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At least 181 records · Page 10

Empowering Scientific Discovery Through Computing at the Advanced Photon Source

This paper explores the challenges and solutions for managing and processing the vast amount of data generated by the Advanced Photon Source (APS), a synchrotron light source facility producing ultra-bright x-rays for diverse scientific domains. With 68 experimental beamlines covering materials research, biology, and more, the APS serves a wide user base across academia, government, and industry. The ongoing upgrade of the APS storage ring and installation of new instruments will amplify data generation and processing demands. This paper discusses the approach to address these demands through automated data processing using standardized workflows that produce faster scientific insights. The APS Data Management System coordinates various data related tasks to manage storage, data transfer, metadata cataloging, data processing, and interfaces with tools provided by Globus. Through integration with the Argonne Leadership Computing Facility (ALCF), APS users can efficiently access high-performance computing resources. Standardized workflows have led to reduced computational burdens on scientists and greater accessibility of high performance computing resources. We demonstrate how standardization and collaboration enable scientists to rapidly convert raw data into meaningful scientific results, establishing a streamlined path from data collection to analysis and ultimately to publication.

Parraga, Hannah↗

Pulsed Magnet Power Systems at NSLS-II

The National Synchrotron Light Source - II (NSLS-II) is a 3 GeV X-ray user facility with 29 beamlines. The NSLS-II pulsed power system consists of an event generator for timely injection and extraction of beam in the transport line from linac to booster at 170 MeV, and from booster to storage ring at 3 GeV. We will discuss current pulsed power systems and the future upgrades/improvements on those systems.

43 PARTICLE ACCELERATORS↗

Crystal structure of perfluorononanoic acid, C 9 HF 17 O 2

The crystal structure of perfluorononanoic acid (PFNA) was solved via parallel tempering using synchrotron powder diffraction data obtained from the Brockhouse X-ray Diffraction and Scattering (BXDS) Wiggler Lower Energy (WLE) beamline at the Canadian Light Source. PFNA crystallizes in monoclinic space group P2 1 /c (#14) with lattice parameters a = 26.172(1) Å, b = 5.6345(2) Å, c = 10.9501(4) Å, and β = 98.752(2)°. The crystal structure is composed of dimers, with pairs of PFNA molecules connected by hydrogen bonds via the carboxylic acid functional groups. The Rietveld-refined structure was compared to a density functional theory-optimized structure, and the root-mean-square Cartesian difference was larger than normally observed for correct powder structures. The powder data likely exhibited evidence of disorder which was not successfully modeled.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

Demonstrating Cross-Facility Data Processing at Scale with Laue Microdiffraction

In February and April 2023 live, at-scale data processing demonstrations were conducted between the Advanced Photon Source (APS), a synchrotron light source, and the Argonne Leadership Computing Facility (ALCF). These tests were run as part of a novel beamline technique: coded aperture laue micro-diffraction. This technique requires a significant amount of compute to decode appeture patterns embedded in the detector stream. An autonomous system was able to send data to ALCF during an experiment, utilize 50 nodes of the Polaris supercomputer to process 6-12 hour scans, and return the data back to the APS within 12-15 minutes behind the detector. With scan points arriving every 72 seconds, the system kept up with the beamline, potentially enabling in-experiment analysis. The data processing system utilizes Globus infrastructure and an on-demand queue to dynamically acquire nodes on Polaris. The underlying reconstruction algorithms were parallelized via MPI and accelerated with custom CUDA kernels.

Prince, Michael↗

A wide-field micro-computed tomography detector: micron resolution at half-centimetre scale

Ideal three-dimensional imaging of complex samples made up of micron-scale structures extending over mm to cm, such as biological tissues, requires both wide field of view and high resolution. For existing optics and detectors used for micro-CT (computed tomography) imaging, sub-micron pixel resolution can only be achieved for fields of view of <2 mm. This article presents a unique detector system with a 6 mm field-of-view image circle and 0.5 µm pixel size that can be used in micro-CT units utilizing both synchrotron and commercial X-ray sources. A resolution-test pattern with linear microstructures and whole adult Daphnia magna were imaged at beamline 8.3.2 of the Berkeley Advanced Light Source. Volumes of 10000 × 10000 × 7096 isotropic 0.5 µm voxels were reconstructed over a 5.0 mm × 3.5 mm field of view. Measurements in the projection domain confirmed a 0.90 µm measured spatial resolution that is largely Nyquist-limited. This unprecedented combination of field of view and resolution dramatically reduces the need for sectional scans and computational stitching for large samples, ultimately offering the means to elucidate changes in tissue and cellular morphology in the context of larger, whole, intact model organisms and specimens. This system is also anticipated to benefit micro-CT imaging in materials science, microelectronics, agricultural science and biomedical engineering.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Twin-pulse seeding enables pump-probe capabilities in the EUV to soft X-ray spectrum at synchrotron light sources

Having previously reported that separating the two stages of echo-enabled harmonic generation (EEHG) with one or more bending magnet (BM) sections allows the BMs to serve as the desired source of momentum compaction, here we demonstrate that this arrangement can greatly reduce the total energy modulation required by any 4th generation synchrotron light source, leading to higher repetition rates as well as stronger coherent radiation output power, with significant benefits. Since the EEHG beamline performance is mainly determined by the momentum compaction, beam emittances and beta functions of a storage ring lattice, allowing for different separations between the two stages is a straightforward way to increase the momentum compaction of chicane 1. This also enables pump-probe capabilities in a novel context, where twin-pulse seeding on the same electron bunch would allow two distinct radiation pulses with an adjustable delay in the range of 0.1 to 10 ps. In the twin-pulse seeding scheme, the same electron bunch could undergo modulation from two distinct laser pulses. Later stages would produce independent harmonics in subsequent straight sections. There are two variations of this twin-pulse seeding scheme, supporting different scientific applications. With a common modulation in stage 1, the first option allows simultaneously two independent radiation sources, with a full coverage of the EUV (2.5 to 50 nm) to soft X-ray (1.25 to 2.5 nm) spectrum; for the second option, the same stage 2 undulator could generate two coherent pulses both fitting within the FEL bandwidth, or at distinct harmonics. We present particle tracking simulation studies based on the APS-U lattice, including quantum excitation and radiation damping. These simulations indicate that there is no degradation of the modulated longitudinal phase space even when the two stages are separated by as many as 10 BM sections.

36 MATERIALS SCIENCE↗

Toward fully coherent soft x-ray free-electron laser via echo-enabled harmonic generation in fourth generation synchrotron light sources

Having previously reported on bunching via echo-enabled harmonic generation (EEHG) as an effective way to improve the longitudinal coherence in the NSLS-II storage ring [X. Yang et al., Sci. Rep. 12, 9437 (2022)], we demonstrate that this EEHG scheme can be easily adopted to any fourth generation diffraction-limited synchrotron light source with significant benefits. The advantage of the scheme is that it requires no change of the lattice and is fully compatible with other beamlines. Since the EEHG performance is mainly determined by the momentum compaction, beam emittances, and beta functions of a SR lattice, we have identified these crucial parameters and successfully built a generalized model, which can predict the performance of nearly any SLS. Regarding the fourth generation SLSs, momentum compactions are often significantly smaller; thus, to cover the x rays with a photon energy of up to 1 keV, we utilize a specific design, including a 250 nm seed-laser wavelength. Our model predicts that for most of the current and future fourth generation SLSs, the EEHG scheme can produce significant prebunching up to harmonic 200 and, thus, generate a few MW scale peak power at 1.25 nm wavelength.

47 OTHER INSTRUMENTATION↗

AMX – the highly automated macromolecular crystallography (17-ID-1) beamline at the NSLS-II

The highly automated macromolecular crystallography beamline AMX/17-ID-1 is an undulator-based high-intensity (>5 × 10 12 photons s −1 ), micro-focus (7 µm × 5 µm), low-divergence (1 mrad × 0.35 mrad) energy-tunable (5–18 keV) beamline at the NSLS-II, Brookhaven National Laboratory, Upton, NY, USA. It is one of the three life science beamlines constructed by the NIH under the ABBIX project and it shares sector 17-ID with the FMX beamline, the frontier micro-focus macromolecular crystallography beamline. AMX saw first light in March 2016 and started general user operation in February 2017. At AMX, emphasis has been placed on high throughput, high capacity, and automation to enable data collection from the most challenging projects using an intense micro-focus beam. Here, the current state and capabilities of the beamline are reported, and the different macromolecular crystallography experiments that are routinely performed at AMX/17-ID-1 as well as some plans for the near future are presented.

36 MATERIALS SCIENCE↗

ORBIT CORRECTION STUDIES ON THE ELECTRON TRANSPORT LINE FROM RCS TO ESR

A dedicated electron transfer line from Rapid Cycling Synchrotron (RCS) to Electron Storage Ring (ESR), referred to as the RTE line has been designed for the Electron-Ion Collider (EIC). The beamline follows a straight-line geometry, with a length of 133 m, and is consists with two matching sections and a FODO section for beam diagnostics. Imperfections with magnet alignments introduce orbit distortions, making orbit correction scheme a critical component in the design. To facilitate orbit correction, each quadrupole magnet is equipped with a pair of beam position monitors (BPMs) and kickers. The Singular Value Decomposition (SVD) algorithm is used for orbit correction and tolerance studies. This paper presents the ongoing progress in the optics design and error correction scheme of the RTE line.

Neththikumara, I. [Thomas Jefferson National Accel↗

hkl-projects/ioc-hkl

HKL-IOC is an open source EPICS IOC that performs real‑time crystallographic HKL calculations for diffractometers and scattering instruments. It integrates the Python hkl library with EPICS through PyDevice, exposing HKL calculations and diffractometer geometry transformations as standard EPICS process variables. This allows beamline and laboratory control systems to convert between motor positions and reciprocal‑space coordinates, configure diffractometer geometries, and drive scans directly in HKL space. The software is written in Python and designed to run alongside existing EPICS deployments without requiring changes to core EPICS components. It is intended for use at synchrotron and neutron scattering facilities, as well as laboratory X‑ray diffractometers, where reliable and reproducible HKL calculations are needed for experiment control, data collection, and automation. HKL-IOC is distributed under the GNU General Public License v3.0 (GPL‑3.0) and contributions and extensions for additional geometries and beamlines are welcomed.

Baekey, Alex↗

Three-dimensional mapping of mineral in intact shark centra with energy dispersive x-ray diffraction

The centra of shark vertebrae consist of cartilage mineralized by a bioapatite similar to bone's carbonated hy-droxyapatite, and, without a repair mechanism analogous to remodeling in bone, these structures still survive millions of cycles of high-strain loading. The main structures of the centrum are an hourglass-shaped double cone and the intermedialia which supports the cones. Little is known about the nanostructure of shark centra, spe-cifically the relationship between bioapatite and cartilage fibers, and this study uses energy dispersive diffraction (EDD) with polychromatic synchrotron x-radiation to study the spatial organization of the mineral phase and its crystallographic texture. The unique energy-sensitive detector array at beamline 6-BM-B, the Advanced Photon Source, enables EDD to quantify the texture within each sampling volume with one exposure while constructing 3D maps via specimen translation across the sampling volume. Herein this study maps a centrum from two shark orders, a carcharhiniform and a lamniform, with different intermedialia structures. In the blue shark (Prionace glauca, Carcharhiniformes), the bioapatite's c-axes are oriented laterally within the centrum's cone walls but axially within the wide wedges of the intermedialia; the former is interpreted to resist lateral deformation, the latter to support axial loads. In the shortfin mako (Isurus oxyrinchus, Lamniformes), there is some tendency for c-axis variation with position, but the situation is unclear because one dimension of the sampling volume is consid-erably larger than the thickness and spacing of the intermedialia's radially-oriented lamellae. Because elastic modulus in collagen plus bioapatite mineralized tissues varies significantly with both volume fraction of bio-apatite and crystallographic texture, the present 3D EDD-derived maps should inform future 3D numerical models of shark centra under applied load.

59 BASIC BIOLOGICAL SCIENCES↗

Experimental setup for high-resolution characterization of crystal optics for coherent X-ray beam applications

Stanford Synchrotron Radiation Lightsource serves a wide scientific community with its variety of X-ray capabilities. Recently, a wiggler X-ray source located at beamline 10-2 has been employed to perform high-resolution rocking curve imaging (RCI) of diamond and silicon crystals. X-ray RCI is invaluable for the development of upcoming cavity-based X-ray sources at SLAC, including the cavity-based X-ray free-electron laser and X-ray laser oscillator. In this paper, the RCI apparatus is described and experimental results are provided to validate its design. Future improvements of the setup are also discussed.

36 MATERIALS SCIENCE↗

Permanent Magnets for the CEBAF 24GeV Upgrade

An upgrade of the CEBAF facility to double its present energy of 12GeV has been proposed. To provide double the number of linac passes using the existing five stacked arc beamlines, some beamlines are replaced by fixed-field accelerator (FFA) arcs, allowing multiple energies to pass through the same magnets. A solution is presented in which two of the existing electromagnetic beamlines are replaced with permanent magnet non-scaling FFA arcs, as demonstrated at CBETA. The two-stage design reduces peak magnetic field and synchrotron radiation loss compared to using a single stage. FFAs do not pulse their magnets, making permanent magnets a promising and power-efficient technology option. However, the magnetic field requirements are still at the high end of accelerator permanent magnets produced thus far (1.6T peak on beam), while the magnets must also be combined-function, having a gradient with a dipole offset. Designs using a novel oval aperture and open midplane within an adapted Halbach magnet are presented.

Brooks, S. J.↗

The Electron Spectro-Microscopy (ESM) Beamline at NSLS-II

Photoelectron spectroscopy is a primary tool for the study of the electronic structure of materials and the chemical composition of surfaces. High-resolution angle-resolved photoemission spectroscopy (ARPES) has the unique ability to map the energy bands in momentum space. Furthermore, going beyond the single particle picture, the self-energy corrections caused by correlations in solids can be extracted from the analysis of the emission line shape. The current level of refinement, in terms of energy and angular resolution (ΔE < 1 meV, Δθ < 0.1°), makes the technique sensitive to the lowest energy excitations and the dynamics of electrons, which in turn virtually determine all the macroscopic properties of any system and govern the chemical, electrical, magnetic, and physical processes. Similarly important, X-ray photoelectron microscopy (XPEEM), combined with the low-energy electron microscopy (LEEM), is indispensable in probing the complexity of chemical, structural, electronic and magnetic properties of surfaces and shallow interfaces, with the spatial resolution of few tens of nanometer (nm). The Electron-Spectro-Microscopy beamline (ESM) has been recently commissioned at NSLS-II and is now in operation. The primary spectroscopic technique is photoemission, performed over a wide energy range with control of light polarization and in a variety of flux/resolution conditions. The beamline has two experimental end stations that allow to perform ARPES and XPEEM/LEEM, separately. The ARPES end station focuses on high energy-resolution work, with spot-size of a few microns. The XPEEM/LEEM end station is a full-field microscope (XPEEM) operating either with the synchrotron generated X-rays (XPEEM), or with an internal electron gun (LEEM). Spatial resolution is crucial in studies of newly synthesized complex materials since they are often initially available only as small specimens (typically micron size). Furthermore, chemical inhomogeneities on surfaces are often an integral part of surface chemical processes. Finally, the ESM beamline with X-ray spots of few microns is optimized to study the electronic structure of novel materials with microscopy capabilities.

47 OTHER INSTRUMENTATION↗

Embedded EPICS server for PowerPMAC motion controllers

An embedded server layer of Experimental Physics and Industrial Control System (EPICS) for PowerPMAC motion controllers has been developed and deployed at two undulator beamlines of the National Institute of General Medical Sciences and the National Cancer Institute (GM/CA) Structural Biology Facility at the Advanced Photon Source (APS). This compact, open source solution makes the power and versatility of PowerPMAC motion controls directly accessible to distributed EPICS clients. At GM/CA the system controls about 200 servo and stepper motors — both encoded and unencoded — and multiple digital and analog I/O accessories. The server stack comprises two sublayers: a lower-level driver and database that communicates directly with PowerPMAC, and a facility-specific soft sublayer built on top. The paper describes installing EPICS on PowerPMAC, the implementation of both layers and client examples, including on-the-fly scanning.

EPICS↗

In situ synchrotron X-ray total scattering measurements and analysis of colloidal CsPbX 3 nanocrystals during flow synthesis

In situ X-ray scattering measurements of CsPbX 3 (X = Cl, Br, I) nanocrystal formation and halide exchange at NSLS-II beamlines were performed in an automated flow reactor. Total scattering measurements were performed at the 28-ID-2 (XPD) beamline and small-angle X-ray scattering at the 16-ID (LiX) beamline. Nanocrystal structural parameters of interest, including size, size distribution and atomic structure, were extracted from modeling the total scattering data. The results highlight the potential of these beamlines and the measurement protocols described in this study for studying dynamic processes of colloidal nanocrystal synthesis in solution with timescales on the order of seconds.

nucleation↗

APS: High-Energy X-rays Expediting Applied and Fundamental Research

The Advanced Photon Source (APS) at Argonne National Laboratory (ANL) was designed and built as one of the first large 3rd generation synchrotrons operated at 7 GeV. The United States Department of Energy (DOE) Office of Science funded the construction and continues to fund the operation of this national facility. Furthermore, the beamlines were originally operated by Collaborative Access Teams (CAT), which allowed a strong involvement of research institutes, universities, and industry. Today 43 of 68 beamlines are operated by the X-ray Science Division (XSD) and 35 beamlines are directly funded by the DOE Office of Science. The APS became operational in 1995, and was planned right from the beginning with 4 beamlines dedicated to high-energy x-rays above 40 keV: 1-ID designed to study engineering materials science, 6-ID-D for magnetism and condensed matter research, 11-ID-B dedicated to magnetic Compton scattering using an Elliptical Multipole Wiggler, and 11-ID-C for materials science and condensed matter physics. These stations were later joined by the bending magnet beamlines 6-BM for white beam studies and 17-BM for rapid powder diffraction. CAT operated beamlines such as 15-ID for crystallography or 16-ID for high-pressure studies also use the high-energy x-ray regime frequently. The program in Compton scattering ended in 2004 and the wiggler was replaced by an undulator. 11-ID-B became the first dedicated station for Pair Distribution Function (PDF) Analysis.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Sulphur variations in annually layered stalagmites using benchtop micro-XRF

Variation of sulphur in annually laminated stalagmites can be used to infer the impact of past volcanic activities, anthropogenic pollution, and climate change due to increased bushfire activity. The synchrotron radiation micro-X-Ray fluorescence (SR-XRF) microprobe is a powerful tool to analyse and image sulphur recorded in stalagmites with micrometre resolution. However, access to SR-XRF beamlines can be limited, so researchers must select the most promising stalagmites for imaging. Benchtop micro-XRF is an effective tool for trace elemental analysis of speleothem samples and is a candidate for routine laboratory measurement of sulphur along stalagmite laminae and screening for SR-XRF. Here, this study describes a protocol using matrix-matched standards to measure annual variations of sulphur at trace to percent level along the laminae of two Western Australian stalagmites, one of which already having been analysed using SR-XRF. Parameters that affected quantitation include X-ray tube voltage and current, spot size of the X-ray beam and stalagmite surface roughness and porosity. The use of a 20 μm X-ray spot size provides sub-annual spatial resolution that can be completed in an overnight scan. The features in a 1000 point micro-XRF analysis of sulphur along a 20 mm transect show good consistency with SR-XRF microprobe data. Micro-XRF mapping was also performed to produce chemical images on the stalagmite and compared with Raman and X-ray diffraction (XRD) to confirm that the stalagmite is exclusively calcite, with no aragonite, and that the source of sulphur in the samples was gypsum and anhydrite. Regions of very high sulphur in the micro-XRF maps were found to be artefacts due to diffraction of the incident beam but these could be efficiently removed by using a multiple point statistics approach to produce a clean image suitable for analysis of the laminae. This work shows the potential of micro-XRF for routine analysis of sulphur in stalagmites, and to streamline sample characterisation before SR-XRF imaging.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗