind in the BSY by these experiments have now been cleared – a job that took 300 employees and subcontractors almost 24,000 hours of work in the period from December 2016 to May 2017. They removed 325 cubic yards, or about 24 tons, of material – enough to fill eight sea-land shipping containers – and more than 300,000 feet of cables.

    “Considering the monumental task we had ahead of us, it’s truly impressive how well this project went,” DeBarger says. “It involved many people from inside and outside the lab, and every single one of them was absolutely needed.”

    Building the Future of X-ray Science

    After clearing out the BSY, members of the Reconfiguration Project installed a new beamline that runs from the copper linac to the current LCLS undulator. In parallel, the system to extract electrons for the End Station A line was put in place by another project team.

    “We also installed the very first LCLS-II beam pipe at the end of a ‘muon shield’ that is constructed of 5- and 10-ton steel blocks and shields the beam transport hall downstream of the BSY, allowing access while beams are tuned in the BSY,” says Dean Hanquist, control account manager on Chan’s team.

    “In the end, we had to make sure that everything works properly again for LCLS, which has now resumed its experimental program,” says BSY Area Physicist Tonee Smith. “For example, all of the magnets used in the beamline to focus the electron beam and make small corrections to it were refurbished, and we had to remeasure and test them.”

    The remaining beamlines and junctions will be installed during a yearlong LCLS downtime, which will start in the summer of 2018. Once completed, the new BSY “metro system” will be ready to transport electron trains to the new X-ray laser facility, where they will power groundbreaking X-ray science for years to come.

    Crew members gather at the conclusion of the BSY Reconfiguration Project. (Dawn Harmer/SLAC National Accelerator Laboratory)

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

    The interior of the east portion of the Beam Switch Yard (BSY) showing three “tracks” that electrons accelerated in SLAC’s linear accelerator can be directed into. All of the beams for LCLS and LCLS-II are sent through the central tunnel. In early 2017, as part of the LCLS-II project, the steel Muon Shield was reconfigured to permit installation of a new beamline that will transport beams to a new Soft X-Ray Undulator. (Chris Smith/SLAC National Accelerator Laboratory)

    Workers install the shield pipe that will position and protect the LCLS-II vacuum chamber within the Muon Shield. (Chris Smith/SLAC National Accelerator Laboratory)

    Surveyors Bryan Rutledge and Francis Gaudreault measure the position of the LCLS beamline prior to its disassembly. (Chris Smith/SLAC National Accelerator Laboratory)

    Mechanical Engineer Alev Ibrahimov, left, and Transport Systems CAM Dean Hanquist inspect the LCLS-II installation location in Sector 30. (Dawn Harmer/SLAC National Accelerator Laboratory)

    Rigger Scot Johnson positions a movable hoist. (Chris Smith/SLAC National Accelerator Laboratory)

    A crane removes the D-10 Tune-up Dump. This dump has five apertures, visible at the end of the device, which over the years allowed beams to head to various downstream experimental areas including LCLS, End Station A, End Station B and SPEAR. (Chris Smith/SLAC National Accelerator Laboratory)

    See the full article here .

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    SLAC is a multi-program laboratory exploring frontier questions in photon science, astrophysics, particle physics and accelerator research. Located in Menlo Park, California, SLAC is operated by Stanford University for the DOE’s Office of Science.

  • richardmitnick 12:22 pm on June 27, 2017 Permalink | Reply
    Tags: 1 billion suns: World’s brightest laser sparks new behavior in light, Diocles Laser, Extreme Light Laboratory, Focusing laser light to a brightness 1 billion times greater than the surface of the sun, , , , U Nebraska, X-ray Technology   

    From U Nebraska – Lincoln: “1 billion suns: World’s brightest laser sparks new behavior in light” 

    University of Nebraska -Lincoln

    Scott Schrage

    A rendering of how changes in an electron’s motion (bottom) alter the scattering of light (top), as measured in a new experiment that scattered more than 500 photons of light from a single electron. Previous experiments had managed to scatter no more than a few photons at a time. Donald Umstadter and Wenchao Yan

    Brighter than a billion suns: A scientist at work in the Extreme Light Laboratory. Diocles Laser.
    University of Nebraska-Lincoln. COSMOS.

    Physicists from the University of Nebraska-Lincoln are seeing an everyday phenomenon in a new light.

    By focusing laser light to a brightness 1 billion times greater than the surface of the sun — the brightest light ever produced on Earth — the physicists have observed changes in a vision-enabling interaction between light and matter.

    Those changes yielded unique X-ray pulses with the potential to generate extremely high-resolution imagery useful for medical, engineering, scientific and security purposes. The team’s findings, detailed June 26 in the journal Nature Photonics, should also help inform future experiments involving high-intensity lasers.

    Donald Umstadter and colleagues at the university’s Extreme Light Laboratory fired their Diocles Laser at helium-suspended electrons to measure how the laser’s photons — considered both particles and waves of light — scattered from a single electron after striking it.

    Under typical conditions, as when light from a bulb or the sun strikes a surface, that scattering phenomenon makes vision possible. But an electron — the negatively charged particle present in matter-forming atoms — normally scatters just one photon of light at a time. And the average electron rarely enjoys even that privilege, Umstadter said, getting struck only once every four months or so.

    Though previous laser-based experiments had scattered a few photons from the same electron, Umstadter’s team managed to scatter nearly 1,000 photons at a time. At the ultra-high intensities produced by the laser, both the photons and electron behaved much differently than usual.

    “When we have this unimaginably bright light, it turns out that the scattering — this fundamental thing that makes everything visible — fundamentally changes in nature,” said Umstadter, the Leland and Dorothy Olson Professor of Physics and Astronomy.

    A photon from standard light will typically scatter at the same angle and energy it featured before striking the electron, regardless of how bright its light might be. Yet Umstadter’s team found that, above a certain threshold, the laser’s brightness altered the angle, shape and wavelength of that scattered light.

    “So it’s as if things appear differently as you turn up the brightness of the light, which is not something you normally would experience,” Umstadter said. “(An object) normally becomes brighter, but otherwise, it looks just like it did with a lower light level. But here, the light is changing (the object’s) appearance. The light’s coming off at different angles, with different colors, depending on how bright it is.”

    That phenomenon stemmed partly from a change in the electron, which abandoned its usual up-and-down motion in favor of a figure-8 flight pattern. As it would under normal conditions, the electron also ejected its own photon, which was jarred loose by the energy of the incoming photons. But the researchers found that the ejected photon absorbed the collective energy of all the scattered photons, granting it the energy and wavelength of an X-ray.

    The unique properties of that X-ray might be applied in multiple ways, Umstadter said. Its extreme but narrow range of energy, combined with its extraordinarily short duration, could help generate three-dimensional images on the nanoscopic scale while reducing the dose necessary to produce them.

    Using a laser focused to the brightest intensity yet recorded, physicists at the Extreme Light Laboratory produced unique X-ray pulses with greater energy than their conventional counterparts. The team demonstrated these X-rays by imaging the circuitry of a USB drive. Extreme Light Laboratory | University of Nebraska-Lincoln.

    Those qualities might qualify it to hunt for tumors or microfractures that elude conventional X-rays, map the molecular landscapes of nanoscopic materials now finding their way into semiconductor technology, or detect increasingly sophisticated threats at security checkpoints. Atomic and molecular physicists could also employ the X-ray as a form of ultrafast camera to capture snapshots of electron motion or chemical reactions.

    As physicists themselves, Umstadter and his colleagues also expressed excitement for the scientific implications of their experiment. By establishing a relationship between the laser’s brightness and the properties of its scattered light, the team confirmed a recently proposed method for measuring a laser’s peak intensity. The study also supported several longstanding hypotheses that technological limitations had kept physicists from directly testing.

    “There were many theories, for many years, that had never been tested in the lab, because we never had a bright-enough light source to actually do the experiment,” Umstadter said. “There were various predictions for what would happen, and we have confirmed some of those predictions.

    “It’s all part of what we call electrodynamics. There are textbooks on classical electrodynamics that all physicists learn. So this, in a sense, was really a textbook experiment.”

    Umstadter authored the study with Sudeep Banerjee and Shouyuan Chen, research associate professors of physics and astronomy; Grigory Golovin and Cheng Liu, senior research associates in physics and astronomy; Wenchao Yan, Ping Zhang, Baozhen Zhao and Jun Zhang, postdoctoral researchers in physics and astronomy; Colton Fruhling and Daniel Haden, doctoral students in physics and astronomy; along with Min Chen and Ji Luo of Shanghai Jiao Tong University.

    The team received support from the Air Force Office for Scientific Research, the National Science Foundation, the U.S. Department of Energy’s Office of Science, the Department of Homeland Security’s Domestic Nuclear Detection Office, and the National Science Foundation of China.

    See the full article here .

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    The University of Nebraska–Lincoln, often referred to as Nebraska, UNL or NU, is a public research university in the city of Lincoln, in the state of Nebraska in the Midwestern United States. It is the state’s oldest university, and the largest in the University of Nebraska system.

    The state legislature chartered the university in 1869 as a land-grant university under the 1862 Morrill Act, two years after Nebraska’s statehood into the United States. Around the turn of the 20th century, the university began to expand significantly, hiring professors from eastern schools to teach in the newly organized professional colleges while also producing groundbreaking research in agricultural sciences. The “Nebraska method” of ecological study developed here during this time pioneered grassland ecology and laid the foundation for research in theoretical ecology for the rest of the 20th century. The university is organized into eight colleges on two campuses in Lincoln with over 100 classroom buildings and research facilities.

    Its athletic program, called the Cornhuskers, is a member of the Big Ten Conference. The Nebraska football team has won 46 conference championships, and since 1970, five national championships. The women’s volleyball team has won four national championships along with eight other appearances in the Final Four. The Husker football team plays its home games at Memorial Stadium, selling out every game since 1962. The stadium’s capacity is about 92,000 people, larger than the population of Nebraska’s third-largest city.

  • richardmitnick 10:24 am on June 23, 2017 Permalink | Reply
    Tags: , , , , Bragg Projection Ptychography, Crystal lattice of nanoscale materials, Hard X-ray Nanoprobe (HXN) beamline at NSLS-II, , Stephan Hruszkewycz, X-ray Technology   

    From BNL- “National Synchrotron Light Source II User Profile: Stephan Hruszkewycz” 

    Brookhaven Lab

    June 19, 2017
    Laura Mgrdichian

    Stephan Hruszkewycz. No image credit.

    Stephan Hruskewycz is an assistant physicist in the Materials Science Division at the U.S. Department of Energy’s (DOE) Argonne National Laboratory.

    While he regularly conducts research at Argonne’s own synchrotron user facility, the Advanced Photon Source (APS), his work on the nanoscale structure and behavior of materials has led him to book beamtime at the DOE’s newest synchrotron, the National Synchrotron Light Source II (NSLS-II). Both NSLS-II and APS are DOE Office of Science User Facilities.





    What are you studying at NSLS-II?

    The focus of our NSLS-II experiments has been to image defects and imperfections in the crystal lattice of nanoscale materials using a new imaging technique known as Bragg Projection Ptychography. Specifically, we have been studying stacking faults in nanowires made of III-V semiconductors, a class of semiconductor that results from the combination of elements from column III on the periodic table (mainly aluminum, gallium, and indium) and column V (nitrogen, phosphorous, arsenic, and antimony). These materials have properties that make them excellent for certain applications; for example, solar cells made of III-V cells are very efficient.

    During our next run, we will be imaging strain fields in complex oxide thin-film nanostructures. These classes of materials have potential uses for energy conversion in solar and fuel cell applications, and their nanoscale structure plays a large role in performance. By studying these structures in detail, we may be able to figure out how to make these materials perform better.

    Why is NSLS-II is particularly suited to your work?

    The Hard X-ray Nanoprobe (HXN) beamline at NSLS-II delivers a coherent hard x-ray beam focused to a few tens of nanometers and the ability to rotate the sample and detector to enable Bragg diffraction with a nanofocused beam. We are capitalizing on the coherence and stability of the focused beam to convert a series of Bragg diffraction patterns measured from different overlapping positions of the sample into an image of the lattice structure inside a specific region of the crystal. The result provides an image with a resolution down to just a few nanometers, as well as picometer-level sensitivity to lattice distortions.

    Tell us about your background and how you arrived at this field of research.

    I have been interested for some time in developing new methods to exploit coherent hard x-rays to reveal of the structure and dynamics of materials. Recently, I have focused on applying these methods to materials with inhomogeneous internal lattice structures that dictate their overall properties, such as nanostructured oxide thin films and semiconductors. To me, this is an exciting area of research, one where cutting-edge materials science questions can be answered with new x-ray imaging methods at state-of-the-art synchrotron sources that deliver highly coherent beams.

    Who else is involved in this work?

    So far, I have been joined at NSLS-II by Megan Hill, a graduate student in Northwestern University’s Materials Science and Engineering Department; Martin Holt, a staff scientist in Argonne’s Center for Nanoscale Materials; and Brian Stephenson, a senior physicist in Argonne’s Materials Science Division.

    See the full article here .

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

  • richardmitnick 8:41 am on June 23, 2017 Permalink | Reply
    Tags: , , Building blocks of bacteria, , , Organelle’s protein shell, , X-ray Technology   

    From LBNL: “Study Sheds Light on How Bacterial Organelles Assemble” 

    Berkeley Logo

    Berkeley Lab

    June 22, 2017
    Sarah Yang
    (510) 486-4575

    Cheryl Kerfeld and Markus Sutter handle crystallized proteins at Berkeley Lab’s Advanced Light Source. (Credit: Marilyn Chung/Berkeley Lab)

    Researchers at Berkeley Lab and MSU have obtained the first atomic-level view of an intact bacterial microcompartment, shown here. Credit: Markus Sutter/Berkeley Lab and MSU

    Scientists with joint appointments at DOE’s Lawrence Berkeley National Laboratory and Michigan State University reveal the building blocks of bacteria. (Video Credit: Michigan State University)

    Scientists are providing the clearest view yet of an intact bacterial microcompartment, revealing at atomic-level resolution the structure and assembly of the organelle’s protein shell.

    The work, led by scientists at the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) and Michigan State University (MSU), will appear in the June 23 issue of the journal Science. They studied the organelle shell of an ocean-dwelling slime bacteria called Haliangium ochraceum.

    “It’s pretty photogenic,” said corresponding author Cheryl Kerfeld, a Berkeley Lab structural biologist with a joint appointment as a professor at the MSU-DOE Plant Research Laboratory. “But more importantly, it provides the very first picture of the shell of an intact bacterial organelle membrane. Having the full structural view of the bacterial organelle membrane can help provide important information in fighting pathogens or bioengineering bacterial organelles for beneficial purposes.”

    These organelles, or bacterial microcompartments (BMCs), are used by some bacteria to fix carbon dioxide, Kerfeld noted. Understanding how the microcompartment membrane is assembled, as well as how it lets some compounds pass through while impeding others, could contribute to research in enhancing carbon fixation and, more broadly, bioenergy. This class of organelles also helps many types of pathogenic bacteria metabolize compounds that are not available to normal, non-pathogenic microbes, giving the pathogens a competitive advantage.

    The contents within these organelles determine their specific function, but the overall architecture of the protein membranes of BMCs are fundamentally the same, the authors noted. The microcompartment shell provides a selectively permeable barrier which separates the reactions in its interior from the rest of the cell. This enables higher efficiency of multi-step reactions, prevents undesired interference, and confines toxic compounds that may be generated by the encapsulated reactions.

    Unlike the lipid-based membranes of eukaryotic cells, bacterial microcompartments (BMCs) have polyhedral shells made of proteins.

    “What allows things through a membrane is pores,” said study lead author Markus Sutter, MSU senior research associate and affiliate scientist at Berkeley Lab’s Molecular Biophysics and Integrated Bioimaging (MBIB) division. “For lipid-based membranes, there are membrane proteins that get molecules across. For BMCs, the shell is already made of proteins, so the shell proteins of BMCs not only have a structural role, they are also responsible for selective substrate transfer across the protein membrane.”

    Earlier studies revealed the individual components that make up the BMC shell, but imaging the entire organelle was challenging because of its large mass of about 6.5 megadaltons, roughly equivalent to the mass of 6.5 million hydrogen atoms. This size of protein compartment can contain up to 300 average-sized proteins.

    The researchers were able to show how five different kinds of proteins formed three different kinds of shapes: hexagons, pentagons and a stacked pair of hexagons, which assembled together into a 20-sided icosahedral shell.

    The intact shell and component proteins were crystallized at Berkeley Lab, and X-ray diffraction data were collected at Berkeley Lab’s Advanced Light Source and the Stanford Synchrotron Radiation Lightsource, both DOE Office of Science User Facilities.



    The study authors said that by using the structural data from this paper, researchers can design experiments to study the mechanisms for how the molecules get across this protein membrane, and to build custom organelles for carbon capture or to produce valuable compounds.

    Other co-authors of the study are Basil Greber, an affiliate of Berkeley Lab’s MBIB division and a UC Berkeley postdoctoral fellow in the California Institute for Quantitative Biosciences, and Clement Aussignargues, a postdoctoral fellow at the MSU-DOE Plant Research Laboratory.

    See the full article here .

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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, , , , X-ray Technology   

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

    SLAC Lab

    June 22, 2017
    Amanda Solliday

    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.



    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.

  • richardmitnick 8:06 am on June 23, 2017 Permalink | Reply
    Tags: A Single Electron’s Tiny Leap Sets Off ‘Molecular Sunscreen’ Response, , , , , , , X-ray Technology   

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

    SLAC Lab

    June 22, 2017
    Glennda Chui

    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.


    “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.

    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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