Modern Synchrotron Research Articles

Partially coherent X-ray wavefront propagation simulations including grazing-incidence focusing optics.

X-ray beamlines in modern synchrotron radiation sources make extensive use ofgrazing-incidence reflective optics, in particular Kirkpatrick-Baez elliptical mirror systems. These systems can focus the incoming X-rays down to nanometer-scale spot sizes while maintaining relatively large acceptance apertures and high flux in the focused radiation spots. In low-emittance storage rings and in free-electron lasers such systems are used with partially or even nearly fully coherent X-ray beams and often target diffraction-limited resolution. Therefore, their accurate simulation and modeling has to be performed within the framework of wave optics. Here the implementation and benchmarking of a wave-optics method for the simulation of grazing-incidence mirrors based on the local stationary-phase approximation or, in other words, the local propagation of the radiation electric field along geometrical rays, is described. The proposed method is CPU-efficient and fully compatible with the numerical methods of Fourier optics. It has been implemented in the Synchrotron Radiation Workshop (SRW) computer code and extensively tested against the geometrical ray-tracing code SHADOW. The test simulations have been performed for cases without and with diffraction at mirror apertures, including cases where the grazing-incidence mirrors can be hardly approximated by ideal lenses. Good agreement between the SRW and SHADOW simulation results is observed in the cases without diffraction. The differences between the simulation results obtained by the two codes in diffraction-dominated cases for illumination with fully or partially coherent radiation are analyzed and interpreted. The application of the new method for the simulation of wavefront propagation through a high-resolution X-ray microspectroscopy beamline at the National Synchrotron Light Source II (Brookhaven National Laboratory, USA) is demonstrated.

In-line SEC-SAXS and MALS/DLS/RI for the Analysis of Polydisperse Macromolecules

Small Angle X-ray Scattering (SAXS) is a powerful tool for the structural analysis of biological macromolecules in solution and has seen a surge in popularity amongst structural biologists in the past decade. In part, this is because SAXS benefits greatly from the sensitivity and throughput that can be achieved at modern high brightness synchrotron sources. However, the critical need for highly monodisperse samples in SAXS analysis can be a challenge, and as such a number of labs have moved to develop in-line Size Exclusion Chromatography (SEC) at the beamline. Real-time SAXS on elution profiles not only improves monodispersity of samples and provides information on possible oligomeric states, but it also offers new modes of data analysis that can take advantage of the inherent concentration profiles underlying elution peaks and distributions of partially resolved species. Efforts to extend the synergy between SEC and SAXS to other biophysical methods are ongoing. The newly commissioned G1 BioSAXS facility at MacCHESS now offers the option of combining real-time SEC-SAXS with multi-angle static (MALS) and dynamic (DLS) light scattering along with refractive index (RI) detection. In this talk we give a brief overview of the performance and capabilities of the new BioSAXS station at MacCHESS with emphasis on detection limits and signal quality. We then discuss how the complementary light scattering techniques can be combined to offer new insights for complex inhomogeneous samples in terms of biological information and data quality assessment. We also discuss the limitations and possible future developments of these approaches as biologists seek to investigate more dynamic systems as well as shorter time scales.

Neutron and X-ray Diffraction from Exotic Magnets in Pulsed Magnetic Fields

Magnetic fields obtained by discharging a large capacitor bank through Helmholtz coils can be produced in excess of 25 T for relatively short periods of time, ~ 1 msec and longer. When combined with modern facilities for diffraction at modern neutron and synchrotron x-ray sources, one can study the structure and phase diagrams of new materials under extremes of magnetic field. I will present two such studies, each focussing on a new magnetic material which exhibit exotic low temperature states. I will show time-resolved neutron Laue diffraction on the multiferroic magnet MnWO4 [1], and time-resolved synchrotron x-ray studies of large magneto-elastic effects in the geometrically-frustarted pyrochlore magnet Tb2Ti2O7 [2], both in magnetic fields up to ~ 30 T. Such studies of new materials in extreme sample environments can be very revealing as to the nature of their exotic low temperature states.

The use of workflows for macromolecular crystallography experiments at the ESRF.

The high performance of modern synchrotron facilities means there is an increasing reliance on automated data analysis and collection methods. The EMBL and ESRF are actively involved in designing and implementing such automated methods. However, as these methods are evolving there is also a need to continually integrate newer and more sophisticated data analysis and collection protocols with experimental control. This integration often poses a challenge, requiring a high level software environment to automatically coordinate beamline control with data acquisition and analysis. This is why we have extended the Eclipse RCP version of the workflow tool Passerelle into a user friendly GUI for experiment design by scientists and programmers [1], which is now part of the Data Analysis WorkbeNch (DAWN) collaboration (http://www.dawnsci.org). The execution of several complex workflows using this technology are now fully integrated in the new version of MxCuBE [2] and deployed on the ESRF macromolecular crystallography beamlines. Here, I will present their current implementation and the data quality improvements that can be achieved. In particular we have developed automated crystal re-orientation workflows that can improve the success of ab initio phasing experiments and help mitigate against radiation damage effect [3]. Other protocols implemented include a 3D diffraction based centring routine, a dehydration protocol and the automated measurement of a crystals radiation sensitivity. Lastly I will present our future plans for other new advanced diffraction based workflow routines, including automated crystal screening and data collection protocols.

Evaluation of Fluorescence Detectors for XAFS at High Flux Beamlines

Detector technologies appropriate for fluorescence detection of XAFS are compared. The current workhorse methods of multi-element solid state detectors and filter-slit systems [1] need continued development to take full advantage of the fluxes available at modern synchrotron beamlines. These high fluxes create the potential for pushing XAFS measurements to extreme levels of diluteness (ppb) if the signal can be separated from the background. Both measurements and calculations are used to explore the ultimate limits for these technologies, and to compare them to alternative methods such as diffraction based analyzers. The measurements include the use of polycapillary optics as coupling optics for crystal analyzers and as improved slits in filter based detectors. The confocal nature of the polycapillaries significantly reduces the background for many samples, and they can be used for nearly perfect rejection of the filter refluorescence in filter based systems. The ultimate limit will be determined by processes such as inelastic scattering that produce backgrounds at the same energy as the fluorescence. These can be minimized but not eliminated by using detectors with high energy resolution.

Synchrotron powder diffraction simplified; management of an APS mail-in program

Synchrotrons have revolutionized powder diffraction. They enable rapid collection of data with tremendous angular resolution and exceptional statistics. High resolution powder diffraction beamlines employing multiple single crystal analyzer detectors routinely reveal subtle crystallographic distortions undetectable on other powder instruments, and are an important tool at most modern synchrotrons for structural studies of a diverse range of materials. Beamline 11-BM at the Advanced Photon Source (APS) is a dedicated high resolution (ΔQ/Q ~2×10-4) powder diffraction instrument which uses vertical and horizontal beam focusing capabilities and a counting system consisting of twelve perfect crystal analyzers paired with scintillator detectors. This APS beamline supports both traditional on-site experiments and a highly successfully rapid access mail-in program mode. This mail-in program has greatly simplified access for a growing user community (> 250 in 2013) to world-class synchrotron quality powder data for their research and resulting publications (> 100 11-BM citations in 2013). The presentation will provide an overview of 11-BM's unique mail-in program. It will be presented both from the view of an external remote user, and will also highlight the numerous alignment, calibration, correction and merging software routines needed to efficiently and accurately reduce the numerous multi-bank detector datasets associated with a high throughput user program. An integrated web interface has been developed to serve as a user-friendly relational database interface for tracking of samples and datasets throughout all stages of the measurements; from the initial user request to sample disposal. The database and software tools critical for this high-throughput synchrotron powder diffraction program will be discussed in detail. More information about the 11-BM and its mail-in program can be found on the beamline webpage: http://11bm.xray.aps.anl.gov

A compact time-of-flight SANS instrument optimised for measurements of small sample volumes at the European Spallation Source

The high flux at European Spallation Source (ESS) will allow for performing experiments with relatively small beam-sizes while maintaining a high intensity of the incoming beam. The pulsed nature of the source makes the facility optimal for time-of-flight small-angle neutron scattering (ToF-SANS). We find that a relatively compact SANS instrument becomes the optimal choice in order to obtain the widest possible q-range in a single setting and the best possible exploitation of the neutrons in each pulse and hence obtaining the highest possible flux at the sample position. The instrument proposed in the present article is optimised for performing fast measurements of small scattering volumes, typically down to 2×2×2 mm3, while covering a broad q-range from about 0.0051/Å to 0.51/Å in a single instrument setting. This q-range corresponds to that available at a typical good BioSAXS instrument and is relevant for a wide set of biomacromolecular samples. A central advantage of covering the whole q-range in a single setting is that each sample has to be loaded only once. This makes it convenient to use the fully automated high-throughput flow-through sample changers commonly applied at modern synchrotron BioSAXS-facilities. The central drawback of choosing a very compact instrument is that the resolution in terms of δλ/λ obtained with the short wavelength neutrons becomes worse than what is usually the standard at state-of-the-art SANS instruments. Our McStas based simulations of the instrument performance for a set of characteristic biomacromolecular samples show that the resulting smearing effects still have relatively minor effects on the obtained data and can be compensated for in the data analysis. However, in cases where a better resolution is required in combination with the large simultaneous q-range characteristic of the instrument, we show that this can be obtained by inserting a set of choppers.

A comprehensive facility for EXAFS measurements at the INDUS-2 synchrotron source at RRCAT, Indore, India

The EXAFS technique, which deals with fine structure oscillations observed in the X-ray absorption spectrum of an element from 50 eV to ~700 eV above its absorption edge, gives precise information regarding the short range order and local structure around the particular atomic species in the material. With the advent of modern bright synchrotron radiation sources, EXAFS has emerged to be the most powerful local structure determination technique, which can be applied to any type of material viz. amorphous, polycrystalline, polymers, surfaces and solutions etc. Over the last few years a comprehensive facility for carrying out EXAFS measurements with synchrotron radiation over variety of samples has been developed at the 2.5 GeV, Synchrotron Radiation Source (INDUS-2) at RRCAT, Indore, India. The facility consists of two operational beamlines viz., the energy dispersive EXAFS beamline (BL-08) and the Energy Scanning EXAFS beamline (BL-09).

At-wavelength metrology of hard X-ray mirror using near field speckle

We present a method to measure the surface profile of hard X-ray reflective optics with nanometer height accuracy and sub-millimetre lateral resolution. The technique uses X-ray near-field speckle, generated by a scattering membrane translated using a piezo motor, to infer the deflection of X-rays from the surface. The method provides a nano-radian order accuracy on the mirror slopes in both the tangential and sagittal directions. As a demonstration, a pair of focusing mirrors mounted in a Kirkpatrick-Baez (KB) configuration were characterized and the results were in good agreement with offline metrology data. It is hoped that the new technique will provide feedback to optic manufacturers to improve mirror fabrication and be useful for the online optimization of active, nano-focusing mirrors on modern synchrotron beamlines.

Ultrafast Streaming Camera Platform for Scientific Applications

X-ray computer tomography is a powerful method for nondestructive investigations in many fields. Three-dimensional images of internal structure are reconstructed from a sequence of two-dimensional projections. The polychromatic high density photon flux of modern synchrotron light sources offer hard X-ray imaging with spatio-temporal resolution up to the micrometer and micrometers range. Existing indirect X-ray image detection systems can be adapted for fast image acquisition by high-speed visible-light cameras. In this paper, we present a platform for custom high-speed CMOS cameras with embedded field-programmable gate array (FPGA) processing. This modular system is characterized by a high-throughput PCI Express (PCIe) interface and efficient communication blocks. It has been used to develop a novel architecture for a self-event trigger that increases the effective image frame rate and reduces the amount of received data. Thanks to a low-noise design, high frame rates in the kilohertz range, and high-throughput data transfer, this camera is well suited for ultrafast synchrotron-based X-ray radiography and tomography. The camera setup is accomplished by high-throughput Linux drivers and a seamless integration in our GPU computing framework.

Squeezing the most from every crystal: the fine details of data collection.

Modern synchrotron beamlines offer instrumentation of unprecedented quality, which in turn encourages increasingly marginal experiments, and for these, as much as ever, the ultimate success of data collection depends on the experience, but especially the care, of the experimenter. A representative set of difficult cases has been encountered at the Structural Genomics Consortium, a worldwide structural genomics initiative of which the Oxford site currently deposits three novel human structures per month. Achieving this target relies heavily on frequent visits to the Diamond Light Source, and the variety of crystal systems still demand customized data collection, diligent checks and careful planning of each experiment. Here, an overview is presented of the techniques and procedures that have been refined over the years and that are considered synchrotron best practice.

Magnetic states in low-pinning high-anisotropy material nanostructures suitable for dynamic imaging

We present magnetic domain states in a material configuration with high (perpendicular) magnetic anisotropy and particularly low magnetic pinning. This material, a B-doped Co/Pt multilayer configuration, exhibits a strong magnetic contrast in x-ray transmission experiments, making it apt for dynamic imaging with modern synchrotron techniques, providing high spatial and high temporal resolution simultaneously. By analyzing the static spin structures in nanodisks at variable external fields, we show that CoB/Pt multilayers exhibit low enough domain wall pinning to manipulate the domain pattern with weak stimuli and in particular to move domains and domain walls. We demonstrate in a proof-of-principle experiment using pump-probe x-ray holographic imaging that moderate magnetic fields can induce elastic and deterministic and hence repeatable small variations of the domain configuration in CoB/Pt multilayers, which is the key to perform high-resolution imaging of the domain wall motion to gain insight to the details of the local magnetization dynamics.

A wave-optical toolbox for multiple CRL transfocators

Modern synchrotron radiation sources are usually equipped with state-of-the-art focusing setups. In the last decade, modular arrays of compound refractive lenses, the so called transfocators, have emerged as adjustable focusing optics elements. Several arrays of more than one hundred lenses are distributed in the x-ray beam path to obtain optimal focusing; however, fully wave-optical simulations of such set-ups are still missing.We present a simple toolbox of distributed computer codes to numerically propagate an x-ray beam through a sequence of transfocators, illuminated by a point-source and a partially coherent extended source.

Discovery of some 400 million year-old sensory structures in the compound eyes of trilobites.

Fossilised arthropod compound eyes have frequently been described. Among the oldest known are those from the lower Cambrian of the Chengjiang Lagerstätte (China, c 525 Ma). All these compound eyes, though often excellently preserved, however, represent just the outer shells, because soft tissues, or even individual cells, usually do not fossilise. Using modern techniques, including μct-scanning and synchrotron radiation analysis we present the discovery of the sensory cell system of compound eyes, belonging to trilobites around 400 million years old, which allows their description and analysis. They are interpreted as forming part of an apposition-like ommatidium, which is a basic functional type of compound eye present in arthropods of today. Considered in greater detail, it is similar to the compound eye of the horseshoe crab Limulus, generally regarded as a ‘living fossil’, which probably retained this ancient basal system successfully until today.

Structural investigation of GaInP nanowires using X-ray diffraction

In this work the structure of ternary GaxIn1−xP nanowires is investigated with respect to the chemical composition and homogeneity. The nanowires were grown by metal–organic vapor-phase epitaxy. For the investigation of ensemble fluctuations on several lateral length scales, X-ray diffraction reciprocal space maps have been analyzed. The data reveal a complicated varying materials composition across the sample and in the nanowires on the order of 20%. The use of modern synchrotron sources, where beam-sizes in the order of several 10μm are available, enables us to investigate compositional gradients along the sample by recording diffraction patterns at different positions. In addition, compositional variations were found also within single nanowires in X-ray energy dispersive spectroscopy measurements.

High-resolution resonant inelastic soft X-ray scattering applied to liquids

The brilliance of modern synchrotron radiation sources and capabilities of new instrumentation facilitate resonant inelastic soft X-ray scattering of liquids and molecular materials with high spectral quality. Especially, when the energy resolution approaches the natural line widths a detailed analysis provides information about local potential surfaces, dynamic coupling between nuclear and electronic degrees of freedom, and intermolecular interactions. After briefly commenting on various sample handling systems we review the recent high-resolution RIXS results on liquid acetone. The experimental RIXS spectra excited at the O K edge demonstrate that the CO stretching mode dominates the vibrational progressions, and that softer modes are little affected by the nuclear dynamics in the intermediate state. It is shown that intermolecular coupling can be neglected in this specific case, and it is predicted that such interaction significantly broadens spectral features in liquids with larger dipole–dipole interaction. Analysis of the data further shows that initial state thermal excitations at room temperature have a noticeable influence on the spectral features.

Synchrotron X-ray imaging for crystal growth studies

Abstract The features associated with modern synchrotron radiation machines (intense and coherent beams) result in a substantial extension of X-ray imaging capabilities in terms of spatial and temporal resolution, phase contrast and 3D images. This allows crystal growth-related information to be obtained which is not available otherwise. After briefly describing the main synchrotron radiation based imaging techniques of interest, we give original examples illustrating the new capabilities for crystal growth: characterisation of crystals grown for applications, such as ice tri-crystals produced for mechanical deformation studies; SiC; crystalline silicon for solar photovoltaic cells; in situ and in real time studies of quasicrystal growth (AlPdMn); and ultrafast tomography for the study of the growth of dendrites in metallic alloys.

(p,T,H) Phase Diagram of Heavy Fermion Systems: Some Systematics and Some Surprises from Ytterbium

Pressure is the cleanest way to tune heavy fermion systems to a quantum phase transition in order to study the rich physics and competing phases, and the comparison between ytterbium and cerium systems is particularly fruitful. We briefly review the mechanisms in play and show some examples of expected and unexpected behaviour. We emphasise the importance of the valence changes under pressure and show how modern synchrotron techniques can accurately determine this, including at low temperature.

X-Ray Interference by Nanocrystalline Domains

Regular arrangement of nanocrystalline domains can introduce interference effects which alter considerably the powder diffraction pattern. Role of nanocrystal alignment (local texture) and mutual positioning are different, with the latter much more effective in controlling the interference effect. While it is demonstrated that these effects are unlikely to be observed on a conventional laboratory instrument, coherence conditions available at modern synchrotron radiation beamlines might support further investigations of interference in systems made of very fine nanocrystals.

Monte Carlo simulation for the Touschek effect with the crab-waist scheme

The Touschek effect is one of the dominant loss mechanisms for lepton storage rings of low emittance (i.e. high bunch density) and low or moderate beam energy. So, in the past years, for all lepton circular machines, either colliders or modern synchrotron light sources, either due to high bunch density or to beam energy, more and more efforts have been made for a comprehensive evaluation of this effect. This paper describes the simulation tool developed to evaluate the actions relevant to minimize the Touschek effect, such as position and shape of scrapers and detector shieldings, interaction region optics design with a particular attention to sextupoles for their relevant nonlinear effects. Relevant results obtained through the years at the low energy ${\mathrm{e}}^{+}{\mathrm{e}}^{\ensuremath{-}}$ collider DA\cyrchar\CYRF{}NE are presented. A reduction of the luminosity normalized to the background of more than 1 order of magnitude is obtained with an increase in luminosity from ${10}^{31}$ to ${10}^{32}\text{ }\text{ }{\mathrm{cm}}^{\ensuremath{-}2}\text{ }{\mathrm{s}}^{\ensuremath{-}1}$ and a small decrease in lifetime. The corresponding data Monte Carlo simulation comparison for each action taken is presented, showing an overall good agreement.