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  • richardmitnick 7:39 am on September 27, 2018 Permalink | Reply
    Tags: , , , BioXFEL- short for Biology with X-ray Free Electron Lasers, HWI-Hauptman-Woodward Medical Research Institute, HWI-High-Throughput Crystallization Center, UB-University at Buffalo SUNY, , X-ray free-electron lasers, X-ray Laser technology   

    From University at Buffalo: UB, HWI and partners awarded $22.5 million to capture biology at the atomic level using X-ray lasers” 

    U Buffalo bloc.

    From University at Buffalo

    September 26, 2018
    Ellen Goldbaum
    News Content Manager
    Medicine
    Tel: 716-645-4605
    goldbaum@buffalo.edu

    BioXFEL is revolutionizing bioimaging through collaborations with academia and industry, including Google Brain.

    A research consortium led by the University at Buffalo has been awarded $22.5 million from the National Science Foundation (NSF) to continue its groundbreaking work developing advanced imaging techniques for critical biological processes that are difficult, if not impossible, to see with conventional methods.

    1
    No image credit

    BioXFEL, an NSF Science and Technology Center and UB’s first such center, was created in November 2013 with an initial, $25 million award to UB, Hauptman-Woodward Medical Research Institute (HWI) and partner institutions.

    “The successful renewal of UB’s first NSF Science and Technology Center award confirms Western New York’s leadership in the areas of X-ray crystallography and structural biology, historically based in the Hauptman-Woodward Medical Research Institute and related departments at UB, including, most recently, the Department of Materials Design and Innovation,” said Venu Govindaraju, PhD, vice president for research and economic development at UB.

    “BioXFEL center scientists have made revolutionary advances in just a few years, using X-ray lasers to probe phenomena previously hidden from view,” he said. “They have discovered about 350 new molecular structures, expanding the knowledge base by describing these structures in more than 500 publications. With these incredibly powerful new tools, they are helping us better understand some of society’s most intractable health and science problems.”

    In addition to UB and HWI, BioXFEL partners include Arizona State University, the University of Wisconsin-Milwaukee, Stanford University, Cornell University, Rice University, the University of California, San Francisco and Miami University in Ohio.

    The goal of the research is to harness the power of X-ray lasers to transform a broad range of scientific fields, focused on structural biology and drug development and extending to potential innovations in environmental technologies and the development of new materials.

    Intensely bright, incredibly short pulses

    Called BioXFEL, short for Biology with X-ray Free Electron Lasers, the consortium of UB, HWI and their partners, is dedicated to using X-ray free electron lasers, which produce incredibly intense X-rays in extremely short pulses.

    “X-ray lasers provide two huge advantages over conventional methods,” explained Edward Snell, PhD, BioXFEL director, president and CEO of HWI and professor in the Department of Materials Design and Innovation in the School of Engineering and Applied Sciences at UB. “They are intensely bright beams that allow us to see much smaller things, like nanocrystals. And their pulses are incredibly short, which allows us to see critical processes, like how drugs bind, at rates as fast as a billionth of a billionth of a second.”

    BioXFEL is developing the next-generation of X-ray-based structural biology research, a field in which Buffalo has a long and rich history. In 1985, the Nobel Prize was awarded to the late Herbert Hauptman and Jerome Karle for their work developing the groundbreaking direct methods technique, a robust means of obtaining the shape and form of pharmaceuticals and their targets that is still used today, Snell explained.

    From photograph to movie

    In the few years that BioXFEL has existed, Snell explained, its researchers have significantly expanded the detail with which biological and other processes can be imaged. “Initially, the molecular images we made were based on distinct snapshots of molecules at certain timepoints,” he said. “Now we’re going from the photograph to the movie, we’re able to see the continuous process. With this renewal, we will be able to understand the complete dynamics of biological mechanisms.”

    HWI’s role in BioXFEL stems from its high-throughput crystallization center that over the past two decades has generated 180 million images from crystallization experiments. Many of these crystals were too small to be analyzed by conventional techniques, but may be deciphered using the power of X-ray lasers.

    The same images have attracted a collaboration with Google Brain, in this case promoting the use of artificial intelligence to expedite new discoveries in protein crystallization. “Buried within all those images are clues about how to go about finding the useful data in them more easily, but there is a lot of noise and we’ve got to work out a way to tease out the clues by somehow automating the process,” he said.

    “It’s well-known that we have this archive of images at HWI generated by our High-Throughput Crystallization Center, so crystallization centers and major pharmaceutical companies worldwide have been eager to collaborate with us,” Snell said.

    Particles in solution

    UB scientist Thomas Grant, PhD, based at HWI, has used X-ray free laser techniques to develop a new way to look at molecular structures in solution, critical for understanding how proteins function in the human body. Other BioXFEL advances include:

    · Developing a method that dramatically reduces the amount of sample needed for analysis.

    · Viewing the motions of molecules during reactions called time-resolved imaging dynamics, which allowed researchers to see how antibiotic resistance develops in tuberculosis and how a virus infects its host.

    · Using X-ray lasers to probe molecular motion studies for new technologies and materials.

    · Eight supported faculty at Arizona State University, where a compact campus XFEL is under construction, who use worldwide XFEL facilities to obtain movies of molecular machines at work in photosynthesis, viruses and drugs, while developing experimental techniques and new algorithms.

    · Four supported faculty at the University of Wisconsin-Milwaukee, leading to the first movies of biological processes underlying vision, antibiotic resistance, and the extrusion of the genome from a virus.

    · New technology developed at Cornell University that has enabled the first millisecond scale mix and inject experiments: watching proteins as they work with near atomic resolution.

    The scientific work of BioXFEL takes place through collaborations between all of the partner institutions. The initial X-ray laser experiments can only be done at the Linac Coherent Light Source at BioXFEL partner Stanford University, where a mile-long facility produces a beam one-tenth of the thickness of a human hair. A handful of these facilities are opening worldwide and BioXFEL is leading research at all of them.

    SLAC/LCLS

    BioXFEL has also implemented a diverse and vigorous set of training programs to help prepare young scientists for careers in XFEL science, including summer intern programs, graduate student support, and postdoctoral career development activities.

    BioXFEL is headquartered at 700 Ellicott St. on the Buffalo Niagara Medical Campus in the building that houses both HWI and members of the UB Department of Materials Design and Innovation.

    The NSF Science and Technology Centers: Integrative Partnerships program supports innovative, potentially transformative research and education projects that require large-scale, long-term awards. The centers foster cutting-edge research, education of the next generations of scientists and broad distribution of the knowledge and technology produced.

    See the full article here .

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  • richardmitnick 12:58 pm on July 19, 2017 Permalink | Reply
    Tags: , , New Droplet-on-Tape Method Assists Biochemical Research at X-Ray Lasers, , , X-ray free-electron lasers   

    From SLAC: “New Droplet-on-Tape Method Assists Biochemical Research at X-Ray Lasers” 


    SLAC Lab

    February 27, 2017 [Never saw this one before]

    1
    Acoustic droplet ejection allows scientists to deposit nanoliters of sample directly into the X-ray beam, considerably increasing the efficiency of sample consumption. A femtosecond pulse from an X-ray free-electron laser then intersects with a droplet that contains protein crystals. (SLAC National Accelerator Laboratory)

    SLAC/LCLS

    2
    As the drops move forward, they are hit with pulses of visible light or treated with oxygen gas, which triggers different chemical reactions depending on the sample studied. (SLAC National Accelerator Laboratory)

    Biological samples studied with intense X-rays at free-electron lasers are destroyed within nanoseconds after they are exposed. Because of this, the samples need to be continually refreshed to allow the many images needed for an experiment to be obtained. Conventional methods use jets that supply a continuous stream of samples, but this can be very wasteful as the X-rays only interact with a tiny fraction of the injected material.

    To help address this issue, scientists at the Department of Energy’s Lawrence Berkeley National Laboratory, SLAC National Accelerator Laboratory, Brookhaven National Laboratory, and other institutes designed a new assembly-line system that rapidly replaces exposed samples by moving droplets along a miniature conveyor belt, timed to coincide with the arrival of the X-ray pulses.

    The droplet-on-tape system now allows the team to study the biochemical reactions in real-time from microseconds to seconds, revealing the stages of these complex reactions.

    In their approach, protein solution or crystals are precisely deposited in tiny liquid drops, made as ultrasound waves push the liquid onto a moving tape. As the drops move forward, they are hit with pulses of visible light or treated with oxygen gas, which triggers different chemical reactions depending on the sample studied. This allows the study of processes such as photosynthesis, which determines how plants absorb light from the sun and convert it into useable energy.

    Finally, powerful X-ray pulses from SLAC’s X-ray laser, the Linac Coherent Light Source (LCLS), probe the drops. In this study published in Nature Methods, the X-ray light scattered from the sample onto two different detectors simultaneously, one for X-ray crystallography and the other for X-ray emission spectroscopy. These are two complementary methods that provide information about the geometric and electronic structure of the catalytic sites of the proteins and allowed them to watch with atomic precision how the protein structures changed during the reaction.

    Below, see the conveyor belt in action at LCLS, a Department of Energy Office of Science User Facility.

    3
    Droplet-on-tape conveyor belt system delivers samples at the Linac Coherent Light Source (LCLS). (SLAC National Accelerator Laboratory)

    See the full article here .

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    SLAC is a multi-program laboratory exploring frontier questions in photon science, astrophysics, particle physics and accelerator research. Located in Menlo Park, California, SLAC is operated by Stanford University for the DOE’s Office of Science.
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  • richardmitnick 5:46 pm on June 20, 2017 Permalink | Reply
    Tags: , , , , Superconducting undulators, X-ray free-electron lasers,   

    From LBNL: “R&D Effort Produces Magnetic Devices to Enable More Powerful X-ray Lasers” 

    Berkeley Logo

    Berkeley Lab

    June 20, 2017
    Glenn Roberts Jr.
    geroberts@lbl.gov
    (510) 486-5582

    Berkeley Lab demonstrates a record-setting magnetic field for a prototype superconducting undulator.

    1
    This Berkeley Lab-developed device, a niobium tin superconducting undulator prototype, set a record in magnetic field strength for a device of its kind. This type of undulator could be used to wiggle electron beams to emit light for a next generation of X-ray lasers.
    (Credit: Marilyn Chung/Berkeley Lab)

    Researchers at the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) and Argonne National Laboratory have collaborated to design, build, and test two devices, called superconducting undulators, which could make X-ray free-electron lasers (FELs) more powerful, versatile, compact, and durable.

    X-ray FELs are powerful tools for studying the microscopic structure and other properties of samples, such as proteins that are key to drug design, exotic materials relevant to electronics and energy applications, and chemistry that is central to industrial processes like fuel production.

    The recent development effort was motivated by SLAC National Accelerator Laboratory’s upgrade of its Linac Coherent Light Source (LCLS), the nation’s only X-ray FEL.

    SLAC LCLS-II

    This upgrade, now underway, is known as LCLS-II. All existing X-ray FELS, including both LCLS and LCLS-II, use permanent magnet undulators to generate intense pulses of X-rays. These devices produce X-ray light by passing high-energy bunches of electrons through alternating magnetic fields produced by a series of permanent magnets.

    Superconducting undulators (SCUs) offer another technical solution and are considered among the most promising technologies to improve the performance of the next generation FELs, and of other types of light sources, such as Berkeley Lab’s Advanced Light Source (ALS) and Argonne’s Advanced Photon Source (APS).

    LBNL/ALS

    ANL APS

    SCUs replace the permanent magnets in the undulator with superconducting coils. The prototype SCUs have successfully produced stronger magnetic fields than conventional undulators of the same size. Higher fields, in turn, can produce higher-energy free-electron laser light to open up a broader range of experiments.

    Berkeley Lab’s 1.5-meter-long prototype undulator, which uses a superconducting material known as niobium-tin (Nb3Sn), set a record in magnetic field strength for a device of its design during testing at the Lab in September 2016.

    “This is a much-anticipated innovation,” agreed Wim Leemans, Director, Accelerator Technology and Applied Physics (ATAP) . “Higher performance in a smaller footprint is something that benefits everyone – the laboratories that host the facilities, the funding agencies, and above all, the user community.”

    Argonne’s test of another superconducting material, niobium-titanium, successfully reached its performance goal, and additionally passed a bevy of quality tests. Niobium-titanium has a lower maximum magnetic field strength than niobium-tin, but is further along in its development.

    3
    The superconducting undulator R&D project at Berkeley Lab was a team effort. Among the contributors: (from left) Heng Pan, Jordan Taylor, Soren Prestemon, Ross Schlueter, Diego Arbelaez, Jim Swanson, Ahmet Pekedis, Scott Myers, Tom Lipton, and Xiaorong Wang. (Credit: Marilyn Chung/Berkeley Lab)

    Researchers at the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) and Argonne National Laboratory have collaborated to design, build, and test two devices, called superconducting undulators, which could make X-ray free-electron lasers (FELs) more powerful, versatile, compact, and durable.

    X-ray FELs are powerful tools for studying the microscopic structure and other properties of samples, such as proteins that are key to drug design, exotic materials relevant to electronics and energy applications, and chemistry that is central to industrial processes like fuel production.

    The recent development effort was motivated by SLAC National Accelerator Laboratory’s upgrade of its Linac Coherent Light Source (LCLS), the nation’s only X-ray FEL. This upgrade, now underway, is known as LCLS-II. All existing X-ray FELS, including both LCLS and LCLS-II, use permanent magnet undulators to generate intense pulses of X-rays. These devices produce X-ray light by passing high-energy bunches of electrons through alternating magnetic fields produced by a series of permanent magnets.

    Superconducting undulators (SCUs) offer another technical solution and are considered among the most promising technologies to improve the performance of the next generation FELs, and of other types of light sources, such as Berkeley Lab’s Advanced Light Source (ALS) and Argonne’s Advanced Photon Source (APS).

    SCUs replace the permanent magnets in the undulator with superconducting coils. The prototype SCUs have successfully produced stronger magnetic fields than conventional undulators of the same size. Higher fields, in turn, can produce higher-energy free-electron laser light to open up a broader range of experiments.

    Berkeley Lab’s 1.5-meter-long prototype undulator, which uses a superconducting material known as niobium-tin (Nb3Sn), set a record in magnetic field strength for a device of its design during testing at the Lab in September 2016.

    “This is a much-anticipated innovation,” agreed Wim Leemans, Director, Accelerator Technology and Applied Physics (ATAP) . “Higher performance in a smaller footprint is something that benefits everyone – the laboratories that host the facilities, the funding agencies, and above all, the user community.”

    Argonne’s test of another superconducting material, niobium-titanium, successfully reached its performance goal, and additionally passed a bevy of quality tests. Niobium-titanium has a lower maximum magnetic field strength than niobium-tin, but is further along in its development.
    Photo – The superconducting undulator R&D project at Berkeley Lab was a team effort. Among the contributors: (from left) Heng Pan, Jordan Taylor, Soren Prestemon, Ross Schlueter, Diego Arbelaez, Jim Swanson, Ahmet Pekedis, Scott Myers, Tom Lipton, and Xiaorong Wang. (Credit: Marilyn Chung/Berkeley Lab)

    The superconducting undulator R&D project at Berkeley Lab was a team effort. Among the contributors: (from left) Heng Pan, Jordan Taylor, Soren Prestemon, Ross Schlueter, Diego Arbelaez, Jim Swanson, Ahmet Pekedis, Scott Myers, Tom Lipton, and Xiaorong Wang. (Credit: Marilyn Chung/Berkeley Lab)

    “The superconducting technology in general, and especially with the niobium tin, lived up to its promise of being the highest performer,” said Ross Schlueter, Head of the Magnetics Department in Berkeley Lab’s Engineering Division. “We’re very excited about this world record. This device allows you to get a much higher photon energy” from a given electron beam energy.

    “We have expertise here both in free-electron laser undulators, as demonstrated in our role in leading the construction of LCLS-II’s undulators, and in synchrotron undulator development at the ALS,” noted Soren Prestemon, Director of the Berkeley Center for Magnet Technology (BCMT), which brings together the Accelerator Technology and Applied Physics Division (ATAP) and Engineering Division, to design and build a range of magnetic devices for scientific, medical, and other applications.

    “The Engineering Division has a long history of forefront research on undulators, and this work continues that tradition,” states Henrik von der Lippe, Director, Engineering Division.

    Diego Arbelaez, the lead engineer in the development of Berkeley Lab’s device, said earlier work at the Lab in building superconducting undulator prototypes for a different project were useful in informing the latest design, though there were still plenty of challenges.

    Niobium-tin is a brittle material that cannot be drawn into a wire. For practical use, a pliable wire, which contains the components that will form niobium-tin when heat-treated, is used for winding the undulator coils. The full undulator coil is then heat-treated in a furnace at 1,200 degrees Fahrenheit.

    The niobium-tin wire is wound around a steel frame to form tightly wrapped coils in an alternating arrangement. The precision of the winding is critical for the performance of the device. Arbelaez said, “One of the questions was whether you can maintain precision in its winding even though you are going through these large temperature variations.”

    After the heat treatment, the coils are placed in a mold and impregnated with epoxy to hold the superconducting coils in place. To achieve a superconducting state and demonstrate its record-setting performance, the device was immersed in a bath of liquid helium to cool it down to about minus 450 degrees Fahrenheit.

    4
    Ahmet Pekedis, left, and Diego Arbelaez inspect the completed niobium tin undulator prototype. (Credit: Marilyn Chung/Berkeley Lab)

    Another challenge was in developing a fast shutoff to prevent catastrophic failure during an event known as “quenching.” During a quench, there is a sudden loss of superconductivity that can be caused by a small amount of heat generation. Uncontrolled quenching could lead to rapid heating that might damage the niobium-tin and surrounding copper and ruin the device.

    This is a critical issue for the niobium-tin undulators due to the extraordinary current densities they can support. Berkeley Lab’s Marcos Turqueti led the effort to engineer a quench-protection system that can detect the occurrence of quenching within a couple thousandths of a second and shut down its effects within 10 thousandths of a second.

    Arbelaez also helped devise a system to correct for magnetic-field errors while the undulator is in its superconducting state.

    SLAC’s Paul Emma, the accelerator physics lead for LCLS-II, coordinated the superconducting undulator development effort.

    Emma said that the niobium-tin superconducting undulator developed at Berkeley Lab shows potential but may require more extensive continuing R&D than Argonne’s niobium-titanium prototype. Argonne earlier developed superconducting undulators that are in use at its APS, and Berkeley Lab also hopes to add superconducting undulators at its ALS.

    “With superconducting undulators,” Emma said, “you don’t necessarily lower the cost but you get better performance for the same stretch of undulator.”

    5
    A close-up view of the superconducting undulator prototype developed at Berkeley Lab. To construct the undulator, researchers wound a pliable wire in alternating coils around a steel frame. The pliable wire was baked to form a niobium-tin compound that is very brittle but can achieve high magnetic fields when chilled to superconducting temperatures. (Credit: Marilyn Chung/Berkeley Lab)

    A superconducting undulator of an equivalent length to a permanent magnetic undulator could produce light that is at least two to three times – perhaps up to 10 times – more powerful, and could also access a wider range in X-ray wavelengths, Emma said, producing a more efficient FEL.

    Superconducting undulators also have no macroscopic moving parts, so they could conceivably be tuned more quickly with high precision. Superconductors also are far less prone to damage by high-intensity radiation than permanent-magnet materials, a significant issue in high-power accelerators such as those that will be installed for LCLS-II.

    There appears to be a clear path forward to developing superconducting undulators for upgrades of existing and new X-ray free-electron lasers, Emma said, and for other types of light sources.

    “Superconducting undulators will be the technology we go to eventually, whether it’s in the next 10 or 20 years,” he said. “They are powerful enough to produce the light we are going to need – I think it’s going to happen. People know it’s a big enough step, and we’ve got to get there.”

    James Symons, Berkeley Lab’s Associate Director for Physical Sciences, said, “We look forward to building on this effort by furthering our R&D on superconducting undulator systems.

    The Advanced Light Source, Advanced Photon Source, and Linac Coherent Light Source are DOE Office of Science User Facilities. The development of the superconducting undulator prototypes was supported by the DOE’s Office of Science.”

    See the full article here .

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