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At least 19 records

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↗

FMX – the Frontier Microfocusing Macromolecular Crystallography Beamline at the National Synchrotron Light Source II

Two new macromolecular crystallography (MX) beamlines at the National Synchrotron Light Source II, FMX and AMX, opened for general user operation in February 2017 [Schneider et al. (2013). J. Phys. Conf. Ser. 425 , 012003; Fuchs et al. (2014). J. Phys. Conf. Ser. 493 , 012021; Fuchs et al. (2016). AIP Conf. Proc. SRI2015 , 1741 , 030006]. FMX, the micro-focusing Frontier MX beamline in sector 17-ID-2 at NSLS-II, covers a 5–30 keV photon energy range and delivers a flux of 4.0 × 10 12 photons s −1 at 1 Å into a 1 µm × 1.5 µm to 10 µm × 10 µm (V × H) variable focus, expected to reach 5 × 10 12 photons s −1 at final storage-ring current. This flux density surpasses most MX beamlines by nearly two orders of magnitude. The high brightness and microbeam capability of FMX are focused on solving difficult crystallographic challenges. The beamline's flexible design supports a wide range of structure determination methods – serial crystallography on micrometre-sized crystals, raster optimization of diffraction from inhomogeneous crystals, high-resolution data collection from large-unit-cell crystals, room-temperature data collection for crystals that are difficult to freeze and for studying conformational dynamics, and fully automated data collection for sample-screening and ligand-binding studies. FMX's high dose rate reduces data collection times for applications like serial crystallography to minutes rather than hours. With associated sample lifetimes as short as a few milliseconds, new rapid sample-delivery methods have been implemented, such as an ultra-high-speed high-precision piezo scanner goniometer [Gao et al. (2018). J. Synchrotron Rad. 25 , 1362–1370], new microcrystal-optimized micromesh well sample holders [Guo et al. (2018). IUCrJ , 5 , 238–246] and highly viscous media injectors [Weierstall et al. (2014). Nat. Commun. 5 , 3309]. The new beamline pushes the frontier of synchrotron crystallography and enables users to determine structures from difficult-to-crystallize targets like membrane proteins, using previously intractable crystals of a few micrometres in size, and to obtain quality structures from irregular larger crystals.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Sextupole reduction via chaos suppression at the National Synchrotron Light Source II

We revisit the nonlinear lattice design approach for the National Synchrotron Light Source II (NSLS-II) storage ring. By suppressing chaos, we identify alternative sextupole configurations to the original design, which relied on the conventional strategy of simultaneously minimizing resonance driving terms (RDTs) and amplitude-dependent detuning (ADD). These alternatives achieve comparable performance while requiring fewer sextupoles. A detailed comparison of two representative solutions is presented and supported by experimental validation. Our results show that the dynamic aperture correlates more strongly with global chaos than with individual RDTs, and that the importance of minimizing ADD may have been overstated in earlier design strategies.

36 MATERIALS SCIENCE↗

Robotic sample changers for macromolecular X-ray crystallography and biological small-angle X-ray scattering at the National Synchrotron Light Source II

In this work, we present two robotic sample changers integrated into the experimental stations for the macromolecular crystallography (MX) beamlines AMX and FMX, and the biological small-angle scattering (bioSAXS) beamline LiX. They enable fully automated unattended data collection and remote access to the beamlines. The system designs incorporate high-throughput, versatility, high-capacity, resource sharing and robustness. All systems are centered around a six-axis industrial robotic arm coupled with a force torque sensor and in-house end effectors (grippers). They have the same software architecture and the facility standard EPICS-based BEAST alarm system. The MX system is compatible with SPINE bases and Unipucks. It comprises a liquid nitrogen dewar holding 384 samples (24 Unipucks) and a stay-cold gripper, and utilizes machine vision software to track the sample during operations and to calculate the final mount position on the goniometer. The bioSAXS system has an in-house engineered sample storage unit that can hold up to 360 samples (20 sample holders) which keeps samples at a user-set temperature (277 K to 300 K). The MX systems were deployed in early 2017 and the bioSAXS system in early 2019.

36 MATERIALS SCIENCE↗

Multimodal, Multidimensional, and Multiscale X-ray Imaging at the National Synchrotron Light Source II

Over the last couple of decades, the synchrotron radiation research community has witnessed tremendous advancement in the field of x-ray imaging and microscopy. Continuing enhancement of the light sources’ brightness, advances in x-ray focusing optics, incorporation of precision instruments, and development of innovative imaging techniques are some of the leading contributors for the rapid progress. New imaging and microscopy beamlines, such as the ones at the National Synchrotron Light Source II (NSLS-II), a Department of Energy (DOE) Office of Science user facility located at DOE’s Brookhaven National Laboratory, are capable of performing more sophisticated and complicated measurements than ever before, either on their own or used together as a suite of tools. These sophisticated and complex measurements exhibit attributes for multimodal, multidimensional, and multiscale imaging. Recent popularity of these methods is strongly driven by the current trends in materials characterizations, where researchers desire to map out hierarchical materials structure over a large range of length scales, to understand structure-property correlation, to quantify materials structures in 3D, and/or to perform operando or in situ experiments. It is important to emphasize that “materials” under investigation are not only synthesized materials but also the natural materials. In this article, we describe multimodal, multidimensional and multiscale x-ray imaging capabilities of the NSLS-II beamlines and how these methods are used to tackle complex scientific problems.

47 OTHER INSTRUMENTATION↗

Recent activities of National Synchrotron Light Source-II Insertion Device Group

Insertion Device (ID) Group at the National Synchrotron Light Source-II (NSLS-II) has been involved in the following activities: Installation and maintenance of the HEX-Superconducting Wiggler (SCW), Laboratory Directed Research and Development (LDRD) for SC adaptive gap undulator (AGU), NSLS-II Experimental Tools II & III (NEXT-II & III) project IDs. Improvement of in-vacuum flip coil bench, development of in-vacuum pulsed wire bench and upgrade of a regular flip coil bench. Development of rotating coil bench for the lattice magnets for future upgrade. This paper describes the specifics of each activity.

47 OTHER INSTRUMENTATION↗

Development of a Superconducting Adaptive Gap Undulator Prototype for NSLS-II

The photon flux and brightness of synchrotron radiation, crucial parameters for any light source, vary significantly depending on the type of source employed. Among the 23 Insertion Device (ID) sources at the National Synchrotron Light Source II (NSLS-II) at Brookhaven National Lab (BNL), the 12-year-old 3m-long In-Vacuum Undulator (IVU20) stands out for its superior performance, although it no longer represents the cutting edge of technology. Recently, there has been a shift in focus towards developing next-generation sources, particularly Superconducting Undulators (SCUs), characterized by smaller gaps, shorter periods, and maximum lengths. However, despite ongoing research and development efforts, SCUs have yet to surpass their predecessors, the Cryogenic Permanent Magnet Undulators (CPMUs), in terms of performance. This is largely attributed to the limitations posed by traditional superconducting wire, as well as challenges in the design of the magnetic structure and vacuum chamber. In this paper, we aim to overcome such limitations through the development of a unique prototype Superconducting Adaptive Gap Undulator (SC-AGU) magnet core and vacuum chamber design. This paper will outline a novel technical approach aimed at constructing a compact prototype magnet array utilizing state-of-the-art superconducting wire technology. This approach provides a more efficient magnetic structure, allowing for enhanced magnetic field strength and stability.

36 MATERIALS SCIENCE↗

NSUF FY 2024 Annual Report: Microscopy and Characterization Suite (MaCS) and National Synchrotron Light Source-II (NSLS-II)

The Microscopy and Characterization Suite (MaCS) laboratory at the Center for Advanced Energy Studies (CAES) and the National Synchrotron Light Source-II (NSLS-II) at Brookhaven National Laboratory (BNL) partner with the Nuclear Science User Facilities (NSUF). This partnership provides funding that allows researchers to access these facilities at no cost for studying irradiation effects on nuclear fuels and materials. Through NSUF, both MaCS and NSLS-II support post-irradiation examination (PIE) and irradiation activities for NSUF Rapid Turnaround Experiments (RTE) and NSUF Consolidated Innovative Nuclear Research (CINR) awards. This report details the work completed at these facilities for NSUF competitively selected awards during fiscal year 2024.

99 GENERAL AND MISCELLANEOUS↗

Advanced flip-coil system for magnetic field integral measurements of insertion devices

A novel flip-coil measurement system has been developed for the National Synchrotron Light Source II (NSLS-II) at Brookhaven National Laboratory. This paper describes the design, implementation, and commissioning of the new measurement bench, highlighting its key features, including improved mechanical stability, advanced data acquisition, and enhanced reproducibility. The system enables precise characterization of field integrals and multipole components, ensuring the optimal performance of Insertion Devices (IDs) before installation in the NSLS-II storage ring. The flip-coil system incorporates an innovative approach to minimize mechanical and electrical errors, which significantly improves the reproducibility of measurements. In addition, the system features a state-of-the-art data acquisition system that enables real-time monitoring and analysis, further enhancing the efficiency and accuracy of the measurement process. Furthermore, preliminary tests have demonstrated that the new system meets the stringent requirements for magnetic field characterization of advanced insertion devices, making it an essential tool for future ID commissioning and quality assurance at NSLS-II.

36 MATERIALS SCIENCE↗

Microscopy and Characterization Suite (MaCS) and National Synchrotron Light Source-II (NSLS-II) FY 2025 Annual Report

The Microscopy and Characterization Suite (MaCS) laboratory at the Critical Materials and Energy Systems Innovation Center (CMESIC), formerly the Center for Advanced Energy Studies (CAES) and the National Synchrotron Light Source-II (NSLS-II) at Brookhaven National Laboratory (BNL) partner with the Nuclear Science User Facilities (NSUF). These partnerships provide funding that allows researchers to access these facilities at no cost for studying irradiation effects on nuclear fuels and materials. Through NSUF, both MaCS and NSLS-II support post-irradiation examination (PIE) and irradiation activities for NSUF Rapid Turnaround Experiments (RTE) and NSUF Consolidated Innovative Nuclear Research (CINR) awards.

36 - MATERIALS SCIENCE↗

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↗

Field Harmonic Measurement of High-Gradient Permanent Magnet Quadrupoles for NSLS- II Upgrade

The National Synchrotron Light Source II (NSLS-II) is preparing for a major upgrade based on a new lattice concept, known as “Complex Bend,” to replace its existing double bend achromat (DBA) lattice. Here, this novel lattice will use high-gradient permanent magnet quadrupoles (PMQs) with small apertures in the range of 16–22 mm. A prototype complex bend branch with PMQs has been installed in the NSLS-II linac to evaluate the lattice's performance. An accurate and precise magnetic measurement system is required for field harmonic characterization and magnetic tuning of these PMQs. As part of this project a Rotating-Coil bench, based on a Printed Circuit Board (PCB) coil with a 12 mm diameter, has been configured to measure nine PMQs with bore diameter of 12.7 mm. This PCB coil has an active length of 270 mm, and is able to measure fields up to the 15th harmonic of the main field at a reference radius of 5 mm, while maintaining field quality levels within 10 ppm of the main field. This article presents the PCB coil setup, the harmonic measurement results and their temperature dependencies and repeatability. Simulation results on compensation of undesired multipoles using “IDBuilder”, a genetic algorithm-based optimizer code for magnetic tuning is included for field harmonic corrections.

36 MATERIALS SCIENCE↗

Advances in scientific literature mining for interpreting materials characterization

Abstract Using synchrotron light sources, such as the National Synchrotron Light Source II at Brookhaven National Laboratory, scientists in fields as diverse as physics, biology, and materials science, identify the atomic structure, chemical composition, or other important properties of varied specimens. x-ray spectroscopy from light sources is particularly valuable for materials research with vast information available about reference spectra in the scientific literature. However, as the technique is applicable to many science domains, searching for information about select x-ray spectroscopy spectra is impeded by the sheer number of publications. Moreover, useful information about the context of an experiment or figures presented in papers can be buried among the details, which takes time to assess. This work presents a scientific literature mining system that supports data acquisition, information extraction, and user interaction for referencing x-ray spectra identification and spectral interpretation. The goal is to provide efficient access to useful spectral data to researchers who may spend only a few days at a synchrotron light source. With this system, users browse a classification tree for papers arranged according to x-ray spectroscopic methods, chemical elements, and x-ray absorption spectroscopy edges. Relevant figures are extracted with sentences from the paper that explain them, known as ‘figure explanatory text.’ Notably, this system focuses on semantic aspects (logical analysis) to find figure explanatory text using deep contextualized word embeddings techniques and contains an interface to obtain labeled data from domain experts that is used to evaluate and improve the model.

Park, Gilchan (ORCID:0000000201536646)↗

Specimen-displacement correction for powder X-ray diffraction in Debye–Scherrer geometry with a flat area detector

The effect of small changes in the specimen-to-detector distance on the unit-cell parameters is examined for synchrotron powder diffraction in Debye–Scherrer (transmission) geometry with a flat area detector. An analytical correction equation is proposed to fix the shift in 2θ values due to specimen capillary displacement. This equation does not require the use of an internal reference material, is applied during the Rietveld refinement step, and is analogous to the specimen-displacement correction equations for Bragg–Brentano and curved-detector Debye–Scherrer geometry experiments, but has a different functional form. The 2θ correction equation is compared with another specimen-displacement correction based on the use of an internal reference material in which new integration and calibration parameters of area-detector images are determined. Example data sets showing the effect of a 3.3 mm specimen displacement on the unit-cell parameters for 25°C CeO 2 , including both types of displacement correction, are described. These experiments were performed at powder X-ray diffraction beamlines at the National Synchrotron Light Source II at Brookhaven National Laboratory and the Advanced Photon Source at Argonne National Laboratory.

36 MATERIALS SCIENCE↗

Long Island Steatite Sourcing from Rhode Island Quarries During the Late Holocene Era

This study aimed to investigate the possible sourcing of Long Island steatite artifacts from quarries in Rhode Island. Seven steatite samples from archeological sites on Long Island including Nassau County, Suffolk County (North Fork and South Fork) and Shelter Island were compared to two Rhode Island quarry sample putative sources using X-ray fluorescence (XRF) microscopy at the Submicron Resolution X-ray spectroscopy (SRX) beamline of the National Synchrotron Light Source II at Brookhaven National Laboratory. The site-derived steatite samples displayed numerous similarities in elemental composition compared to the two Rhode Island quarries, Oaklawn and Ochee Springs. This study provides new evidence to support the possible sourcing of Long Island steatite from Rhode Island during the late Holocene era.

54 ENVIRONMENTAL SCIENCES↗

Long Island Steatite Sourcing from Rhode Island Quarries During the Late Holocene Era

This study aimed to investigate the possible sourcing of Long Island steatite artifacts from quarries in Rhode Island. Seven steatite samples from archeological sites on Long Island including Nassau County, Suffolk County (North Fork and South Fork) and Shelter Island were compared to two Rhode Island quarry sample putative sources using X-ray fluorescence (XRF) microscopy at the Submicron Resolution X-ray spectroscopy (SRX) beamline of the National Synchrotron Light Source II at Brookhaven National Laboratory. The site-derived steatite samples displayed numerous similarities in elemental composition compared to the two Rhode Island quarries, Oaklawn and Ochee Springs. This study provides new evidence to support the possible sourcing of Long Island steatite from Rhode Island during the late Holocene era.

54 ENVIRONMENTAL SCIENCES↗

Magnetic excitations in Nd 𝑛+1⁢ Ni 𝑛⁢ O 3⁢𝑛+1 Ruddlesden-Popper nickelates observed via resonant inelastic x-ray scattering

Magnetic interactions are thought to play a key role in the properties of many unconventional superconductors, including cuprates, iron pnictides, and square-planar nickelates. Superconductivity was also recently observed in the bilayer and trilayer Ruddlesden-Popper nickelates, the electronic structure of which is expected to differ from that of cuprates and square-planar nickelates. Here we study how electronic structure and magnetic interactions evolve with the number of layers, 𝑛, in thin film Ruddlesden-Popper nickelates Nd 𝑛+1 ⁢Ni 𝑛 ⁢O 3⁢𝑛+1 with 𝑛 = 1,3, and 5 using resonant inelastic x-ray scattering (RIXS). The RIXS spectra are consistent with a high-spin |3⁢𝑑 8 ⁢ $\underline{𝐿}$⟩ electronic configuration, resembling that of La 2−𝑥 ⁢Sr 𝑥 ⁢NiO 4 and the parent perovskite, NdNiO 3 . The magnetic excitations soften to lower energy in the structurally self-doped, higher-𝑛 films. In conclusion, our observations confirm that structural tuning is an effective route for altering electronic properties, such as magnetic superexchange, in this prominent family of materials.

36 MATERIALS SCIENCE↗