Development Of Synchrotron Radiation Sources Research Articles

A distributed data processing scheme based on Hadoop for synchrotron radiation experiments.

With the development of synchrotron radiation sources and high-frame-rate detectors, the amount of experimental data collected at synchrotron radiation beamlines has increased exponentially. As a result, data processing for synchrotron radiation experiments has entered the era of big data. It is becoming increasingly important for beamlines to have the capability to process large-scale data in parallel to keep up with the rapid growth of data. Currently, there is no set of data processing solutions based on the big data technology framework for beamlines. Apache Hadoop is a widely used distributed system architecture for solving the problem of massive data storage and computation. This paper presents a set of distributed data processing schemes for beamlines with experimental data using Hadoop. The Hadoop Distributed File System is utilized as the distributed file storage system, and Hadoop YARN serves as the resource scheduler for the distributed computing cluster. A distributed data processing pipeline that can carry out massively parallel computation is designed and developed using Hadoop Spark. The entire data processing platform adopts a distributed microservice architecture, which makes the system easy to expand, reduces module coupling and improves reliability.

Structure-guided fragment-based drug discovery at the synchrotron: screening binding sites and correlations with hotspot mapping.

Structure-guided drug discovery emerged in the 1970s and 1980s, stimulated by the three-dimensional structures of protein targets that became available, mainly through X-ray crystal structure analysis, assisted by the development of synchrotron radiation sources. Structures of known drugs or inhibitors were used to guide the development of leads. The growth of high-throughput screening during the late 1980s and the early 1990s in the pharmaceutical industry of chemical libraries of hundreds of thousands of compounds of molecular weight of approximately 500 Da was impressive but still explored only a tiny fraction of the chemical space of the predicted 1040 drug-like compounds. The use of fragments with molecular weights less than 300 Da in drug discovery not only decreased the chemical space needing exploration but also increased promiscuity in binding targets. Here we discuss advances in X-ray fragment screening and the challenge of identifying sites where fragments not only bind but can be chemically elaborated while retaining their positions and binding modes. We first describe the analysis of fragment binding using conventional X-ray difference Fourier techniques, with Mycobacterium abscessus SAICAR synthetase (PurC) as an example. We observe that all fragments occupy positions predicted by computational hotspot mapping. We compare this with fragment screening at Diamond Synchrotron Light Source XChem facility using PanDDA software, which identifies many more fragment hits, only some of which bind to the predicted hotspots. Many low occupancy sites identified may not support elaboration to give adequate ligand affinity, although they will likely be useful in drug discovery as ‘warm spots’ for guiding elaboration of fragments bound at hotspots. We discuss implications of these observations for fragment screening at the synchrotron sources.This article is part of the theme issue ‘Fifty years of synchrotron science: achievements and opportunities’.

Synchrotron radiation sources in Brazil.

The development of synchrotron radiation sources in Brazil is described from a brief historical point of view followed by a description of the Sirius project, a new 3 GeV fourth-generation synchrotron light source with 518 m circumference and 0.25 nm.rad emittance, in final construction stage at the Brazilian Synchrotron Light Laboratory campus, in Campinas. As one of the pioneer fourth-generation machines, many accelerator engineering challenges were studied in depth and resulted in quite a few innovative developments. In this paper, we review some of these developments. This article is part of the theme issue 'Fifty years of synchrotron science: achievements and opportunities'.

Synchrotron radiation in Novosibirsk: The first 13 years

We describe the development of activity at the Siberian Center for Synchrotron and Terahertz Radiation at Budker Institute of Nuclear Physics (BINP), SB RAS, since 1974, when the history of experiments with synchrotron radiation (SR) in the world was just beginning–there were no dedicated sources of radiation and works can be carried out at several nuclear centers in the world. BINP made a significant contribution to the development of synchrotron radiation sources, and SB RAS institutes did their part for development of SR application to problems of chemistry, catalysis, biology, geology and materials science. The experiments were made at VEPP-3/VEPP-4 installation.

Synchrotron radiation: A continuing revolution in X-ray science—Diffraction limited storage rings and beyond

Electron spectroscopy and the investigation of the electronic properties of matter have been largely impacted by the development of synchrotron radiation sources providing highly brilliant, easily tunable X-ray beams with selectable polarization properties. In this brief review the development of synchrotron radiation sources over the last 50 years will be described and the scientific opportunities presented by ongoing and future source developments will be briefly highlighted.

Plasmon Line Width in Liquid Metals

With the recent development of synchrotron radiation sources and the instrumentations, inelastic X-ray scattering (IXS) has become an important tool for observing plasmons in materials. One of the significant advantages of IXS is that it can be applied to liquid samples, which is considerably difficult for electron energy loss spectroscopy. Thus far, the IXS study of plasmons in liquid samples has been performed for several systems such as liquid lithium, liquid aluminum, or lithium ammonia solutions. However, the properties of plasmons in the liquid phase are less clearly understood than those in the crystalline phase. One of such properties is the plasmon line width. For the solid state, the finite line width observed in experiments can be evaluated using the formulations derived in previous theoretical studies, in which the effect of interband transitions, phonon-assisted intraband (or interband) transitions, and the excitations of two electron–hole (e–h) pairs are considered. These effects should also play an important role in liquid, because a finite line width is also observed in liquid samples. The effects of phonon and two e–h pairs are readily extended to liquid systems, since these effects can be calculated without using information on the ionic structure. On the other hand, the effect of interband transitions is difficult to extend to the liquid state, because it strongly depends on the ionic structure. In this work, we show the derivation of a formula for evaluating the plasmon line width at the zero momentum transfer, q 1⁄4 0, in metallic liquid. The formula describes how the ionic structure influences the plasmon line width for metallic liquid. The application of the formula to liquid alkali metals is also shown. The plasmon line width at q 1⁄4 0, E1=2ð0Þ, is written as E1=2ð0Þ 1⁄4 h !p Im ð!pÞ; ð1Þ

A Unique Rheology / SAXS Combination at DESY / Petra III

Progress in the development of synchrotron radiation sources, x-ray optics and detectors brings new possibilities in x-ray instrumentation. At the P10 beamline of PETRA III, a unique rheology / SAXS setup was successfully integrated and commissioned to gain new insight in the molecular arrangement of complex fluids and soft matter under shear conditions. The setup is based on an inverted Thermo Fisher Haake Mars II rheometer with a horizontal plate/plate or cone/plate geometry, specifically designed to be probed by a vertically deflected synchrotron X-ray beam. The main advantage of this kind of configuration is the unique possibility to scan the molecular arrangement of fluid matter along the shear gradient under a variety of shear conditions. In this way, very well defined experimental conditions can be provided and molecular arrangements that are otherwise inaccessible in plate / plate geometries can be directly examined.

Mineral-Aqueous Solution Interfaces and Their Impact on the Environment

This Perspective describes an area of geochemistry that involves minerals, their surfaces, and the interactions of these surfaces with water and the ions and molecules present in water, some of which, like arsenic, are highly toxic to organisms. The importance of these interactions, together with those between microorganisms and mineral surfaces, cannot be overestimated, for they control the composition of our natural environment and mitigate some of the anthropogenic perturbations that are changing our environment in ways that are often unpredictable and sometimes detrimental. Following overviews of our scientific careers to date, including acknowledgments of our former and current students and research collaborators, we highlight some of the scientific contributions of Victor Goldschmidt, Irving Langmuir, Linus Pauling, Konrad Krauskopf, Werner Stumm , and others that led directly or indirectly to the evolution of this field, recalling personal interactions with some of these pioneers. In all fields of science, advances are made when new experimental methods, new characterisation and computational tools, and new theories become available. The field of mineral-water interface geochemistry is no different and has advanced significantly over the past 30–40 years due to enormous changes in molecular-level experimental methods, particularly those involving the extremely intense X-ray sources known as synchrotrons, in digital computers, and in molecular-level theories. We (GB and GC) offer our perspectives on the development of synchrotron radiation sources and their applications to mineral-water interface processes, based on our personal experiences starting in the early days of these major user facilities. We discuss some of these new methods and theories and their applications to mineral-water interface processes through various examples. Because of the complexity of mineral-water interfaces, particularly in natural Earth surface environments, where natural organic matter and microorganisms play very important roles, we adopt a reductionist approach and consider simple model systems of increasing complexity in our quest to understand the chemical processes occurring at these interfaces at the molecular level. We start with a discussion of the acid-base chemistry of metal-oxide surfaces in contact with bulk water and empirical models of the electrical double layer (EDL) that is thought to develop at solid-water interfaces. We then consider experimental and theoretical studies of the EDL, which show that the classical Helmholtz-Gouy-Chapman-Stern-Grahame model is qualitatively correct. Following a story about some of the new, controversial research on the structure of water, we discuss (1) experimental and theoretical studies of the reaction of water with metal-oxide surfaces, (2) the structure of hydrated mineral surfaces, (3) the uptake of cations and anions on metal-oxide surfaces, (4) X-ray absorption spectroscopy studies of lead and arsenic adsorption complexes at mineral-water interfaces, (5) the adsorption of organic molecules at mineral-water interfaces, (6) the effect of organic and microbial biofilm coatings on the reactivity of mineral surfaces, and (7) the effect of particle size on the structure and properties of nanoparticles, using ferrihydrite as an example of a natural nanomineral and silver nanoparticles as an example of an engineered nanoparticle. In keeping with the spirit of Geochemical Perspectives , we interspersed personal experiences resulting from our involvement in most of these research areas. To put the results of this more basic research in context we end by discussing selected applications of mineral-water interface geochemistry to environmental and Earth science problems, including (1) sorption reactions in real environmental systems that were anthropogenically perturbed, focusing on lead-polluted sites in the USA and France and As-polluted areas in southern Asia and France, (2) dissolution and weathering mechanisms of silicate minerals and zircon, (3) the interaction of aluminum with diatom surfaces, (4) the interaction of cobalt with manganese oxides, (5) the role of mineral-surface reactions in isotope fractionation, (6) the role of mineral surfaces in mineral-carbonation reactions, and (7) the surface chemistry associated with alteration of nuclear waste glasses. We finish with our thoughts on what has and has not been learned about mineral-water interface processes over the past 30 years and offer our opinions about some of the exciting research opportunities in this field that await the next generation of geochemists.

Introduction: synchrotron radiation time resolved concurrent experiments—a new Italian route to China

On November 11, 2010 in Shanghai qualified Chinese and Italian scientists met for the first Bilateral Italo/Chinese Workshop on Synchrotron Radiation Time Resolved Concurrent Experiments: Advantages and Future Applications. The workshop had been conceived to increase the scientific exchange between Italy and the P.R. China with the main goal to promote the development of new and unique methods of investigation by the means of synchrotron radiation. From its discovery in 1947 the development of synchrotron radiation sources and the growth of the related applications have been impressive and continuous all over the world, in particular in the major industrialized countries. In more than 50 years since its discovery, facilities around the world constantly evolved to provide beams in different forms, at different energies and with different properties for an incredible number of applications. Experimental researches based on this technology involve many academic disciplines and synchrotron radiation is nowadays an essential tool in many frontier disciplines. Because of its outstanding features, synchrotron radiation is a high-level multidisciplinary experimental platform that plays an essential role in many researches and technological applications, being universally acknowledged by the scientific community, the society as well as the governments. Actually, with more than 50 operational storage rings existing all over the world, laboratories based on synchrotron radiation sources are the most widely operated large-scale facilities with a total investment in the range of billions of dollars. Synchrotron radiation helped to push forward a huge number of researches that led to important discoveries. The reconstruction of the atomic structure of many proteins or of the local structure of high critical temperature superconductors may give just an idea of the

Using nuclear accelerator technology to make intense X-rays

Electron accelerators, originally developed for nuclear and high energy physics research, have become by far the most intense infrared, ultraviolet and X-ray sources in the world. The increase in availability of these sources (there are now about 60 in operation around the world) has had a revolutionary effect on many branches of basic and applied research resulting in a major impact on science and society in developing countries as well as in technologically well-developed countries. Synchrotron radiation facilities in developing countries have produced hundreds of PhD students who did not have to leave their country, and they have attracted dozens of mid-career scientists to return to their country of origin, where they can continue to perform frontier research. In addition, scientists in these developing countries are able to use intense synchrotron radiation to address local environmental and biomedical issues and concerns. This paper presents: 1) a brief historical account of the development of synchrotron radiation sources from the first to the fourth generation; 2) a summary of the properties of synchrotron radiation; 3) an overview of synchrotron radiation facilities in developing countries; 4) a description of the UNESCO-sponsored Synchrotron-light for Experimental Science and Applications in the Middle East (SESAME) project which is constructing a regional, international third-generation synchrotron radiation research centre in the Middle East in close analogy to CERN.

Review/Synthèse Synchrotron radiation in atomic physics

Much of present understanding of atomic and molecular structure and dynamicswas gained through studies of photon--atom interactions. In particular,observations of the emission, absorption, and scattering of X rays havecomplemented particle-collision experiments in elucidating the physics ofatomic inner shells. Grounded on Max von Laue's theoretical insight andthe invention of the Bragg spectrometer, the field's potential underwent astep function with the development of synchrotron-radiation sources. Notablycurrent third-generation sources have opened new horizons in atomicand molecular physics by producing radiation of wide tunability andexceedingly high intensity and polarization, narrow energy bandwidth, andsharp time structure. In this review, recent advances insynchrotron-radiation studies in atomic and molecular science are outlined.Some tempting opportunities are surveyed that arise for future studiesof atomic processes, including many-body effects, aspects offundamental photon--atominteractions, and relativistic and quantum-electrodynamic phenomena.PACS Nos.: 32.20J, 32.20R, and 07.65E

The use of synchrotron x rays to exploit the Warren–Mavel fluorescence detection technique in studies of disordered systems

Although the early structural studies of liquids and amorphous systems used x-ray diffraction, the advent of high flux reactor sources led to neutron diffraction becoming the preferred technique. There are several advantages: high scattering vector information is not form factor limited and, where isotopes exist, the variation in scattering length allows more detailed structural information to be extracted in many cases. However, the development of synchrotron radiation sources has generated renewed interest in x-ray measurements. High intensity is available at wavelengths short enough to give reasonable access to the high scattering vector region and, in theory, the tunability can be used to maximize anomalous scattering effects and so allow element specific scattering to be recorded. Another use of the tunability is for largely removing the Compton scattering which can often dominate the total scattered intensity and which contains no structural information. This technique requires a choice of incident photon energy such that the x rays scattered without energy loss excite fluorescence in a metal foil in the detection system while most of the Compton scattering has insufficient energy to do so. Hence, recording the fluorescence intensity effectively gives a measurement of the elastic scattering only. Whereas early experiments were limited by the available x-ray emission lines of conventional sources, synchrotron radiation can be tuned so that the incident energy is much closer to the absorption edge of the metal foil thus maximizing the efficiency of the technique. We demonstrate the power of this method and suggest where its application may continue to develop interest in x-ray experiments.

The location of redox centers in biological membranes determined by resonance X-ray diffraction. I. Observation of the resonance effect

We have developed resonance X-ray diffraction methods to locate for the first time intrinsic metal atoms associated with redox centers within biological membrane systems. The study of membranes containing dilute concentrations of resonant scatterers has been made possible by the development of synchrotron radiation sources of X-rays. The technique permits altering the scattering power of a particular atom relative to others by varying the incident X-ray energy. Thus, this method may be used to locate a metal atom within a complex integral protein without chemical modification of the membrane. We present resonance diffraction data taken with synchroton radiation for two different membrane systems: cytochrome oxidase incorporated into lipid vesicles and a photosynthetic reaction center-cytochrome c complex also reincorporated into lipid vesicles.

Electron spectroscopy of surfaces

Abstract Electron spectroscopic methods can be applied to investigate the crystallography, the chemistry and the electronic structure associated with atoms in the outermost atomic layers of a solid. In this article the application of electron energy loss spectroscopy and photoelectron spectroscopy to investigate both occupied and unoccupied electronic states in solids are described. The recent development of synchrotron radiation sources and angularly resolving spectroscopic techniques has made the detection of surface states and resonances more straightforward and has enabled the dispersion of surface and bulk states to be investigated. Angularly resolving photoelectron spectroscopic techniques are also enabling information about the adsorption sites, the nature of the chemical bonding, and the orientation of atoms and molecules adsorbed on surfaces to be obtained. Examples are considered.