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At least 91 records · Page 5

Structural biology at the National Synchrotron Light Source II

The structural biology program at the National Synchrotron Light Source II presents a coordinated set of instruments, software and research opportunities for the interested user. We describe in some detail the research capabilities enabled by the Center for BioMolecular Structure. The evolution of the resources is described in detail, considering three major themes: automation, micro-focusing and computation prediction.

36 MATERIALS SCIENCE↗

Towards High-Efficiency Particle Detection Using Superconducting Microwire Arrays

We present a detailed study of an 8-channel $1\times1$~mm$^{2}$ WSi superconducting microwire single photon detector (SMSPD) array exposed to 120~GeV hadron beam and 120~GeV muon beam at the CERN Super Proton Synchrotron H6 beamline. Following up on our first detailed characterization of the efficiency and response of an SMSPD fabricated on a 3~nm WSi film, we report measurements of enhanced particle detection efficiency using a sensor fabricated from a thicker 4.7~nm-thick WSi film. We also report the first SMSPD detection efficiency measurement made for muons. Measurements are enabled by a silicon tracking telescope providing 10~$\mu$m in situ spatial resolution. The results show a detection efficiency of 75\% and a time resolution of about 130~ps across pixels. These findings represent a significant advancement toward developing high-efficiency SMSPD charged particle tracking systems with simultaneous precision timing, with potential applications in future accelerator-based experiments such as the FCC-ee and Muon Collider.

Wang, Christina [Fermilab]↗

Reduction and Agglomeration of Supported Metal Clusters Induced by High-Flux X-ray Absorption Spectroscopy Measurements

Supported metal clusters are widely used in catalysis for many important reactions. To understand the catalytic properties, in situ/operando characterization techniques, such as X-ray absorption spectroscopy (XAS), provide essential details of the size, shape, and chemical composition of the cluster and the nature of the active sites. New-generation synchrotrons combined with focusing beamlines provide high-flux-density X-rays for improved detection sensitivity as well as higher time and spatial resolution. Understanding the effects of a high-flux-density X-ray beam on the catalyst during the actual measurement, whether XAS or another synchrotron-based technique, is crucial. This is especially important for in situ and operando studies where both the high flux density and reaction conditions can affect the catalyst structure. In this work, we investigated the effect of the flux density on rhodium clusters supported on Al 2 O 3 at two different beamlines: National Synchrotron Light Source II beamline 08-ID and Stanford Synchrotron Radiation Light Source (SSRL) beamline 4-1. We show that the higher flux density at beamline 08-ID causes the reduction of the highly dispersed RhO x /Al 2 O 3 catalyst, even at room temperature. Additionally, exposure to the higher flux density X-rays at beamline 08-ID during in situ reduction results in significant agglomeration of the Rh clusters. The final size of the Rh nanoparticles reduced at 310 °C is equivalent to that of particles formed after the reduction at 600–650 °C in the absence of the beam. Significant beam-induced reduction and agglomeration is also shown for Ni supported on beta zeolite during in situ reduction at an intermediate-flux-density beamline 9-3 at SSRL, indicating that beam-induced changes in heterogeneous catalysts could be common at intermediate- and high-flux-density beamlines. We provide precautions and recommendations for detecting and minimizing beam damage during in situ/operando XAS measurements.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Application and performance of the novel Elcomat 5000 autocollimator in slope-measuring profilometry of beamline optics

Autocollimators are used in profilometers for the precise form measurement of beam-shaping optics for synchrotron light sources and x-ray free-electron lasers. This application requires using an aperture stop, typically 2.5 mm in diameter, which limits the footprint of the autocollimator’s measuring beam on the optics to achieve a sufficiently high lateral resolution. Central to the development of profilometry has been the availability of commercial autocollimators, such as the Elcomat 3000 from Möller–Wedel Optical. Although autocollimators are generally not designed for use with small apertures, this device has proven capable and has become the de facto standard. Now that it has been replaced by the Elcomat 5000, we evaluate the performance of several autocollimators of this type at small apertures, including the characterization of instrument transfer functions with a chirped height profile. We demonstrate that the Elcomat 5000 is capable of repeatable angle measurements with a standard deviation of 0.014 arcsec at an aperture diameter of 1.6 mm, whereas the Elcomat 3000 achieves 0.03 arcsec at 2.5 mm, comparing models with modified reticle designs. Here, we also investigate the influence of optical aberrations of the autocollimator’s objective and their changes with the path length to the surface under test. We characterize the sensitivity of the angle measurement to changes in environmental parameters, in particular, barometric pressure. These efforts are aimed at approaching fundamental limits in the characterization of the shape of optical surfaces with autocollimator-based profilometers so that these are ready for characterizing the next generation of synchrotron and XFEL beamline optics.

angle metrology↗

Synchrotron Catalysis Consortium (SCC) at NSLS-II: Dedicated Beamline Facilities for In Situ and Operando Characterization of Catalysts

The Synchrotron Catalysis Consortium (SCC) was funded and established in September 2005 at the National Synchrotron Light Source (NSLS) at Brookhaven National Laboratory (BNL). For more than a decade, the SCC was the first of its kind in the United States, with a mission to promote the utilization of synchrotron techniques for cutting-edge catalysis research under in-situ conditions. The consortium consists of three Principal Investigators (Jingguang Chen, Columbia University, Anatoly Frenkel, Stony Brook University/BNL, and Jose Rodriguez, BNL) and scientific staff member Nebojsa Marinkovic. The initial team also included Radoslav Adzic, BNL, and collaborators from academic, national, and industrial laboratories. During the first decade of its operations at three NSLS beamlines (X18A, X18B, and X19A) until the closing of NSLS on September 30, 2014, the primary goal of the SCC team was to provide assistance and to develop new sciences/techniques to the catalysis community...This report outlines a brief history, specifications, techniques, and training and outreach for the facility.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Combining diagnostics, modeling, and control systems for automated alignment of the TES beamline

X-ray beamlines are essential components of all synchrotron light sources. Practical operations involve frequent variation in beamline component positions and orientation, particularly when photon beam parameters shift due to experimental needs, or due to variations in the incoming photon beam. The alignment process can be time consuming and takes away from valuable beam time for experimental data collection. We describe progress in the automation of certain alignment tasks on the tender-energy X-ray spectroscopy (TES) beamline at the National Synchrotron Light Source II (NSLS-II). The beamline is controlled using the BlueSky software in which high level experimental plans guide the beamline components during an experiment. Numerous software packages exist for beamline modeling, and they may be tied to the beamline control system using a package we are continuing to develop called Sirepo-Bluesky. The photon beam distribution may be measured with fluorescent screens, and a relation between beam and machine state can be found by varying the mirror and aperture settings over a multi-dimensional range. We describe the results of such parameter varying measurements and how we are combining Sirepo-Bluesky with machine learning methods and reduced models to automate mirror alignment on the TES beamline.

36 MATERIALS SCIENCE↗

Metalloproteins in an Era of Modern Crystallography and Why the Beamline Matters

The Structural Molecular Biology (SMB) macromolecular crystallography (MC) group at the Stanford Synchrotron Radiation Lightsource (SSRL) have developed state-of-the-art capabilities tailored for metalloenzyme structural analysis. Metalloproteins sit at the center of biology’s most audacious chemistry. From multi-electron redox catalysis to radical rearrangements and light-driven transformations, metal sites give proteins access to reaction landscapes that would otherwise be inaccessible under ambient conditions. Yet their study presents a fundamental paradox for MC studies: the very X-rays we use to reveal atomic structure can alter the electronic states we seek to understand. As the field moves beyond static snapshots toward mechanistic insight, success increasingly depends on our ability to maintain metal centers in their native state throughout the experiment. The SSRL SMB-MC beamlines integrate a suite of capabilities specifically designed to address these challenges. By combining in situ spectroscopic verification, intelligent dose management, controlled reaction initiation, optimized anomalous diffraction, and real-time crystallographic diffraction analysis, these tools enable researchers to interrogate metalloproteins with unprecedented rigor. This article explores how these complementary approaches are reshaping our ability to capture metalloprotein chemistry, and what this means for mechanistic studies at synchrotron beamlines.

Maggiolo, Ailiena O. [SLAC National Accelerator La↗

UV/VUV radiometric calibrations at SURF II

Since 1981 more than 150 instrument calibrations have been performed on the radiometric instrumentation calibration beamline at the Synchrotron Ultraviolet Radiation Facility (SURF II) at the National Institute of Standards and Technology (NIST) in Gaithersburg, Maryland. This 300 MeV electron storage ring operates routinely at electron currents greater than 250 mA. The spectrometer calibration beamline provides a continuum of radiation from 4 nm through the visual spectral region in the form of an intense beam with total angular divergence of 1.2 mrad. The probable uncertainty for the flux ranges from about 5 percent at 4 nm to less than 2 percent above 20 nm. The new system will radiometrically trace to SURF II, and thus is expected to reduce the calibration uncertainty for diodes in this region by a factor of five to the 1-2 percent level.

Furst, Mitchell L.↗

A general Bayesian algorithm for the autonomous alignment of beamlines

Autonomous methods to align beamlines can decrease the amount of time spent on diagnostics, and also uncover better global optima leading to better beam quality. The alignment of these beamlines is a high-dimensional expensive-to-sample optimization problem involving the simultaneous treatment of many optical elements with correlated and nonlinear dynamics. Bayesian optimization is a strategy of efficient global optimization that has proved successful in similar regimes in a wide variety of beamline alignment applications, though it has typically been implemented for particular beamlines and optimization tasks. In this paper, we present a basic formulation of Bayesian inference and Gaussian process models as they relate to multi-objective Bayesian optimization, as well as the practical challenges presented by beamline alignment. We show that the same general implementation of Bayesian optimization with special consideration for beamline alignment can quickly learn the dynamics of particular beamlines in an online fashion through hyperparameter fitting with no prior information. We present the implementation of a concise software framework for beamline alignment and test it on four different optimization problems for experiments on X-ray beamlines at the National Synchrotron Light Source II and the Advanced Light Source, and an electron beam at the Accelerator Test Facility, along with benchmarking on a simulated digital twin. We discuss new applications of the framework, and the potential for a unified approach to beamline alignment at synchrotron facilities.

47 OTHER INSTRUMENTATION↗

Improvements to the characterization of Agfa x-ray film for use on opacity spectroscopy diagnostics

The National Ignition Facility uses a soft x-ray opacity spectrometer for x-ray spectral imaging in high-energy-density experiments. The increased demand for a better spectral resolution prompted the investigation into the Agfa D4 film. Characterization is already under way for the film. A Manson x-ray source using six different anodes was used to expose film to the linear optical density (OD) region. This is a continuation of the previous work, and the updated analysis process is communicated here. The identified uncertainties have been reduced with the updated steps that improve the results of the characterization process. In conclusion, when the Stanford Synchrotron Radiation Lightsource Beamline 16-2 was operational, the film was characterized at that source. Its beam offered a higher fluency with a lower exposure time needed to reach saturation. Results for both sources are compared in this paper.

47 OTHER INSTRUMENTATION↗

Peculiarities of planar shockwave interaction with air–water interface and solid target

We present the results of the research on underwater electrical explosion of planar copper wire arrays, accompanied by the generation of a planar shock, using the synchrotron-based phase-contrast radiography imaging capabilities of the ID19 beamline at the European Synchrotron Radiation Facility. It is shown that the interaction of a strong shock with an air–water interface leads to additional acceleration of the wire expansion due to a rarefaction wave along with the emergence of micro-jets. In the case of a target placed above the array, we observed the formation of a cavity between the array and the target due to the interaction of two rarefaction waves. Furthermore, the results of two-dimensional hydrodynamic simulations of the wire explosion and the interaction of the generated shock with the water–air and water-target interfaces showed good agreement with experimental results.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Application of sulfur SAD to small crystals with a large asymmetric unit and anomalous substructure

The application of sulfur single-wavelength anomalous dispersion (S-SAD) to determine the crystal structures of macromolecules can be challenging if the asymmetric unit is large, the crystals are small, the size of the anomalously scattering sulfur structure is large and the resolution at which the anomalous signals can be accurately measured is modest. Here, as a study of such a case, approaches to the SAD phasing of orthorhombic Ric-8A crystals are described. The structure of Ric-8A was published with only a brief description of the phasing process [Zeng et al. (2019), Structure , 27 , 1137–1141]. Here, alternative approaches to determining the 40-atom sulfur substructure of the 103 kDa Ric-8A dimer that composes the asymmetric unit are explored. At the data-collection wavelength of 1.77 Å measured at the Frontier micro-focusing Macromolecular Crystallography (FMX) beamline at National Synchrotron Light Source II, the sulfur anomalous signal strength, |Δ ano |/σΔ ano ( d ′′/sig), approaches 1.4 at 3.4 Å resolution. The highly redundant, 11 000 000-reflection data set measured from 18 crystals was segmented into isomorphous clusters using BLEND in the CCP 4 program suite. Data sets within clusters or sets of clusters were scaled and merged using AIMLESS from CCP 4 or, alternatively, the phenix.scale_and_merge tool from the Phenix suite. The latter proved to be the more effective in extracting anomalous signals. The HySS tool in Phenix , SHELXC / D and PRASA as implemented in the CRANK 2 program suite were each employed to determine the sulfur substructure. All of these approaches were effective, although HySS , as a component of the phenix.autosol tool, required data from all crystals to find the positions of the sulfur atoms. Critical contributors in this case study to successful phase determination by SAD included (i) the high-flux FMX beamline, featuring helical-mode data collection and a helium-filled beam path, (ii) as recognized by many authors, a very highly redundant, multiple-crystal data set and (iii) the inclusion within that data set of data from crystals that were scanned over large ω ranges, yielding highly isomorphous and highly redundant intensity measurements.

59 BASIC BIOLOGICAL SCIENCES↗

Flatfielding of hybrid pixel detectors in tender x-ray scattering

The ability of the soft matter interfaces beamline at National Synchrotron Light Source II to access x-ray energy in the tender x-ray regime, i.e., from 2.1 to 5 keV, enables new resonant x-ray scattering studies at the sulfur K-edge and others. We present a new approach to correct data acquired in the tender x-ray regime with a Pilatus3 detector in order to improve the data quality and to correct the various artifacts inherent to hybrid pixel detectors, such as variations in modules’ efficiency or noisy detector module junctions. Further, this new flatfielding significantly enhances the data quality and enables detection of weak scattering signals.

47 OTHER INSTRUMENTATION↗

Designing linear lattices for round beam in electron storage rings using the solution by linear matrices analysis

For some synchrotron light source beamline applications, a round beam is preferable to a flat one. A conventional method of obtaining round beam in an electron storage ring is to shift its tune close to a linear difference resonance. The linearly coupled beam dynamics is analyzed with perturbation theories, which have certain limitations. In this paper, we adopt the Solution by LInear Matrices (SLIM) analysis to calculate exact beam sizes to design round beam lattices. The SLIM analysis can deal with a generally linearly coupled accelerator lattice. The effects of various coupling sources on beam emittances and sizes can be studied within a self-consistent frame. Both the on- and off-resonance schemes to obtain round beams are explained with examples. The SLIM formalism for two widely used magnet models: combined-function bending magnets, and planar wigglers and undulators, is also derived.

43 PARTICLE ACCELERATORS↗

Power density calculation of spontaneous radiation emission from a finite emittance electron beam in planar undulators

We extend the angular power density formulae for spontaneous radiation emission from planar undulators to include finite emittance and angular misalignment of the electron beam. Then we calculate and compare power densities estimated from integral approach with Gaussian beam distribution and summation approach with macro-particle allocation covering particle beam phase space. After showing that both approaches converge to each other, we apply the macro-particle approach to study power absorbed and transmitted by various apertures at front end of 9-ID beamline at National Synchrotron Light Source-II for misaligned electron beam. Our analysis indicate that the electron beam misalignment could lead to unwarranted power deposition at tighter apertures that would have been otherwise difficult to account for during the aperture design/choice process.

43 PARTICLE ACCELERATORS↗

Searching for the Best Protein Crystals: Synchrotron Based Measurements of Protein Crystal Quality

We are developing X-ray diffraction methods to quantitatively evaluate the quality of protein crystals. The ultimate use for these crystal quality will be to optimize crystal growth and freezing conditions to obtain the best diffraction data. We have combined super fine-phi slicing with highly monochromatic, low divergence synchrotron radiation and the ADSC Quantum 4 CCD detector at the Stanford Synchrotron Radiation laboratory beamline 1.5 to accurately measure crystal mosaicity. Comparisons of microgravity versus earth-grown insulin crystals using these methods will be presented.

Borgstahl, Gloria↗

High power density soft x-ray GaAs photodiodes with tailored spectral response

GaAs photodiode arrays have been designed for non-destructive monitoring of x-ray beam position in soft coherent beamline front ends in synchrotron light sources. A shallow p-on-n junction was employed to reduce the device photocurrent density to optimize the operation with beam power densities up to 20 W mm -2 , mainly coming from hard x-rays. With this approach, the photocurrent is primarily defined by the excess carriers generated by low-energy x-ray photons absorbed near the detector surface. The p–n junction structures were grown by molecular beam epitaxy and processed into 64-element linear photodiode arrays. The devices were characterized first in the visible range with a high-power Ar-ion laser and then tested in the soft and hard x-ray regions up to 10 keV at two beamlines of the National Synchrotron Light Source II. The responsivity was measured to be 0.16 A W -1 at 0.7 keV and 0.05 A W -1 at 6 keV in agreement with modeling. At higher x-ray energies the measured responsivity was lower than predicted in the framework of the carrier diffusion model; a possible explanation is discussed.

36 MATERIALS SCIENCE↗

Development of the high energy engineering X-ray (HEX) superconducting wiggler, magnetic measurement, installation, and commissioning

The High energy Engineering X-ray (HEX) diffraction beamline at the National Synchrotron Light Source II (NSLS-II) at Brookhaven National Lab (BNL) is the first high-energy beamline capable of reaching 200 keV for a monochromatic beam. With the 3 GeV electron beam energy for the NSLS-II ring, only the superconducting wiggler (SCW) producing greater than 4 T peak field can cover these ranges with a sufficient number of photons. The 1.2 m-long HEX-SCW has a period length of 70 mm and a field strength on-axis of 4.3 T. It utilizes no liquid helium, and the vertical aperture size of the electron beam vacuum chamber is 8 mm. Unlike regular undulators/wigglers, there is no standard configuration for the magnetic measurement system for superconducting insertion devices. The NSLS-II Insertion Devices group has developed, in collaboration with the vacuum group, a novel in-vacuum Hall mapper with a 1.75 m in-vacuum linear motor and an in-vacuum flip coil system utilizing many commercial-off-the-shelf products. The measurements were conducted at the BNL, and the device was installed in the ring and commissioned. Here, this paper provides a description of the SCW and its magnetic measurement systems, as well as a brief account of the installation and commissioning efforts.

36 MATERIALS SCIENCE↗