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  • richardmitnick 2:07 pm on February 10, 2016 Permalink | Reply
    Tags: , Biomolecules, , , , X-ray Technology   

    From DESY: “New method opens crystal clear views of biomolecules” 


    No writer credit found

    A scientific breakthrough gives researchers access to the blueprint of thousands of molecules of great relevance to medicine and biology. The novel technique, pioneered by a team led by DESY scientist Professor Henry Chapman from the Center for Free-Electron Laser Science CFEL and reported this week in the scientific journal Nature, opens up an easy way to determine the spatial structures of proteins and other molecules, many of which are practically inaccessible by existing methods. The structures of biomolecules reveal their modes of action and give insights into the workings of the machinery of life. Obtaining the molecular structure of particular proteins, for example, can provide the basis for the development of tailor-made drugs against many diseases. “Our discovery will allow us to directly view large protein complexes in atomic detail,” says Chapman, who is also a professor at the University of Hamburg and a member of the Hamburg Centre for Ultrafast Imaging CUI.

    Dimer crystals Detec of complex biomolecules like that of the photosystem II molecule shown here
    Slightly disordered crystals of complex biomolecules like that of the photosystem II molecule shown here produce a complex continous diffraction pattern (right, the disorder is greatly exaggerated) under X-ray light that contains far more information than the so-called Bragg peaks of a strongly ordered crystal alone (left). Credit: DESY, Eberhard Reimann

    To determine the spatial structure of a biomolecule, scientists mainly rely on a technique called crystallography. The new work offers a direct route to “read” the atomic structure of complex biomolecules by crystallography without the usual need for prior knowledge and chemical insight. “This discovery has the potential to become a true revolution for the crystallography of complex matter,” says the chairman of DESY’s board of directors, Professor Helmut Dosch.

    In crystallography, the structure of a crystal and of its constituents can be investigated by shining X-rays on it. The X-rays scatter from the crystal in many different directions, producing an intricate and characteristic pattern of numerous bright spots, called Bragg peaks (named after the British crystallography pioneers William Henry and William Lawrence Bragg). The positions and strengths of these spots contain information about the structure of the crystal and of its constituents. Using this approach, researchers have already determined the atomic structures of tens of thousands of proteins and other biomolecules.

    But the method suffers from two significant barriers, which make structure determination extremely difficult or sometimes impossible. The first is that the molecules must be formed into very high quality crystals. Most biomolecules do not naturally form crystals. However, without the necessary perfect, regular arrangement of the molecules in the crystal, only a limited number of Bragg peaks are visible. This means the structure cannot be determined, or at best only a fuzzy “low resolution” facsimile of the molecule can be found. This barrier is most severe for large protein complexes such as membrane proteins. These systems participate in a range of biological processes and many are the targets of today’s drugs. Great skill and quite some luck are needed to obtain high-quality crystals of them.

    Extreme Sudoku in three dimensions

    The second barrier is that the structure of a complex molecule is still extremely difficult to determine, even when good diffraction is available. “This task is like extreme Sudoku in three dimensions and a million boxes, but with only half the necessary clues,” explains Chapman. In crystallography, this puzzle is referred to as the phase problem. Without knowing the phase – the lag of the crests of one diffracted wave to another – it is not possible to compute an image of the molecule from the measured diffraction pattern. But phases can’t be measured. To solve the tricky phase puzzle, more information must be known than just the measured Bragg peaks. This additional information can sometimes be obtained by X-raying crystals of chemically modified molecules, or by already knowing the structure of a closely-related molecule.

    When thinking about why protein crystals do not always “diffract”, Chapman realised that imperfect crystals and the phase problem are linked. The key lies in a weak “continuous” scattering that arises when crystals become disordered. Usually, this non-Bragg, continuous diffraction is thought of as a nuisance, although it can be useful for providing insights into vibrations and dynamics of molecules. But when the disorder consists only of displacements of the individual molecules from their ideal positions in the crystal then the “background” takes on a much more complex character – and its rich structure is anything but diffuse. It then offers a much bigger prize than the analysis of the Bragg peaks: the continuously-modulated “background” fully encodes the diffracted waves from individual “single” molecules.

    “If you would shoot X-rays on a single molecule, it would produce a continuous diffraction pattern free of any Bragg spots,” explains lead author Dr. Kartik Ayyer from Chapman’s CFEL group at DESY. “The pattern would be extremely weak, however, and very difficult to measure. But the ‘background’ in our crystal analysis is like accumulating many shots from individually-aligned single molecules. We essentially just use the crystal as a way to get a lot of single molecules, aligned in common orientations, into the beam.” With imperfect, disordered crystals, the continuous diffraction fills in the gaps and beyond the Bragg peaks, giving vastly more information than in normal crystallography. With this additional gain in information, the phase problem can be uniquely solved without having to resort to other measurements or assumptions. In the analogy of the Sudoku puzzle, the measurements provide enough clues to always arrive at the right answer.

    The best crystals are imperfect crystals

    This novel concept leads to a paradigm shift in crystallography — the most ordered crystals are no longer the best to analyse with the novel method. Instead, the best crystals are imperfect crystals. “For the first time we have access to single molecule diffraction – we have never had this in crystallography before,” he explains. “But we have long known how to solve single-molecule diffraction if we could measure it.” The field of coherent diffractive imaging, spurred by the availability of laser-like beams from X-ray free-electron lasers, has developed powerful algorithms to directly solve the phase problem in this case, without having to know anything at all about the molecule. “You don’t even have to know chemistry,” says Chapman, “but you can learn it by looking at the three-dimensional image you get.”

    To demonstrate their novel analysis method, the Chapman group teamed up with the group of Professor Petra Fromme from the Arizona State University (ASU), and other colleagues from ASU, University of Wisconsin, the Greek Foundation for Research and Technology – Hellas FORTH, and SLAC National Accelerator Laboratory in the U.S. They used the world’s most powerful X-ray laser LCLS at SLAC to X-ray imperfect microcrystals of a membrane protein complex called Photosystem II that is part of the photosynthesis machinery in plants.

    SLAC LCLS Inside
    Inside LCLS

    Including the continuous diffraction pattern into the analysis immediately improved the spatial resolution around a quarter from 4.5 Ångström to 3.5 Ångström (an Ångström is 0.1 nanometres). The obtained image gave fine definition of molecular features that usually require fitting a chemical model to see. “That is a pretty big deal for biomolecules,” explains co-author Dr. Anton Barty from DESY. “And we can further improve the resolution if we take more patterns.” The team had only a few hours of measuring time for these experiments, while full-scale measuring campaigns usually last a couple of days.

    The scientists hope to obtain even clearer and higher resolution images of photosystem II and many other macromolecules with their new technique. “This kind of continuous diffraction has actually been seen for a long time from many different poorly-diffracting crystals,” says Chapman. “It wasn’t understood that you can get structural information from it and so analysis techniques suppressed it. We’re going to be busy to see if we can solve structures of molecules from old discarded data.”

    Macromolecular diffractive imaging using imperfect crystals; Kartik Ayyer et al.; Nature (2016); DOI: 10.1038/nature16949

    See the full article here .

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    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 9:16 am on February 5, 2016 Permalink | Reply
    Tags: , , , X-ray Technology   

    From DESY: “Scientists film exploding nanoparticles” 


    No writer credit found

    Imaging nanoscale dynamics with unparalleled detail and speed

    Using a super X-ray microscope, an international research team has “filmed” the explosion of single nanoparticles. The team led by Tais Gorkhover from Technische Universität Berlin, currently working at the SLAC National Accelerator Laboratory in the U.S. as a fellow of the Volkswagen Foundation, and Christoph Bostedt from the Argonne National Laboratory and Northwestern University has managed to combine a temporal resolution of 100 femtoseconds and a spatial resolution of eight nanometres for the first time. A nanometre is a billionth of a metre, and a femtosecond is a mere quadrillionth of a second. For their experiments, the scientists used the so-called free-electron X-ray laser LCLS.

    SLAC LCLS Inside
    LCLS at SLAC

    The exposure time of the individual images was so short that the rapidly moving particles in the gas phase appeared frozen in time. Therefore, they did not have to be fixed on substrates as it is commonly done in other microscopy approaches. The team, including researchers from the Center for Free-Electron Laser Science CFEL at DESY, reports its results in the scientific journal Nature Photonics.

    Xenon nanoparticle exploding
    Three states of an exploding xenon nanoparticle. The ultra short flashes of the X-ray laser record these states as a so-called diffraction pattern. From these, the state of the sample can be calculated. Credit: Tais Gorkhover/SLAC

    Most imaging approaches are severely limited when a combination of high spatial resolution and extreme shutter speed is required. Ultrafast optical approaches have a rather coarse resolution due to the long wavelength. Conversely, electron microscopy can yield ultrahigh resolution but demands a rather long exposure time and it requires the particles being fixed to substrates. Therefore ultrafast processes in free nanometre-sized particles cannot be directly imaged with conventional methods. However, the ability to image and understand the dynamics in nanostructures and aggregates is of relevance in many fields, ranging from climate models to nanotechnology.

    The properties and dynamics of nanoparticles can significantly change when they are deposited on a substrate. To avoid any modification, the particles, made of frozen xenon and with a diameter of around 40 nanometres, were imaged during their flight through a vacuum chamber. “Using the intense light of an infrared laser, the nanoparticles where superheated and exploded,” explains DESY scientist Jochen Küpper, who is also a professor at the University of Hamburg and a member of the Hamburg Centre for Ultrafast Imaging (CUI). The explosion was imaged with ultrafast X-ray flashes at different time steps. Küpper’s group helped to implement this so-called pump-probe technique. “The experiment was repeated over and over with a new nanoparticle every time and slightly increased delay of the X-ray flash,” reports Lotte Holmegaard from Küpper’s CFEL group. Subsequently the images were assembled to a „movie“.

    „To our big surprise the exploding particles appeared to be shrinking with time instead of expanding as intuitively expected“ says Gorkhover. This unexpected result could be explained with theoretical models that describe the explosion as a melting process starting on the surface instead of a homogenous expansion. In this process, the solid part of the particle’s core gets smaller and smaller what causes the illusion of a shrinking particle.

    Another very interesting aspect of this new imaging approach is that it is possible to directly image the dynamics in single, free nanoparticles. Most time resolved studies are based on ensembles of many particles and averaging statements in which some important differences such as size and shapes of the particles get lost. “We have already demonstrated the importance to look at one particle at a time in earlier static experiments. Now this approach is also available for time-resolved studies,” says Gorkhover.

    “Our experiments yield unprecedented insight into the non-equilibrium physics of superheated nanoparticles. Moreover, they open the door for a multitude of new experiments where the ultrafast dynamics of small samples is important.“ explains Bostedt. Such dynamics may be of relevance in the formation of aerosols which are of major importance in climate models as they are in a large part responsible for absorption and reflection of sunlight. They may also be interesting for research on laser driven fusion in small targets or the rapidly developing area of nanoplasmonics in which the properties of nanoparticles are manipulated with intense light fields.

    Femtosecond and nanometre visualization of structural dynamics in superheated nanoparticles; Tais Gorkhover, Christoph Bostedt et al.; „Nature Photonics“, 2016; DOI: 10.1038/NPHOTON.2015.264

    See the full article here .

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    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 5:21 pm on January 29, 2016 Permalink | Reply
    Tags: , , X-ray Technology   

    From SLAC: “Tiniest Particles Shrink Before Exploding When Hit With SLAC’s X-ray Laser” 

    SLAC Lab

    January 29, 2016

    nanometer-sized clusters of xenon atoms (center) first shrink before exploding after being hit with very intense X-rays. In the experiment at LCLS
    Nanometer-sized clusters of xenon atoms (center) first shrink before exploding after being hit with very intense X-rays at LCLS.

    SLAC Experimental setup at LCLS used to determine that nanometer-sized particles first shrink before exploding after being hit with very intense X-rays.
    Experimental setup at LCLS used to determine that nanometer-sized particles first shrink before exploding after being hit with very intense X-rays. The researchers exposed tiny xenon clusters (injected from top left) to two consecutive X-ray pulses (green and red wavelets coming in from bottom left). The first pulse rapidly heats the cluster, while the second pulse probes how its structure changes over a period of 80 quadrillionths of a second. The structural changes are tracked with an X-ray detector (right). (SLAC National Accelerator Laboratory)

    Researchers assumed that tiny objects would instantly blow up when hit by extremely intense light from the world’s most powerful X-ray laser at the Department of Energy’s SLAC National Accelerator Laboratory. But to their astonishment, these nanoparticles initially shrank instead – a finding that provides a glimpse of the unusual world of superheated nanomaterials that could eventually also help scientists further develop X-ray techniques for taking atomic images of individual molecules.

    The experiments took place at the Linac Coherent Light Source (LCLS) X-ray laser, a DOE Office of Science User Facility. Its pulses are so bright that they can be used to turn solids into highly ionized gases, or plasmas, that blow up within a fraction of a second. Fortunately, for many samples researchers can take the data they need before the damage sets in – an approach that has been used to reveal never-before-seen details of a variety of samples relevant to chemistry, materials science, biology and energy research.

    The ultimate limits of this approach are, however, not well understood. One of the key visions for X-ray laser science is to image individual, one-of-a-kind particles with single X-ray pulses. To do so in a quantitative manner, researchers need to understand precisely how each molecule responds to the intense X-ray light. The new study, published today in Science Advances, provides an unexpected insight into this aspect.

    “So far, all models have assumed that a very small system would immediately explode when we pump a lot of energy into it with the X-ray laser,” says former LCLS researcher Christoph Bostedt, who is now at Argonne National Laboratory and Northwestern University. “But our experiments showed otherwise.”

    At LCLS, Bostedt and his fellow researchers exposed minuscule clusters of xenon atoms to two consecutive X-ray pulses. The clusters, which were merely three millionths of an inch across, were heated by the first pulse for 10 quadrillionths of a second, or 10 femtoseconds. The second pulse then probed the clusters’ atomic structures over the next 80 femtoseconds.

    “The unique nature of the LCLS X-ray pulse allowed us to create a freeze-frame movie of the response, with a resolution of about a tenth of the width of a single xenon atom,” says LCLS and Stanford University graduate student Ken Ferguson, who led the data analysis. The researchers believe that the effect is a result of how electrons, which were initially localized around individual xenon atoms, redistribute over the entire cluster after the first X-ray pulse.

    “This phenomenon had never been observed before, nor had it been predicted by any of the existing theories,” he says. “We expect it to have implications for many ultrafast X-ray laser experiments, especially those geared toward single-particle imaging with very intense X-ray pulses.”

    The research could benefit studies in other areas as well, such as investigations of warm dense matter – a state of matter between a solid and a plasma that exists in the cores of certain planets and is also important in the pursuit of nuclear fusion with high-power lasers.

    Other institutions involved in the study were Technical University of Berlin, Germany; Tohoku University, Japan; National Science Foundation BioXFEL Science and Technology Center, Buffalo; and Kyoto University, Japan.

    Citation: K. R. Ferguson et al., Science Advances, 29 January 2016 (10.1126/sciadv.1500837).

    See the full article here .

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

  • richardmitnick 4:56 am on January 22, 2016 Permalink | Reply
    Tags: , , SLAC LCLS MFX, X-ray Technology   

    From SLAC: “New MFX Experimental Station at LCLS Sees First X-ray Light” 

    SLAC Lab

    No writer credit found

    Instrument Expands X-ray Laser’s Capability and Flexibility for Biological Experiments

    For the first time in three years, LCLS has added a new instrument to its set of experimental stations. Staff from Stanford and SLAC gathered on Jan. 12 in the X-ray laser’s Far Experimental Hall to celebrate the arrival of the first X-rays in the brand new MFX hutch. LCLS’s seventh instrument, MFX will expand the facility’s capability and capacity by generating more opportunities for all kinds of groundbreaking user experiments.

    Although MFX can support a variety of experimental settings, it was specifically designed for macromolecular femtosecond crystallography. This technique provides atomic-resolution X-ray images and ultrafast movies of biomolecules in action. It will aid researchers in unravelling crucial biological processes, from finding new ways of fighting disease to developing methods to harness solar energy similar to photosynthesis.

    “MFX is going to make a big difference for the biosciences community, which has a growing demand for X-ray laser studies,” said SLAC and Stanford researcher Soichi Wakatsuki, the principal investigator for the MFX grants that initiated the project. “The instrument will increase the number of biological experiments at LCLS and will allow us to do them more efficiently.”

    SLAC LCLS Far Experimental Hall
    LCLS’s new instrument for macromolecular femtosecond crystallography, MFX, is located in the X-ray laser’s Far Experimental Hall. (SLAC National Accelerator Laboratory)

    So far, studies of biological samples have taken place at several other LCLS instruments, including AMO and SXR, but primarily at XPP and CXI. Their versatile, multi-purpose research programs require frequent, time-consuming changes in the experimental setups and limit the time available for biostudies. MFX will help alleviate both issues.

    But the addition of the new experimental station will benefit more than just bio-interested users. Since the X-ray beam can now be distributed between more instruments than before, there will be more experimental time for non-MFX users as well. The new in-hutch instrumentation, which is the focus of ongoing and future R&D, is rapidly expanding the MFX scientific capabilities in new directions.

    Building the new hutch in the Far Experimental Hall took place over the past six months. Now, more equipment will be brought in to prepare for the first MFX user experiments in July.
    A Collaborative Effort

    “It only took a little more than two-and-a-half years from the initial idea for MFX to today’s first light,” said LCLS scientist and MFX project manager Sébastien Boutet. “None of this would have happened without the collaboration of many great people – technicians, designers, engineers, researchers and construction workers.”

    LCLS ALD Mike Dunne said, “MFX is a great example of the successful collaboration between Stanford, SLAC’s Biosciences Division, SSRL and LCLS, and it may be a model for future projects that bring people together to do something remarkable.”

    Similar statements were also made by others at the first-light event.

    Persis Drell, dean of the Stanford School of Engineering and former SLAC director, emphasized that it was the inspiration of researchers from both SLAC and Stanford that laid the ground for the new instrument, which will make LCLS more accessible to users from around the world.

    SSRL Science Director Britt Hedman pointed out that MFX is also a gateway for scientists who want to do new types of crossover experiments that make use of both X-ray light sources, LCLS and SSRL. On the SSRL side, MFX efforts are led by researcher Aina Cohen, who also oversaw the development of a broadly used experimental setup at XPP that will now be used at MFX.


    “Today’s first light is a major milestone, but it’s not the end of MFX construction yet,” Wakatsuki said. “In the near future, we’ll install advanced instrumentation capable of rapid and automated use of LCLS’s X-rays, and turn MFX into a highly optimized system that will further increase the scientific productivity of the facility.”

    The MFX project received financial support from the Department of Energy’s Office of Science, Biological and Environmental Research (BER) and Basic Energy Sciences (BES); the National Institute of General Medical Sciences; Stanford University and the Howard Hughes Medical Institute.

    See the full article here .

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

  • richardmitnick 12:19 pm on January 20, 2016 Permalink | Reply
    Tags: , EMBL, Molecular Biology, X-ray Technology   

    From EMBL: “The cellular crystal factory” 

    EMBL European Molecular Biology Laboratory bloc

    European Molecular Biology Laboratory

    EMBL icon
    Free-electron laser beam hits a peroxisome containing protein crystals. IMAGE: EMBL/CFEL, Thomas Seine

    Scientists from the Wilmanns group have teamed up with experts across the Deutsches Elektronen-Synchrotron (DESY) research campus in Hamburg and at the SLAC National Accelerator Laboratory in California to show that naturally formed crystals can diffract X-rays. The first crystals successfully analysed with a free-electron laser inside the cells that produced them are unlikely to be the last.

    While structural biologists are familiar with the concept of growing protein crystals in the lab for X-ray crystallography experiments, many may not know that some organisms produce crystals naturally within their cells. “When we heard about these naturally forming crystals, we wondered whether we could use them for crystallography experiments,” says Daniel Passon, a postdoc in the Wilmanns group at EMBL Hamburg. “Producing protein crystals in the lab for crystallography experiments is not always easy – imagine if we could get cells to do this for us: a tiny crystal factory in a cell!”

    Crystallography uses X-rays to probe the 3D atomic structure of proteins that have been captured in their crystalline form, but the technique has its limitations. In a study published recently in the International Union of Crystallography Journal (IUCrJ), the team of Hamburg scientists instead used crystals grown inside yeast cells for crystallography experiments at the Linac Coherent Light Source [LCLS], an X-ray free-electron laser facility.

    SLAC LCLS Inside
    Inside the LCLS

    “This study would not have been possible without access to one of only two X-ray Free-Electron Lasers currently operational in the world,” says Matthias Wilmanns, Head of EMBL Hamburg, who oversaw the research, “It is a great example of the importance and potential of emerging infrastructures for the field of structural biology.”

    Size matters

    The group studied crystals that occur naturally in parts of the cell called peroxisomes. These organelles break down large molecules such as fatty acids, keeping toxic processes safely within their bounds and away from the rest of the cell. In Hansenula polymorpha yeast cells, a protein called alcohol oxidase breaks down methanol molecules into useful byproducts.

    To make effective use of the restricted space within the peroxisome, alcohol oxidase molecules are packed tightly into crystals; despite being so densely packed, the enzyme molecules inside this crystal are still active. “We think of crystals as rigid entities, but in fact they are not entirely solid,” explains Arjen Jakobi, a postdoc in the Wilmanns group and the Sachse group at EMBL Heidelberg, who carried out the work together with Passon and Wilmanns. “The methanol molecules pass through the crystals, reacting with the oxidase to become detoxified.”

    Temp 2
    Daniel Passon prepares nozzles for sample delivery via liquid jet. PHOTO: EMBL/Daniel Passon

    While all of these yeast cells have peroxisomes, some cells have more peroxisomes than others, and peroxisome size varies from cell to cell, too. This natural variation posed a problem, as the researchers needed the crystals to be as large as possible, and as similar to each other as possible.

    The Wilmanns group worked closely with colleagues at the University of Groningen who identified a mutant strain of yeast that only produces one large peroxisome per cell, each containing one large crystal. “Large is of course relative,” says Passon. At 0.001mm, the crystals were still too small for observations at even the most advanced synchrotrons, where they were likely to be combusted before data could be collected. “Free-Electron Lasers produce a large amount of photons in small bursts and have a very small parallel beam,” explains Wilmanns, “This makes them ideal for looking at such small crystals.”

    A novel experience

    The experiment was novel not only for EMBL’s scientists. “This field is its infancy and there are few leading experts worldwide,” says Wilmanns. “We teamed up with the Coherent Imaging Division at the neighbouring Center for Free Electron Laser Science (CFEL) at DESY and University of Hamburg, and benefited from the considerable experience and expertise of division Director, Henry Chapman and his group” he adds.

    Having done some initial validation experiments on the beamlines in Hamburg, Wilmanns, Chapman and their teams set off to the Linac Coherent Light Source at SLAC with their precious peroxisomes. “For such a novel and exciting experiment, I was really keen to be there in person!” says Wilmanns. “It reminded me of being at the synchrotron 20 years ago – it is a very experimental set-up, but the SLAC staff are skilled and efficient.”

    Temp 5
    Wilmanns checks that nozzles for sample delivery are working during a test run. PHOTO: EMBL/Daniel Passon

    A complementary method

    The group prepared two types of samples for the experiment: one with the peroxisomes inside their cells and the other with just the peroxisomes, removed from cells. “Surprisingly, we got better data when we measured the peroxisome inside the cell,” says Jakobi. “There was a lot less interference from the surrounding cell material than we expected.”

    Having shown that it is possible to get data from crystals within a cell, the group now hopes to harness the natural ability of the peroxisome to produce crystals of other proteins, thereby side-stepping the need for laborious crystallisation experiments. “This could become a complementary method for structural biologists studying challenging proteins,” Wilmanns concludes.


    Jakobi A J et al. IUCrJ (published online 12 January 2016). DOI: 10.1107/S2052252515022927

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    EMBL European Molecular Biology Laboratory campus

    EMBL is Europe’s flagship laboratory for the life sciences, with more than 80 independent groups covering the spectrum of molecular biology. EMBL is international, innovative and interdisciplinary – its 1800 employees, from many nations, operate across five sites: the main laboratory in Heidelberg, and outstations in Grenoble; Hamburg; Hinxton, near Cambridge (the European Bioinformatics Institute), and Monterotondo, near Rome. Founded in 1974, EMBL is an inter-governmental organisation funded by public research monies from its member states. The cornerstones of EMBL’s mission are: to perform basic research in molecular biology; to train scientists, students and visitors at all levels; to offer vital services to scientists in the member states; to develop new instruments and methods in the life sciences and actively engage in technology transfer activities, and to integrate European life science research. Around 200 students are enrolled in EMBL’s International PhD programme. Additionally, the Laboratory offers a platform for dialogue with the general public through various science communication activities such as lecture series, visitor programmes and the dissemination of scientific achievements.

  • richardmitnick 3:56 pm on January 19, 2016 Permalink | Reply
    Tags: , , , , , X-ray Technology   

    From Symmetry: “A speed trap for dark matter” 


    Manuel Gnida

    Analyzing the motion of X-ray sources could help researchers identify dark matter signals.

    Temp 1
    ASTRO-H, an X-ray satellite of the Japan Aerospace Exploration Agency

    Dark matter or not dark matter? That is the question when it comes to the origin of intriguing X-ray signals scientists have found coming from space.

    In a theory paper published today in Physical Review Letters, scientists have suggested a surprisingly simple way of finding the answer: by setting up a speed trap for the enigmatic particles.

    Eighty-five percent of all matter in the universe is dark: It doesn’t emit light, nor does it interact much with regular matter other than through gravity.

    The nature of dark matter remains one of the biggest mysteries of modern physics. Most researchers believe that the invisible substance is made of fundamental particles, but so far they’ve evaded detection. One way scientists hope to prove their particle assumption is by searching the sky for energetic light that would emerge when dark matter particles decayed or annihilated each other in space.

    Over the past couple of years, several groups analyzing data from two X-ray satellites—the European Space Agency’s XMM-Newton and NASA’s Chandra X-ray space observatories—reported the detection of faint X-rays with a well-defined energy of 3500 electronvolts (3.5 keV).

    ESA XMM Newton

    NASA Chandra Telescope

    The signal emanated from the center of the Milky Way; its nearest neighbor galaxy, Andromeda; and a number of galaxy clusters.

    Andromeda Galaxy. Adam Evans

    Some scientists believe it might be a telltale sign of decaying dark matter particles called sterile neutrinos—hypothetical heavier siblings of the known neutrinos produced in fusion reactions in the sun, radioactive decays and other nuclear processes. However, other researchers argue that there could be more mundane astrophysical origins such as hot gases.

    There might be a straightforward way of distinguishing between the two possibilities, suggest researchers from Ohio State University and the Kavli Institute for Particle Astrophysics and Cosmology [KIPAC], a joint institute of Stanford University and SLAC National Accelerator Laboratory.

    It involves taking a closer look at the Doppler shifts of the X-ray signal. The Doppler effect is the shift of a signal to higher or lower frequencies depending on the relative velocity between the signal source and its observer. It’s used, for instance, in roadside speed traps by the police, but it could also help astrophysicists “catch” dark matter particles.

    “On average, dark matter moves differently than gas,” says study co-author Ranjan Laha from KIPAC. “Dark matter has random motion, whereas gas rotates with the galaxies to which it is confined. By measuring the Doppler shifts in different directions, we can in principle tell whether a signal—X-rays or any other frequency—stems from decaying dark matter particles or not.”

    Researchers would even know if the signal were caused by the observation instrument itself because then the Doppler shift would be zero for all directions

    Although a promising approach, it can’t just yet be applied to the 3.5-keV X-rays because the associated Doppler shifts are very small. Current instruments either don’t have enough energy resolution for the analysis or they don’t operate in the right energy range.

    However, this situation may change very soon with ASTRO-H, an X-ray satellite of the Japan Aerospace Exploration Agency, whose launch is planned for early this year. As the researchers show in their paper, it will have just the right specifications to return a verdict on the mystery X-ray line. Dark matter had better watch its speed.

    See the full article here .

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  • richardmitnick 1:37 pm on December 8, 2015 Permalink | Reply
    Tags: , Ribosome research, , X-ray Technology   

    From SLAC: “Innovation Boosts Study of Fragile Biological Samples at SLAC’s X-ray Laser” 

    SLAC Lab

    December 8, 2015

    Hasan DeMirci, a SLAC scientist with the Stanford PULSE Institute, with equipment used to prepare delicate biological samples for study with the lab’s X-ray laser, the Linac Coherent Light Source. (SLAC National Accelerator Laboratory)

    Hasan DeMirci and Raymond Sierra

    Diagram of the experimental setup at SLAC’s Linac Coherent Light Source. Gently prepared samples of fragile biological complexes are dropped into the path of the X-ray laser pulses, which enter from bottom right (yellow dashed line). At the interaction point where they meet, X-rays bounce off atoms in the sample and scatter into a detector, bottom left, producing patterns that are used to reconstruct the sample’s atom-by-atom structure. (R. Sierra et al., Nature Methods)

    Researchers at the Department of Energy’s SLAC National Accelerator Laboratory have found a simple new way to study very delicate biological samples – like proteins at work in photosynthesis and components of protein-making machines called ribosomes – at the atomic scale using SLAC’s X-ray laser.

    Hasan DeMirci, a SLAC scientist with the Stanford PULSE Institute who teamed up with graduate student Raymond Sierra on the new system, has been using the Linac Coherent Light Source (LCLS) X-ray laser – a DOE Office of Science User Facility – to zero in on the details of ribosomes at work.

    SLAC LCLS Inside

    In addition to their universal role in deciphering the genetic code to build proteins, ribosomes are also important targets for antibiotic treatments.

    It is difficult to form ribosomes into crystals so they can be studied with X-rays because they are very fragile. The new system sprang from a desire to better preserve the ribosome crystals.

    The research team did this by keeping the tiny crystals in the same solution they were grown in at temperatures approaching those in their natural environment, and by finding a more gentle way to deliver or “inject” them into a vacuum chamber, where they are struck by LCLS X-ray pulses.

    One Stream Protects Another

    The new system, dubbed coMESH, uses low-cost, off-the-shelf components to shape and protect a stream of crystallized proteins with a surrounding stream of electrically charged fluid. It was successfully tested in a 2014 experiment and featured in the Nov. 30 online edition of Nature Methods.

    “Our strategy was to come up with an injector that can handle anything, not just ribosomes,” DeMirci said. “We are addressing a definite need in the scientific community for a more universal way to deliver samples to LCLS.”

    In addition to demonstrating that the new system worked, the experiments also gave the scientists a more detailed, 3-D look at how one component of the ribosome binds to an antibiotic called paromomycin that is used to treat parasitic infections. “Now we have a more realistic picture of how this antibiotic interacts with ribosomes at temperatures close to those in their natural environment,” DeMirci said.

    The new system consists of a thin tube, about one-tenth of a millimeter in diameter, inside a slightly larger tube; the sizes can vary based on the dimensions of the crystal samples.

    A charging electrode applies low electrical current to the fluid in the larger tube, which focuses the flow to a thin filament. Both tubes end at the same point and the electrical current in the outer fluid greatly narrows both streams of fluid as they emerge from the tubes.

    Less Damage and Waste

    The system is also designed to waste fewer crystals in experiments than some other sample delivery methods. The thickness and flow rate of the inner stream can be fine-tuned by changing the applied voltage and the width of the tubing to maximize the rate at which X-ray pulses strike the crystals flowing into their path.

    DeMirci and Sierra said that based on the 3-D atomic-scale details they were able to see in the ribosome-drug complex and in samples of a photosynthetic protein complex known as photosystem-II, it doesn’t appear the voltage damaged the protein structures.

    “It’s like birds sitting on an electrical wire,” DeMirci said.

    DeMirci and Sierra said they expect the coMESH system will find wider use by other scientists conducting experiments at LCLS. “We want this to be ‘plug-and-play,'” Sierra said, “so all they have to think about during their experiment is collecting data and not troubleshooting sample delivery.”

    Citation: R.G. Sierra et al. Nature Methods, 30 November 2015 (10.1038/nmeth.3667)

    See the full article here .

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  • richardmitnick 12:24 pm on November 30, 2015 Permalink | Reply
    Tags: , Intermediate Energy X-ray (IEX) beamline, X-ray Technology   

    From APS at ANL: “Novel intermediate energy X-ray beamline opening for researchers” 

    News APS at Argonne National Laboratory

    November 20, 2015
    John Spizzirri

    Researchers working to create next-generation electronic systems and to understand the fundamental properties of magnetism and electronics to tackle grand challenges such as quantum computing have a new cutting-edge tool in their arsenal. The Advanced Photon Source (APS), a U.S. Department of Energy (DOE) Office of Science User Facility located at Argonne National Laboratory, recently unveiled a new capability: the Intermediate Energy X-ray (IEX) beamline at sector 29.

    Intermediate Energy X-ray (IEX) beamline at sector 29

    Using relatively low-energy X-rays, the IEX beamline at the APS will help illuminate electronic ordering and emergent phenomena in ordered materials to better understand the origins of distinct electronic properties. Another important feature for users is a greater ability to adjust X-ray parameters to meet experimental needs.

    Currently in commissioning phase, the IEX beamline begins its first user runs in January 2016. With its state-of-the-art electromagnetic insertion device, highly adaptive X-ray optics, and compatible endstation techniques for X-ray photoelectron spectroscopy and scattering, it opens a new era for X-ray research in sciences ranging from condensed matter physics and materials science to molecular chemistry.

    “The nice thing about having both spectroscopy and scattering techniques available here is that there are different communities addressing the same science questions with different approaches,” said Jessica McChesney, an assistant physicist and beamline scientist at the APS who is responsible for operating the beamline and starting the user program. “We hope people will actually work together and talk to each other, and drive the science that way.”

    “The idea is, we’re going to look at electronic order in materials that may one day end up in your cell phone, either as battery materials, interconnects, or in the logic,” McChesney added. “Possibly one day, when we have spintronic devices, the materials may be something we studied here.”

    Conventional electronics use current, or the flow of electrons, while spintronics relies on the flow of the electrons’ spins, not just their charges. Other materials that can be studied at the IEX beamline include high-temperature superconductors, magnetic materials, and polymer self-assemblies.

    The new beamline was built to meet the specific requirements of its two shared scientific endstations that offer users varied but complementary techniques. Using Einstein’s discovery of the photoelectric effect, the angle-resolved photoemission spectroscopy (ARPES) endstation measures the energy and angle of emitted electrons and, by using conservation of energy and momentum, can reveal what the properties of these photoemitted electrons were before they left the material. The resonant soft X-ray scattering (RSXS) uses resonance, the tuning of the X-ray beam to a specific electronic excitation, to scatter off of an ordered electronic state to determine electron density.

    “So there was this freak convergence of a lot of different things: the right combination of science, geography, and technology all at the same time.”

    How it all started

    Like the formation of a new particle in a collider, it was the research trajectory of two scientists that forged the foundations for IEX beamline. Physicists Juan Carlos Campuzano of the University of Illinois at Chicago (UIC) and Peter Abbamonte of the University of Illinois in Urbana Champaign (UIUC) both studied the complicated dynamics of high-temperature superconducting materials.

    By 1985, Campuzano had already proposed a similar, but less advanced, beamline at the Swiss Light Source, in Villingen, Switzerland, while Abbamonte, as a postdoc, had been on the team that pioneered the RSXS endstation, at Brookhaven National Laboratory in Upton, NY. Eventually, both took jobs within the University of Illinois system and were seeking an intermediate energy X-ray source in the Midwest to conduct their research.

    Given the challenges presented by these superconducting materials, they decided a better, brighter beamline was in order. They wrote a proposal that garnered funding from the National Science Foundation (NSF), which suggested they build the instrument at the newly established APS at Argonne, where Campuzano held a joint appointment.

    They reached out to APS beamline scientist George Srajer, now deputy associate laboratory director for Photon Sciences, to forge a partnership with DOE to fine-tune the concept and secure the remaining funding. A beamline was born.

    “So there was this freak convergence of a lot of different things: the right combination of science, geography, and technology all at the same time,” said Abbamonte, now professor of physics at UIUC.

    “There is no other like it in the world.”

    Making the beamline unique

    With several similar beamlines in Japan and Europe already operating, the toughest challenge in requesting funds for and building the new IEX beamline at the APS was to create something unique, noted Campuzano.

    “And it doesn’t seem like a big deal, but deciding what not to do was very important,” added Abbamonte. “You build a $15 million machine and people want to make it do everything. But that ends up costing more and the experiment that is supposed to do everything ends up doing nothing, because the more versatile an instrument is the more difficult it is to make it work. So we decided to focus and pick a few really important things.”

    A key feature unique to IEX at the APS is the beamline’s insertion device (ID), the magnetic system responsible for shaping the properties of X-rays provided to the beamline.

    According to Srajer, there is no other like it in the world.

    The ID is an electromagnetic variable polarizing undulator (EMVPU), operating in a range of 250 to 2,500 electron volts (eV). Like a fixed magnet device, users can change the energy of the X-rays and polarization at the sample. But the new ID also allows the source to run in quasi-periodic mode, which suppresses the higher harmonics in the X-ray beamline, resulting in a much higher signal-to-noise ratio that is ideal for detecting small signals in a large background.

    One advantage to developing a lower-energy beamline at a high-energy storage ring is that the intensity produced by the undulator is rather flat across the whole 250- to 2500-eV energy range. This minimizes the need for normalization, unlike at lower-energy storage rings where users must switch between the different undulator harmonics.

    To accurately deliver the X-rays produced by the ID to the endstations required the complicated design and manufacturing of X-ray optics that precisely adjust X-ray parameters, such as focus, energy resolution, and coherence fraction. Users can further tailor the X-ray beam for a given experiment by selecting between one of three gratings in the monochromator, optimizing the total intensity or flux (109–1012 photons per second) and energy resolution (5–300 milli-electron volts [meV]).

    A means to the end(stations)

    Superconductors with transition temperatures above the temperature of liquid nitrogen hold the promise of practical applications, such as the efficient production and transport of electricity. However, how those moderate- to high-temperature superconductors function is not well understood.

    When Campuzano and Abbamonte joined forces to develop the IEX beamline, their shared interest in high-temperature superconductivity became the focal point for the design of its two scientific endstations. Years of collective work in photoemission spectroscopy and X-ray scattering, respectively, would culminate in a powerful combination of tools located in one place.

    Campuzano was already using ultraviolet ARPES and was considered one of the leading experts in the field when he set his sights to building a new APS beamline.

    “We already knew that low-energy photons released electrons mostly from the surface of a material, which is not necessarily representative of what’s going on inside it,” said Campuzano. “The way to get around that was to build a beamline that had much higher-energy photons, soft X-rays.”

    The IEX ARPES experimental station, designed and built by Campuzano’s team at UIC, uses photons in a relatively high-energy range of 1000 eV to probe electrons deeper within a solid. As electrons absorb incoming photons, they are ejected from the structure. This lets users better analyze the dynamics of electron, the electronic excitations, in a sample.

    By understanding what happens to the electronic structure when macroscopic properties are changed, scientists get a better idea of how they can manipulate those properties to their advantage, whether it’s finding the best remnant magnetic fields for spintronics or determining transition temperatures in superconductors.

    Where ARPES lets researchers know how electrons propagate in a material, the RSXS endstation lets them know where those electrons are located. Designed and built by Abbamonte’s team at UIUC, resonant soft X-ray scattering is a photon-in-photon-out technique that yields real-space information about electronic ordering and information about correlation lengths.

    For Abbamonte, the technique is central to his research in determining whether heterogeneity is relevant for optimizing superconductivity.

    “Set the beam energies to the right resonance value, and when the photons hit the sample, they’ll scatter in all different directions because of this heterogeneity that we’re interested in,” he explained. “Then you use an angle-resolving detector to scan and measure the angle dependence of the light to back out what the form of that heterogeneity is.”

    In addition to the traditional microchannel plate angle-resolving detector, the RSXS endstation is equipped with a two-dimensional energy-resolving detector, another of the highly unique applications on this beamline. Considered among the most sensitive energy-resolving detectors in the world, it is based on transition-edge sensor (TES) technology pioneered by the National Institute of Standards and Technology (NIST) for cosmology applications, such as research in cosmic microwave background radiation.

    This is the first time TES technology has been used for scattering, and could prove 1000 times more sensitive to heterogeneity than any previous technology.

    The development of IEX was jointly funded by DOE and NSF.

    See the full article here .

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  • richardmitnick 1:20 pm on November 24, 2015 Permalink | Reply
    Tags: , , X-ray Technology   

    From MIT: “A new way to make X-rays” 

    MIT News

    November 23, 2015
    David L. Chandler

    MIT researchers have found a phenomenon that might lead to more compact, tunable X-ray devices made of graphene.

    By using plasmons to “wiggle” a free electron in a sheet of graphene, researchers have developed a new method for generating X-rays. In this image of one of their simulations, the color and height represent the intensity of radiation (with blue the lowest intensity and red the highest), at a moment in time just after an electron (grey sphere) moving close to the surface generates a pulse. Courtesy of the researchers

    The most widely used technology for producing X-rays – used in everything from medical and dental imaging, to testing for cracks in industrial materials – has remained essentially the same for more than a century. But based on a new analysis by researchers at MIT, that might potentially change in the next few years.

    The finding, based on a new theory backed by exact simulations, shows that a sheet of graphene – a two-dimensional form of pure carbon – could be used to generate surface waves called plasmons when the sheet is struck by photons from a laser beam. These plasmons in turn could be triggered to generate a sharp pulse of radiation, tuned to wavelengths anywhere from infrared light to X-rays.

    What’s more, the radiation produced by the system would be of a uniform wavelength and tightly aligned, similar to that from a laser beam. The team says this could potentially enable lower-dose X-ray systems in the future, making them safer. The new work is reported this week in the journal Nature Photonics, in a paper by MIT professors Marin Soljačić and John Joannopoulos and postdocs Ido Kaminer, Liang Jie Wong (now at the Singapore Institute of Manufacturing Technology), and Ognjen Ilic.

    Soljačić says that there is growing interest in finding new ways of generating sources of light, especially at scales that could be incorporated into microchips or that could reduce the size and cost of the high-intensity beams used for basic scientific and biomedical research. Of all the wavelengths of electromagnetic radiation commonly used for applications, he says, “coherent X-rays are particularly hard to create.” They also have the highest energy. The new system could, in principle, create ultraviolet light sources on a chip and table-top X-ray devices that could produce the sorts of beams that now require huge, multimillion-dollar particle accelerators.

    To make focused, high-power X-ray beams, “the usual approach is to create high-energy charged particles [using an accelerator] and ‘wiggle’ them,” says Kaminer. “The oscillations will produce X-rays. But that approach is very expensive,” and the few facilities available nationwide that can produce such beams are highly oversubscribed. “The dream of the community is to make them small and inexpensive,” he says.

    Most sources of X-rays rely on extremely high-energy electrons, which are hard to produce. But the new method gets around that, using the tightly-confined power of the wave-like plasmons that are produced when a specially patterned sheet of graphene gets hit by photons from a laser beam. These plasmons can then release their energy in a tight beam of X-rays when triggered by a pulse from a conventional electron gun similar to those found in electron microscopes.

    “The reason this is unique is that we’re substantially bypassing the problem of accelerating the electrons,” he says. “Every other approach involves accelerating the electrons. This is unique in producing X-rays from low-energy electrons.”

    In addition, the system would be unique in its tunability, able to deliver beams of single-wavelength light all the way from infrared, through visible light and ultraviolet, on into X-rays. And there are three different inputs that can be used to control the tuning of the output, Kaminer explains – the frequency of the laser beam to initiate the plasmons, the energy of the triggering electron beam, and the “doping” of the graphene sheet.

    Such beams could have applications in crystallography, the team says, which is used in many scientific fields to determine the precise atomic structure of molecules. Because of its tight, narrow beam, the system might also allow more precise pinpointing of medical and dental X-rays, thus potentially reducing the radiation dose received by a patient, they say.

    So far, the work is theoretical, based on precise simulations, but the group’s simulations in the past have tended to match quite well with experimental results, Soljačić says. “We have the ability in our field to model these phenomena very exactly.”

    They are now in the process of building a device to test the system in the lab, starting initially with producing ultraviolet sources and working up to the higher-energy X-rays. “We hope to have solid confirmation of the principles within a year, and X-rays, if that goes well, optimistically within three years,” Soljačić says.

    But as with any drastically new technology, he acknowledges, the devil is in the details, and unexpected issues could crop up. So his estimate of when a practical X-ray device could emerge from this, he says with a smile, is “from three years, to never.”

    Hrvoje Buljan, a professor of physics at the University of Zagreb in Croatia, who was not involved in this study, says the work provides “a significant new approach to produce X-ray radiation.” He adds, “The experimental implementation still needs to be performed. Based on the proposal, all of the ingredients for the proof of principle experiments are there, and such experiments will be feasible.”

    The work was supported by the U.S. Army Research Laboratory and the U.S. Army Research Office, through the Institute for Soldier Nanotechnologies, by the Science and Engineering Research Council, A*STAR, Singapore, and by the European Research Council Marie Curie IOF grant.

    See the full article here .

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  • richardmitnick 8:11 am on November 17, 2015 Permalink | Reply
    Tags: , , X-ray Technology   

    From SLAC: “X-ray Microscope Reveals ‘Solitons,’ a Special Type of Magnetic Wave” 

    SLAC Lab

    November 16, 2015

    Scientists Hope to Control its Properties to Create a New Form of Electronics

    X-rays at SSRL (purple) measure a special type of magnetic wave, called a spin wave soliton, that has the ability to hold its shape as it moves across a magnetic material. The arrows, like reorienting compass needles, represent localized changes in the material’s magnetic orientation. (SLAC National Accelerator Laboratory)

    Researchers used a powerful, custom-built X-ray microscope at the Department of Energy’s SLAC National Accelerator Laboratory to directly observe the magnetic version of a soliton, a type of wave that can travel without resistance. Scientists are exploring whether such magnetic waves can be used to carry and store information in a new, more efficient form of computer memory that requires less energy and generates less heat.

    Magnetic solitons are remarkably stable and hold their shape and strength as they travel across a magnetic material, just as tsunamis maintain their strength and form while traversing the ocean. This offers an advantage over materials used in modern electronics, which require more energy to move data due to resistance, which causes them to heat up.

    In experiments at SLAC’s Stanford Synchrotron Radiation Lightsource [SSRL] , a DOE Office of Science User Facility, researchers captured the first X-ray images of solitons and a mini-movie of solitons that were generated by hitting a magnetic material with electric current to excite rippling magnetic effects. Results from two independent experiments were published Nov. 16 in Nature Communications and Sept. 17 in Physical Review Letters.

    SLAC SSRL Tunnel

    “Magnetism has been used for navigation for thousands of years and more recently to build generators, motors and data storage devices,” said co-author Hendrik Ohldag, a scientist at SSRL. “However, magnetic elements were mostly viewed as static and uniform. To push the limits of energy efficiency in the future we need to understand better how magnetic devices behave on fast timescales at the nanoscale, which is why we are using this dedicated ultrafast X-ray microscope.”

    “This is an exciting observation because it shows that small magnetic waves – known as spin-waves – can add up to a large one in a magnet,” explains Andrew Kent, a professor of physics at New York University and a senior author for one of the studies.. “A specialized X-ray method that can focus on particular magnetic elements with very high resolution enabled this discovery and should enable many more insights into this behavior.”

    Solitons are a form of spin waves, which are disturbances that propagate in a magnetic material as a patterned, rippling response in the material’s electrons. This response is related to the spin of electrons, a fundamental particle property that can be thought of as either “up” or “down” – like the head or tail sides of a coin.

    An ultrafast camera coupled to a custom-built X-ray microscope at SLAC’s Stanford Synchrotron Radiation Lightsource allowed researchers to produce a six-frame “movie” of the soliton’s motion. It took about 12 hours to record enough X-ray data to produce the movie. (Stefano Bonetti/Stockholm University)

    In 1834 John Scott Russell, a Scottish civil engineer and shipbuilder, first described his observation of the soliton phenomenon in a boat-produced wave that held a uniform shape for over a mile as it traveled down a canal. Solitons had for decades been theorized to occur in magnets, but it took a specialized X-ray microscope like the one at SLAC to directly observe the effect.

    “We built a microscope that allowed us to look at these magnetic waves in a new way,” said Stefano Bonetti, the leading author of the study published in Nature Communications. Bonetti is a Stanford University postdoctoral fellow now at Stockholm University. “With this new microscope, we can actually see them moving,” he said. “We can see things directly.”

    An ultrafast camera coupled to the microscope allowed researchers to record six images that were compiled in sequence to form a “movie” of the soliton’s motion. It took about 12 hours to record enough X-ray data to produce the movie.

    The high resolution of the X-ray microscope revealed an anomaly in the spin-wave effects: While researchers expected the soliton to fully flip the local magnetic alignment of the material, like a compass switching from north to south, they found that the soliton caused the material’s magnetic orientation to change only slightly.

    “We would expect to see this reverse, or flip,” Bonetti said. “But it didn’t reverse – it just tilted about 25 degrees. The situation is not as simple as people thought.”

    Also, in one of the experiments researchers saw the soliton split in two: it was expected to take a spherical or circular form, but instead appeared split down the middle, as if an approaching ocean wave had split into two separate waves that were mirror images of each other. “In the simulations we were using before, we were blind to this possibility,” Bonetti said.

    More experiments are needed to understand both the tilting effect and the way that the soliton can split into a mirrored form, Bonetti said. Simulations could help researchers learn how to convert the mirrored pattern of the soliton into a more uniformly symmetrical shape, he said, or to understand how to use the split form for data applications.

    Researchers from Stanford University; SIMES, the Stanford Institute for Materials and Energy Sciences at SLAC; University of Barcelona in Spain; KTH Royal Institute of Technology in Sweden; New York University; HGST, a Western Digital Company; and Emory University in Georgia also contributed to the study. The work was supported by Everspin Technologies, the DOE Office of Science, the Knut and Alice Wallenberg Foundation, the Swedish Research Council, the Catalan Government, the National Science Foundation, the Forsk Foundation, the European Commission, the U.S. Army Research Office and Brookhaven National Laboratory.

    Citations: S. Bonetti, et al., Nature Communications, 16 November 2015 (10.1038/NCOMMS9889)

    D. Backes, et al., Physical Review Letters, 17 September 2015 (10.1103/PhysRevLett.115.127205)

    See the full article here .

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