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At least 1,387 records · Page 77

Validated ligand geometries for macromolecular refinement restraints and molecular-mechanics force fields

In macromolecular structure refinement, the low observation-to-parameter ratio and the lack of high-resolution data are countered by using a priori information in the form of restraints. Having accurate geometries of the chemical entities in the sample is paramount for generating accurate chemical restraints and, therefore, accurate macromolecular structures. In particular, it is desirable to have accurate restraints for known and novel ligand entities. Quantum mechanics (QM) can minimize the energy of a ligand by adjusting its geometry, and these geometries can be used to generate restraints for macromolecular refinement. This article describes a library of approximately 37 000 small molecules extracted from the Chemical Component Dictionary in the Protein Data Bank and minimized by density-functional QM. The library includes restraint files for use in crystallography or cryo-EM refinement, along with files suitable for molecular-dynamics simulation. Because the geometries are validated using the Cambridge Structural Database, the restraints library provides users with both functional restraints and minimized geometries. This work also provides procedures for generating new and accurate restraints.

Amber↗

Conversion kinetics of container glass batch melting

Abstract Understanding the batch‐to‐glass conversion process is fundamental to optimizing the performance of glass‐melting furnaces and ensuring that furnace modeling can correctly predict the observed outcome when batch materials or furnace conditions change. To investigate the kinetics of silica dissolution, gas evolution, and primary foam formation and collapse, we performed X‐ray diffraction, thermal gravimetry, feed expansion tests, and evolved gas analysis of batch samples heated at several constant heating rates. We found that gas evolving reactions, foaming, and silica dissolution depend on the thermal history of the batch in a similar manner: the kinetic parameters of each process were linear functions of the square root of the heating rate. This kinetic similarity reflects the stronger‐than‐expected interdependence of these processes. On the basis of our results, we suggest that changes in furnace operating conditions, such as firing or boosting, influence the melting rate less than what one would expect without consideration of batch conversion kinetics.

Ueda, Nanako↗

An Approach to Bayesian Optimization for Design Feasibility Check on Discontinuous Black-Box Functions

The paper presents a novel approach to applying Bayesian Optimization (BO) in predicting an unknown constraint boundary, also representing the discontinuity of an unknown function, for a feasibility check on the design space, thereby representing a classification tool to discern between a feasible and infeasible region. Bayesian optimization is a low-cost black-box global optimization tool in the Sequential Design Methods where one learns and updates knowledge from prior evaluated designs, and proceeds to the selection of new designs for future evaluation. However, BO is best suited to problems with the assumption of a continuous objective function and does not guarantee true convergence when having a discontinuous design space. This is because of the insufficient knowledge of the BO about the nature of the discontinuity of the unknown true function. In this paper, we have proposed to predict the location of the discontinuity using a BO algorithm on an artificially projected continuous design space from the original discontinuous design space. The proposed approach has been implemented in a thin tube design with the risk of creep-fatigue failure under constant loading of temperature and pressure. The stated risk depends on the location of the designs in terms of safe and unsafe regions, where the discontinuities lie at the transition between those regions; therefore, the discontinuity has also been treated as an unknown creep-fatigue failure constraint. The proposed BO algorithm has been trained to maximize sampling toward the unknown transition region, to act as a high accuracy classifier between safe and unsafe designs with minimal training cost. The converged solution has been validated for different design parameters with classification error rate and function evaluations at an average of <1% and ~150, respectively. Finally, the performance of our proposed approach in terms of training cost and classification accuracy of thin tube design is shown to be better than the existing machine learning (ML) algorithms such as Support Vector Machine (SVM), Random Forest (RF), and Boosting.

Engineering↗

Preliminary Design of a New Pulsed-Neutron Die--Away Experiments with Absorbers (IER-552 CED-1)

This report presents the preliminary design (CED-1) of IER-552, pulsed-neutron die-away (PNDA) experiments with absorbers, to be conducted by Lawrence Livermore National Laboratory (LLNL). The goal of the PNDA experiments with absorbing materials is to produce high-quality, low-cost integral benchmarks that can be used to validate cross sections that are high priority nuclear data for the Department of Energy’s Nuclear Criticality Safety Program (NCSP). PNDA experiments can be used to generate nuclear data validation benchmarks quickly and cheaply, as they do not require fissile material or a nuclear facility to conduct them. The original PNDA experiments were set up at LLNL under IER-501. Extending the PNDA experiments to include absorbing materials leverages existing facilities and resources at LLNL to validate cross sections, with a basic experiment design that uses a neutron generator to impinge a short, mono-energetic neutron pulse on a poisoned, moderating target sample. The neutron pulse lasts 100 µs, after which the neutron population in the sample reaches thermal equilibrium and later spatial equilibrium. In this fully equilibrized state, the neutron population has a characteristic decay-time eigenvalue. The eigenvalue can be used as an integral parameter to validate nuclear data involved with neutron scattering and absorption. Two observables can be measured: the neutron population and the population of secondary γ-rays produced by inelastic and capture reactions. This report explores the feasibility of both approaches. For γ-ray measurements, this allows for direct measurement of reactions of interest for validation. During the neutron burst time, inelastic (prompt) γ-rays dominate, and these data can be isolated for validation of neutron inelastic scattering data. After the pulse ends, neutron capture (delayed) γ-rays dominate and are produced by many reaction channels as neutrons slow down to thermal energies. Two sets of γ-ray spectra (inelastic, capture) can be produced for validation. Additionally, the time-dependent decay of the capture γ-ray population when the neutron population is thermalized and in its fundamental mode can be used for validation. Two experiments can be imagined where pulsed neutrons are used to validate the nuclear data of absorbing materials. The first integrates well into the existing PNDA testbed at LLNL. The absorber material would be introduced into a moderating target and the same neutron generator, neutron detectors, electronics, and shielding box used for IER-501 would be employed. From the same experimental setup, many absorbing materials can be validated by simply changing the neutron poison in the moderator. The only significant modification would be the introduction of a γ-ray detector. Such an experiment would primarily serve to validate nuclear data in the thermal energy range. The second kind of experiment would validate the fast and epithermal energy range. It would involve pulsing neutron into a bare assembly of the absorber material and measuring the die-away of neutrons. The fast leakage of such an assembly requires nanosecond neutron-generator pulse widths and fast detectors/electronics that could measure ~200 ns die-away curves. This kind of experiment would ideally be performed at a cyclotron, like that available at Lawrence Berkeley National Laboratory.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Effect of laser power on roughness and porosity in laser powder bed fusion of stainless steel 316L alloys measured by X-ray tomography

The quality of metal objects fabricated via laser powder bed fusion are highly affected by process parameters, and their influence on final products is yet to be fully explored. In this work, pyrometry signals of the melt pool were collected from a set of stainless-steel samples during manufacturing and the effect of laser power on porosity and roughness of final printed parts was analyzed. Results show that the melt pool pyrometry signal of contours increases with higher laser power, whereas it is lower and decreases for the infilled part. Post-built X-ray computed tomography imaging reveals that porosity decreases while sample roughness increases upon increasing laser power. The decrease in porosity with increasing laser power is attributed to the larger size of the contour welds that were printed first, leading to an increase in dimension of the final products.

36 MATERIALS SCIENCE↗

Power Prediction of Airborne Wind Energy Systems Using Multivariate Machine Learning

Kites can be used to harvest wind energy at higher altitudes while using only a fraction of the material required for conventional wind turbines. In this work, we present the kite system of Kyushu University and demonstrate how experimental data can be used to train machine learning regression models. The system is designed for 7 kW traction power and comprises an inflatable wing with suspended kite control unit that is either tethered to a fixed ground anchor or to a towing vehicle to produce a controlled relative flow environment. A measurement unit was attached to the kite for data acquisition. To predict the generated tether force, we collected input–output samples from a set of well-designed experimental runs to act as our labeled training data in a supervised machine learning setting. We then identified a set of key input parameters which were found to be consistent with our sensitivity analysis using Pearson input–output correlation metrics. Finally, we designed and tested the accuracy of a neural network, among other multivariate regression models. The quality metrics of our models show great promise in accurately predicting the tether force for new input/feature combinations and potentially guide new designs for optimal power generation.

17 WIND ENERGY↗

Prediction of Silicon Content in a Blast Furnace via Machine Learning: A Comprehensive Processing and Modeling Pipeline

Silicon content plays an important role in determining the operational efficiency of blast furnaces (BFs) and their downstream processes in integrated steelmaking; however, existing sampling methods and first-principles models are somewhat limited in their capability and flexibility. Current data-based prediction models primarily rely on a limited set of manually selected furnace parameters. Additionally, different BFs present a diverse set of operating parameters and state variables that are known to directly influence the hot metal’s silicon content, such as fuel injection, blast temperature, and raw material charge composition, among other process variables that have their own impacts. The expansiveness of the parameter set adds complexity to parameter selection and processing. This highlights the need for a comprehensive methodology to integrate and select from all relevant parameters for accurate silicon content prediction. Providing accurate silicon content predictions would enable operators to adjust furnace conditions dynamically, improving safety and reducing economic risk. To address these issues, a two-stage approach is proposed. First, a generalized data processing scheme is proposed to accommodate diverse furnace parameters. Second, a robust modeling pipeline is used to establish a machine learning (ML) model capable of predicting hot metal silicon content with reasonable accuracy. The method employed herein predicted the average Si content of the upcoming furnace cast with an accuracy of 91% among 200 target predictions for a specific furnace provisioned by the XGBoost model. This prediction is achieved using only the past shift’s operating conditions, which should be available in real time. This performance provides a strong baseline for the modeling approach with potential for further improvement through provision of real-time features.

Chemistry↗

mosartwmpy sample input data; 1980 - 1985

Sample input data spanning the years 1980-1985 for running the `mosartwmpy` water routing and management model: https://github.com/IMMM-SFA/mosartwmpy. More information is available in the README.md. Changelog: v0.0.6: updates reservoir parameters to indicate which reservoirs should follow generic operating rules and which should follow ISTARF data-driven operating rules. v0.0.5: adds supporting files for running the Farmer Agent Based Model of adaptive water demand.

Rexer, Emily↗

The impact of environment on the lives of disc galaxies as revealed by SDSS-IV MaNGA

Environment has long been known to have significant impact on the evolution of galaxies, but here we seek to quantify the subtler differences that might be found in disc galaxies, depending on whether they are isolated, the most massive galaxy in a group (centrals), or a lesser member (satellites). The MaNGA survey allows us to define a large mass-matched sample of 574 galaxies with high-quality integrated spectra in each category. Initial examination of their spectral indices indicates significant differences, particularly in low-mass galaxies. Semi-analytic spectral fitting of a full chemical evolution model to these spectra confirms these differences, with low-mass satellites having a shorter period of star formation and chemical enrichment typical of a closed box, while central galaxies have more extended histories, with evidence of ongoing gas accretion over their lifetimes. The derived parameters for gas infall time-scale and wind strength suggest that low-mass satellite galaxies have their hot haloes of gas effectively removed, while central galaxies retain a larger fraction of gas than isolated galaxies due to the deeper group potential well in which they sit. S0 galaxies form a distinct subset within the sample, particularly at higher masses, but do not bias the inferred lower mass environmental impact significantly. The consistent picture that emerges underlines the wealth of archaeological information that can be extracted from high-quality spectral data using techniques like semi-analytic spectral fitting.

79 ASTRONOMY AND ASTROPHYSICS↗

Scaling behavior of low-temperature orthorhombic domains in the prototypical high-temperature superconductor La 1.875 Ba 0.125 CuO 4

Structural symmetry breaking and recovery in condensed-matter systems are closely related to exotic physical properties such as superconductivity (SC), magnetism, spin density waves, and charge density waves (CDWs). The interplay between different order parameters is intricate and often subject to intense debate, as in the case of CDW order and superconductivity. In La 1.875 Ba 0.125 CuO 4 (LBCO), the low-temperature structural domain walls are hypothesized as nanometer-scale pinning sites for the CDWs. Coherent x-ray diffraction techniques have been employed here to visualize the domain structures associated with these symmetry changes directly during phase transition. We have pushed Bragg coherent diffractive imaging (BCDI) into the cryogenic regime where most phase transitions in quantum materials reside. Utilizing BCDI, we image the structural evolution of LBCO microcrystal samples during the high-temperature tetragonal to low-temperature orthorhombic (LTO) phase transition. Our results show the formation of LTO domains close to the transition temperature and how the domain size decreases with temperature. In conclusion, the number of domains follows the secondary order parameter (or orthorhombic strain) measurement with a critical exponent that is consistent with the three-dimensional universality class.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Laser diagnostics to characterize the in-flame growth of platinum nanoparticles manufactured by the reactive spray deposition technology

Reactive Spray Deposition Technology (RSDT) is an atmospheric pressure, flame-based advanced manufacturing method used to fabricate Membrane Electrode Assemblies (MEAs) for proton exchange fuel cells and water electrolyzers. RSDT combines the flame synthesis of catalyst nanoparticles and their deposition onto the membrane in one step. The properties of the synthesized nanoparticles, such as their Size Distribution Function (SDF), determine the manufactured electrodes’ performance, which can be evaluated when the deposition is complete via ex-situ characterization of the products. Efforts to improve RSDT for manufacturing state-of-the-art MEAs can be significantly enhanced with integrated laser diagnostics that enable in situ measurement of the synthesized catalyst nanoparticles. This paper reports the implementation of laser diagnostics in an RSDT facility and evaluates their potential to assist the manufacturing process. Laser Light Scattering (LS) and Laser-Induced Incandescence (LII) measurements are performed in the oxygen-rich zone of the flame at various distances from the flame fuel jet nozzle downstream of its luminous region. The measurements quantitatively track the evolution in size and volume fraction of platinum-based nanoparticles in two flames that yield different catalytic properties in the manufactured electrodes. The profiles of the measured nanoparticles’ volume fraction along the flame axis can be estimated a priori so that the average nanoparticle sizes can be measured in quasi-real time via LS. Nanoparticles experience an extremely slow growth rate while being convected at distances from 150 nm to 300 nm from the fuel nozzle. Complementary characterizations of the synthesized nanoparticles are performed ex-situ via High-Angle Annular Darkfield Scanning Transmission Electron Microscopy (HAADF-STEM) image analyses of samples collected on grids at a fixed distance from the fuel jet nozzle. Comparing the results from laser and microscopy techniques not only cross-validates the findings but also provides the parameters to infer the bimodal SDF in-situ and yields evidence that the coagulation efficiency of the synthesized nanoparticles has extremely low values in the investigated zone of the flames.

Rayleigh Light Scattering (LS)↗

Spectrally-dependent positive and negative photo-plastic effects in CdZnTe and CdZnTeSe

We studied the Vickers microhardness HV0.025 of CdZnTe and CdZnTeSe samples upon illumination with quasi-monochromatic light with wavelengths ranging between 750 and 1540 nm. We observed that light with a wavelength close to or above the bandgap of the samples results in a positive photo-plastic effect (hardening), and light in the spectral range well below the band gap can lead both to positive or negative effects depending on the parameters of deep levels in the bandgap. We performed measurements of spectrally dependent photoconductivity and compared them with HV0.025. Based on the analysis, we propose a complex qualitative model explaining the spectral dependence of HV0.025 by the charging and neutralization of deep levels by optical transitions between the valence and conduction bands and between the bands and deep levels in the band gap. Tuning of parameters of deep levels could be used to control the sign and magnitude of the photo-plastic effect.

36 MATERIALS SCIENCE↗

Characterization of volcanic tuff pores pre- and post-underground nuclear detonation using ultra-small and small angle neutron scattering

The ability to accurately model the subsurface transport of radionuclides is fundamental to the remote detection and characterization of underground nuclear explosion (UNE) events. Developing more sophisticated transport models presents a significant opportunity to enhance monitoring capabilities, particularly in the reliable prediction of signature migration. Experimentally determined characterization of geologic materials associated with transport properties is the pertinent base information for such robust model development and calibration. Here, we report results from an unprecedented study demonstrating changes to the pore and fracture network structures in geological materials in response to UNEs over nanometer to micrometer length scales. Volcanic tuffs of five different lithological formations from pre- and post-UNE environments were collected from the Nevada National Security Site. Combined ultra-small and small-angle neutron scattering techniques were used to characterize the tuff pore structure. The results demonstrate measurable differences in the specific surface area and porosity of samples pre- and post-shot from texturally similar lithological formations, indicating that pore properties can serve as a direct physical signature of a UNE. The results also provide experimentally determined transport parameters in support of advanced model development through the integration of gas migration, hydrodynamic simulations, and geologic framework models.

54 ENVIRONMENTAL SCIENCES↗

A multifrequency study of sub-parsec jets with the Event Horizon Telescope

Context. The 2017 observing campaign of the Event Horizon Telescope (EHT) delivered the first very long baseline interferometry (VLBI) images at the observing frequency of 230 GHz, leading to a number of unique studies on black holes and relativistic jets from active galactic nuclei (AGN). In total, eighteen sources were observed, including the main science targets, Sgr A* and M 87, and various calibrators. Sixteen sources were AGN.Aims. We investigated the morphology of the sixteen AGN in the EHT 2017 data set, focusing on the properties of the VLBI cores: size, flux density, and brightness temperature. We studied their dependence on the observing frequency in order to compare it with the Blandford-Königl (BK) jet model. In particular, we aimed to study the signatures of jet acceleration and magnetic energy conversion.Methods. We modeled the source structure of seven AGN in the EHT 2017 data set using linearly polarized circular Gaussian components (1749+096, 1055+018, BL Lac, J0132–1654, J0006–0623, CTA 102, and 3C 454.3) and collected results for the other nine AGN from dedicated EHT publications, complemented by lower frequency data in the 2–86 GHz range. Combining these data into a multifrequency EHT+ data set, we studied the dependences of the VLBI core component flux density, size, and brightness temperature on the frequency measured in the AGN host frame (and hence on the distance from the central black hole), characterizing them with power law fits. We compared the observations with the BK jet model and estimated the magnetic field strength dependence on the distance from the central black hole.Results. Our observations spanning event horizon to parsec scales indicate a deviation from the standard BK model, particularly in the decrease of the brightness temperature with the observing frequency. Only some of the discrepancies may be alleviated by tweaking the model parameters or the jet collimation profile. Either bulk acceleration of the jet material, energy transfer from the magnetic field to the particles, or both are required to explain the observations. For our sample, we estimate a general radial dependence of the Doppler factor δ ∝ r≤0.5. This interpretation is consistent with a magnetically accelerated sub-parsec jet. We also estimate a steep decrease of the magnetic field strength with radius B ∝ r−3, hinting at jet acceleration or efficient magnetic energy dissipation.Key words: techniques: interferometric / galaxies: active / galaxies: jets / galaxies: nuclei / quasars: general / quasars: supermassive black holes⋆⋆ Deceased.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Energy dispersive x-ray diffraction of luminescent powders: A complement to visible phosphor thermometry

Energy-dispersive x-ray diffraction of thermographic phosphors has been explored as a complementary temperature diagnostic to visible phosphor thermometry in environments where the temperature-dependent optical luminescence of the phosphors is occluded. Powder phosphor samples were heated from ambient to 300°C in incremental steps and probed with polychromatic synchrotron x rays; scattered photons were collected at a fixed diffraction angle of 3.9°. Crystal structure, lattice parameters, and coefficients of thermal expansion were calculated from the diffraction data. Finally, of the several phosphors surveyed, YAG:Dy, ZnO:Ga, and GOS:Tb were found to be excellent candidates for diffraction thermometry due to their strong, distinct diffraction peaks that shift in a repeatable and linear manner with temperature.

47 OTHER INSTRUMENTATION↗

Deriving effective electrode–ion interactions from free-energy profiles at electrochemical interfaces

Understanding ion adsorption at electrified metal–electrolyte interfaces is essential for accurate modeling of electrochemical systems. Here, in this study, we systematically investigate the free energy profiles of Na + , Cl − , and F − ions at the Au(111)–water interface using enhanced sampling molecular dynamics with both classical force fields and machine-learned interatomic potentials (MLIPs). Our classical metadynamics results reveal a strong dependence of predicted ion adsorption on the Lennard-Jones parameters, highlighting that—without due care—standard mixing rules can lead to qualitatively incorrect descriptions of ion–metal interactions. We present a systematic methodology for tuning the cross term LJ parameters to control adsorption energetics in agreement with more accurate models. As a surrogate for an ab initio model, we employed the recently released Universal Models for Atoms MLIP, which validates classical trends and displays strong specific adsorption for chloride, weak adsorption for fluoride, and no specific adsorption for sodium, in agreement with experimental and theoretical expectations. By integrating molecular-level adsorption free energies into continuum models of the electric double layer, we show that specific ion adsorption substantially alters the interfacial ion population, the potential of zero charge, and the differential capacitance of the system. Our results underscore the critical importance of force field parameterization and advanced interatomic potentials for the predictive modeling of ion-specific effects at electrified interfaces and provide a robust framework for bridging molecular simulations and continuum electrochemical models.

Roncoroni, Fabrice [Lawrence Berkeley National Lab↗

Red Dragon: a redshift-evolving Gaussian mixture model for galaxies

ABSTRACT Precision-era optical cluster cosmology calls for a precise definition of the red sequence (RS), consistent across redshift. To this end, we present the Red Dragon algorithm: an error-corrected multivariate Gaussian mixture model (GMM). Simultaneous use of multiple colours and smooth evolution of GMM parameters result in a continuous RS and blue cloud (BC) characterization across redshift, avoiding the discontinuities of red fraction inherent in swapping RS selection colours. Based on a mid-redshift spectroscopic sample of SDSS galaxies, an RS defined by Red Dragon selects quiescent galaxies (low specific star formation rate) with a balanced accuracy of over $90{{\ \rm per\ cent}}$. This approach to galaxy population assignment gives more natural separations between RS and BC galaxies than hard cuts in colour–magnitude or colour–colour spaces. The Red Dragon algorithm is publicly available at bitbucket.org/wkblack/red-dragon-gamma/.

79 ASTRONOMY AND ASTROPHYSICS↗

Magnetic multilayer edges in Bernal-stacked hexagonal boron nitride

Single-layer h-BN is known to have edges with unique magnetism; however, in the commonly fabricated multilayer AA'-h-BN, edge relaxations occur that create interlayer bonds and eliminate the unpaired electrons at the edge. Recently, a robust method of growing the unconventional Bernal-stacked h-BN (AB-h-BN) has been reported. Here, we use theoretical approaches to investigate the nitrogen-terminated zigzag edges in AB-h-BN that can be formed in a controlled fashion using a high-energy electron beam. We find that these "open"edges remain intact in bilayer and multilayer AB-h-BN, enabling researchers potentially to investigate these edge states experimentally. We also investigate the thermodynamics of the spin configurations at the edge by constructing a lattice model that is based on parameters extracted from a set of first-principles calculations. We find that the edge spins in neighboring layers interact very weakly, resulting in a sequence of independent spin chains in multilayer samples. By solving this model using Monte Carlo simulations, we can determine nm-scale correlation lengths at liquid-N 2 temperatures and lower. At low temperatures, these edges may be utilized in magnetoresistance and spintronics applications.

1-dimensional spin chains↗