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  • richardmitnick 1:22 pm on August 7, 2018 Permalink | Reply
    Tags: Catching the dance of antibiotics and ribosomes at room temperature, , , , RNA studies, , SLAC LCLS,   

    From SLAC National Accelerator Lab: “Catching the dance of antibiotics and ribosomes at room temperature” 

    From SLAC National Accelerator Lab

    August 6, 2018
    Ali Sundermier

    Hasan DeMirci refers to ribosomes as the 3D printers of the human body because they synthesize proteins, which are essential to life. (Dawn Harmer/SLAC National Accelerator Laboratory)

    Interns in DeMirci’s lab help grow ribosome crystals. Once grown and suspended in a special chemical solution called “mother liquor,” the crystals are imaged at the LCLS to uncover how they interact with antibiotics. (Dawn Harmer/SLAC National Accelerator Laboratory)

    Antibiotics have been a pillar of modern medicine since the 1940s. Streptomycin, which belongs to a class of antibiotics called aminoglycosides, was the first hint of light in the millennia-long search for a treatment for tuberculosis, which remains one of the deadliest infectious diseases in human history.

    Today, aminoglycosides are the most commonly prescribed antibiotics in the world due to their low cost and high effectiveness in tackling a broad spectrum of bacterial infections. But they also bring along side effects that can have lifelong impacts. Depending on the dosage and the particular antibiotic, an estimated 10 to 20 percent of patients who take aminoglycosides suffer kidney damage and 20 to 60 percent end up with irreversible hearing loss.

    Now researchers at the Department of Energy’s SLAC National Accelerator Laboratory have developed a new imaging technique to better understand the mechanisms that lead to hearing loss when aminoglycosides are introduced to the body. Using the lab’s Linac Coherent Light Source (LCLS) X-ray laser and Stanford Synchrotron Lightsource (SSRL), SLAC researchers, in collaboration with researchers at Stanford University, were able to observe interactions between the drugs and bacterial ribosomes at both extremely low and room temperatures, revealing never-before-seen details.



    They also demonstrated how small modifications to the antibiotics can lead to dramatic changes in ribosome shape that eliminate hearing loss. The research could lead to a better understanding of which parts of a drug molecule cause unwanted reactions in the body, which will enable the development of more effective antibiotics with fewer side effects.

    The group was led by research associate and senior author Hasan DeMirci. Their results were published in Nucleic Acids Research.

    3D printing proteins

    Hasan DeMirci refers to ribosomes – tiny molecular machines made up of tangles of RNA and proteins clumped together and intricately wired like ramen noodles in soup – as “the 3D printers of the human body.” The ribosomes synthesize proteins using the genetic information contained in DNA, “building our bodies from the ground up.”

    Ribosomes (shown here) are tiny molecular machines made up of tangles of RNA and proteins clumped together and intricately wired like ramen noodles in soup. (Hasan DeMirci/SLAC National Accelerator Laboratory)

    “While one subunit of the ribosome, its brain, deciphers and translates the genetic code, the other, its hands, links together amino acids to form proteins,” DeMirci said.

    Unlike viruses, which have to leech off hosts to survive, bacteria have their own ribosomes, which is where antibiotics come into play. Bacterial ribosomes are the targets of many antibiotics. So-called “cidal” antibiotics like aminoglycosides function by attacking the brains of bacterial ribosomes, causing them to make mistakes and fill the cells with protein-like garbage molecules.

    “It’s like a house with a lot of hoarded junk,” DeMirci says. “There’s no going back. From that point the bacteria just die.”

    The problem with this strategy is that human cells contain energy-producing factories called mitochondria that have their very own ribosomes – and since those ribosomes are dangerously similar to those found in bacteria, they’re also vulnerable to antibiotic attack.

    “We’re killing the bacteria, but the same drug gets into our mitochondria and destroys the ribosomes there,” DeMirci says. “Now we cannot produce those enzymes that power us. You take an antibiotic and you start losing your hearing, your kidney fails.”

    Insights into molecular machinery

    DeMirci has a strong interest in aminoglycosides because he can use them to gain insight into the molecular machinery of the ribosome.

    “What I really want to know is what those drugs can teach us about how ribosomes decipher the genetic code,” DeMirci said. “Drugs give us an opportunity to stop that process at different stages to understand how each and every step is catalyzed by the ribosome.”

    To better understand this process, he struck up a collaboration with Anthony Ricci, a biophysicist and professor of medicine at Stanford who focuses on the inner ear. In previous research, Ricci found that aminoglycosides infiltrate specialized channels to target the sensory cells essential to hearing.

    “You can think of it as a roach motel,” Ricci says. “The drugs can get in but they can’t get out. They start to build up, binding to the ribosomes and altering protein synthesis. This puts a huge metabolic load on the sensory cells, which eventually leads to their deaths.”

    A major goal of Ricci’s lab has been to design and develop new aminoglycosides that kill bacteria but cannot squeeze through the channel. In order to do this, the researchers need to understand exactly how the aminoglycosides interact with the ribosomes so they can modify parts of the drug without weakening its bacteria-killing properties.

    Defrosting interactions

    The best way to reach this understanding, researchers have found, is through a technique called X-ray crystallography. In X-ray crystallography, researchers use the patterns formed when a beam of X-rays scatters off a crystal sample to form a 3D model of how its atoms and molecules are arranged. This technique allows researchers to observe how a drug binds to a ribosome.

    While the key interactions in these processes happen at body temperature, around 37 degrees Celsius, X-ray crystallography usually has to be done at extremely low, or cryogenic, temperatures, around minus 180 degrees Celsius. This leads to gaps in the data, obscuring tiny details that could greatly inform future experiments.

    “Our bodies are warm, so the important biology is happening at body temperature,” DeMirci said, “but in crystallography everything is frozen. When you cool these processes down, you miss out on thermal fluctuations, tiny movements that could change your understanding of how the drugs and ribosomes are behaving.”

    In order to design better antibiotics, they need to get as close a view as they can of this interaction happening under physiological conditions. At the LCLS, using a technique called serial femtosecond crystallography, DeMirci is able to catch the intricate waltz of the drugs and ribosomes at room temperature. Rather than freeze the ribosome crystals, the researchers suspend them in ‘mother liquor,’ a special chemical solution they were grown in that keeps them stable, so they are “swimming happily, still wiggling and fluctuating,” he says.

    The crystals travel from a reservoir to the interaction region through a single capillary, like a garden hose. Once in the interaction region, the crystals are zapped with a beam of X-rays from the LCLS, which scatters off of them into a detector and provides the researchers with patterns they can use to build detailed 3D models of the ribosome before and after they’ve bound with the drugs. They then use these models to piece together a simulation of the interaction.

    At LCLS, crystallized ribosomes travel through a capillary into the interaction region, where they are zapped with a beam of X-rays. The X-rays scatter off the crystals into a detector, providing the researchers with patterns they can use to build detailed 3D models of interactions between the drug and ribosome. (Greg Stewart/SLAC National Accelerator Laboratory)

    Uncovering hidden wiggles

    To demonstrate their technique, the researchers imaged modified and unmodified drugs binding to ribosomes at both cryogenic and room temperatures to see if they could catch any differences. They found that the drug molecules were less flexible at cryogenic temperatures: Tiny wiggles essential to a better understanding of their interactions with ribosomes were frozen in place.

    “Despite the fact that we’ve recorded hundreds of thousands of structures of ribosomal interactions, less than a handful of new-generation drugs have been designed based on these cryogenic structures,” DeMirci said. “That’s because every small interaction makes a huge difference, even a single hydrogen bond.”

    With the images taken at room temperature, Ricci’s group identified a site where the drug could be modified without altering its effectiveness.

    “We now have some idea that when the drug binds with the ribosome, a global change occurs in the ribosome that might actually be important for the function of the antibiotic and the sensitivity of the ribosome,” Ricci said.

    Refining the jigsaw pieces

    In the next phase of experiments, DeMirci hopes to design a setup in which the antibiotics aren’t introduced until the last second before the ribosome is imaged so that they can watch as it binds to the ribosome, rather than just taking images before and after.

    Up to this point, Ricci said, his group had been doing drug synthesis with very little information or insight into how the antibiotic interacts with the ribosome.

    “What this paper and overall collaboration allow is a direct investigation of the drug-ribosome interaction,” he said. “It’s like having more defined pieces to the jigsaw puzzle. You don’t have to guess about what’s happening.”

    Developing antibiotics that can fight off drug-resistant bacteria with minimal side effects is essential because the rise of antibiotic resistant strains is currently the biggest threat to modern medicine, DeMirci said.

    “Every year more than a million people die from tuberculosis and nearly half a million are HIV positive,” he said. “People don’t usually die from HIV or cancer, they die because their immune system is suppressed and they can’t fight off bacterial infections. That’s when you need antibiotics. But what if you don’t have one that’s effective against the resistant strains? That’s exactly what’s happening right now. This research can help us make informed decisions when designing the next generation of drugs.”

    The research team included scientists from LCLS; SSRL; SLAC’s Biosciences Division; the Stanford PULSE Institute; and the Stanford School of Medicine.

    See the full article here .

    Please help promote STEM in your local schools.

    Stem Education Coalition

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

  • richardmitnick 1:56 pm on May 16, 2018 Permalink | Reply
    Tags: , , SLAC LCLS, Water is more complicated than it seems, X-ray Laser Reveals Ultrafast Dance of Liquid Water,   

    From SLAC Lab: “X-ray Laser Reveals Ultrafast Dance of Liquid Water” 

    From SLAC Lab

    May 16, 2018
    Water is more complicated than it seems. Now a study led by researchers at Stockholm University has probed the movements of its molecules on a timescale of millionths of a billionth of a second.

    An illustration shows the “blurring” effect caused by water molecules moving during imaging with the X-ray laser. As the laser pulse gets longer, from left to right, the diffraction pattern produced by X-rays hitting the molecules changes (bottom row), reflecting the motion of the water molecules (top row). Experiments at SLAC’s LCLS X-ray laser were able to provide the timescale of the water dynamics by using pulses less than 100 millionths of a billionths of a second long. (Fivos Perakis/Stockholm University)

    Water’s lack of color, taste and smell make it seem simple – and on a molecular level, it is. However, when many water molecules come together they form a highly complex network of hydrogen bonds. This network is believed to be responsible for many of the peculiar properties of liquid water, but its behavior is not yet fully understood.

    Now researchers have probed the movements of molecules in liquid water that occur in less than 100 millionths of a billionth of a second, or femtoseconds. An international team led by researchers at Stockholm University carried out the experiments with the Linac Coherent Light Source (LCLS) X-ray laser at the Department of Energy’s SLAC National Accelerator Laboratory. They published their report this week in Nature Communications.


    The study is the first to “photograph” water molecules on this timescale with a technique called ultrafast X-ray photon correlation spectroscopy, which bounces X-rays pulses off the molecules to produce a series of diffraction patterns. Varying the duration of the X-ray pulses essentially varies the exposure time, and any motion of the water molecules during an exposure will blur the resulting picture. By analyzing the blurring produced by different exposure times, the scientists were able to extract information about the molecular motion.

    On this timescale, it was assumed that water molecules move randomly due to heat, behaving more like a gas than a liquid. However, the experiments indicate that the network of hydrogen bonds plays a role even on this ultrafast timescale, coordinating the motions of water molecules in an intricate dance, which becomes even more pronounced when water is “supercooled” below its normal freezing point.

    “The key to understanding water on a molecular level is watching the changes of the hydrogen-bond network, which can play a major role in biological activity and life as we know it,” says Anders Nilsson, a professor at Stockholm University and former professor at SLAC.

    Adds Stockholm University researcher Fivos Perakis, “It is a brand-new capability to be able to use X-ray lasers to see the motion of molecules in real time. This can open up a whole new field of investigations on these timescales, combined with the unique structural sensitivity of X-rays.”

    The experimental results were reproduced by computer simulations, which indicate that the coordinated dance of water molecules is due to the formation of transient tetrahedral structures.

    “I have studied the dynamics of liquid and supercooled water for a long time using computer simulations, and it is very exciting to finally be able to directly compare with experiments,” says Gaia Camisasca, a postdoctoral researcher at Stockholm University who performed the computer simulations for this study. “I look forward to seeing the future results that can come out from this technique, which can help improve the current water computer models.”

    LCLS is a DOE Office of Science user facility. SLAC’s Thomas J. Lane, Sanghoon Song, Takahiro Sato, Marcin Sikorski, Andre Eilert, Trevor McQueen, Hirohito Ogasawara, Dennis Nordlund, Jake Koralek, Silke Nelson, Philip Hart, Roberto Alonso-Mori, Yiping Feng, Diling Zhu and Aymeric Robert contributed to this study, along with researchers from KTH Royal Institute of Technology in Stockholm and DESY in Hamburg.

    See the full article here .

    Please help promote STEM in your local schools.


    Stem Education Coalition

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

  • richardmitnick 4:41 pm on May 10, 2018 Permalink | Reply
    Tags: , , , SLAC LCLS   

    From SLAC Labs: “SLAC’s X-ray Laser Opens New View on Proteins Related to Alzheimer’s Disease” 

    From SLAC Labs

    May 9, 2018
    Angela Anderson

    Experiments at SLAC’s Linac Coherent Light Source show the promise of using X-ray free-electron lasers to better understand the structure and function of amyloid fibrils, tiny protein strands that play a role in diseases like Alzheimer’s and Parkinson’s. In this illustration, X-ray light penetrates a sample of amyloid fibrils placed on the honeycomb-like carbon lattice of graphene, a new method that produces cleaner data because the thin graphene virtually disappears from view. (Greg Stewart/SLAC)


    To learn more about diseases such as Alzheimer’s and Parkinson’s, scientists have zeroed in on invisibly small protein filaments that bunch up to form fibrous clusters called amyloids in the brain: How do these fibrils form and how do they lead to disease?

    Until now, the best tools for studying them have generated limited views, largely because the fibrils strands are so complex and tiny, just a few nanometers thick.

    Now an international research team has come up with a new method with potential for revealing the structure of individual amyloid fibrils with powerful beams of X-ray laser light. They describe it in a report published today in Nature Communications.

    In experiments conducted at the Linac Coherent Light Source (LCLS) at the Department of Energy’s SLAC National Accelerator Laboratory, the scientists placed up to 50 fibrils at a time on a layer of graphene, whose carbon atoms are arranged in a honeycomb-like pattern, and hit them with bursts of X-ray laser light. The graphene, it turned out, was almost transparent to the X-rays, and this allowed them to probe the structures of the delicate fibrils without picking up significant extraneous signals from the graphene layer in individual snapshots.

    While the team did not uncover the complete fibril structure, they said the innovative method they developed at LCLS opens up a promising path for amyloid studies using X-ray free-electron lasers, or XFELs, such as LCLS.

    Carolin Seuring, a scientist at the Center for Free-Electron Laser Science (CFEL) at DESY in Germany and principal author of the paper, said the results suggest this technique could even be used to determine the structure of individual fibrils.

    “There is a common consensus that it is not the amyloid fiber alone, but rather the protofilaments composing the fiber and the process of fibril formation that are toxic to the cell,” she said. “XFEL-based experiments have the potential to overcome the challenges we’ve faced in better understanding amyloid fibrils.”

    The Problem with Amyloids

    While amyloid fibrils are believed to play a major role in the development of neurodegenerative diseases, scientists have recently discovered that they also have other functions, Seuring said.

    “The ‘feel-good hormone’ endorphin, for example, can form amyloid fibrils in the pituitary gland,” she said. “They dissolve into individual molecules when the acidity of their surroundings changes, after which these molecules can fullfil their purpose in the body. Other amyloid proteins, such as those found in post-mortem brains of patients suffering from Alzheimer’s, accumulate as amyloid fibrils in the brain, and cannot be broken down and therefore impair brain function in the long term.”

    Accurate information about the structure of amyloid fibrils can inform scientists about their function, she added.

    “Our aim is to understand the role of the formation and structure of amyloid fibrils in the body and in the development of neurodegenerative diseases,” Seuring said.

    One barrier to studying amyloid fibrils is that they cannot be grown as crystals, which are the conventional targets for structural studies using X-rays. And because individual amyloid fibrils are so small, they don’t produce a measurable signal when exposed to X-rays. Scientists typically line up millions of fibrils parallel to each other to amplify the signal, but information about their individual differences is lost in the process.

    “A major part of our understanding about amyloid fibrils is derived from nuclear magnetic resonance and cryo-electron microscopy data,” Seuring said. But these methods are also of limited value for seeing individual differences between amyloid fibrils or observing their formation. “The structural analysis of amyloids is complex and examining them using existing methods is hampered by differences between the fibrils within a single sample,’” she said “Being able to look at the individual components of the sample would make it possible to determine the 3D structure of one type of fibril at a time.”

    The New Approach

    Earlier attempts to study fibrils at X-ray lasers delivered them into the path of the beam in jets of fluid. Switching to a solid graphene carrier gave the team two advantages, according to CFEL’s Henry Chapman, a professor at the University of Hamburg and a lead scientist at DESY.

    Because graphene is just one layer of atoms thick, it leaves hardly a trace in the diffraction patterns formed by X-rays scattering off the fibrils, which are used to determine their structures, he said. And the regular structure of the graphene encourages the fibrils to all line up in the same direction.

    This allows diffraction patterns to be obtained from fewer than 50 amyloid fibrils. Based on the results, the team hopes to eventually get patterns from single fibrils. To get to that goal, new methods of exposing a single fibril to the XFEL beam will need to be developed, according to Seuring: “With enough snapshots, a full 3D data set of a single fibril should be possible.”

    The exceptionally bright and narrowly focused beam at LCLS’s Coherent X-ray Imaging instrument was also key to the team’s success in taking data from such a small number of fibrils, according to SLAC staff scientist Mengning Liang.

    Intense X-ray pulses at XFELs limit the exposure of delicate samples to damaging X-rays. In this study, the fibrils were exposed for only a few femtoseconds, or millionths of a billionth of a second. Before the molecules are destroyed, information about their structure can be read by detectors.

    “Fibrils are a third category of samples that can be studied with the ‘diffract before destroy’ method at XFELs, in addition to single particles and crystals,” Liang said. “In some regards, fibrils fit between the other two: they have regular, recurring variations in structure like crystals, but without the rigid crystal structure.”

    The scientists tested their method on samples of well-studied tobacco mosaic virus filaments and smaller amyloid fibrils, some of which are associated with certain types of cancer. The tests produced structural data with a high degree of accuracy: The resolution in the diffraction images was almost on the scale of a single atom.

    “It is amazing that we are essentially carrying out the same experiments as Rosalind Franklin did on DNA in 1952, which led to the discovery of the double helix, but now we are reaching the level of single molecules,” says Chapman.

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

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

  • richardmitnick 3:42 pm on May 5, 2018 Permalink | Reply
    Tags: , , , , , Freeze-framing nanosecond movements of nanoparticles, , SLAC LCLS,   

    From DESY: “Freeze-framing nanosecond movements of nanoparticles” 

    From DESY

    No writer credit

    New method allows to monitor fast movements at hard X-ray lasers.

    A team of scientists from DESY, the Advanced Photon Source APS and National Accelerator Laboratory SLAC, both in the USA, have developed and integrated a new method for monitoring ultrafast movements of nanoscopic systems.

    Argonne APS


    With the light of the X-ray laser LCLS at the research center SLAC in California, they took images of the movements of nanoparticles taking only the billionth of a second (0,000 000 001 s).


    In their experiments now published in the journal Nature Communications they overcame the slowness of present-day two-dimensional X-ray detectors by splitting individual laser flashes of LCLS, delaying one half of it by a nanosecond and recording a single picture of the nanoparticle with these pairs of X-ray pulses. The tunable light splitter for hard X-rays which the scientists developed for these experiments enables this new technique to monitor movements of nanometer size fluctuations down to femtoseconds and at atomic resolution. For comparison: modern synchrotron radiation light sources like PETRA III at DESY can typically measure movements on millisecond timescales.

    DESY Petra III interior

    Scheme of the experiment: An autocorrelator developed at DESY splits the ultrashort X-ray laser pulses into two equal intensity pulses which arrive with a tunable delay at the sample. The speckle pattern of the sample is collected in a single exposure of the 2-D detector (picture: W. Roseker/DESY).

    he intense light flashes of X-ray lasers are coherent which means that the waves of the monochromatic laser light propagate in phase to each other. Diffracting coherent light by a sample usually results in a so-called speckle diffraction pattern showing apparently randomly ordered light spots. However, this speckle is also a map of the sample arrangement, and movements of the sample constituents result in a different speckle pattern.

    For their experiments the researchers developed a special optical setup – a so-called optical autocorrelator – capable of splitting 100 femtosecond long XFEL pulses into two sub-pulses, deviate them into separated detours and recombining their paths with a tunable time delay between zero and a few nanoseconds. These pairs of XFEL pulses hit the sample with the tuned delay, spotting the sample´s structure at the two exposure times. The sum of both speckle pictures was recorded by a two-dimensional photon detector within one exposure time. The trick: If the constituents of the sample move during the two illuminations, the speckle pattern changes, resulting in an integrated picture of less contrast at the detector. The contrast is a measure on how strong the photon intensity varies on the detector. However, the intensity and especially the intensity difference measured at the detector are very weak. In their experiments the researchers had to work with only some 1000 detected photons on the one-million-pixels size detector.

    “Such type of experiments has been done for much slower movements of nanoparticles at storage ring light sources,” explains first author Wojciech Roseker from DESY. “But now, the high coherence and intensity of the X-ray laser light at XFELs open up the opportunity to get pictures bright enough to provide reasonable information about quick movements in the nanosecond to femtosecond regime.”

    In their work the researchers around Roseker used a suspension of two nanometers size gold particles undergoing Brownian motion. The experiment was in perfect agreement with the theoretical predictions thus proving not only the performance of the autocorrelator setup but also the validity of the data analysis procedure, demonstrating the first successful experiment of this kind. One of the challenges in this experiment, carried out at the XCS experimental station at LCLS, was to autocorrelate thousands of extremely weak double shot 2D images which was achieved with the help of a newly developed maximum likelihood analysis technique.

    “This experiment paves the way to dynamics experiments of materials on atomic length and femtosecond-nanosecond timescales,” explains Gerhard Grübel, head of the DESY FS-CXS group. “Split-pulse X-ray Photon Correlation Spectroscopy (XPCS) can potentially track atomic scale fluctuations in liquid metals, multi-scale dynamics in water, heterogeneous dynamics about the glass transition, and atomic scale surface fluctuations.” Additionally, time-domain XPCS at FEL sources, especially at the European XFEL, is well suited for studying fluctuations in non-equilibrium processes that go beyond time-averaged structural descriptions.

    DESY European XFEL

    European XFEL

    This will allow the elucidation of dynamics of ultrafast magnetization processes and can address open questions concerning photo-induced phonon dynamics and phase transitions.

    See the full article here .

    Please help promote STEM in your local schools.

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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 7:45 pm on April 26, 2018 Permalink | Reply
    Tags: , DESY FLASH free-electron laser at Germany’s Deutsches Elektronen-Synchrotron, Flowing sheets of liquid just 100 water molecules thick that persist for days in a vacuum, Images of samples suspended in water with two types of light – infrared and ‘soft’, , , Researchers used X-ray pulses to heat the liquid sheets to thousands of degrees to simulate the extremely warm dense form of water present in giant planets like Jupiter, SLAC LCLS, The nozzle is a tiny glass chip with three microscopic channels, There are many mysteries in those big planets and they’re important for understanding the evolution of our planetary system as well as others, Thin free-flowing sheets 100 times thinner than any produced before, X-Ray Scientists Create Tiny Super-Thin Sheets of Flowing Water that Shimmer Like Soap Bubbles   

    From SLAC: “X-Ray Scientists Create Tiny, Super-Thin Sheets of Flowing Water that Shimmer Like Soap Bubbles” 

    SLAC Lab

    April 26, 2018
    Glennda Chui

    The liquid sheets – less than 100 water molecules thick – will let researchers probe chemical, physical and biological processes, and even the nature of water itself, in a way they could never do before.

    This tiny glass chip creates super-thin sheets of flowing liquid for X-ray experiments at SLAC’s X-ray laser, LCLS. A stream of liquid flowing through the middle channel is shaped by flows of gas coming in from the channels on either side. (Dawn Harmer/SLAC National Accelerator Laboratory.)

    Water is an essential ingredient for life as we know it, making up more than half of the adult human body and up to 90 percent of some other living things. But scientists trying to examine tiny biological samples with certain wavelengths of light haven’t been able to observe them in their natural, watery environments because the water absorbs too much of the light.

    Now there’s a way around that problem: A team led by scientists at the Department of Energy’s SLAC National Accelerator Laboratory turned tiny liquid jets that carry samples into the path of an X-ray beam into thin, free-flowing sheets, 100 times thinner than any produced before. They’re so thin that X-rays pass through them unhindered, so images of the samples they carry come out clear.

    The new method opens new windows on critical processes in chemistry, physics and biology, including the nature of water itself, the researchers said in an April 10 report in Nature Communications.

    The method was developed at SLAC’s X-ray free-electron laser, the Linac Coherent Light Source (LCLS), but they said it can also work in experiments with synchrotron light sources, tabletop lasers and electron beams.


    A series of movies shows how increasing flows of gas that shape a stream of liquid affects the formation of liquid sheets and their soap-bubble-like sheen.

    “This opens up possibilities in a lot of fields,” said SLAC staff scientist Jake Koralek, who led the research with Daniel DePonte, leader of the LCLS Sample Environment Department.

    “Until now, we haven’t been able to make images of samples suspended in water with two types of light – infrared and ‘soft’, lower-energy X-rays – that are important for studying basic processes in physics, chemistry and biology, including the physics of water,” Koralek said.

    “The new nozzle we developed, which can create flowing sheets of liquid just 100 water molecules thick that persist for days in a vacuum, solves that problem. The sheets can even be used to image samples with electron beams that resolve even smaller details.”

    Shaping Liquid with Gas

    The nozzle is a tiny glass chip with three microscopic channels. A stream of liquid flows through the middle channel, shaped by flows of gas coming in from the channels on either side. This particular nozzle was made with photolithography, a technique used to manufacture computer chips, but it could also be crafted with 3-D printing, the researchers noted.

    As the scientists turn up the speed of the gas flow, the liquid stream spreads into a series of sheets whose width and thickness can be precisely controlled. The sheet closest to the nozzle is the widest and thinnest; the farther they get from the nozzle, the narrower and thicker the sheets become until they finally merge into a cylindrical stream.

    These images show the formation of tiny sheets of liquid shaped by jets of gas from a nozzle developed at SLAC. Top: As the gas flow increases, the liquid sheets become bigger. Bottom: The nozzle produces a series of liquid sheets; the one closest to the nozzle is the widest and thinnest. Each sheet is perpendicular to the previous one, so we are seeing the second and fourth sheets from the side.

    The sheets shimmer like soap bubbles in a variety of colors, the result of light reflecting off both the front and back surfaces of the sheet. And just as the contour lines on a topographic map mark differences in elevation, the hue and spacing of a sheet’s ever-changing bands of color indicate how thick it is and how much the thickness changes from one point to another.

    “It’s a very flexible and reliable design for creating both ultrathin and slightly thicker liquid sheets, which can be desirable for some applications” said Linda Young, a distinguished fellow at DOE’s Argonne National Laboratory and professor at the University of Chicago who was not involved in the study.

    She said she will be using the nozzle to make slightly thicker sheets of water for an LCLS study of how water molecules behave after one of their electrons has been ripped away. These ionized water molecules persist for only a few hundred femtoseconds, or millions of a billionth of a second, and “the X-rays provide a completely new and clean wayto monitor their electronic response in their natural environment, so that’s why we’re excited about it,” Young said.

    A New Way to Study Extreme Forms of Water

    The liquid sheets have already been used in experiments that explore the properties of water in extreme environments like those on giant planets, said co-author Siegfried Glenzer, a SLAC professor and head of the lab’s High Energy Density Science Division.

    Those experiments were performed with the FLASH free-electron laser at Germany’s Deutsches Elektronen-Synchrotron (DESY).

    DESY FLASH free-electron laser at Germany’s Deutsches Elektronen-Synchrotron.

    Researchers used X-ray pulses to heat the liquid sheets to thousands of degrees to simulate the extremely warm, dense form of water present in giant planets like Jupiter. Then they measured the reflectivity and conductivity of the super-hot water with optical laser pulses in the instant before the water vaporized. These measurements could only be made on a flat sheet of water.

    “There are many mysteries in those big planets and they’re important for understanding the evolution of our planetary system as well as others,” Glenzer said. “This is a beautiful tool for studying water itself, and in the future we will also study other materials that we can mix into it.”

    A SLAC research team at the LCLS experimental station where they carried out experiments with the sheet-forming nozzle this week. From left: Paper co-authors Zhijiang Chen, Stefan Moeller, Siegfried Glenzer, Jake Koralek and Chandra Curry and area manager Bob Sublett of the LCLS Sample Environment Department. (Dawn Harmer/SLAC National Accelerator Laboratory)

    The team measured the thickness of the sheets with a beam of infrared light at the Advanced Light Source at the DOE’s Lawrence Berkeley National Laboratory, and also demonstrated that the sheets could be used for infrared spectroscopy, where light absorbed by a material reveals its chemical makeup.


    LCLS and the Advanced Light Source are DOE Office of Science user facilities. In addition to researchers from SLAC, Berkeley Lab and DESY, scientists from the ELI Beamlines Institute of Physics of the Czech Academy of Sciences, Dartmouth College, the University of Alberta in Canada and the European X-ray Free-Electron Laser Facility (European XFEL) in Germany contributed to this work. Major funding came from the DOE Office of Science and the National Institutes of Health, National Institute of General Medical Sciences.

    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 8:56 am on April 16, 2018 Permalink | Reply
    Tags: , Attosecond X-ray science, , , , SLAC LCLS, , XLEAP X-ray Laser-Enhanced Attosecond Pulse generation   

    From European XFEL: “Entering the realm of attosecond X-ray science” 

    XFEL bloc

    European XFEL

    European XFEL


    New methods for producing and characterizing attosecond X-ray pulses.

    Ultrashort X-ray pulses (pink) at the Linac Coherent Light Source ionize neon gas at the center of a ring of detectors. An infrared laser (orange) sweeps the outgoing electrons (blue) across the detectors with circularly polarized light. Scientists read data from the detectors to learn about the time and energy structure of the pulses, information they will need for future experiments. Copyright: Terry Anderson / SLAC National Accelerator Laboratory.


    European XFEL produces unfathomably fast X-ray pulses that are already being used by scientists to explore the unchartered territory of the atomic and molecular cosmos. Intense X-ray pulses lasting only a few femtoseconds – or a few millionths of a billionth of a second – are being used to reveal insights into the dynamics of chemical reactions and the atomic structures of biological molecules such as proteins and viruses. And while there is much more to discover in this femtosecond time range, scientists are already looking to take European XFEL to the next time dimension, exploring reactions and dynamics that occur on an even briefer time scale – the attosecond time regime.

    If you leave the shutter of your camera open for too long while photographing a race, the resulting pictures will only be a smear of colour. To capture clear and sharp images of the athletes’ movements you need to make sure the shutter is only open for the shortest time; in fact the best shutter speed to capture a clear snapshot of the runners’ legs frozen in action would be faster than the time the runner needed to move their legs. Good light conditions help too to make sure your photos are sharp and in focus. And so it is as scientists attempt to take snapshots of some of nature’s fastest processes such as the movements of electrons within atoms and molecules. To capture snapshots of these movements in action we need pulses of intense X-rays that reflect the timescale on which these reactions occur – and these reactions can occur even down to the attosecond timescale.


    Attosecond X-ray science is expected to allow scientists to delve even deeper into ultrafast chemical and molecular processes and the tiniest details of our world than already possible. But how to produce X-ray flashes that are even shorter than the already ultrafast femtosecond flashes? One of the methods currently being explored by scientists is ‘X-ray Laser-Enhanced Attosecond Pulse generation’ (XLEAP). The method, being developed at the SLAC National Accelerator Laboratory in the USA, is expected to be possible with only moderate modifications to the layout of existing FEL facilities. If successful, the usually chaotic time and energy structure of XFEL (X-ray Free-Electron Laser) pulses, consisting of a sequence of many intensity spikes based on the so-called SASE (Self-Amplification by Spontaneous Emission) principle, can be reliably narrowed down to one single, coherent intensity spike of only few hundreds of attoseconds. In a recent review article in the Journal of Optics, European XFEL scientists propose how the XLEAP method might be implemented at the SASE 3 branch of the facility, eventually providing attosecond pulses for experiments.

    European XFEL scientist Markus Ilchen working on the original angle resolving time-of-flight spectrometer at PETRA III, DESY. Copyright: European XFEL

    DESY Petra III

    DESY Petra III interior

    Angular Streaking diagnostics

    While the free-electron laser technology is almost ready to provide attosecond pulses, another hurdle is to actually prove and characterize their existence. Experiments to date at XFEL facilities have often relied on indirect measurements and simulations of X-ray pulses to calibrate results. However, only with detailed information from direct measurements of the exact time and energy structure of each X-ray pulse, can X-ray science enter a new era of time resolved and coherence dependent experiments.

    With this in mind, a novel experimental approach was conceived as part of an international collaboration including scientists from SLAC, Deutsches Elektronen-Synchrotron (DESY), European XFEL, the Technical University of Munich, University of Kassel, University of Gothenburg, University of Bern, University of Colorado, University of the Basque Country in Spain, and Lomonosov Moscow State University in Russia. In a study published in the journal Nature Photonics, the international groupdemonstrated the capability of a so-called ‘angular streaking’ method to characterize the time and energy structure of X-ray spikes. The scientists used the shortest pulses available at the Linac Coherent Light Source (LCLS) at SLAC in the USA for their experiment. Using the new angular streaking diagnostic method, millions of pulses, each of a few femtoseconds in length, were successfully captured and analyzed. “Being able to get the precise information about the energy spectrum, as well as the time and intensity structure of every single X-ray pulse is unprecedented” explains Markus Ilchen from the Small Quantum Systems group at European XFEL, one of the principal investigators of this work. “This is really one of the holy grails of FEL diagnostics” he adds enthusiastically.

    The new angular streaking technique works by using the rotating electrical field of intense circularly polarized optical laser pulses to extract the time and energy structure of the XFEL pulses. Interaction with the XFEL pulse causes atoms to eject electrons which are then strongly kicked around by the surrounding laser field. Information about the electron’s exact time of birth is not only imprinted in the energy of the electron but also in the ejecting angle. This all provides a ‘clock’ by which to sort the resulting experimental data. Pulses generated by the SASE process, as implemented at European XFEL and SLAC, are intrinsically variable and chaotic. Some of the recorded pulses during the experiment at SLAC were, therefore, already single spikes in the attosecond regime which then were fully characterized for their time-energy structure.

    Angle resolving time-of-flight spectrometer

    An illustration of the ring-shaped array of 16 individual detectors arranged in a circle like numbers on the face of a clock. An X-ray laser pulse hits a target at the center and sets free electrons that are swept around the detectors. The location, where the electrons reach the “clock,” reveals details such as the variation of the X-ray energy and intensity as a function of time within the ultrashort pulse itself. Copyright: Frank Scholz & Jens Buck, DESY.

    he underlying spectroscopic method is based on an angle resolving time-of-flight spectrometer setup consisting of 16 individual spectrometers aligned in a plane perpendicular to the XFEL beam. These are used to characterize the X-ray beam by correlating the electrons’ energies and their angle dependent intensities. An adapted version of the spectrometer setup originally developed at the PETRA III storage ring at DESY, was built in the diagnostics group of European XFEL and provided for the beamtime at SLAC.

    At European XFEL the diagnostic goal is that scientists will eventually be able to use the method to extract all information online during their experiments and correlate and adjust their data analysis accordingly. Furthermore, although the method has so far only been designed and tested for soft X-rays, Ilchen and his colleagues are optimistic that it could also be used for experiments using hard X-rays. “By reducing the wavelength of the optical laser, we could even resolve the few hundreds of attosecond broad spikes of the hard X-ray pulses here at the SASE 1 branch of European XFEL” Ilchen says.

    Time-resolved experiments

    During the experiment at SLAC the scientists also showed that it was even possible to use the acquired data to select pulses with exactly two intensity spikes with a variable time delay between them. This demonstrates the capability of FELs to enable time-resolved X-ray measurements attosecond to few femtosecond delay. “By determining the time duration and distance of those two spikes, we can sort our data for matching pulse properties and use them to understand how certain reactions and processes have progressed on an attosecond timescale” explains Ilchen. “Since our method gives us precise information about the pulse structure, we will be able to reliably reconstruct what is happening in our samples by producing a sequence of snapshots, so that much like a series of photographs pasted together makes a moving film sequence, we can make ‘movies’ of the reactions” he adds.

    From principle to proof

    Due to the limited pulse repetition rate currently available at most XFELs, however, moving from a proof-of-principle experiment to actually using specifically structured pulses for so-called pump-probe experiments requires a large leap of the imagination. European XFEL, however, already provides more pulses per second than other similar facilities, and will eventually provide 27,000 pulses per second, making the dream of attosecond time-resolved experiment a real possibility. “Although, currently, no machine in the world can provide attosecond X-ray pulses with variable time delay below the femtosecond regime in a controlled fashion,” says Ilchen, “the technologies available at European XFEL in combination with our method, could enable us to produce so much data that we can pick the pulse structures of interest and sort the rest out while still getting enough statistics for new scientific perspectives.”

    Further reading:

    News from SLAC – “Tick, Tock on the ‘Attoclock’: Tracking X-Ray Laser Pulses at Record Speeds

    Overview of options for generating high-brightness attosecond x-ray pulses at free-electron lasers and applications at the European XFEL
    S. Serkez et al., Journal of Optics, 9 Jan 2018 doi:10.1088/2040-8986/aa9f4f

    See the full article here .

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    XFEL Campus

    XFEL Tunnel

    XFEL Gun

    The Hamburg area will soon boast a research facility of superlatives: The European XFEL will generate ultrashort X-ray flashes—27 000 times per second and with a brilliance that is a billion times higher than that of the best conventional X-ray radiation sources.

    The outstanding characteristics of the facility are unique worldwide. Started in 2017, it will open up completely new research opportunities for scientists and industrial users.

  • richardmitnick 3:52 pm on April 9, 2018 Permalink | Reply
    Tags: , , , SLAC LCLS, , Superconducting electron gun   

    From SLAC: “SLAC Produces First Electron Beam with Superconducting Electron Gun” 

    SLAC Lab

    Image of the first electron beam (bright colors) produced with a superconducting electron gun at SLAC and analyzed with an energy spectrometer. The beam energy was more than a million electronvolts. (SLAC National Accelerator Laboratory)

    April 9, 2018
    Manuel Gnida

    Making a high-quality beam of high-energy electrons starts with an electron gun: It knocks electrons out of atoms with a laser beam so they can be accelerated to nearly the speed of light for experiments that explore nature’s fastest atomic processes.

    Now accelerator scientists at the Department of Energy’s SLAC National Accelerator Laboratory are testing a new type of electron gun for a future generation of instruments that take snapshots of the atomic world in never-before-seen quality and detail, with applications in chemistry, biology, energy and materials science.

    Unlike other electron sources at SLAC, the new one is superconducting: When chilled to extremely low temperatures, some of its key components conduct electricity with nearly 100 percent efficiency. This allows it to produce superior, almost continuous electron beams that will be needed for future high-energy X-ray lasers and ultrafast electron microscopes. The new superconducting electron gun recently produced its first beam of electrons at SLAC.

    “This is an important milestone,” says Xijie Wang, who leads the project. “The use of superconducting accelerator technology represents the beginning of a new era at the lab that will create unforeseen research opportunities, and will keep us at the forefront of science for decades to come.”

    SLAC’s accelerator scientists are testing a superconducting electron gun (inside the large vessel at center), a new type of electron source that could be used in next-generation X-ray lasers and ultrafast electron microscopes. (Dawn Harmer/SLAC National Accelerator Laboratory)

    A Superior Electron Source

    At SLAC and other labs, beams of high-energy electrons are used as tools to precisely examine the atomic fabric of our world and to look at atomic-scale processes that occur within femtoseconds, or millionths of a billionth of a second. The beams are used directly, in instruments for ultrafast electron diffraction and microscopy (UED/UEM), or indirectly in X-ray lasers like SLAC’s Linac Coherent Light Source (LCLS), where the energy of the electron beam is converted into powerful X-ray light.


    In both approaches, the electrons are produced with an electron gun. It consists of a photocathode, where electrons are released when a metal is hit by a laser pulse; a hollow metal cavity, which accelerates the electrons with a radiofrequency field; and a magnetic lens that bundles the electrons into a tight beam.

    Conventional electron guns use cavities made of normal-conducting metals like copper. But the new device’s cavity is made of niobium, which becomes superconducting at temperatures close to absolute zero. Several groups around the world are actively pursuing the superconducting technology for next-generation particle accelerators and X-ray lasers.

    “Superconducting electron guns have the potential to outperform current guns,” says accelerator physicist Theodore Vecchione, coordinator of the SLAC project. “For instance, while the electron gun that’s being installed as part of the future LCLS-II will generate electron pulses at an extremely high repetition rate, the superconducting gun should be able to produce similar pulses at four times higher beam energy.

    SLAC/LCLS II projected view

    It should also be able to achieve twice the beam acceleration over a given distance, producing a tighter beam of electrons with extraordinary average brightness.”

    SLAC schematic of superconducting electron gun

    LCLS-II will already use superconducting cryomodules to bring electrons up to speed, which will allow the X-ray laser to fire 8,000 times faster after the upgrade. A superconducting electron gun could be ready for a future high-energy upgrade that would further enhance its scientific potential.

    “In addition to advancing X-ray science, the superconducting technology could also turn into an electron source for the UED/UEM techniques we’re developing,” says SLAC accelerator physicist Renkai Li. “It would further improve the quality of atomic-level images and movies we’re able to capture now.”

    A Top R&D Priority

    The SLAC team is testing a superconducting gun that was originally built for a project at the University of Wisconsin, Madison. About two years ago, the DOE relocated the gun to SLAC, asking the lab to recommission it for R&D work in the field of future electron sources.

    “There is a lot of excitement at the lab and the DOE about the opportunity to develop the superconducting technology into something that will drive future applications that require powerful electron beams,” says Bruce Dunham, associate lab director for SLAC’s Accelerator Directorate. “It’s very exciting to see the new gun produce its first electron beam, as it represents the very first step toward that future.”

    Over the past few months, the team installed the gun at SLAC’s Next Linear Collider Test Accelerator (NLCTA) facility and built an experimental setup with diagnostics needed to analyze the generated electron beam. “This successful effort involved many different groups around the lab, including people working on lasers, metrology, vacuum and controls,” says Keith Jobe, the NLCTA facility manager. “We’re also grateful to Bob Legg and other members of the original Wisconsin team, who were very helpful in getting this effort underway here.”

    Now that the team has demonstrated the superconducting gun is working and capable of producing electron beams with energies above a million electronvolts, they are planning their next steps. They first want to make a number of upgrades to improve the gun’s performance, including an overhaul of its refrigeration system. Then, they will be ready to push the technology to higher beam energies that could pave the way for future applications.

    The project is funded by the DOE Office of Science. LCLS is a DOE Office of Science user facility.

    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 4:14 pm on April 4, 2018 Permalink | Reply
    Tags: , , SLAC LCLS, , Tick Tock on the ‘Attoclock:’ Tracking X-Ray Laser Pulses at Record Speeds,   

    From SLAC: “Tick, Tock on the ‘Attoclock:’ Tracking X-Ray Laser Pulses at Record Speeds” 

    SLAC Lab

    April 4, 2018
    Amanda Solliday
    Angela Anderson

    In this illustration, ultrashort X-ray pulses (pink) at the Linac Coherent Light Source ionize neon gas at the center of a ring of detectors.


    An infrared laser (orange) sweeps the outgoing electrons (blue) across the detectors with circularly polarized light. Scientists read data from the detectors to learn about the time and energy structure of the pulses, information they will need for future experiments. (Terry Anderson / SLAC National Accelerator Laboratory)

    When it comes to making molecular movies, producing the world’s fastest X-ray pulses is only half the battle. A new technique reveals details about the timing and energy of pulses that are less than a millionth of a billionth of a second long, which can be used to probe nature’s processes at this amazingly fast attosecond timescale.

    To catch chemistry in action, scientists at the Department of Energy’s SLAC National Accelerator Laboratory use the shortest possible flashes of X-ray light to create “molecular movies” that capture the motions of atoms in chemical reactions and reveal new details about the most fundamental processes in nature.

    Future experiments at the Linac Coherent Light Source (LCLS), SLAC’s X-ray free-electron laser, will use pulses that last just attoseconds (billionths of a billionth of a second). Such experiments will be even more powerful because they’ll be able to detect the motions of electrons within molecules during chemical reactions. However, to design such ultrafast experiments, researchers need meticulous measurements of the X-ray pulses so they can use that information to interpret the data they collect on the samples they study.

    Now an international team, including SLAC scientists, has created an X-ray “attoclock” that lets them analyze X-ray pulses on the attosecond timescale of electron motions.

    “Using this method, we can resolve details of the pulses in the attosecond domain for the first time,” says Ryan Coffee, a senior scientist at LCLS and the Stanford PULSE Institute and a principal investigator on the team. “This paves the way for X-ray free-electron laser science at a timescale that is key to understanding physical chemistry.”

    The team’s research was published in Nature Photonics on March 5.

    Timekeeping in Attoseconds

    An illustration of the ring-shaped array of 16 individual detectors arranged in a circle like numbers on the face of a clock. An X-ray laser pulse hits a target at the center and sets free electrons that are swept around the detectors. The location, where the electrons reach the “clock,” reveals details such as the variation of the X-ray energy and intensity as a function of time within the ultrashort pulse itself. (Frank Scholz & Jens Buck / DESY)

    The term “attoclock” was coined by Swiss physicist Ursula Keller, who first demonstrated a technique to study attosecond processes with circularly polarized light 10 years ago. However, the LCLS version is the first one designed to measure individual X-ray pulses, one by one.

    It consists of a ring of detectors arranged like numbers on the face of a clock. When an X-ray pulse hits a target at the center of the clock, it knocks electrons out of the target’s atoms. Those electrons are hit by circularly polarized laser light that whirls the electrons around the ring before they land on one of the detectors. The position of that detector – the number on the clock face – tells scientists how much energy the X-ray pulse contained and when exactly it hit the target.

    “It’s like reading a watch,” Coffee says. “An electron may strike a detector positioned at one o’clock or three o’clock or anywhere around the clock face. We can tell from where it hits exactly when it was generated by the X-ray pulse.”

    In an experiment designed to test the technique, the researchers hit neon gas with an attosecond X-ray pulse and then read which of the 16 detectors arrayed around the attoclock the freed electrons hit.

    “In coming up with this technique, we combined ideas from different fields,” says principal investigator Wolfram Helml, then a Marie Curie research fellow at SLAC and the Technical University of Munich and now at the Ludwig-Maximilian University of Munich. “For our purposes, it just made sense to combine the circularly polarized light used in the original attoclock with a ring-shaped detector that has been used in other kinds of experiments.”

    Finding the True Colors

    The technique will be especially important for pump-probe experiments, in which a molecule is first excited with a “pump” pulse and then analyzed by a second “probe” pulse to see how it reacted.

    As short as they are, these pulses can contain many different colors or wavelengths. “The color can also vary widely from pulse to pulse, and our technique can sift through the pulses, finding those that are interesting for the experiment,” Coffee says, noting the importance that such sifting will have for the data deluge expected when an upgrade to the X-ray laser, LCLS-II, comes online a couple years from now.

    SLAC/LCLS II projected view

    With pulses that arrive up to a million times per second, LCLS-II will produce as much data in a few minutes as LCLS currently collects in a month.

    “For instance, only a certain color may excite a molecule when it is ‘pumped,’” Helml said. “With the attoclock we can see what part of the pulse is actually exciting the molecule because we know exactly when particular colors of light arrive. This lets us pinpoint more precisely when changes occur in the molecule as a result of the interaction with light.”

    What’s more, scientists can potentially excite individual elements in separate parts of the molecule at the same time using different colors of X-rays.

    “With this technique we could look within a single molecule at the interplay between atoms. For example, what’s going on with an oxygen atom and how might that affect the chemical environment surrounding a nearby nitrogen atom?” Helml says. “With that level of detail, we can discern completely new chemical behavior.”

    Progress in Motion

    The attoclock team is now working on a proposal to build more refined detectors.

    “With the next detector, we are aiming to precisely identify a broader spectrum of energies,” Coffee says. “This will be an important feature for our upgraded X-ray laser, LCLS-II, which will produce pulses with an even wider energy range and more multi-color flexibility than our current machine.”

    This is one of several ideas being tested at SLAC to give scientists detailed information about attosecond pulses. Two other teams are building similar systems with different types of detectors, including one at LCLS and PULSE that recently published a study in Optics Express.

    The international team on the Nature Photonics study also included scientists from Deutsches Elektronen-Synchrotron (DESY) and the European X-ray Free-electron Laser (Eu-XFEL), both in Germany, who also provided the unique ring-shaped detector; University of Kassel in Germany; University of Gothenburg in Sweden; University of Bern in Switzerland; University of Colorado at Boulder; University of the Basque Country in Spain; and Lomonosov Moscow State University in Russia.

    LCLS is a DOE Office of Science user facility.

    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 2:08 pm on February 1, 2018 Permalink | Reply
    Tags: , Magnetic Trick Triples the Power of SLAC’s X-Ray Laser, , SLAC LCLS,   

    From SLAC: “Magnetic Trick Triples the Power of SLAC’s X-Ray Laser” 

    SLAC Lab

    January 31, 2018
    Mark Shwartz

    The new technique will allow researchers to observe ultrafast chemical processes previously undetectable at the atomic scale.

    Scientists at the Department of Energy’s SLAC National Accelerator Laboratory have discovered a way to triple the amount of power generated by the world’s most powerful X-ray laser. The new technique, developed at SLAC’s Linac Coherent Light Source (LCLS), will enable researchers to observe the atomic structure of molecules and ultrafast chemical processes that were previously undetectable at the atomic scale.


    From left, SLAC’s Yauntao Ding and Marc Guetg discuss their work at the lab’s Accelerator Control Room where beams that feed the X-ray laser are monitored.(Dawn Harmer/SLAC)

    The results, published in a Jan. 3 study in Physical Review Letters (PRL), will help address long-standing mysteries about photosynthesis and other fundamental chemical processes in biology, medicine and materials science, according to the researchers.

    “LCLS produces the world’s most powerful X-ray pulses, which scientists use to create movies of atoms and molecules in action,” said Marc Guetg, a research associate at SLAC and lead author of the PRL study. “Our new technique triples the power of these short pulses, enabling higher contrast.”

    The research team, from left: back row, Yuantao Ding, Matt Gibbs, Nora Norvell, Alex Saad, Uwe Bergmann, Zhirong Huang; front row, Marc Guetg and Timothy Maxwell. (Dawn Harmer/SLAC)

    Magnetic Wiggles

    The X-ray pulses at LCLS are generated by feeding beams of high-energy electrons through a long array of magnets. The electrons, which travel near the speed of light, wiggle back and forth as they pass along the magnets. This wiggling motion causes the electrons to emit powerful X-ray pulses that can be used for nanoscale imaging.

    “When you image an atomic structure, you have a race going on,” said study co-author Uwe Bergmann, a distinguished staff scientist at SLAC. “You need an X-ray pulse strong enough to get a good image, but that pulse will destroy the very structure that you’re trying to measure. However, if the pulse is short enough, about 10 femtoseconds, you can outrun the damage. You can take the snapshot before the patient feels the pain.”

    One femtosecond is one millionth of a billionth of a second. Generating high-power X-ray pulses that last only 10 femtoseconds has been a major challenge.

    “The trick is to have the electrons packed together as tightly as possible when they start wiggling around,” Guetg explained. “It’s difficult to do, because electrons don’t like each other. They’re all negatively charged, so they repel one another. It’s a battle. We’re constantly trying to force them to together, and they’re constantly trying to move apart.”

    To win the battle, Guetg and his SLAC colleagues used a special combination of magnets designed to bring the electrons closer together before they start emitting X-rays.

    “One problem when you compress electrons is that they start kicking each other,” Guetg said. “As a result, the electron beam gets tilted, which impairs the light production and therefore the power of the X-ray pulses.”

    In previous studies, Guetg had theorized that correcting the tilt would compress the electrons and produce shorter, more powerful bursts of X-rays.

    “The electron beam is shaped like a banana,” said co-author Zhirong Huang, an associate professor at SLAC and at Stanford University. “We corrected the curvature of the banana to make it a straight, pencil-like beam.”

    Dramatic Results

    The results were dramatic. Straightening the beam increased the power of the X-ray pulses by 300 percent, and each pulse lasted only 10 femtoseconds.

    “In an ingenious way, Marc and his colleagues were able to compress these electrons like a pancake before they drifted apart,” Bergmann said. “That allowed them to create very short X-ray pulses that are about 1,000 times more powerful than if you focused all the sunlight that hits the Earth onto one square centimeter. It’s an incredible power.”

    Bergmann has already used the new technique to create nanoscale images of transition metals such as manganese, which is essential for splitting water to form oxygen molecules (O2) during photosynthesis.

    “By pushing the frontier of laser science we can now see more and hopefully learn more about chemical reactions and molecular processes,” he said.

    The SLAC team hopes to build on their results in future experiments.

    “We want to make the new technique operational and robust so that anyone can use it,” Huang said. “We also want to keep improving the power with this technique and others. I would not call this the final limit.”

    The study is co-authored by SLAC staff scientists Alberto Lutman, Yuantao Ding, Timothy Maxwell and Franz-Josef Decker. Financial support was provided by the Department of Energy’s Office of Science. LCLS is a DOE Office of Science user facility.

    See the full article here .

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  • richardmitnick 4:30 pm on December 19, 2017 Permalink | Reply
    Tags: , , CERN Large Hadron Collider, , , , , Large Electron-Positron Collider, , , , SLAC LCLS, ,   

    From Symmetry: “Machine evolution” 

    Symmetry Mag

    Amanda Solliday

    Courtesy of SLAC

    Planning the next big science machine requires consideration of both the current landscape and the distant future.

    Around the world, there’s an ecosystem of large particle accelerators where physicists gather to study the most intricate details of matter.

    These accelerators are engineering marvels. From planning to construction to operation to retirement, their lifespans stretch across decades.

    But to get the most out of their investments of talent and funding, laboratories planning such huge projects have to think even longer-term: What could these projects become in their next lives?

    The following examples show how some of the world’s big physics machines have evolved to stay at the forefront of science and technology.

    Same tunnel, new collisions

    Before CERN research center in Geneva, Switzerland, had its Large Hadron Collider, it had the Large Electron-Positron Collider. LEP was the largest electron-positron collider ever built, occupying a nearly 17-mile circular tunnel dug beneath the border of Switzerland and France. The tunnel took three years to completely excavate and build.

    The first particle beam traveled around the LEP circular collider in 1989. Long before then, the international group of CERN physicists and engineers were already thinking about what CERN’s next machine could be.

    “People were saying, ‘Well, if we do build LEP, then we should make it compatible with the [then-proposed] Large Hadron Collider,’” says James Gillies, a senior communications advisor and member of the strategic planning and evaluation unit at CERN. “If you want to have a future facility, you often have to engage the people who just finished designing one machine to start thinking about the next one.”

    LEP’s designers chose an energy for the collider that would mass-produce Z bosons, fundamental particles discovered by earlier experiments at CERN. The LHC would be a step up from LEP, reaching higher energies that scientists hoped could produce the Higgs boson. In the 1960s, theorists proposed the Higgs as a way to explain the origin of the mass of elementary particles. And the new machine to look for it could be built in the same 17-mile tunnel excavated for LEP.

    Engineers began working on the LHC while LEP was still running. The new machine required enlargements to underground areas—it needed bigger detectors and new experimental halls.

    “That was challenging because these caverns are huge. As they were being excavated, the pressure on the LEP tunnel was reduced and the LEP beamline needed realignment,” Gillies says. “So you constantly had to realign the collider for experiments as you were digging.”

    After LEP reached its highest energy in 2000, it was switched off. The tunnel remained the same, says Gillies, but there were many other changes. Only one of the LEP detectors, DELPHI, remains underground at CERN as a visitors’ point.

    In 2012, LHC scientists announced the discovery of the long-sought Higgs boson. The LHC is planned to continue running until at least 2035, gradually increasing the intensity of its particle collisions. The research and development into the accelerator’s successor is already happening. The possibilities include a higher energy LHC, a compact linear collider or an even larger circular collider.


    Large Electron-Positron Collider
    Location: CERN—Geneva, Switzerland
    First beam: 1989
    Link to LEP Timeline: Timeline
    Courtesy of CERN


    CERN/LHC Map

    CERN LHC Tunnel

    CERN LHC particles

    Large Hadron Collider
    Location: CERN—Geneva, Switzerland
    First beam: 2008
    Link to LHC Timeline: Timeline
    Courtesy of CERN

    High-powered science
    Decades before the LHC came into existence, a suburb of Chicago was home to the most powerful collider in the world: the Tevatron. A series of accelerators at Fermi National Accelerator Laboratory boosted protons and antiprotons to nearly the speed of light. In the final, 4-mile Tevatron ring, the particles reached record energy levels, and more than 1000 superconducting magnets steered them into collisions. Physicists used the Tevatron to make the first direct measurement of the tau neutrino and to discover the top quark, the last observed lepton and quark, respectively, in the Standard Model.

    The Tevatron shut down in 2011 after the LHC came up to speed, but the rest of Fermilab’s accelerator infrastructure was still hard at work powering research in particle physics—particularly on the abundant, mysterious and difficult-to-detect neutrino.

    Starting in 1999, a brand-new, 2-mile circular accelerator called the Main Injector was added to the Fermilab complex to increase the number of Tevatron particle collisions tenfold. It was joined in its tunnel by the Recycler, a permanent magnet ring that stored and cooled antiprotons.

    But before the Main Injector was even completed, scientists had identified a second purpose: producing powerful beams of neutrinos for experiments in Illinois and 500 miles away in Minnesota.

    FNAL/NOvA experiment map

    By 2005, the proton beam circulating in the Main Injector was doing double duty: sending ever-more-intense beams to the Tevatron collider and smashing into a target to produce neutrinos. Following the shutdown of the Tevatron, the Recycler itself was recycled to increase the proton beam power for neutrino research.

    “I’m still amazed at how we are able to use the Recycler. It can be difficult to transition if a machine wasn’t originally built for that purpose,” says Ioanis Kourbanis, the head of the Main Injector department at Fermilab.

    Fermilab’s high-energy neutrino beam is already the most intense in the world, but the laboratory plans to enhance it with future improvements to the Main Injector and the Recycler, and to build a brand-new neutrino beamline.

    Neutrinos almost never interact with matter, so they can pass straight through the Earth on their way to detectors onsite and others several hundred miles away. Scientists hope to learn more about neutrinos and their possible role in shaping our early universe.

    The new beamline will be part of the Long-Baseline Neutrino Facility, which will send neutrinos 800 miles underground to the massive, mile-deep detectors of the Deep Underground Neutrino Experiment.

    FNAL LBNF/DUNE from FNAL to SURF, Lead, South Dakota, USA

    FNAL DUNE Argon tank at SURF

    Surf-Dune/LBNF Caverns at Sanford

    SURF building in Lead SD USA

    Scientists from around the world will use the DUNE data to answer questions about neutrinos, thanks to the repurposed pieces of the Fermilab accelerator complex.


    FNAL Tevatron

    FNAL/Tevatron map

    FNAL/Tevatron DZero detector

    FNAL/Tevatron CDF detector

    Location: Fermilab—Batavia, Illinois
    First beam: 1983
    Link to Tevatron Timeline: Timeline
    Courtesy of Fermilab


    Neutrinos at the Main Injector (NuMI) beam
    Location: Fermilab—Batavia, Illinois
    First beam: 2004
    Link to Fermilab Timeline: Timeline
    Courtesy of Fermilab

    A monster accelerator

    When physicists first came up with the idea to build a two-mile linear accelerator at what is now called SLAC National Accelerator Laboratory, managed by Stanford University, they called it “Project M” for “Monster.” Engineers began building it from hand-drawn designs. Once completed, the machine was able to accelerate electrons to near the speed of light, producing its first particle beam in May 1966.

    SLAC Campus

    The accelerator’s scientific purpose has gone through several iterations of particle physics experiments over the decades, from fixed-target experiments to the Stanford Linear Collider (the only electron-positron linear collider ever built) to an injector for a circular collider, the Positron-Electron Project.

    These experiments led to the discovery that protons are made of quarks, the first evidence that the charm quark existed (through observations of the J/psi particle, co-discovered with researchers at MIT) and the discovery of the tau lepton.

    In 2009, the lab used the accelerator as the backbone for a different type of science machine—an X-ray free-electron laser, the Linac Coherent Light Source.

    “Looking around, SLAC was the only place in the world with a linear accelerator capable of driving a free-electron laser,” says Claudio Pellegrini, a distinguished professor emeritus of physics at the University of California, Los Angeles and a visiting scientist and consulting professor at SLAC. Pellegrini first proposed the idea to transform SLAC’s linear accelerator.

    The new machine, a DOE Office of Science user facility, would be the world’s first laser of its kind that could produce extremely bright hard X-rays, the high-energy X-rays that let scientists take snapshots of atoms and molecules.

    “Much of the physics and many of the tools learned and developed during the operation of the Stanford Linear Collider were directly applicable to the free electron laser,” says Lia Merminga, head of the accelerator directorate at SLAC. “This was a big factor in the LCLS being commissioned in record time. Without the Stanford Linear Collider experience, this significant body of work would have to be reinvented and reproduced almost from scratch.”

    Little about the accelerator itself needed to change. But to create a free-electron laser, scientists needed to design a new part: an electron gun, a device that generates electrons to be injected into the accelerator. A collaboration of several national labs and UCLA created a new type of electron gun for LCLS, while other national labs helped build undulators, a series of magnets that would wiggle the electrons to create X-rays.

    LCLS used only the last third of SLAC’s original linear accelerator. In part of the remaining section, scientists are developing plasma wakefield and other new particle acceleration techniques.

    For the X-ray laser’s next iteration, LCLS-II, scientists are aiming for an even brighter laser that will fire 1 million pulses per second, allowing them to observe rare and exceptionally transient events.


    To do this, they will need to replace the original copper structures with superconducting technology. The technology is derived from designs for a large International Linear Collider [ILC] proposed to be built in Japan.

    ILC schematic

    “I’m in awe of the foresight of the original builders of SLAC’s linear accelerator,” Merminga adds. “We’ve been able to do so much with this machine, and the end is not yet in sight.”


    Fixed target and collider experiments

    Location: SLAC—Menlo Park, California
    First beam: 1966
    Link to SLAC Timeline: Timeline
    Courtesy of SLAC


    Linac Coherent Light Source
    Location: SLAC—Menlo Park, California
    First beam: 2009
    Link to SLAC Timeline: Timeline
    Courtesy of SLAC

    See the full article here .

    Please help promote STEM in your local schools.

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    Stem Education Coalition

    Symmetry is a joint Fermilab/SLAC publication.

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