313 results on '"X-ray free electron laser"'
Search Results
152. XFEL data analysis for structural biology
- Author
-
Liu, Haiguang and Spence, John C. H.
- Published
- 2016
- Full Text
- View/download PDF
153. Effects of Space Charge and Multiple Scattering on the Gain of an X-Ray Free Electron Laser Using Stimulated Transition Radiation.
- Author
-
Yoshimori, Shigeru and Kawamura, Mitsuo
- Subjects
- *
SPACE charge , *CARRIER waves , *ELECTRIC charge , *X-rays , *FREE electron lasers , *RADIATION - Abstract
For the X-ray free electron laser using stimulated transition radiation in periodic stacks of metal foils or polymer films, the effects considered are those that are due to: (1) the space charge of the relativistic electron beam; (2) multiple scattering of the electron beam passing through the stacks; and (3) both the space charge and multiple scattering simultaneously. Taking these respective effects into account in a Boltzmann transport equation, dispersion relations are derived and gain coefficients of the laser are calculated and compared. As a result, it is found that the effect of multiple scattering is large and it depends also on the magnitude of the electron beam energy, e.g., for the case of 50 (3eV, the gain coefficient is decreased by seven! dB. The effect of the space charge is relatively small. Also, the gain coefficient generally decreases with the beam energy. [ABSTRACT FROM AUTHOR]
- Published
- 1995
- Full Text
- View/download PDF
154. Radiation shielding design of the PAL-XFEL
- Author
-
Jung, Nam-Suk, Lee, Hee-Seock, Oh, Joo-Hee, and Kim, Bum-Jong
- Published
- 2015
- Full Text
- View/download PDF
155. The Effect of Intensity Fluctuations on Sequential X-ray Photon Correlation Spectroscopy at the X-ray Free Electron Laser Facilities.
- Author
-
Cao, Yue, Sheyfer, Dina, Jiang, Zhang, Maddali, Siddharth, You, Hoydoo, Wang, Bi-Xia, Ye, Zuo-Guang, Dufresne, Eric M., Zhou, Hua, Stephenson, G. Brian, and Hruszkewycz, Stephan O.
- Subjects
FREE electron lasers ,LIGHT beating spectroscopy ,X-ray spectroscopy ,X-rays ,SEQUENTIAL analysis - Abstract
How materials evolve at thermal equilibrium and under external excitations at small length and time scales is crucial to the understanding and control of material properties. X-ray photon correlation spectroscopy (XPCS) at X-ray free electron laser (XFEL) facilities can in principle capture dynamics of materials that are substantially faster than a millisecond. However, the analysis and interpretation of XPCS data is hindered by the strongly fluctuating X-ray intensity from XFELs. Here we examine the impact of pulse-to-pulse intensity fluctuations on sequential XPCS analysis. We show that the conventional XPCS analysis can still faithfully capture the characteristic time scales, but with substantial decrease in the signal-to-noise ratio of the g 2 function and increase in the uncertainties of the extracted time constants. We also demonstrate protocols for improving the signal-to-noise ratio and reducing the uncertainties. [ABSTRACT FROM AUTHOR]
- Published
- 2020
- Full Text
- View/download PDF
156. Beyond X-rays: an overview of emerging structural biology methods.
- Author
-
Schaffer JE, Kukshal V, Miller JJ, Kitainda V, and Jez JM
- Subjects
- Crystallography, X-Ray, Molecular Biology, X-Rays, Electrons, Lasers
- Abstract
Structural biologists rely on X-ray crystallography as the main technique for determining the three-dimensional structures of macromolecules; however, in recent years, new methods that go beyond X-ray-based technologies are broadening the selection of tools to understand molecular structure and function. Simultaneously, national facilities are developing programming tools and maintaining personnel to aid novice structural biologists in de novo structure determination. The combination of X-ray free electron lasers (XFELs) and serial femtosecond crystallography (SFX) now enable time-resolved structure determination that allows for capture of dynamic processes, such as reaction mechanism and conformational flexibility. XFEL and SFX, along with microcrystal electron diffraction (MicroED), help side-step the need for large crystals for structural studies. Moreover, advances in cryogenic electron microscopy (cryo-EM) as a tool for structure determination is revolutionizing how difficult to crystallize macromolecules and/or complexes can be visualized at the atomic scale. This review aims to provide a broad overview of these new methods and to guide readers to more in-depth literature of these methods., (© 2021 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society and the Royal Society of Biology.)
- Published
- 2021
- Full Text
- View/download PDF
157. Formation of diamonds in laser-compressed hydrocarbons at planetary interior conditions
- Author
-
Kraus, D., Vorberger, J., Pak, A., Hartley, N. J., Fletcher, L. B., Frydrych, S., Galtier, E., Gamboa, E. J., Gericke, D. O., Glenzer, S. H., Granados, E., Macdonald, M. J., Mackinnon, A. J., Mcbride, E. E., Nam, I., Neumayer, P., Roth, M., Saunders, A. M., Sun, P., Driel, T., Döppner, T., Falcone, R. W., Kraus, D., Vorberger, J., Pak, A., Hartley, N. J., Fletcher, L. B., Frydrych, S., Galtier, E., Gamboa, E. J., Gericke, D. O., Glenzer, S. H., Granados, E., Macdonald, M. J., Mackinnon, A. J., Mcbride, E. E., Nam, I., Neumayer, P., Roth, M., Saunders, A. M., Sun, P., Driel, T., Döppner, T., and Falcone, R. W.
- Abstract
The effects of hydrocarbon dissociation and subsequent diamond precipitation on the internal structure and evolution of icy giant planets like Neptune and Uranus have been discussed for more than three decades. Inside these celestial bodies, gravity compresses mixtures of light elements to densities of several grams per cubic centimeter while the temperature reaches thousands of Kelvins resulting in thermal energies on the order of chemical bonding and above. Under these conditions, simple hydrocarbons like methane, which are highly abundant in the atmospheres of these planets, are believed to undergo structural transitions that release molecular hydrogen from deeper layers and may lead to compact stratified cores. Indeed, the isentropes of Uranus and Neptune intersect temperature-pressure conditions where first polymerization occurs, and then, in deeper layers, a phase separation into diamond and hydrogen may be possible. Here we show experimental evidence for this phase separation process obtained by in situ X-ray diffraction from polystyrene samples dynamically compressed to 150GPa and 5000 K, which resembles the environment ~10,000 km below the surfaces of Neptune and Uranus. Our findings demonstrate the necessity of high pressures for initiating carbon-hydrogen demixing and imply that diamond precipitation may require ~10x higher pressures than previously suggested by experiments investigating non-isolated hydrocarbons. Besides underlining the general importance of chemical processes inside giant planets, these results will inform evolutionary models of Uranus and Neptune, where carbon-hydrogen demixing can be a significant source for the convection necessary to explain their unusual magnetic fields. Additionally, our experiment demonstrates an alternative path for producing nanodiamonds for scientific and industrial applications that may be superior to current methods using oxygen-deficient explosives.
- Published
- 2017
158. A Dispersive Inelastic X-ray Scattering Spectrometer for Use at X-ray Free Electron Lasers
- Author
-
Christopher J. Milne, Joanna Czapla–Masztafiak, Maarten Nachtegaal, S. Peredkov, Daniel Grolimund, Jakub Szlachetko, and Gregor Knopp
- Subjects
Free electron model ,Diffraction ,dispersive X-ray spectrometer ,02 engineering and technology ,segmented crystal ,01 natural sciences ,lcsh:Technology ,law.invention ,von Hamos geometry ,Crystal ,lcsh:Chemistry ,Optics ,law ,0103 physical sciences ,General Materials Science ,010306 general physics ,Instrumentation ,lcsh:QH301-705.5 ,Fluid Flow and Transfer Processes ,Physics ,Spectrometer ,Scattering ,business.industry ,lcsh:T ,Process Chemistry and Technology ,inelastic X-ray scattering ,Resolution (electron density) ,General Engineering ,Radius ,021001 nanoscience & nanotechnology ,Laser ,lcsh:QC1-999 ,Computer Science Applications ,X-ray free electron laser ,SwissFEL ,lcsh:Biology (General) ,lcsh:QD1-999 ,lcsh:TA1-2040 ,0210 nano-technology ,business ,lcsh:Engineering (General). Civil engineering (General) ,lcsh:Physics - Abstract
We report on the application of a short working distance von Hamos geometry spectrometer to measure the inelastic X-ray scattering (IXS) signals from solids and liquids. In contrast to typical IXS instruments where the spectrometer geometry is fixed and the incoming beam energy is scanned, the von Hamos geometry allows measurements to be made using a fixed optical arrangement with no moving parts. Thanks to the shot-to-shot capability of the spectrometer setup, we anticipate its application for the IXS technique at X-ray free electron lasers (XFELs). We discuss the capability of the spectrometer setup for IXS studies in terms of efficiency and required total incident photon flux for a given signal-to-noise ratio. The ultimate energy resolution of the spectrometer, which is a key parameter for IXS studies, was measured to the level of 150 meV at short crystal radius thanks to the application of segmented crystals for X-ray diffraction. The short working distance is a key parameter for spectrometer efficiency that is necessary to measure weak IXS signals.
- Published
- 2017
159. SwissFEL: The Swiss X-ray Free Electron Laser
- Author
-
Bill Pedrini, Paul Beaud, Hans-Heinrich Braun, Edwin Divall, G. Marinkovic, Matthias Ringele, Roberto Dinapoli, Vladimir Arsov, H. Brands, Ralf Menzel, Christof Zellweger, Yunpei Deng, Christoph P. Hauri, Christoph Kittel, Marta Csatari Divall, Thomas Schietinger, Thierry Zamofing, Pavle Juranić, Rasmus Ischebeck, Roger Kalt, Markus Janousch, I. Gorgisyan, M. Stadler, Florian Gärtner, C. Lopez-Cuenca, Volker Schlott, Terence Garvey, Claude Pradervand, Gian Luca Orlandi, Meitian Wang, Leonid Rivkin, M. Jurcevic, Marie Ruat, Mark Dällenbach, Paolo Craievich, Nicole Hiller, Christian Erny, Martin Paraliev, Uwe Flechsig, Patrick Pollet, Wolfgang Tron, Bruce D. Patterson, B. Keil, Elke Zimoch, T. Schilcher, L. Stingelin, Rafael Abela, Sladana Dordevic, Ezequiel Panepucci, J. Alex, A. Hauff, Jean-Yves Raguin, Sven Reiche, Arturo Alarcon, Marco Pedrozzi, S. Redford, Peter Radi, A. Trisorio, Henrik T. Lemke, Alexander Dietrich, Didier Voulot, Michael D’Amico, Karol Nass, Ingo Brunnenkant, Hansrudolf Fitze, Albert Romann, Aldo Mozzanica, Rolf Follath, C. Ruder, Florian Löhl, Cigdem Ozkan Loch, Tadej Humar, Christopher J. Milne, Babak Kalantari, M. Aiba, Jakub Szlachetko, F. Marcellini, Gerhard Ingold, S. Vetter, Xintian Shi, Alexander Anghel, Isabelle Martiel, Carlo Vicario, Andreas Dax, Eduard Prat, Thomas J. Schmidt, Bernd Schmitt, A. Citterio, Luc Patthey, Marco Calvi, F. Frei, M. Bopp, Carl Beard, Stephan Hunziker, Zheqiao Geng, Manuel Brönnimann, Lionel Schebacher, R. Zennaro, D. Thattil, Maik Kaiser, Fabian Märki, Thomas Lippuner, W. Koprek, Werner Sturzenegger, Romain Ganter, D. Treyer, C. Gough, Daniel Llorente Sancho, Simona Bettoni, J. Rittmann, Simon Ebner, Jens Rehanek, Leonardo Sala, Gregor Knopp, and Julien Réhault
- Subjects
X-ray photon diagnostics ,X-ray detector ,serial femtosecond crystallography ,Photon ,X-ray free electron laser ,linac ,X-rays ,undulator ,SwissFEL ,X-ray optics ,ultrafast X-ray science ,JUNGFRAU ,lcsh:Technology ,01 natural sciences ,Linear particle accelerator ,lcsh:Chemistry ,Optics ,0103 physical sciences ,General Materials Science ,010306 general physics ,lcsh:QH301-705.5 ,Instrumentation ,Fluid Flow and Transfer Processes ,Physics ,lcsh:T ,010308 nuclear & particles physics ,business.industry ,Process Chemistry and Technology ,General Engineering ,Free-electron laser ,X-ray ,Undulator ,lcsh:QC1-999 ,Computer Science Applications ,lcsh:Biology (General) ,lcsh:QD1-999 ,lcsh:TA1-2040 ,lcsh:Engineering (General). Civil engineering (General) ,business ,lcsh:Physics - Abstract
The SwissFEL X-ray Free Electron Laser (XFEL) facility started construction at the Paul Scherrer Institute (Villigen, Switzerland) in 2013 and will be ready to accept its first users in 2018 on the Aramis hard X-ray branch. In the following sections we will summarize the various aspects of the project, including the design of the soft and hard X-ray branches of the accelerator, the results of SwissFEL performance simulations, details of the photon beamlines and experimental stations, and our first commissioning results.
- Published
- 2017
- Full Text
- View/download PDF
160. Opportunities for Chemistry at the SwissFEL X-ray Free Electron Laser
- Author
-
Gerhard Ingold, Pavle Juranić, Bill Pedrini, Christian Erny, Paul Beaud, Christopher J. Milne, Gregor Knopp, Christoph P. Hauri, Rolf Follath, Yunpei Deng, Peter Radi, Henrik T. Lemke, Luc Patthey, and Uwe Flechsig
- Subjects
0301 basic medicine ,030103 biophysics ,Chemical research ,Free-electron laser ,02 engineering and technology ,General Medicine ,General Chemistry ,021001 nanoscience & nanotechnology ,Laser ,Engineering physics ,law.invention ,X-ray free electron laser ,Chemistry ,03 medical and health sciences ,Sample composition ,law ,Material structure ,Research community ,0210 nano-technology ,QD1-999 ,Swissfel - Abstract
X-ray techniques have long been applied to chemical research, ranging from powder diffraction tools to analyse material structure to X-ray fluorescence measurements for sample composition. The development of high-brightness, accelerator-based X-ray sources has allowed chemists to use similar techniques but on more demanding samples and using more photon-hungry methods. X-ray Free Electron Lasers (XFELs) are the latest in the development of these large-scale user facilities, opening up new avenues of research and the possibility of more advanced applications for a range of research. The SwissFEL XFEL project at the Paul Scherrer Institute will begin user operation in the hard X-ray (2.1–12.4 keV) photon energy range in 2018 with soft X-ray (240–1930 eV) user operation to follow and here we will present the details of this project, it's operating capabilities, and some aspects of the experimental stations that will be particularly attractive for chemistry research. SwissFEL is a revolutionary new machine that will complement and extend the time-resolved chemistry efforts in the Swiss research community.
- Published
- 2017
161. Populations and coherence in femtosecond time resolved X-ray crystallography of the photoactive yellow protein
- Author
-
C. Hutchison, Jasper J. van Thor, and Engineering & Physical Science Research Council (EPSRC)
- Subjects
photoactive yellow protein ,0306 Physical Chemistry (Incl. Structural) ,0307 Theoretical And Computational Chemistry ,Physics::Optics ,PUMP-PROBE SPECTROSCOPY ,02 engineering and technology ,Physics, Atomic, Molecular & Chemical ,010402 general chemistry ,01 natural sciences ,ABSORPTION-SPECTROSCOPY ,linear response theory ,0202 Atomic, Molecular, Nuclear, Particle And Plasma Physics ,RAMAN-SPECTROSCOPY ,Serial femtosecond crystallography ,Physical and Theoretical Chemistry ,PRIMARY PHOTOCHEMISTRY ,PHOTORECEPTOR PROTEIN ,Photoactive yellow protein ,PHOTOINDUCED DYNAMICS ,Science & Technology ,Chemical Physics ,Chemistry ,Chemistry, Physical ,Physics ,vibrational coherence ,Free-electron laser ,ECTOTHIORHODOSPIRA-HALOPHILA ,021001 nanoscience & nanotechnology ,0104 chemical sciences ,EXCITED-STATE DYNAMICS ,X-ray free electron laser ,Crystallography ,FLUORESCENCE SPECTROSCOPY ,NEUTRON-SCATTERING ,Femtosecond ,X-ray crystallography ,Physical Sciences ,0210 nano-technology ,Linear response theory ,Ultrashort pulse ,Coherence (physics) - Abstract
Ultrafast X-ray crystallography of the photoactive yellow protein with femtosecond delays using an X-ray free electron laser has successfully probed the dynamics of an early Franck-Condon species. The femtosecond pump-probe application of protein crystallography represents a new experimental regime that provides an X-ray structural probe for coherent processes that were previously accessible primarily using ultrafast spectroscopy. We address how the optical regime of the visible pump, that is necessary to successfully resolve ultrafast structural differences, affects the motions that are measured using the technique. The sub-picosecond photochemical dynamics in PYP involves evolution of a mixture of electronic ground and excited state populations. Additional to photoisomerisation that is considered to proceed through activated barrier crossing, within the dephasing time structural motion include vibrational coherence arising from excited states, the ground state and a ground state intermediate under experimental conditions used for ultrafast crystallography. Intense optical pulses are required to convert population levels in PYP crystals that allow detection by X-ray crystallography, but the compromise currently needed for the optical bandwidth and power has consequences with regard to the contributions to the motions that are experimentally measured with femtosecond delays. We briefly review the ultrafast spectroscopy literature of the primary photoreactions of PYP and discuss relevant physical models taken from coherent control and femtosecond coherence spectroscopy literature that address both the population transfer as well as the vibrational coherences. We apply linear response theory, with the additional use of a high power approximation, of on-resonance impulsive vibrational coherence in the ground state and the non-impulsive coherence in the excited state and discuss experimental approaches to manipulate the coherence contributions. The results are generalised and extended to discuss the future capabilities of high repetition rate X-ray free electron laser instruments providing enhanced sensitivity to perform the crystallographic equivalent of an impulsive Raman measurement of vibrational coherence.
- Published
- 2017
162. SACLA における連続フェムト秒結晶学のためのデータ処理パイプライン
- Author
-
Nakane, Takanori, 黒田, 知宏, 松田, 文彦, and 楠見, 明弘
- Subjects
X-ray free electron laser ,serial femtosecond crystallography ,realtime processing ,X-ray diffraction ,automation - Published
- 2017
163. Performance of focusing mirror device in EUV beamline of SPring-8 Compact SASE Source (SCSS)
- Author
-
Ohashi, Haruhiko, Senba, Yasunori, Nagasono, Mitsuru, Yabashi, Makina, Tono, Kensuke, Togashi, Tadashi, Kudo, Togo, Kishimoto, Hikaru, Miura, Takanori, Kimura, Hiroaki, and Ishikawa, Tetsuya
- Subjects
- *
PERFORMANCE evaluation , *EXTREME ultraviolet lithography , *PARTICLE beams , *FREE electron lasers , *LASER ablation , *IRRADIATION - Abstract
Abstract: A focusing mirror device was designed and installed in an extreme ultraviolet (EUV) beamline of the SPring-8 Compact SASE Source (SCSS). The horizontal and vertical sizes of the beam at the focal point were measured to be 22 and 26μm with a working distance of 0.94m at a wavelength of 60nm. A high power density over 20TW/cm2 was achieved. Ablation properties of some materials such as silicon, diamond and tantalum have been studied for determining the focused beam profile with a single shot irradiation. [Copyright &y& Elsevier]
- Published
- 2011
- Full Text
- View/download PDF
164. Optical control, selection and analysis of population dynamics in ultrafast protein X-ray crystallography
- Author
-
Jasper J. van Thor, C. Hutchison, Engineering & Physical Science Research Council (EPSRC), and Biotechnology and Biological Sciences Research Council
- Subjects
Free electron model ,General Science & Technology ,General Mathematics ,Population ,Physics::Optics ,General Physics and Astronomy ,PUMP-PROBE SPECTROSCOPY ,DATA-COLLECTION ,law.invention ,optical control ,law ,EXCITATION ,COHERENCE ,TR-SFX ,time-resolved serial femtosecond crystallography ,education ,LAUE CRYSTALLOGRAPHY ,Physics ,education.field_of_study ,Science & Technology ,PHOTOCYCLE ,XFEL ,Protein x ,General Engineering ,REFLECTIONS ,FEMTOSECOND ,Articles ,nuclear coherence ,Laser ,Multidisciplinary Sciences ,X-ray free electron laser ,Crystallography ,RESOLUTION ,Optical control ,Science & Technology - Other Topics ,Ultrashort pulse - Abstract
Ultrafast pump-probe X-ray crystallography has now been established at X-ray free electron lasers that operate at hard X-ray energies. We discuss the performance and development of current applications in terms of the available data quality and sensitivity to detect and analyse structural dynamics. A discussion of technical capabilities expected at future high repetition rate applications as well as future non-collinear multi-pulse schemes focuses on the possibility to advance the technique to the practical application of the X-ray crystallographic equivalent of an impulse time-domain Raman measurement of vibrational coherence. Furthermore, we present calculations of the magnitude of population differences and distributions prepared with ultrafast optical pumping of single crystals in the typical serial femtosecond crystallography geometry, which are developed for the general uniaxial and biaxial cases. The results present opportunities for polarization resolved anisotropic X-ray diffraction analysis of photochemical populations for the ultrafast time domain. This article is part of the theme issue ‘Measurement of ultrafast electronic and structural dynamics with X-rays’.
- Published
- 2019
165. Preventing Bio-Bloopers and XFEL Follies: Best Practices from your Friendly Instrument Staff.
- Author
-
Kupitz, Christopher and Sierra, Raymond G.
- Subjects
FREE electron lasers ,BEST practices ,SLURRY ,BIOLOGICAL systems ,HAPPY hours - Abstract
Serial Femtosecond Crystallography (SFX) at X-ray Free electron Lasers (XFELs) is a relatively new field promising to deliver unparalleled spatial and temporal resolution on biological systems and there dynamics. Over the past decade, though, there have been a handful of results that have truly delivered on these promises. Why? SFX has many paradigm shifting techniques not seen in typical structural biology arenas, such as creating a concentrated slurry of microcrystals rather than a handful of loopable prisms worthy of a catalog photo. Then taking that slurry and high speed jetting them towards the vacuum or helium interation region to destroy less than 1% of your sample and waste the other 99. The literature is full of techniques and methods promising to cure what ails your experiment, yet as an instrument scientist will tell you –and a first author might admit after a few drinks at the conference happy hour—is that there are a lot more failures than the success we published, results may vary. We will walk through a best practices on how to prepare your sample and chose a sample delivery technique that will amerliorate your studies rather than undermine your hardwork and hopefully lead to better experimental planning and execution, inching you closer to that scientific goal and that call from Stockholm. This will be written in a more editorialized fashion and is meant to give the reader an idea of what to try or how they should be thinking. Welcome to SFX, now what? [ABSTRACT FROM AUTHOR]
- Published
- 2020
- Full Text
- View/download PDF
166. High-Throughput 3D Ensemble Characterization of Individual Core-Shell Nanoparticles with X-ray Free Electron Laser Single-Particle Imaging.
- Author
-
Cho DH, Shen Z, Ihm Y, Wi DH, Jung C, Nam D, Kim S, Park SY, Kim KS, Sung D, Lee H, Shin JY, Hwang J, Lee SY, Lee SY, Han SW, Noh DY, Loh ND, and Song C
- Abstract
The structures as building blocks for designing functional nanomaterials have fueled the development of versatile nanoprobes to understand local structures of noncrystalline specimens. Progress in analyzing structures of individual specimens with atomic scale accuracy has been notable recently. In most cases, however, only a limited number of specimens are inspected lacking statistics to represent the systems with structural inhomogeneity. Here, by employing single-particle imaging with X-ray free electron lasers and algorithms for multiple-model 3D imaging, we succeeded in investigating several thousand specimens in a couple of hours and identified intrinsic heterogeneities with 3D structures. Quantitative analysis has unveiled 3D morphology, facet indices, and elastic strain. The 3D elastic energy distribution is further corroborated by molecular dynamics simulations to gain mechanical insight at the atomic level. This work establishes a route to high-throughput characterization of individual specimens in large ensembles, hence overcoming statistical deficiency while providing quantitative information at the nanoscale.
- Published
- 2021
- Full Text
- View/download PDF
167. Attosecond Hard X-ray Free Electron Laser
- Author
-
Heung-Sik Kang, Sandeep Kumar, and Dong Eon Kim
- Subjects
Free electron model ,attosecond pulse generation ,Attosecond ,lcsh:Technology ,law.invention ,lcsh:Chemistry ,Optics ,law ,High harmonic generation ,General Materials Science ,Spontaneous emission ,Instrumentation ,lcsh:QH301-705.5 ,Fluid Flow and Transfer Processes ,Physics ,business.industry ,lcsh:T ,Process Chemistry and Technology ,General Engineering ,Free-electron laser ,Laser ,lcsh:QC1-999 ,Computer Science Applications ,X-ray free electron laser ,lcsh:Biology (General) ,lcsh:QD1-999 ,lcsh:TA1-2040 ,Cathode ray ,business ,lcsh:Engineering (General). Civil engineering (General) ,undulator radiation ,Beam (structure) ,lcsh:Physics - Abstract
In this paper, several schemes of soft X-ray and hard X-ray free electron lasers (XFEL) and their progress are reviewed. Self-amplified spontaneous emission (SASE) schemes, the high gain harmonic generation (HGHG) scheme and various enhancement schemes through seeding and beam manipulations are discussed, especially in view of the generation of attosecond X-ray pulses. Our recent work on the generation of attosecond hard X-ray pulses is also discussed. In our study, the enhanced SASE scheme is utilized, using electron beam parameters of an XFEL under construction at Pohang Accelerator Laboratory (PAL). Laser, chicane and electron beam parameters are optimized to generate an isolated attosecond hard X-ray pulse at 0.1 nm (12.4 keV). The simulations show that the manipulation of electron energy beam profile may lead to the generation of an isolated attosecond hard X-ray of 150 attosecond pulse at 0.1 nm.
- Published
- 2013
168. Time-resolved Bragg coherent X-ray diffraction revealing ultrafast lattice dynamics in nano-thickness crystal layer using X-ray free electron laser
- Author
-
Koki Shimada, Tetsu Ichitsubo, Makina Yabashi, Isao Takahashi, Kazuya Tokuda, Marcus C. Newton, Yoshinori Nishino, Eiichiro Matsubara, Tadashi Togashi, Rena Onitsuka, Kiminori Ito, Tomoya Kawaguchi, Yoshihito Tanaka, T. Nakatani, and Takahiro Sato
- Subjects
Materials science ,business.industry ,X-ray ,Free-electron laser ,Semiconductor ,Nanocrystal ,General Chemistry ,Time-resolved measurement ,Condensed Matter Physics ,Molecular physics ,X-ray free electron laser ,Crystal ,Optics ,Nano ,X-ray crystallography ,Materials Chemistry ,Ceramics and Composites ,Coherent X-ray diffraction ,Diffraction topography ,business ,Electron backscatter diffraction - Abstract
Ultrafast time-resolved Bragg coherent X-ray diffraction (CXD) has been performed to investigate lattice dynamics in a thin crystal layer with a nanoscale thickness by using a SASE (Self-Amplified Spontaneous Emission)-XFEL (X-ray Free Electron Laser) facility, SACLA. Single-shot Bragg coherent diffraction patterns of a 100 nm-thick silicon crystal were measured in the asymmetric configuration with a grazing exit using an area detector. The measured coherent diffraction patterns showed fringes extending in the surface normal direction. By using an optical femtosecond laser-pump and the XFEL-probe, a transient broadening of coherent diffraction pattern profile was observed at a delay time of around a few tens of picosecond, indicating transient crystal lattice fluctuation induced by the optical laser. A perspective application of the time-resolved Bragg CXD method to investigate small sized grains composing ceramic materials is discussed. (C)2013 The Ceramic Society of Japan. All rights reserved.
- Published
- 2013
169. Ultra-short and ultra-intense X-ray free-electron laser single pulse in one-dimensional photonic crystals
- Author
-
Philippe Jonnard, Jean-Michel André, Laboratoire de Chimie Physique - Matière et Rayonnement (LCPMR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Chimie Physique - Matière et Rayonnement ( LCPMR ), and Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Centre National de la Recherche Scientifique ( CNRS )
- Subjects
Nuclear and High Energy Physics ,Materials science ,01 natural sciences ,[ CHIM ] Chemical Sciences ,non-linear processes ,law.invention ,010309 optics ,Optics ,law ,0103 physical sciences ,[CHIM]Chemical Sciences ,010306 general physics ,Instrumentation ,Photonic crystal ,one-dimensional photonic crystal ,Radiation ,business.industry ,Free-electron laser ,Laser ,Pulse (physics) ,X-ray free electron laser ,Transmission (telecommunications) ,Extinction (optical mineralogy) ,Reflection (physics) ,Optoelectronics ,Transient (oscillation) ,business - Abstract
The propagation within a one-dimensional photonic crystal of a single ultra-short and ultra-intense pulse delivered by an X-ray free-electron laser is analysed with the framework of the time-dependent coupled-wave theory in non-linear media. It is shown that the reflection and the transmission of an ultra-short pulse present a transient period conditioned by the extinction length and also the thickness of the structure for transmission. For ultra-intense pulses, non-linear effects are expected: they could give rise to numerous phenomena, bi-stability, self-induced transparency, gap solitons, switching, etc., which have been previously shown in the optical domain.
- Published
- 2016
170. Advances in X-ray free electron laser (XFEL) diffraction data processing applied to the crystal structure of the synaptotagmin-1 / SNARE complex
- Author
-
Aaron S. Brewster, Qiangjun Zhou, William I. Weis, Minglei Zhao, Artem Y. Lyubimov, Monarin Uervirojnangkoorn, Nicholas K. Sauter, Axel T. Brunger, James M. Holton, Tara Michels-Clark, and Oliver B. Zeldin
- Subjects
0301 basic medicine ,Diffraction ,Electron density ,Materials science ,QH301-705.5 ,Science ,General Biochemistry, Genetics and Molecular Biology ,law.invention ,03 medical and health sciences ,Optics ,Microscopy, Electron, Transmission ,macromolecular crystallography ,law ,post-refinement ,Atomic model ,Image Processing, Computer-Assisted ,Biology (General) ,General Immunology and Microbiology ,business.industry ,General Neuroscience ,Resolution (electron density) ,Free-electron laser ,General Medicine ,Laser ,Biophysics and Structural Biology ,Synchrotron ,Data set ,X-ray free electron laser ,030104 developmental biology ,Synaptotagmin I ,radiation damage ,Medicine ,Other ,business ,Crystallization ,SNARE Proteins ,Research Advance - Abstract
X-ray free electron lasers (XFELs) reduce the effects of radiation damage on macromolecular diffraction data and thereby extend the limiting resolution. Previously, we adapted classical post-refinement techniques to XFEL diffraction data to produce accurate diffraction data sets from a limited number of diffraction images (Uervirojnangkoorn et al., 2015), and went on to use these techniques to obtain a complete data set from crystals of the synaptotagmin-1 / SNARE complex and to determine the structure at 3.5 Å resolution (Zhou et al., 2015). Here, we describe new advances in our methods and present a reprocessed XFEL data set of the synaptotagmin-1 / SNARE complex. The reprocessing produced small improvements in electron density maps and the refined atomic model. The maps also contained more information than those of a lower resolution (4.1 Å) synchrotron data set. Processing a set of simulated XFEL diffraction images revealed that our methods yield accurate data and atomic models.
- Published
- 2016
171. LCLS-II: The Next Leap for X-Ray Science
- Published
- 2016
172. Native phasing of x-ray free-electron laser data for a G protein-coupled receptor
- Author
-
Mengchen Pu, Cornelius Gati, Vadim Cherezov, Benjamin Stauch, Gye Won Han, Raymond C. Stevens, Andrii Ishchenko, Wei Liu, Alexander Batyuk, Andrew Aquila, Yun Zhao, Mark S. Hunter, Sébastien Boutet, Mengning Liang, Uwe Weierstall, Petr Popov, Garrett Nelson, Vsevolod Katritch, Lorenzo Galli, Chufeng Li, Ming-Yue Lee, Zhi-Jie Liu, Daniel James, John C. H. Spence, Thomas A. White, Anton Barty, and Petra Fromme
- Subjects
0301 basic medicine ,Diffraction ,serial femtosecond crystallography ,Materials science ,Phase (waves) ,Nanotechnology ,Phase problem ,law.invention ,03 medical and health sciences ,0302 clinical medicine ,GPCR ,law ,Structural Biology ,de novo structure ,Physics::Atomic and Molecular Clusters ,Research Articles ,Quantitative Biology::Biomolecules ,Multidisciplinary ,Crystallography ,Quantitative Biology::Molecular Networks ,Resolution (electron density) ,Free-electron laser ,SciAdv r-articles ,SAD ,x-ray free electron laser ,Laser ,Quantitative Biology::Quantitative Methods ,030104 developmental biology ,Chemical physics ,sulfur ,Femtosecond ,native phasing ,Physics::Accelerator Physics ,ddc:500 ,Structure factor ,lipidic cubic phase ,protein ,030217 neurology & neurosurgery ,Research Article - Abstract
Anomalous signal from sulfur atoms present in most proteins was used for de novo phasing of XFEL data and solving a GPCR structure., Serial femtosecond crystallography (SFX) takes advantage of extremely bright and ultrashort pulses produced by x-ray free-electron lasers (XFELs), allowing for the collection of high-resolution diffraction intensities from micrometer-sized crystals at room temperature with minimal radiation damage, using the principle of “diffraction-before-destruction.” However, de novo structure factor phase determination using XFELs has been difficult so far. We demonstrate the ability to solve the crystallographic phase problem for SFX data collected with an XFEL using the anomalous signal from native sulfur atoms, leading to a bias-free room temperature structure of the human A2A adenosine receptor at 1.9 Å resolution. The advancement was made possible by recent improvements in SFX data analysis and the design of injectors and delivery media for streaming hydrated microcrystals. This general method should accelerate structural studies of novel difficult-to-crystallize macromolecules and their complexes.
- Published
- 2016
173. Three-Dimensional Electron Density Mapping of Shape-Controlled Nanoparticle by Focused Hard X-ray Diffraction Microscopy
- Author
-
Yoshinori Nishino, Eiichiro Matsubara, Tetsuya Ishikawa, Kazuto Yamauchi, Ryosuke Tsutsumi, Yukio Takahashi, and Nobuyuki Zettsu
- Subjects
Diffraction ,Electron density ,Materials science ,Reflection high-energy electron diffraction ,Macromolecular Substances ,Surface Properties ,Molecular Conformation ,Bioengineering ,Atom probe ,law.invention ,Coherent X-ray diffraction microscopy ,Imaging, Three-Dimensional ,Optics ,X-Ray Diffraction ,law ,Materials Testing ,Microscopy ,Energy filtered transmission electron microscopy ,General Materials Science ,electron density ,Particle Size ,Image resolution ,phase retrieval ,business.industry ,Mechanical Engineering ,General Chemistry ,Condensed Matter Physics ,Nanostructures ,X-ray free electron laser ,Microscopy, Electron ,Electron tomography ,business ,shape-controlled nanoparticle - Abstract
Coherent diffraction microscopy using highly focused hard X-ray beams allows us to three-dimensionally observe thick objects with a high spatial resolution, also providing us with unique structural information, i.e., electron density distribution, not obtained by X-ray tomography with lenses, atom probe microscopy, or electron tomography. We measured high-contrast coherent X-ray diffraction patterns of a shape-controlled Au/Ag nanoparticle and successfully reconstructed a projection and a three-dimensional image of the nanoparticle with a single pixel (or a voxel) size of 4.2 nm in each dimension. The small pits on the surface and a hollow interior were clearly visible. The Au-rich regions were identified based on the electron density distribution, which provided insight into the formation of Au/Ag nanoboxes.
- Published
- 2010
174. Untangling the sequence of events during the S 2 → S 3 transition in photosystem II and implications for the water oxidation mechanism.
- Author
-
Ibrahim M, Fransson T, Chatterjee R, Cheah MH, Hussein R, Lassalle L, Sutherlin KD, Young ID, Fuller FD, Gul S, Kim IS, Simon PS, de Lichtenberg C, Chernev P, Bogacz I, Pham CC, Orville AM, Saichek N, Northen T, Batyuk A, Carbajo S, Alonso-Mori R, Tono K, Owada S, Bhowmick A, Bolotovsky R, Mendez D, Moriarty NW, Holton JM, Dobbek H, Brewster AS, Adams PD, Sauter NK, Bergmann U, Zouni A, Messinger J, Kern J, Yachandra VK, and Yano J
- Subjects
- Hydrogen metabolism, Magnesium metabolism, Oxidation-Reduction, Oxygen metabolism, Photons, Photosystem II Protein Complex chemistry, Quinones metabolism, Water metabolism, Photosynthesis, Photosystem II Protein Complex metabolism
- Abstract
In oxygenic photosynthesis, light-driven oxidation of water to molecular oxygen is carried out by the oxygen-evolving complex (OEC) in photosystem II (PS II). Recently, we reported the room-temperature structures of PS II in the four (semi)stable S-states, S
1 , S2 , S3 , and S0 , showing that a water molecule is inserted during the S2 → S3 transition, as a new bridging O(H)-ligand between Mn1 and Ca. To understand the sequence of events leading to the formation of this last stable intermediate state before O2 formation, we recorded diffraction and Mn X-ray emission spectroscopy (XES) data at several time points during the S2 → S3 transition. At the electron acceptor site, changes due to the two-electron redox chemistry at the quinones, QA and QB , are observed. At the donor site, tyrosine YZ and His190 H-bonded to it move by 50 µs after the second flash, and Glu189 moves away from Ca. This is followed by Mn1 and Mn4 moving apart, and the insertion of OX (H) at the open coordination site of Mn1. This water, possibly a ligand of Ca, could be supplied via a "water wheel"-like arrangement of five waters next to the OEC that is connected by a large channel to the bulk solvent. XES spectra show that Mn oxidation (τ of ∼350 µs) during the S2 → S3 transition mirrors the appearance of OX electron density. This indicates that the oxidation state change and the insertion of water as a bridging atom between Mn1 and Ca are highly correlated., Competing Interests: The authors declare no competing interest., (Copyright © 2020 the Author(s). Published by PNAS.)- Published
- 2020
- Full Text
- View/download PDF
175. Improvement of Production and Isolation of Human Neuraminidase-1 in Cellulo Crystals.
- Author
-
Koiwai K, Tsukimoto J, Higashi T, Mafuné F, Miyajima K, Nakane T, Matsugaki N, Kato R, Sirigu S, Jakobi A, Wilmanns M, Sugahara M, Tanaka T, Tono K, Joti Y, Yabashi M, Nureki O, Mizohata E, Nakatsu T, Nango E, Iwata S, Chavas LMG, Senda T, Itoh K, and Yumoto F
- Abstract
In cellulo crystallization is a developing technique to provide crystals for protein structure determination, particularly for proteins that are difficult to prepare by in vitro crystallization. This method has a key advantage: it requires neither a protein purification step nor a crystallization step. However, there is still no systematic strategy for improving the technique of in cellulo crystallization because the process occurs spontaneously. Here we report a protocol to produce and extract in cellulo crystals of human lysosomal neuraminidase-1 (NEU1) in human cultured cells. Overexpression of NEU1 protein by the retransfection of cells pretransfected with neu1 -overexpressing plasmid improved the efficiency of NEU1 crystallization. Microscopic analysis revealed that NEU1 proteins were not crystallized in the lysosome but in the endoplasmic reticulum (ER). Screening of the buffer conditions used to extract crystals from cells further improved the crystal yield. The optimal pH was 7.0, which corresponds to the pH in the ER. Use of a high-yield flask with a large surface area also yielded more crystals. These optimizations enabled us to execute a serial femtosecond crystallography experiment with a sufficient number of crystals to generate a complete data set. Optimization of the in cellulo crystallization method was thus shown to be possible.
- Published
- 2019
- Full Text
- View/download PDF
176. Atomic-Scale Perspective of Ultrafast Charge Transfer at a Dye-Semiconductor Interface
- Author
-
Felix Sturm, Fabian Weise, Robert W. Schoenlein, Stefan Neppl, Nils Huse, William F. Schlotter, Hirohito Ogasawara, Joseph Robinson, Giacomo Coslovich, Chaitanya Das Pemmaraju, Daniel Slaughter, Joshua J. Turner, Stephen R. Leone, Josh Vura-Weis, Daniel M. Neumark, Hendrik Bluhm, David Prendergast, Ming-Fu Lin, Michael P. Minitti, Michael Holmes, Marc Messerschmidt, Ali Belkacem, Hana Cho, Robert A. Kaindl, Oleg Krupin, Katrin R. Siefermann, Champak Khurmi, Jin Z. Zhang, Jinghua Guo, Sheraz Gul, Andrey Shavorskiy, Amy A. Cordones, Camila Bacellar, Matthew L. Strader, Dennis Nordlund, and Oliver Gessner
- Subjects
Chemistry ,constrained density functional theory ,interfacial charge transfer ,Electronic structure ,Photoexcitation ,X-ray free electron laser ,Dye-sensitized solar cell ,time-resolved X-ray photoelectron spectroscopy ,Affordable and Clean Energy ,Ab initio quantum chemistry methods ,Chemical physics ,Excited state ,Atom ,Physical Sciences ,Chemical Sciences ,General Materials Science ,ddc:530 ,Electron configuration ,Physical and Theoretical Chemistry ,Atomic physics ,dye-sensitized solar cells ,Spectroscopy ,photocatalysis - Abstract
Understanding interfacial charge-transfer processes on the atomic level is crucial to support the rational design of energy-challenge relevant systems such as solar cells, batteries, and photocatalysts. A femtosecond time-resolved core-level photoelectron spectroscopy study is performed that probes the electronic structure of the interface between ruthenium-based N3 dye molecules and ZnO nanocrystals within the first picosecond after photoexcitation and from the unique perspective of the Ru reporter atom at the center of the dye. A transient chemical shift of the Ru 3d inner-shell photolines by (2.3 ± 0.2) eV to higher binding energies is observed 500 fs after photoexcitation of the dye. The experimental results are interpreted with the aid of ab initio calculations using constrained density functional theory. Strong indications for the formation of an interfacial charge-transfer state are presented, providing direct insight into a transient electronic configuration that may limit the efficiency of photoinduced free charge-carrier generation. © 2014 American Chemical Society.
- Published
- 2015
177. Structural basis for bifunctional peptide recognition at human $\delta$-opioid receptor
- Author
-
Gye Won Han, Chun Hong Yoon, John C. H. Spence, Wei-Wei Liu, Gustavo Fenalti, Karel Guillemyn, Thomas A. White, Raimund Fromme, Cecilia Betti, Anton Barty, Haitao Zhang, Markus Metz, Chelsie E. Conrad, Peter W. Schiller, Raymond C. Stevens, Shibom Basu, Marc Messerschmidt, Vadim Cherezov, Bryan L. Roth, Dominik Oberthuer, Cornelius Gati, Andrii Ishchenko, Steven Ballet, Petra Fromme, Dingjie Wang, Henry N. Chapman, Daniel James, Patrick T. Giguere, Jesse Coe, Nadia A. Zatsepin, Sébastien Boutet, Vsevolod Katritch, Dirk Tourwé, Uwe Weierstall, Garth J. Williams, and Oleksandr Yefanov
- Subjects
Agonist ,serial femtosecond crystallography ,Stereochemistry ,medicine.drug_class ,ligand binding ,Peptide ,Article ,chemistry.chemical_compound ,Structural Biology ,Opioid receptor ,ddc:570 ,medicine ,G protein-coupled receptor ,protein structure ,Binding site ,Bifunctional ,Opioid peptide ,Molecular Biology ,chemistry.chemical_classification ,Tetrapeptide ,opioid receptor ,3. Good health ,X-ray free electron laser ,chemistry ,Biochemistry ,Bi-functional peptide - Abstract
Nature structural & molecular biology 22(3), 265 - 268(2015). doi:10.1038/nsmb.2965, Bifunctional μ- and δ-opioid receptor (OR) ligands are potential therapeutic alternatives, with diminished side effects, to alkaloid opiate analgesics. We solved the structure of human δ-OR bound to the bifunctional δ-OR antagonist and μ-OR agonist tetrapeptide H-Dmt-Tic-Phe-Phe-NH2 (DIPP-NH2) by serial femtosecond crystallography, revealing a cis-peptide bond between H-Dmt and Tic. The observed receptor-peptide interactions are critical for understanding of the pharmacological profiles of opioid peptides and for development of improved analgesics., Published by Nature Publishing Group, London [u.a.]
- Published
- 2015
178. Status of the SACLA Facility
- Author
-
Hitoshi Tanaka, Makina Yabashi, Tetsuya Ishikawa, and Kensuke Tono
- Subjects
X-ray optics ,02 engineering and technology ,lcsh:Technology ,01 natural sciences ,Linear particle accelerator ,lcsh:Chemistry ,SACLA ,Data acquisition ,Optics ,photon diagnostics ,0103 physical sciences ,Broadband ,General Materials Science ,linac ,010306 general physics ,lcsh:QH301-705.5 ,Instrumentation ,undulator ,Fluid Flow and Transfer Processes ,Physics ,lcsh:T ,business.industry ,Process Chemistry and Technology ,damage-free analysis ,General Engineering ,Free-electron laser ,Undulator ,021001 nanoscience & nanotechnology ,lcsh:QC1-999 ,Computer Science Applications ,X-ray free electron laser ,lcsh:Biology (General) ,lcsh:QD1-999 ,Beamline ,lcsh:TA1-2040 ,ultrafast science ,lcsh:Engineering (General). Civil engineering (General) ,0210 nano-technology ,business ,lcsh:Physics - Abstract
This article reports the current status of SACLA, SPring-8 Angstrom Compact free electron LAser, which has been producing stable X-ray Free Electron Laser (XFEL) light since 2012. A unique injector system and a short-period in-vacuum undulator enable the generation of ultra-short coherent X-ray pulses with a wavelength shorter than 0.1 nm. Continuous development of accelerator technologies has steadily improved XFEL performance, not only for normal operations but also for fast switching operation of the two beamlines. After upgrading the broadband spontaneous-radiation beamline to produce soft X-ray FEL with a dedicated electron beam driver, it is now possible to operate three FEL beamlines simultaneously. Beamline/end-station instruments and data acquisition/analyzation systems have also been upgraded to allow advanced experiments. These efforts have led to the production of novel results and will offer exciting new opportunities for users from many fields of science.
- Published
- 2017
179. Feasibility considerations of a soft-x-ray distributed feedback laser pumped by an x-ray free electron laser
- Author
-
Karine Le Guen, Jean-Michel André, Philippe Jonnard, Laboratoire de Chimie Physique - Matière et Rayonnement (LCPMR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Chimie Physique - Matière et Rayonnement ( LCPMR ), and Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Centre National de la Recherche Scientifique ( CNRS )
- Subjects
Soft x ray ,Distributed feedback laser ,[PHYS.PHYS.PHYS-OPTICS]Physics [physics]/Physics [physics]/Optics [physics.optics] ,Materials science ,[ PHYS.PHYS.PHYS-OPTICS ] Physics [physics]/Physics [physics]/Optics [physics.optics] ,business.industry ,Free-electron laser ,X-ray ,FOS: Physical sciences ,x-ray free electron laser ,Condensed Matter Physics ,Distributed Bragg reflector ,7. Clean energy ,Industrial and Manufacturing Engineering ,Atomic and Molecular Physics, and Optics ,Optics ,multilayer Bragg reflector ,soft-x-ray distributed feedback laser ,business ,Instrumentation ,Optics (physics.optics) ,Physics - Optics - Abstract
We discuss the feasibility of a soft-x-ray distributed feedback laser (DFL) pumped by an x-ray free electron laser (X-FEL). The DFL under consideration is a Mg/SiC bi-layered Bragg reflector pumped by a single X-FEL bunch at 57.4 eV, stimulating the Mg L2,3 emission at 49 eV corresponding to the 3s-3d -> 2p1/2,3/2 transition. Based on a model developed by Yariv and Yeh and an extended coupled-wave theory, we show that it would be possible to obtain a threshold gain compatible with the pumping provided by available X-FEL facilities., This paper has 7 pages and is published in Laser Physics 24, 085001 (2014). The webpage of the editor is http://iopscience.iop.org/1555-6611/24/8/085001/
- Published
- 2014
180. Accelerator-based X-ray sources: synchrotron radiation, X-ray free electron lasers and beyond.
- Author
-
Ishikawa T
- Abstract
The evolution of synchrotron radiation (SR) sources and related sciences is discussed to explain the 'generation' of the SR sources. Most of the contemporary SR sources belong to the third generation, where the storage rings are optimized for the use of undulator radiation. The undulator development allowed to reduction of the electron energy of the storage ring necessary for delivering 10 keV X-rays from the initial 6-8 GeV to the current 3 Gev. Now is the transitional period from the double-bend-achromat lattice-based storage ring to the multi-bend-achromat lattice to achieve much smaller electron beam emittance. Free electron lasers are the other important accelerator-based light sources which recently reached hard X-ray regime by using self-amplified spontaneous emission scheme. Future accelerator-based X-ray sources should be continuous wave X-ray free electron lasers and pulsed X-ray free electron lasers. Some pathways to reach the future case are discussed. This article is part of the theme issue 'Fifty years of synchrotron science: achievements and opportunities'.
- Published
- 2019
- Full Text
- View/download PDF
181. Snapshot of an oxygen intermediate in the catalytic reaction of cytochrome c oxidase.
- Author
-
Ishigami I, Lewis-Ballester A, Echelmeier A, Brehm G, Zatsepin NA, Grant TD, Coe JD, Lisova S, Nelson G, Zhang S, Dobson ZF, Boutet S, Sierra RG, Batyuk A, Fromme P, Fromme R, Spence JCH, Ros A, Yeh SR, and Rousseau DL
- Subjects
- Animals, Catalysis, Catalytic Domain, Cattle, Copper chemistry, Crystallography, X-Ray, Electron Transport Complex IV genetics, Oxidation-Reduction, Protein Conformation, Electron Transport Complex IV chemistry, Heme chemistry, Iron chemistry, Oxygen chemistry
- Abstract
Cytochrome c oxidase (C c O) reduces dioxygen to water and harnesses the chemical energy to drive proton translocation across the inner mitochondrial membrane by an unresolved mechanism. By using time-resolved serial femtosecond crystallography, we identified a key oxygen intermediate of bovine C c O. It is assigned to the P
R -intermediate, which is characterized by specific redox states of the metal centers and a distinct protein conformation. The heme a3 iron atom is in a ferryl (Fe4+ = O2- ) configuration, and heme a and CuB are oxidized while CuA is reduced. A Helix-X segment is poised in an open conformational state; the heme a farnesyl sidechain is H-bonded to S382, and loop-I-II adopts a distinct structure. These data offer insights into the mechanism by which the oxygen chemistry is coupled to unidirectional proton translocation., Competing Interests: The authors declare no conflict of interest.- Published
- 2019
- Full Text
- View/download PDF
182. Recent innovations in membrane-protein structural biology.
- Author
-
Allen JP
- Subjects
- Cryoelectron Microscopy, Electrons, Lasers, Protein Structural Elements, X-Ray Diffraction, Membrane Proteins physiology
- Abstract
Innovations are expanding the capabilities of experimental investigations of the structural properties of membrane proteins. Traditionally, three-dimensional structures have been determined by measuring x-ray diffraction using protein crystals with a size of least 100 μm. For membrane proteins, achieving crystals suitable for these measurements has been a significant challenge. The availabilities of micro-focus x-ray beams and the new instrumentation of x-ray free-electron lasers have opened up the possibility of using submicrometer-sized crystals. In addition, advances in cryo-electron microscopy have expanded the use of this technique for studies of protein crystals as well as studies of individual proteins as single particles. Together, these approaches provide unprecedented opportunities for the exploration of structural properties of membrane proteins, including dynamical changes during protein function., Competing Interests: No competing interests were disclosed.No competing interests were disclosed.No competing interests were disclosed.No competing interests were disclosed.
- Published
- 2019
- Full Text
- View/download PDF
183. Non-cryogenic structure of a chloride pump provides crucial clues to temperature-dependent channel transport efficiency.
- Author
-
Yun JH, Li X, Park JH, Wang Y, Ohki M, Jin Z, Lee W, Park SY, Hu H, Li C, Zatsepin N, Hunter MS, Sierra RG, Koralek J, Yoon CH, Cho HS, Weierstall U, Tang L, Liu H, and Lee W
- Subjects
- Crystallography, X-Ray, Protein Domains, Actinomycetales chemistry, Chloride Channels chemistry, Rhodopsins, Microbial chemistry
- Abstract
Non-cryogenic protein structures determined at ambient temperature may disclose significant information about protein activity. Chloride-pumping rhodopsin (ClR) exhibits a trend to hyperactivity induced by a change in the photoreaction rate because of a gradual decrease in temperature. Here, to track the structural changes that explain the differences in CIR activity resulting from these temperature changes, we used serial femtosecond crystallography (SFX) with an X-ray free electron laser (XFEL) to determine the non-cryogenic structure of ClR at a resolution of 1.85 Å, and compared this structure with a cryogenic ClR structure obtained with synchrotron X-ray crystallography. The XFEL-derived ClR structure revealed that the all- trans retinal (ATR) region and positions of two coordinated chloride ions slightly differed from those of the synchrotron-derived structure. Moreover, the XFEL structure enabled identification of one additional water molecule forming a hydrogen bond network with a chloride ion. Analysis of the channel cavity and a difference distance matrix plot (DDMP) clearly revealed additional structural differences. B-factor information obtained from the non-cryogenic structure supported a motility change on the residual main and side chains as well as of chloride and water molecules because of temperature effects. Our results indicate that non-cryogenic structures and time-resolved XFEL experiments could contribute to a better understanding of the chloride-pumping mechanism of ClR and other ion pumps.
- Published
- 2019
- Full Text
- View/download PDF
184. Scanning coherent x-ray microscopy as a tool for XFEL nanobeam characterization
- Author
-
Schropp, Andreas, Hoppe, Robert, Patommel, Jens, Seiboth, Frank, Uhlén, Fredrik, Vogt, Ulrich, Lee, Hae Ja, Nagler, Bob, Galtier, Eric C, Zastrau, Ulf, Arnold, Brice, Heimann, Philip, Hastings, Jerome B, Schroer, Christian G, Schropp, Andreas, Hoppe, Robert, Patommel, Jens, Seiboth, Frank, Uhlén, Fredrik, Vogt, Ulrich, Lee, Hae Ja, Nagler, Bob, Galtier, Eric C, Zastrau, Ulf, Arnold, Brice, Heimann, Philip, Hastings, Jerome B, and Schroer, Christian G
- Abstract
During the last years, scanning coherent x-ray microscopy, also called ptychography, has revolutionized nanobeam characterization at third generation x-ray sources. The method yields the complete information on the complex valued, nanofocused wave field with high spatial resolution. In an experiment carried out at the Matter in Extreme Conditions (MEC) instrument at the Linac Coherent Light Source (LCLS) we successfully applied the method to an attenuated nanofocused XFEL beam with a size of 180(h) × 150(v) nm2 (FWHM) in horizontal (h) and vertical direction (v), respectively. It was created by a set of 20 beryllium compound refractive lenses (Be-CRLs). By using a fast detector (CSPAD) to record the diffraction patterns and a fast implementation of the phase retrieval code running on a graphics processing unit (GPU), the applicability of the method as a real-time XFEL nanobeam diagnostic is highlighted., QC 20140115
- Published
- 2013
- Full Text
- View/download PDF
185. Time-resolved Bragg coherent X-ray diffraction revealing ultrafast lattice dynamics in nano-thickness crystal layer using X-ray free electron laser
- Author
-
Tanaka, Yoshihito, Ito, Kiminori, Nakatani, Takashi, Onitsuka, Rena, Newton, Marcus, Sato, Takahiro, Togashi, Tadashi, Yabashi, Makina, Kawaguchi, Tomoya, Shimada, Koki, Tokuda, Kazuya, Takahashi, Isao, Ichitsubo, Tetsu, Matsubara, Eiichiro, Nishino, Yoshinori, Tanaka, Yoshihito, Ito, Kiminori, Nakatani, Takashi, Onitsuka, Rena, Newton, Marcus, Sato, Takahiro, Togashi, Tadashi, Yabashi, Makina, Kawaguchi, Tomoya, Shimada, Koki, Tokuda, Kazuya, Takahashi, Isao, Ichitsubo, Tetsu, Matsubara, Eiichiro, and Nishino, Yoshinori
- Abstract
Ultrafast time-resolved Bragg coherent X-ray diffraction (CXD) has been performed to investigate lattice dynamics in a thin crystal layer with a nanoscale thickness by using a SASE (Self-Amplified Spontaneous Emission)-XFEL (X-ray Free Electron Laser) facility, SACLA. Single-shot Bragg coherent diffraction patterns of a 100 nm-thick silicon crystal were measured in the asymmetric configuration with a grazing exit using an area detector. The measured coherent diffraction patterns showed fringes extending in the surface normal direction. By using an optical femtosecond laser-pump and the XFEL-probe, a transient broadening of coherent diffraction pattern profile was observed at a delay time of around a few tens of picosecond, indicating transient crystal lattice fluctuation induced by the optical laser. A perspective application of the time-resolved Bragg CXD method to investigate small sized grains composing ceramic materials is discussed. (C)2013 The Ceramic Society of Japan. All rights reserved.
- Published
- 2013
186. Damage threshold investigation using grazing incidence irradiation by hard X-ray free electron laser
- Author
-
1000020468276, Koyama, T., 1000020423197, Yumoto, H., 1000000353508, Tono, K., Sato, T., 1000060415239, Togashi, T., 1000040506250, Inubushi, Y., 1000090648073, Katayama, T., Kim, J., 1000010423196, Matsuyama, S., 1000030362651, Mimura, H., 1000000372144, Yabashi, M., 1000010174575, Yamauchi, K., 1000030443550, Ohashi, H., 1000020468276, Koyama, T., 1000020423197, Yumoto, H., 1000000353508, Tono, K., Sato, T., 1000060415239, Togashi, T., 1000040506250, Inubushi, Y., 1000090648073, Katayama, T., Kim, J., 1000010423196, Matsuyama, S., 1000030362651, Mimura, H., 1000000372144, Yabashi, M., 1000010174575, Yamauchi, K., 1000030443550, and Ohashi, H.
- Abstract
T. Koyama, H. Yumoto, K. Tono, T. Sato, T. Togashi, Y. Inubushi, T. Katayama, J. Kim, S. Matsuyama, H. Mimura, M. Yabashi, K. Yamauchi, and H. Ohashi "Damage threshold investigation using grazing incidence irradiation by hard x-ray free electron laser", Proc. SPIE 8848, Advances in X-Ray/EUV Optics and Components VIII, 88480T (27 September 2013); https://doi.org/10.1117/12.2025377.
- Published
- 2013
187. Modeling of XFEL induced ionization and atomic displacement in protein nanocrystals
- Author
-
Caleman, Carl, Tîmneanu, Nicusor, Martin, A. V., White, T. A., Scott, H. A., Barty, A., Aquila, A., Chapman, H. N., Caleman, Carl, Tîmneanu, Nicusor, Martin, A. V., White, T. A., Scott, H. A., Barty, A., Aquila, A., and Chapman, H. N.
- Abstract
X-ray free-electron lasers enable high-resolution imaging of biological materials by using short enough pulses to outrun many of the effects of radiation damage. Experiments conducted at the LCLS have obtained diffraction data from single particles and protein nanocrystals at doses to the sample over 3 GGy. The details of the interaction of the X-ray FEL pulse with the sample determine the limits of this new paradigm for imaging. Recent studies suggest that in the case of crystalline samples, such as protein nanocrystals, the atomic displacements and loss of bound electrons in the crystal (due to the high X- ray intensity) has the effect of gating the diffraction signal, and hence making the experiment less radiation sensitive. Only the incident photon intensity in the first part of the pulse, before the Bragg diffraction has died out, is relevant to acquiring signal and the rest of the pulse will mainly contribute to a diffuse background. In this work we use a plasma based non-local thermodynamic equilibrium code to explore the displacement and the ionization of a protein nanocrystal at various X-ray wavelengths and intensities.
- Published
- 2012
- Full Text
- View/download PDF
188. On the Feasibility of Nanocrystal Imaging Using Intense and Ultrashort X-ray Pulses
- Author
-
Caleman, Carl, Huldt, Gösta, Maia, Filipe R. N. C., Ortiz, Carlos, Parak, Fritz G., Hajdu, Janos, van der Spoel, David, Chapman, Henry N., Timneanu, Nicusor, Caleman, Carl, Huldt, Gösta, Maia, Filipe R. N. C., Ortiz, Carlos, Parak, Fritz G., Hajdu, Janos, van der Spoel, David, Chapman, Henry N., and Timneanu, Nicusor
- Abstract
Structural studies of biological macromolecules are severely limited by radiation damage. Traditional crystallography curbs the effects of damage by spreading damage over many copies of the molecule of interest in the crystal. X-ray lasers offer an additional opportunity for limiting damage by out-running damage processes with ultrashort and very intense X-ray pulses Such pulses may allow the imaging of single molecules, clusters; Or nanoparticles: Coherent flash Imaging Will also open up new avenues for structural studies on nano- and microcrystalline substances. This paper addresses the theoretical potentials and limitations of nanocrystallography with extremely intense coherent X-ray pulses. We use urea nanocrystals as a model for generic biological substances and simulate the primary and secondary ionization dynamics in the crystalline sample. The results establish conditions for ultrafast single shot nanocrystallography diffraction experiments as a function of X-ray fluence, pulse duration, and the size of nanocrystals. Nanocrystallography using ultrafast X-ray pulses has the potential to open up a new route in protein crystallography to solve atomic structures of many systems that remain Inaccessible using conventional X-ray sources.
- Published
- 2011
- Full Text
- View/download PDF
189. Fluid sample injectors for x-ray free electron laser at SACLA.
- Author
-
Tono, Kensuke
- Subjects
- *
X-rays , *FREE electron lasers , *FLUIDS , *INJECTORS , *MICROMETERS - Abstract
This paper provides a review on sample injectors which are provided at SPring-8 Angstrom Compact free electron LAser (SACLA) for conducting serial measurement in a ‘diffract-before-destroy’ scheme using an x-ray free electron laser (XFEL). Versatile experimental platforms at SACLA are able to accept various types of injectors, among which liquid-jet, droplet and viscous carrier injectors are frequently utilized. These injectors produce different forms of fluid targets such as a liquid filament with a diameter in the order of micrometer, micro-droplet synchronized to XFEL pulses, and slowly flowing column of highly viscous fluid with a rate below $1~\unicode[STIX]{x03BC}\text{L}~\text{min}^{-1}$. Characteristics and applications of the injectors are described. [ABSTRACT FROM AUTHOR]
- Published
- 2017
- Full Text
- View/download PDF
190. Three-Dimensional Electron Density Mapping of Shape-Controlled Nanoparticle by Focused Hard X-ray Diffraction Microscopy
- Author
-
Takahashi, Yukio, Zettsu, Nobuyuki, Nishino, Yoshinori, Tsutsumi, Ryosuke, Matsubara, Eiichiro, Ishikawa, Tetsuya, Yamauchi, Kazuto, Takahashi, Yukio, Zettsu, Nobuyuki, Nishino, Yoshinori, Tsutsumi, Ryosuke, Matsubara, Eiichiro, Ishikawa, Tetsuya, and Yamauchi, Kazuto
- Published
- 2010
191. Three-Dimensional Electron Density Mapping of Shape-Controlled Nanoparticle by Focused Hard X-ray Diffraction Microscopy
- Author
-
90173864, Takahashi, Yukio, Zettsu, Nobuyuki, Nishino, Yoshinori, Tsutsumi, Ryosuke, Matsubara, Eiichiro, Ishikawa, Tetsuya, Yamauchi, Kazuto, 90173864, Takahashi, Yukio, Zettsu, Nobuyuki, Nishino, Yoshinori, Tsutsumi, Ryosuke, Matsubara, Eiichiro, Ishikawa, Tetsuya, and Yamauchi, Kazuto
- Published
- 2010
192. STUDY OF LONGITUDINAL SPACE CHARGE WAVES IN SPACE-CHARGE DOMINATED BEAMS
- Author
-
Thangaraj, Jayakar Charles Tobin and Thangaraj, Jayakar Charles Tobin
- Abstract
Future x-ray free electron lasers will probe matter at the atomic scale with femtosecond time resolution. Such x-ray sources require a high current electron beam with very low emittance and energy spread. Any density fluctuation in an intense beam can launch space charge waves that lead to energy modulation. The energy modulations may cause further density modulations in any dispersive element and can, for example, excite the microbunching instability in x-ray free electron lasers. Hence, it is important to understand and control the evolution of density modulations on an intense beam. This dissertation focuses on long path-length experimental study of intense beams with density perturbations. The experimental results are compared with theory and computer simulation. We took advantage of the multi-turn operation of the University of Maryland Electron Ring (UMER), to carry out long path-length (100 m) experimental studies of space-charge-dominated beams with density perturbations. First, a single density perturbation is introduced on a space-charge dominated electron beam using photoemission from a laser. The perturbation splits and propagates as a fast and a slow wave on the beam. The speed of the space charge waves is measured experimentally as a function of beam current and perturbation strength. The results are in good agreement with Particle-in-cell (PIC) simulation and 1-D cold fluid theory in the linear regime. We then show that linear space-charge waves can be used as non-interceptive transverse beam diagnostics in UMER. Using time-resolved imaging techniques, we report the transverse effects of a longitudinal perturbation in a circular machine. We introduce multiple perturbations on the beam and show that the fast and the slow waves superpose and cross each other. We then present experimental results on the beam response from introducing a controlled energy modulation on the density modulated beam and compare them with the theory. In the non-linear regime, w
- Published
- 2009
193. Growth of Cuprous Oxide Particles in Liquid-Phase Synthesis Investigated by X-ray Laser Diffraction.
- Author
-
Oroguchi T, Yoshidome T, Yamamoto T, and Nakasako M
- Abstract
Cuprous oxide (Cu
2 O) particles obtained by surfactant-assisted liquid-phase synthesis have cuboid shapes but the internal structures are difficult to be visualized by electron microscopy. Herein, we investigated the internal structures of numerous individual Cu2 O particles with submicrometer dimensions by X-ray diffraction imaging (XDI) using X-ray free-electron laser (XFEL) pulses. The reconstructed two-dimensional electron density maps, which displayed inhomogeneous internal structures, were divided into five classes characterized by the positions and shapes of high and low electron density areas. Further analysis of the maps in each class by a manifold learning algorithm revealed that the internal structures of Cu2 O particles varied in correlation with total electron density while retaining the characteristics within each class. On the basis of the analyses, we proposed a growth mechanism to yield the inhomogeneity in the internal structures of Cu2 O particles in surfactant-mediated liquid-phase synthesis.- Published
- 2018
- Full Text
- View/download PDF
194. Laser power meters as an X-ray power diagnostic for LCLS-II.
- Author
-
Heimann P, Moeller S, Carbajo S, Song S, Dakovski G, Nordlund D, and Fritz D
- Abstract
For the LCLS-II X-ray instruments, laser power meters are being developed as compact X-ray power diagnostics to operate at soft and tender X-ray photon energies. These diagnostics can be installed at various locations along an X-ray free-electron laser (FEL) beamline in order to monitor the transmission of X-ray optics along the beam path. In addition, the power meters will be used to determine the absolute X-ray power at the endstations. Here, thermopile power meters, which measure average power, and have been chosen primarily for their compatibility with the high repetition rates at LCLS-II, are evaluated. A number of characteristics in the soft X-ray range are presented including linearity, calibrations conducted with a photodiode and a gas monitor detector as well as ultra-high-vacuum compatibility tests using residual gas analysis. The application of these power meters for LCLS-II and other X-ray FEL sources is discussed.
- Published
- 2018
- Full Text
- View/download PDF
195. X-ray free electron laser: opportunities for drug discovery.
- Author
-
Cheng RKY, Abela R, and Hennig M
- Subjects
- Crystallography, X-Ray, Data Collection methods, Ligands, Proteins ultrastructure, Synchrotrons, Temperature, X-Ray Diffraction, Drug Discovery methods, Electrons, Lasers, Proteins chemistry, Small Molecule Libraries chemistry
- Abstract
Past decades have shown the impact of structural information derived from complexes of drug candidates with their protein targets to facilitate the discovery of safe and effective medicines. Despite recent developments in single particle cryo-electron microscopy, X-ray crystallography has been the main method to derive structural information. The unique properties of X-ray free electron laser (XFEL) with unmet peak brilliance and beam focus allow X-ray diffraction data recording and successful structure determination from smaller and weaker diffracting crystals shortening timelines in crystal optimization. To further capitalize on the XFEL advantage, innovations in crystal sample delivery for the X-ray experiment, data collection and processing methods are required. This development was a key contributor to serial crystallography allowing structure determination at room temperature yielding physiologically more relevant structures. Adding the time resolution provided by the femtosecond X-ray pulse will enable monitoring and capturing of dynamic processes of ligand binding and associated conformational changes with great impact to the design of candidate drug compounds., (© 2017 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.)
- Published
- 2017
- Full Text
- View/download PDF
196. TESLA : the superconducting electron-positron linear collider with an integrated X-ray laser laboratory. Technical design report. Part 4: A detector for TESLA
- Author
-
Behnke, T., Bertolucci, S., Heuer, R.-D., and Settles, R.
- Subjects
TESLA ,magnetic detector ,FEL ,X-ray free electron laser ,accelerators ,X-ray laser ,e+ e- linear collider ,ddc:539.73606 ,linear collider ,technical design report - Published
- 2001
197. TESLA : the superconducting electron-positron linear collider with an integrated X-ray laser laboratory. Technical design report. Part 6: Appendices
- Author
-
Klanner, R., Telnov, V., Katz, U., Klein, M., Levy, A., Kaiser, R., Nowak, W. D., DeSanctis, E., Laget, J.-M., and Rith, K.
- Subjects
TESLA ,magnetic detector ,FEL ,X-ray free electron laser ,accelerators ,X-ray laser ,e+ e- linear collider ,ddc:539.73606 ,linear collider ,technical design report - Published
- 2001
198. TESLA : the superconducting electron-positron linear collider with an integrated X-ray laser laboratory. Technical design report. Part 5: The X-Ray Free Electron Laser
- Author
-
Materlik, G. and Tschentscher, T.
- Subjects
TESLA ,magnetic detector ,FEL ,X-ray free electron laser ,accelerators ,X-ray laser ,e+ e- linear collider ,XFEL ,ddc:539.73606 ,linear collider ,technical design report - Published
- 2001
199. TESLA : the superconducting electron-positron linear collider with an integrated X-ray laser laboratory. Technical design report. Part 2: The accelerator
- Author
-
Brinkmann, R., Floettmann, K., Rossbach, J., Schmueser, P., Walker, N., and Weise, H.
- Subjects
TESLA ,magnetic detector ,FEL ,X-ray free electron laser ,accelerators ,X-ray laser ,e+ e- linear collider ,ddc:539.73606 ,linear collider ,technical design report - Published
- 2001
200. TESLA: the superconducting electron-positron linear collider with an integrated X-ray laser laboratory. Technical design report. Part 1: Particle physics with the electron-positron linear collider
- Author
-
Richard, F., Schneider, J. R., Trines, D., and Wagner, A.
- Subjects
TESLA ,magnetic detector ,FEL ,X-ray free electron laser ,539.736 ,accelerators ,X-ray laser ,e+ e- linear collider ,linear collider ,technical design report - Abstract
Hamburg : DESY 1 online resource (xvi, 58 pages) : illustrations (2001)., Published by DESY, Hamburg
- Published
- 2001
- Full Text
- View/download PDF
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.