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At least 1,657 records · Page 92

A WISER way for simulating the performance of gratings

Soft X-ray monochromators for synchrotron radiation sources have been continuously developed over the years, improving energy resolution and stability. Great effort has been made in improving the surface quality of the optics involved, reaching values permitting diffraction-limited images. Still, one problem has not been solved, nor fully understood, yet: groove placing errors. Nowadays, these are one of the major factors responsible for resolving the power reduction of diffraction-gratings-based X-ray monochromators. Despite decades of use of gratings, there is not yet a universally established method for predicting and simulating the effect of groove placing errors on monochromator performance. This is especially important in the new scenario of high-coherent X-ray sources, i.e. diffraction-limited storage rings and free-electron lasers. To address this problem, in this article an approach based on WISER (Wavefront propagatIon Simulation codE libRary) is presented. WISER is a physical optics simulation package, also available in the user-friendly Orange Synchrotron Radiation Suite – OASYS. Even though it was originally conceived to assess the focusing performance of X-ray mirrors in the presence of height defects, it perfectly simulates the performance of a periodic (or quasi-periodic) structure like a diffraction grating. In this article, the way to use WISER and its application to a specific case, e.g. the design of a monochromator for the upgrade of a beamline at the Advanced Light Source, are shown. A simple rule for estimating how well the grooves are placed on a grating, based on calculation of the Strehl ratio, is also presented.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Mapping nanocrystal orientations via scanning Laue diffraction microscopy for multi-peak Bragg coherent diffraction imaging

The recent commissioning of a movable monochromator at the 34-ID-C endstation of the Advanced Photon Source has vastly simplified the collection of Bragg coherent diffraction imaging (BCDI) data from multiple Bragg peaks of sub-micrometre scale samples. Laue patterns arising from the scattering of a polychromatic beam by arbitrarily oriented nanocrystals permit their crystal orientations to be computed, which are then used for locating and collecting several non-co-linear Bragg reflections. The volumetric six-component strain tensor is then constructed by combining the projected displacement fields that are imaged using each of the measured reflections via iterative phase retrieval algorithms. Complications arise when the sample is heterogeneous in composition and/or when multiple grains of a given lattice structure are simultaneously illuminated by the polychromatic beam. Here, a workflow is established for orienting and mapping nanocrystals on a substrate of a different material using scanning Laue diffraction microscopy. The capabilities of the developed algorithms and procedures with both synthetic and experimental data are demonstrated. The robustness is verified by comparing experimental texture maps obtained with Laue diffraction microscopy at the beamline with maps obtained from electron back-scattering diffraction measurements on the same patch of gold nanocrystals. Such tools provide reliable indexing for both isolated and densely distributed nanocrystals, which are challenging to image in three dimensions with other techniques.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

VerSoX B07-B: a high-throughput XPS and ambient pressure NEXAFS beamline at Diamond Light Source

The beamline optics and endstations at branch B of the Versatile Soft X-ray (VerSoX) beamline B07 at Diamond Light Source are described. B07-B provides medium-flux X-rays in the range 45-2200 eV from a bending magnet source, giving access to local electronic structure for atoms of all elements from Li to Y. It has an endstation for high-throughput X-ray photoelectron spectroscopy (XPS) and near-edge X-ray absorption fine-structure (NEXAFS) measurements under ultrahigh-vacuum (UHV) conditions. B07-B has a second endstation dedicated to NEXAFS at pressures from UHV to ambient pressure (1 atm). The combination of these endstations permits studies of a wide range of interfaces and materials. The beamline and endstation designs are discussed in detail, as well as their performance and the commissioning process.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Complementarity of neutron, XFEL and synchrotron crystallography for defining the structures of metalloenzymes at room temperature

Room-temperature macromolecular crystallography allows protein structures to be determined under close-to-physiological conditions, permits dynamic freedom in protein motions and enables time-resolved studies. In the case of metalloenzymes that are highly sensitive to radiation damage, such room-temperature experiments can present challenges, including increased rates of X-ray reduction of metal centres and site-specific radiation-damage artefacts, as well as in devising appropriate sample-delivery and data-collection methods. It can also be problematic to compare structures measured using different crystal sizes and light sources. In this study, structures of a multifunctional globin, dehaloperoxidase B (DHP-B), obtained using several methods of room-temperature crystallographic structure determination are described and compared. Here, data were measured from large single crystals and multiple microcrystals using neutrons, X-ray free-electron laser pulses, monochromatic synchrotron radiation and polychromatic (Laue) radiation light sources. These approaches span a range of 18 orders of magnitude in measurement time per diffraction pattern and four orders of magnitude in crystal volume. The first room-temperature neutron structures of DHP-B are also presented, allowing the explicit identification of the hydrogen positions. The neutron data proved to be complementary to the serial femtosecond crystallography data, with both methods providing structures free of the effects of X-ray radiation damage when compared with standard cryo-crystallography. Comparison of these room-temperature methods demonstrated the large differences in sample requirements, data-collection time and the potential for radiation damage between them. With regard to the structure and function of DHP-B, despite the results being partly limited by differences in the underlying structures, new information was gained on the protonation states of active-site residues which may guide future studies of DHP-B.

36 MATERIALS SCIENCE↗

Preliminary results of neutron and X-ray diffraction data collection on a lytic polysaccharide monooxygenase under reduced and acidic conditions

Lytic polysaccharide monooxygenases (LPMOs) are copper-center enzymes that are involved in the oxidative cleavage of the glycosidic bond in crystalline cellulose and other polysaccharides. The LPMO reaction is initiated by the addition of a reductant and oxygen to ultimately form an unknown activated copper–oxygen species that is responsible for polysaccharide-substrate H-atom abstraction. Given the sensitivity of metalloproteins to radiation damage, neutron protein crystallo­graphy provides a nondestructive technique for structural characterization while also informing on the positions of H atoms. Neutron cryo-crystallography permits the trapping of catalytic intermediates, thereby providing insight into the protonation states and chemical nature of otherwise short-lived species in the reaction mechanism. Here, to characterize the reaction-mechanism intermediates of LPMO9D from Neurospora crassa, a cryo-neutron diffraction data set was collected from an ascorbate-reduced crystal. A second neutron diffraction data set was collected at room temperature from an LPMO9D crystal exposed to low-pH conditions to probe the protonation states of ionizable groups involved in catalysis under acidic conditions.

Neurospora crassa↗

Cryotrapping peroxide in the active site of human mitochondrial manganese superoxide dismutase crystals for neutron diffraction

Structurally identifying the enzymatic intermediates of redox proteins has been elusive due to difficulty in resolving the H atoms involved in catalysis and the susceptibility of ligand complexes to photoreduction from X-rays. Cryotrapping ligands for neutron protein crystallography combines two powerful tools that offer the advantage of directly identifying hydrogen positions in redox-enzyme intermediates without radiolytic perturbation of metal-containing active sites. However, translating cryogenic techniques from X-ray to neutron crystallography is not straightforward due to the large crystal volumes and long data-collection times. Here, methods have been developed to visualize the evasive peroxo complex of manganese superoxide dismutase (MnSOD) so that all atoms, including H atoms, could be visualized. The subsequent cryocooling and ligand-trapping methods resulted in neutron data collection to 2.30 Å resolution. The P 6 1 22 crystal form of MnSOD is challenging because it has some of the largest unit-cell dimensions ( a = b = 77.8, c = 236.8 Å) ever studied using high-resolution cryo-neutron crystallography. The resulting neutron diffraction data permitted the visualization of a dioxygen species bound to the MnSOD active-site metal that was indicative of successful cryotrapping.

59 BASIC BIOLOGICAL SCIENCES↗

Serial crystallography with multi-stage merging of thousands of images

KAMO and BLEND provide particularly effective tools to automatically manage the merging of large numbers of data sets from serial crystallography. The requirement for manual intervention in the process can be reduced by extending BLEND to support additional clustering options such as the use of more accurate cell distance metrics and the use of reflection-intensity correlation coefficients to infer `distances' among sets of reflections. This increases the sensitivity to differences in unit-cell parameters and allows clustering to assemble nearly complete data sets on the basis of intensity or amplitude differences. If the data sets are already sufficiently complete to permit it, one applies KAMO once and clusters the data using intensities only. When starting from incomplete data sets, one applies KAMO twice, first using unit-cell parameters. In this step, either the simple cell vector distance of the original BLEND or the more sensitive NCDist is used. This step tends to find clusters of sufficient size such that, when merged, each cluster is sufficiently complete to allow reflection intensities or amplitudes to be compared. One then uses KAMO again using the correlation between reflections with a common hkl to merge clusters in a way that is sensitive to structural differences that may not have perturbed the unit-cell parameters sufficiently to make meaningful clusters. Many groups have developed effective clustering algorithms that use a measurable physical parameter from each diffraction still or wedge to cluster the data into categories which then can be merged, one hopes, to yield the electron density from a single protein form. Since these physical parameters are often largely independent of one another, it should be possible to greatly improve the efficacy of data-clustering software by using a multi-stage partitioning strategy. Here, one possible approach to multi-stage data clustering is demonstrated. The strategy is to use unit-cell clustering until the merged data are sufficiently complete and then to use intensity-based clustering. Using this strategy, it is demonstrated that it is possible to accurately cluster data sets from crystals that have subtle differences.

36 MATERIALS SCIENCE↗

Fragment-based determination of a proteinase K structure from MicroED data using ARCIMBOLDO_SHREDDER

Structure determination of novel biological macromolecules by X-ray crystallography can be facilitated by the use of small structural fragments, some of only a few residues in length, as effective search models for molecular replacement to overcome the phase problem. Independence from the need for a complete pre-existing model with sequence similarity to the crystallized molecule is the primary appeal of ARCIMBOLDO , a suite of programs which employs this ab initio algorithm for phase determination. Here, the use of ARCIMBOLDO is investigated to overcome the phase problem with the electron cryomicroscopy (cryoEM) method known as microcrystal electron diffraction (MicroED). The results support the use of the ARCIMBOLDO_SHREDDER pipeline to provide phasing solutions for a structure of proteinase K from 1.6 Å resolution data using model fragments derived from the structures of proteins sharing a sequence identity of as low as 20%. ARCIMBOLDO_SHREDDER identified the most accurate polyalanine fragments from a set of distantly related sequence homologues. Alternatively, such templates were extracted in spherical volumes and given internal degrees of freedom to refine towards the target structure. Both modes relied on the rotation function in Phaser to identify or refine fragment models and its translation function to place them. Model completion from the placed fragments proceeded through phase combination of partial solutions and/or density modification and main-chain autotracing using SHELXE . The combined set of fragments was sufficient to arrive at a solution that resembled that determined by conventional molecular replacement using the known target structure as a search model. This approach obviates the need for a single, complete and highly accurate search model when phasing MicroED data, and permits the evaluation of large fragment libraries for this purpose.

59 BASIC BIOLOGICAL SCIENCES↗

Learning with Adaptive Conservativeness for Distributionally Robust Optimization: Incentive Design for Voltage Regulation

Information asymmetry between the Distribution System Operator (DSO) and Distributed Energy Resource Aggregators (DERAs) obstructs designing effective incentives for voltage regulation. To capture this effect, we employ a Stackelberg game-theoretic framework, where the DSO seeks to overcome the information asymmetry and refine its incentive strategies by learning from DERA behavior over multiple iterations. We introduce a model-based online learning algorithm for the DSO, aimed at inferring the relationship between incentives and DERA responses. Given the uncertain nature of these responses, we also propose a distributionally robust incentive design model to control the probability of voltage regulation failure and then reformulate it into a convex problem. This model allows the DSO to periodically revise distribution assumptions on uncertain parameters in the decision model of the DERA. Finally, we present a gradient-based method that permits the DSO to adaptively modify its conservativeness level, measured by the size of a Wasserstein metric-based ambiguity set, according to historical voltage regulation performance. The effectiveness of our proposed method is demonstrated through numerical experiments.

adaptation models↗

Strym: A Python Package for Real-time CAN Data Logging, Analysis and Visualization to Work with USB-CAN Interface

In this report, we describe a data analysis tool developed for decoding and analyzing vehicle data obtained from a passenger vehicle’s onboard controller area network (CAN) bus. The tool developed in this paper provides a timeseries framework to perform domain-specific analysis at scale when interpreting data from a vehicle or a collection of vehicles in light of how to design intelligent vehicle applications. The tool, called Strym, exploits the CAN bus mechanism of modern vehicles to capture data using commercially available CAN-to-USB hardware Comma.ai Panda devices, managed through open-source software Libpanda. Strym permits the decoding of vendor-specific CAN messages in a vehicle-agnostic manner. Through this, a researcher can characterize data throughput, assess data quality, and perform analyses. Such analyses are useful in a number of research such as studying human driving behavior in mixed-autonomy, new driver models, rare-event detection, traffic flow estimation, and custom control of vehicles.

Performance evaluation, Smart cities, Intelligent ↗

Picosecond Synchronization System for Quantum Networks

The operation of long-distance quantum networks requires photons to be synchronized and must account for length variations of quantum channels. We demonstrate a 200 MHz clock-rate fiber optic-based telecommunication C-band quantum network using off-the-shelf components combined with custom-made electronics. The network is backed by a scalable and fully automated synchronization system with ps-scale timing resolution. Synchronization of the photons is achieved by distributing O-band-wavelength laser pulses between network nodes. Specifically, we distribute photon pairs between three nodes, and measure a reduction of coincidence-to-accidental ratio from 77 to only 42 when the synchronization system is enabled, which permits high-fidelity qubit transmission. Our demonstration sheds light on the role of noise in quantum communication and represents a key step in realizing deployed co-existing classical-quantum networks.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

On Quantum Rainbows: Density Operator in the Frequency-Bin Representation for Entangled Twin-Photons Generated With Sub-Threshold Microcombs

Kerr optical frequency combs are generated by pumping a high-Q integrated microresonator with a resonant laser. Below threshold, the pump laser field mediates the phenomenon of spontaneous four-wave mixing, where two pump photons are symmetrically up- and down-converted as twin photons that can be entangled across up to tens of eigenmodes in the spectral domain. While these room-temperature integrated photonic circuits are expected to play a central role in quantum technology, their high dimensionality and dissipative nature are a challenge for their theoretical description, therefore hindering the understanding of their properties and potential of performance. In this article, we develop a framework that permits to obtain an explicit solution for the density operator of quantum microcombs below threshold. Furthermore, this self-consistent theoretical description allows for their complete characterization, as well as for the analytical determination of various performance metrics such as fidelity, purity, and entropy.

42 ENGINEERING↗

Compliant Intramedullary Stems for Joint Reconstruction

The longevity of current joint replacements is limited by aseptic loosening, which is the primary cause of non-infectious failure for hip, knee, and ankle arthroplasty. Aseptic loosening is typically caused either by osteolysis from particulate wear, or by high shear stresses at the bone-implant interface from over-constraint. Our objective was to demonstrate feasibility of a compliant intramedullary stem that eliminates over-constraint without generating particulate wear. The compliant stem is built around a compliant mechanism that permits rotation about a single axis. We first established several models to understand the relationship between mechanism geometry and implant performance under a given angular displacement and compressive load. We then used a neural network to identify a design space of geometries that would support an expected 100-year fatigue life inside the body. We additively manufactured one representative mechanism for each of three anatomic locations, and evaluated these prototypes on a KR-210 robot. The neural network predicts maximum stress and torsional stiffness with 2.69% and 4.08% error respectively, relative to finite element analysis data. We identified feasible design spaces for all three of the anatomic locations. Simulated peak stresses for the three stem prototypes were below the fatigue limit. Benchtop performance of all three prototypes was within design specifications. Our results demonstrate the feasibility of designing patient- and joint-specific compliant stems that address the root causes of aseptic loosening. Guided by these results, we expect the use of compliant intramedullary stems in joint reconstruction technology to increase implant lifetime.

60 APPLIED LIFE SCIENCES↗

Virtualized Logical Qubits: A 2.5D Architecture for Error-Corrected Quantum Computing

Current, near-term quantum devices have shown great progress in the last several years culminating recently with a demonstration of quantum supremacy. In the medium-term, however, quantum machines will need to transition to greater reliability through error correction, likely through promising techniques like surface codes which are well suited for near-term devices with limited qubit connectivity. We discover quantum memory, particularly resonant cavities with transmon qubits arranged in a 2.5D architecture, can efficiently implement surface codes with substantial hardware savings and performance/fidelity gains. Specifically, we virtualize logical qubits by storing them in layers of qubit memories connected to each transmon. Surprisingly, distributing each logical qubit across many memories has a minimal impact on fault tolerance and results in substantially more efficient operations. Our design permits fast transversal application of CNOT operations between logical qubits sharing the same physical address (same set of cavities) which are 6x faster than standard lattice surgery CNOTs. We develop a novel embedding which saves approximately 10x in transmons with another 2x savings from an additional optimization for compactness. Although qubit virtualization pays a 10x penalty in serialization, advantages in the transversal CNOT and in area efficiency result in fault-tolerance and performance comparable to conventional 2D transmon-only architectures. Our simulations show our system can achieve fault tolerance comparable to conventional two-dimensional grids while saving substantial hardware. Furthermore, our architecture can produce magic states at 1.22x the baseline rate given a fixed number of transmon qubits. Here, this is a critical benchmark for future fault-tolerant quantum computers as magic states are essential and machines will spend the majority of their resources continuously producing them. This architecture substantially reduces the hardware requirements for fault-tolerant quantum computing and puts within reach a proof-of-concept experimental demonstration of around 10 logical qubits, requiring only 11 transmons and 9 attached cavities in total.

quantum computing↗

COSMIC DAWN: Distributed Analysis of Wireless at Nextscale

Distributed Analysis of Wireless at Nextscale (DAWN) is a novel simulation framework for large-scale design-space exploration (DSE) of unmodified software-defined radio (SDR) applications interacting in a scalable, high-fidelity, virtual physics environment. The software-defined nature of the coupled software-physics simulation leverages hardware emulation to permit in-depth examination and modification of not only the electromagnetic environment, including each signal in flight, but also the precise state of system software and components. DAWN supports modular, customizable physics environments allowing realistic propagation effects so that computationally efficient empirical models, reduced order/surrogate models, or large-scale, high-fidelity, site-specific simulations can be used as a propagation medium based on scenario requirements. This paper introduces DAWN’s design and initial implementation, detailing key architectural components, including the Physics Realization Engine (PhyRE), Runtime Infrastructure for Simulation Environments (RISE), and the design space exploration (DSE) suite. It concludes with demonstrations using unmodified 4G/LTE software available from srsRAN on computing resources ranging from a small cluster to ORNL’s Frontier Exascale system.

Wise, Mike [ORNL] (ORCID:0000000266120641)↗

Efficient Quantum Gate Discovery with Optimal Control

Optimal control theory provides a framework for numerical discovery of device controls that implement quantum logic gates, but common objective functions used for optimization often assign arbitrarily high costs to otherwise useful controls. We propose a framework for designing objective functions that permit novel gate designs such as echo pulses or locally-equivalent gates. We use numerical simulations to demonstrate the efficacy of the new objective functions by designing microwave-only pulses that act as entangling gates for superconducting transmon architectures. We observe that the proposed objective functions lead to higher fidelity controls in fewer optimization iterations than obtainable by traditional objective functions.

Kairys, Paul↗

A Refinement-by-Superposition -Method for (curl)- and (div)-Conforming Discretizations

Here, we present refinement-by-superposition (RBS) hp-refinement infrastructure for computational electromagnetics (CEMs), which permits exponential rates of convergence. In contrast to dominant approaches to hp-refinement for continuous Galerkin methods, which rely on explicit constraint equations, the multilevel strategy presented drastically reduces the implementation complexity. Through the RBS methodology, enforcement of continuity occurs by construction, enabling arbitrary levels of refinement with ease, and without the practical (but not theoretical) limitations of constrained-node refinement. We outline the construction of the RBS hp-method for refinement with H (curl)- and H (div)-conforming finite cells. Numerical simulations for the 2-D finite element method (FEM) solution of the Maxwell eigenvalue problem demonstrate the effectiveness of RBS hp-refinement. As an additional goal of this work, we aim to promote the use of mixed-order (low- and high-order) elements in practical CEM applications.

42 ENGINEERING↗

Can High Current Density HTS Magnets be Quench Protected Using Methods Used to Protect High Current Density LTS Magnets?

In the 1970s the Lawrence Berkeley Laboratory (LBL) was testing high current density magnets where the EJ 2 limit was up to two orders of magnitude higher than the quench protection methods of the period would permit at the time. LBL was designing a high current density (J) thin solenoid with a large volume and stored energy (E). The accepted EJ 2 limit at the time was ~10 23 J A 2 m -4 . In order to exceed the EJ 2 limit by two orders of magnitude, one had to greatly increase the quench protection voltages (V) and magnet current (I). In 1977, LBL tested four quench protection methods on a 2-meter diameter high current density solenoid with a stored energy of 2 MJ. Three of these quench protection methods worked well, but the fourth didn't appear to work. These methods will be discussed as to whether they can be applied to HTS or MgB 2 high current density magnets.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗