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At least 127 records · Page 7

The Bi{sub 2}O{sub 3}–Fe{sub 2}O{sub 3}–Sb{sub 2}O{sub 5} system phase diagram refinement, Bi{sub 3}FeSb{sub 2}O{sub 11} structure peculiarities and magnetic properties

The refinement of the Bi{sub 2}O{sub 3}–Fe{sub 2}O{sub 3}–Sb{sub 2}O{sub 5} system phase diagram has been performed and the existence of the two ternary compounds has been confirmed. The first one with a pyrochlore-type structure (sp. gr. Fd 3-barm) exists in the wide solid solution region, (Bi{sub 2−x}Fe{sub x})Fe{sub 1+y}Sb{sub 1−y}O{sub 7±δ}, where x=0.1–0.4 and y=−0.13–0.11. The second one, Bi{sub 3}FeSb{sub 2}O{sub 11}, corresponds to the cubic KSbO{sub 3}-type structure (sp. gr. Pn 3-bar) with unit cell parameter a=9.51521(2) Å. The Rietveld structure refinement showed that this compound is characterized by disordered structure. The Bi{sub 3}FeSb{sub 2}O{sub 11} factor group analysis has been carried out and a Raman spectrum has been investigated. According to magnetization measurements performed at the temperature range 2–300 K it may be concluded that the Bi{sub 3}FeSb{sub 2}O{sub 11} magnetic properties can be substantially described as a superposition of strong short-range antiferromagnetic exchange interactions realizing inside the [(FeSb{sub 2})O{sub 9}] 3D-framework via different pathways. - Graphical abstract: The refinement of the Bi{sub 2}O{sub 3}–Fe{sub 2}O{sub 3}–Sb{sub 2}O{sub 5} system phase diagram has been performed and the existence of the solid solution with a pyrochlore-type structure (sp. gr. Fd 3-barm) and Bi{sub 3}FeSb{sub 2}O{sub 11}, correspond of the cubic KSbO{sub 3}-type structure (sp. gr. Pn 3-bar has been confirmed. The structure refinement, Raman spectroscopy as well as magnetic measurements data of Bi{sub 3}FeSb{sub 2}O{sub 11} are presented. - Highlights: • The Bi{sub 2}O{sub 3}–Fe{sub 2}O{sub 3}–Sb{sub 2}O{sub 5} system phase diagram refinement has been performed. • The Bi{sub 3}FeSb{sub 2}O{sub 11} existence along with pyrochlore structure compound is shown. • It was determined that the Bi{sub 3}FeSb{sub 2}O{sub 11} is of disordered cubic KSbO{sub 3}-type structure. • Factor group analysis of Bi{sub 3}FeSb{sub 2}O{sub 11} vibrational spectrum has been performed. • Short-range antiferromagnetic interactions govern Bi{sub 3}FeSb{sub 2}O{sub 11} magnetic behavior.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Precipitation process in a Mg–Gd–Y alloy grain-refined by Al addition

The precipitation process in Mg–10Gd–3Y (wt.%) alloy grain-refined by 0.8 wt.% Al addition has been investigated by transmission electron microscopy. The alloy was given a solution treatment at 520 °C for 6 h plus 550 °C for 7 h before ageing at 250 °C. Plate-shaped intermetallic particles with the 18R-type long-period stacking ordered structure were observed in the solution-treated state. Upon isothermal ageing at 250 °C, the following precipitation sequence was identified for the α-Mg supersaturated solution: β″ (D0{sub 19}) → β′ (bco) → β{sub 1} (fcc) → β (fcc). The observed precipitation process and age hardening response in the Al grain-refined Mg–10Gd–3Y alloy are compared with those reported in the Zr grain-refined counterpart. - Highlights: • The precipitation process in Mg–10Gd–3Y–0.8Al (wt.%) alloy has been investigated. • Particles with the 18R-type LPSO structure were observed in the solution state. • Upon ageing at 250 °C, the precipitation sequence is: β″ → β′ → β1 (fcc) → β. • The Al grain-refined alloy has a lower hardness than the Zr refined counterpart.

36 MATERIALS SCIENCE↗

H-Atom Assignment and Sb–O Bonding of [Mes 3 SbOH][O 3 SPh] Confirmed by Neutron Diffraction, Multipole Modeling, and Hirshfeld Atom Refinement

Neutron wavelength-resolved Laue diffraction experiments permit accurate refinement of the H-atom positions and anisotropic displacement parameters of [Mes 3 SbOH][O 3 SPh]. A multipole-based charge density refinement and a topological analysis of the refined electron density were also performed. Hirshfeld atom refinement (HAR) recovers the neutron-determined H-atom parameters, and the quantum-mechanical electron density used in HAR recovers the electron density topology from the refined multipole model. We report these results confirm that [Mes 3 SbOH][O 3 SPh] does indeed feature a hydroxystibonium cation with a nominal Sb–O single bond and not a stibine oxide with an Sb=O/Sb + –O – bond.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Adaptive Ensemble Refinement of Protein Structures in High Resolution Electron Microscopy Density Maps with Radical Augmented Molecular Dynamics Flexible Fitting

Recent advances in cryo-electron microscopy (cryo-EM) have enabled modeling macromolecular complexes that are essential components of the cellular machinery. The density maps derived from cryo-EM experiments are often integrated with manual, knowledge or artificial intelligence driven, and physics-guided computational methods to build, fit, and refine molecular structures. Going beyond a single stationary- structure determination scheme, it is becoming more common to interpret the experimental data with an ensemble of models, which contributes to an average observation. Hence, there is a need to decide on the quality of an ensemble of protein structures on-the-fly, while refining them against the density maps. Here, we introduce such an adaptive decision making scheme during the molecular dynamics flexible fitting (MDFF) of biomolecules. Using RADICAL-Cybertools, and the new RADICAL augmented MDFF implementation (R-MDFF) is examined in high-performance computing environments for refinement of two protein systems, Adenylate Kinase and Carbon Monoxide Dehydrogenase. For the test cases, use of multiple replicas in flexible fitting with adaptive decision making in R-MDFF improves the overall correlation to the density by 40% relative to the refinements of the brute-force MDFF. The improvements are particularly significant at high, 2 - 3 Å, map resolutions. More importantly, the ensemble model captures key features of biologically relevant molecular dynamics that is inaccessible to a single-model interpretation. Finally, the pipeline is applicable to systems of growing sizes, which is demonstrated using ensemble refinement of capsid proteins from Chimpanzee adenovirus. The overhead for decision making remaining low and robust to computing environments. The software is publicly available on GitHub and includes a short user guide to install the R-MDFF on different computing environments, from local Linux based workstations to High Performance Computing (HPC) environments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Refining Jets for CMS Run 3 using Fast Simulation

As the LHC moves into its high-luminosity phase, the CMS experiment must handle more complex data collected at much higher rates. While the Geant4-based simulation application (FullSim) provides highly accurate simulation to complement real data, FullSim’s intensive consumption of computing resources becomes an increasing liability as the rates increase, while faster tools offer an advantage. The fast MC production application (FastSim) delivers a complete simulation with a factor of 10 speedup over FullSim, but introduces inaccuracies in some observables. A specialized refinement method, Fast Perfekt, employs machine learning to improve the accuracy of FastSim. An initial report of this work focused on the refinement of jet flavor tagging observables. This article presents an update on the refinement, focusing on PUPPI jets with Run 3 data-taking conditions. Refinement is extended to include jet transverse momentum as well as its propagation to missing transverse momentum. A gridbased framework and real-time monitoring system have been developed to facilitate optimization and scaling of the refinement to a large number of target variables.

Güngördü, Açelya Deniz [Istanbul Tech. U.]↗

Improving assessments of tidal power potential using grid refinement in the Coupled Ocean-Atmosphere-Wave-Sediment Transport model

Tidal currents are a promising source for future power generation given their periodicity and predictability. Therefore, numerical hydrodynamic models are frequently utilized for resource assessments. However, the relevant scales of the simulations and hence modeling techniques depend on the problem at hand. This paper shows the potential of the grid refinement technique for the assessment of tidal current energy for particular sites given its relatively low computational expense and high accuracy for the regions with the refined resolution. Example applications are described for mapping the tidal resources near two facilities (Portsmouth Naval Shipyard in Maine and Key West Naval Station in Florida) for possible future deployments of Marine Hydro-Kinetic technologies. The grid refinement capability in the coupled ocean-atmosphere-wave-sediment transport modeling system is used to improve the spatial resolution in the regions of interest, and has shown significant advantage over the original simulation results for the tidal power assessment. The numerical simulation results from both the original coarse grids and the refined grids are validated with measured tidal constituents at available locations. This study demonstrates how the enhancement of a model system for a regional tidal energy with grid refinement can assist with the performance of site specific resource assessments with modest computational expense.

Yang, Xiufeng↗

Adaptive mesh refinement in binary black holes simulations

Abstract We discuss refinement criteria for the Berger–Rigoutsos (block-based) refinement algorithm in our numerical relativity code GR-Athena++ in the context of binary black hole (BBH) merger simulations. We compare three different strategies: the ‘box-in-box’ approach, the ‘sphere-in-sphere’ approach and a local criterion for refinement based on the estimation of truncation error of the finite difference scheme. We extract and compare gravitational waveforms using the three different mesh refinement methods and compare their accuracy against a calibration waveform and demonstrate that the sphere-in-sphere approach provides the best strategy overall when considering computational cost and the waveform accuracy. Ultimately, we demonstrate the capability of each mesh refinement method in accurately simulating gravitational waves from BBH systems—a crucial aspect for their application in next-generation detectors. We quantify the mismatch achievable with the different strategies by extrapolating the gravitational wave mismatch to higher resolution.

Astronomy & Astrophysics↗

Neural refinement of sample weights

Monte Carlo simulations are an essential tool in particle physics data analysis. Events are typically generated alongside weights that redistribute the cross section of the simulated process across the phase space. These weights can be negative, and several post hoc methods have been developed to eliminate or mitigate the negative values. All of these methods share the common strategy of approximating the average weight as a function of phase space. We introduce an alternative approach, which, instead of reweighting to the average, refines the initial weights with a scaling transformation, utilizing a phase space-dependent factor. Since this new refinement method does not need to model the full weight distribution, it can be more accurate. High-dimensional and unbinned phase space is processed using neural networks for the refinement method. In addition to the refinement method, we introduce a new resampling protocol, which can be used in conjunction with any weight transformation to not only preserve the average weight but also the statistical uncertainties of the initial distribution. Using both realistic and synthetic examples, we show that the new neural refinement method is able to match or exceed the accuracy of similar weight transformations and that the new resampling protocol is simpler in implementation than previous methods while exhibiting equivalent statistical properties.

Artificial neural networks↗

Application of DEN refinement and automated model building to a difficult case of molecular-replacement phasing: the structure of a putative succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum

Phasing by molecular replacement remains difficult for targets that are far from the search model or in situations where the crystal diffracts only weakly or to low resolution. Here, the process of determining and refining the structure of Cgl1109, a putative succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum , at ~3 Å resolution is described using a combination of homology modeling with MODELLER , molecular-replacement phasing with Phaser , deformable elastic network (DEN) refinement and automated model building using AutoBuild in a semi-automated fashion, followed by final refinement cycles with phenix.refine and Coot . This difficult molecular-replacement case illustrates the power of including DEN restraints derived from a starting model to guide the movements of the model during refinement. The resulting improved model phases provide better starting points for automated model building and produce more significant difference peaks in anomalous difference Fourier maps to locate anomalous scatterers than does standard refinement. This example also illustrates a current limitation of automated procedures that require manual adjustment of local sequence misalignments between the homology model and the target sequence.

59 BASIC BIOLOGICAL SCIENCES↗

Exploiting structure similarity in refinement: automated NCS and target-structure restraints in BUSTER

Local structural similarity restraints (LSSR) provide a novel method for exploiting NCS or structural similarity to an external target structure. Two examples are given where BUSTER re-refinement of PDB entries with LSSR produces marked improvements, enabling further structural features to be modelled. Maximum-likelihood X-ray macromolecular structure refinement in BUSTER has been extended with restraints facilitating the exploitation of structural similarity. The similarity can be between two or more chains within the structure being refined, thus favouring NCS, or to a distinct ‘target’ structure that remains fixed during refinement. The local structural similarity restraints (LSSR) approach considers all distances less than 5.5 Å between pairs of atoms in the chain to be restrained. For each, the difference from the distance between the corresponding atoms in the related chain is found. LSSR applies a restraint penalty on each difference. A functional form that reaches a plateau for large differences is used to avoid the restraints distorting parts of the structure that are not similar. Because LSSR are local, there is no need to separate out domains. Some restraint pruning is still necessary, but this has been automated. LSSR have been available to academic users of BUSTER since 2009 with the easy-to-use -autoncs and @@target target.pdb options. The use of LSSR is illustrated in the re-refinement of PDB entries http://scripts.iucr.org/cgi-bin/cr.cgi?rm, where -target enables the correct ligand-binding structure to be found, and http://scripts.iucr.org/cgi-bin/cr.cgi?rm, where -autoncs contributes to the location of an additional copy of the cyclic peptide ligand.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Significant reduction in errors associated with nonbonded contacts in protein crystal structures: automated all-atom refinement with PrimeX

All-atom models derived from moderate-resolution protein crystal structures contain a high frequency of close nonbonded contacts, independent of the major refinement program used for structure determination. All-atom refinement with PrimeX corrects many of these problematic interactions, producing models that are better suited for use in computational chemistry and related applications. All-atom models are essential for many applications in molecular modeling and computational chemistry. Nonbonded atomic contacts much closer than the sum of the van der Waals radii of the two atoms (clashes) are commonly observed in such models derived from protein crystal structures. A set of 94 recently deposited protein structures in the resolution range 1.5–2.8 Å were analyzed for clashes by the addition of all H atoms to the models followed by optimization and energy minimization of the positions of just these H atoms. The results were compared with the same set of structures after automated all-atom refinement with PrimeX and with nonbonded contacts in protein crystal structures at a resolution equal to or better than 0.9 Å. The additional PrimeX refinement produced structures with reasonable summary geometric statistics and similar R{sub free} values to the original structures. The frequency of clashes at less than 0.8 times the sum of van der Waals radii was reduced over fourfold compared with that found in the original structures, to a level approaching that found in the ultrahigh-resolution structures. Moreover, severe clashes at less than or equal to 0.7 times the sum of atomic radii were reduced 15-fold. All-atom refinement with PrimeX produced improved crystal structure models with respect to nonbonded contacts and yielded changes in structural details that dramatically impacted on the interpretation of some protein–ligand interactions.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Structure of ice VII with Hirshfeld atom refinement

In the refinement of the crystal structures of ice, the best results obtained so far have been with neutron diffraction because the most troublemaking aspects are the hydrogen atoms. In nine out of twenty ice structures, the hydrogen atoms are disordered, which makes proper refinement more difficult. In our previous paper describing the structure of ice VI we proved that, using Hirshfeld atom refinement (HAR) based on synchrotron X-ray data, it is possible to obtain results comparable with those from neutron experiments. In this work, we investigate another structure of high-pressure disordered ice, cubo-ice (ice VII). Single crystals of cubo-ice were grown under pressure in diamond anvil cells. X-ray diffraction measurements were conducted at a synchrotron source facility (APS, University of Chicago, USA) as well as on our regular in-house laboratory diffractometer with Ag radiation. The data collected were further refined with HAR. Comparison of the structural parameters obtained with those derived from neutron diffraction showed very good agreement in terms of bond lengths and fairly good agreement in terms of hydrogen atom ADPs. We were also able to perform unconstrained refinements with various split-atom models.

Chemistry↗

Crystal structure refinement with SHELXL

New features added to the refinement program SHELXL since 2008 are described and explained. The improvements in the crystal structure refinement program SHELXL have been closely coupled with the development and increasing importance of the CIF (Crystallographic Information Framework) format for validating and archiving crystal structures. An important simplification is that now only one file in CIF format (for convenience, referred to simply as ‘a CIF’) containing embedded reflection data and SHELXL instructions is needed for a complete structure archive; the program SHREDCIF can be used to extract the .hkl and .ins files required for further refinement with SHELXL. Recent developments in SHELXL facilitate refinement against neutron diffraction data, the treatment of H atoms, the determination of absolute structure, the input of partial structure factors and the refinement of twinned and disordered structures. SHELXL is available free to academics for the Windows, Linux and Mac OS X operating systems, and is particularly suitable for multiple-core processors.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Refined large N duality for knots

We formulate large [Formula: see text] duality of [Formula: see text] refined Chern–Simons theory with a torus knot/link in [Formula: see text]. By studying refined BPS states in M-theory, we provide the explicit form of low-energy effective actions of Type IIA string theory with D4-branes on the [Formula: see text]-background. This form enables us to relate refined Chern–Simons invariants of a torus knot/link in [Formula: see text] to refined BPS invariants in the resolved conifold. Assuming that the extra [Formula: see text] global symmetry acts on BPS states trivially, the duality predicts graded dimensions of cohomology groups of moduli spaces of M2–M5 bound states associated to a torus knot/link in the resolved conifold. Thus, this formulation can be also interpreted as a positivity conjecture of refined Chern–Simons invariants of torus knots/links. We also discuss about an extension to non-torus knots.

Mathematics↗

Magnesium Recycling of Partially Oxidized, Mixed Magnesium-Aluminum Scrap through Combined Refining and Solid Oxide Membrane Electrolysis Processes

Pure magnesium (Mg) is recycled from 19g of partially oxidized 50.5wt.% Mg-Aluminum (Al) alloy. During the refining process, potentiodynamic scans (PDS) were performed to determine the electrorefining potential for magnesium. The PDS show that the electrorefining potential increases over time as the magnesium content inside the Mg-Al scrap decreases. Up to 100% percent of magnesium is refined from the Mg-Al scrap by a novel refining process of dissolving magnesium and its oxide into a flux followed by vapor phase removal of dissolved magnesium and subsequently condensing the magnesium vapor. The solid oxide membrane (SOM) electrolysis process is employed in the refining system to enable additional recycling of magnesium from magnesium oxide (MgO) in the partially oxidized Mg-Al scrap. The combination of the refining and SOM processes yields 7.4g of pure magnesium.

36 MATERIALS SCIENCE↗

Assessment of Energy Efficiency Improvement in the United States Petroleum Refining Industry

Adoption of efficient process technologies is an important approach to reducing CO 2 emissions, in particular those associated with combustion. In many cases, implementing energy efficiency measures is among the most cost-effective approaches that any refiner can take, improving productivity while reducing emissions. Therefore, careful analysis of the options and costs associated with efficiency measures is required to establish sound carbon policies addressing global climate change, and is the primary focus of LBNL’s current petroleum refining sector analysis for the U.S. Environmental Protection Agency. The analysis is aimed at identifying energy efficiency-related measures and developing energy abatement supply curves and CO 2 emissions reduction potential for the U.S. refining industry. A refinery model has been developed for this purpose that is a notional aggregation of the U.S. petroleum refining sector. It consists of twelve processing units and account s for the additional energy requirements from steam generation, hydrogen production and water utilities required by each of the twelve processing units. The model is carbon and energy balanced such that crud e oil inputs and major refinery sector outputs (fuels) are benchmarked to 2010 data. Estimates of the current penetration for the identified energy efficiency measures benchmark the energy requirements to those reported in U.S. DOE 2010 data. The remaining energy efficiency potential for each of the measures is estimated and compared to U.S. DOE fuel prices resulting in estimates of cost- effective energy efficiency opportunities for each of the twelve major processes. A combined cost of conserved energy supply curve is also presented along with the CO 2 emissions abatement opportunities that exist in the U.S. petroleum refinery sector. Roughly 1,200 PJ per year of primary fuels savings and close to 500 GWh per y ear of electricity savings are potentially cost-effective given U.S. DOE fuel price forecasts. This represents roughly 70 million metric tonnes of CO 2 emission reductions assuming 2010 emissions factor for grid electricity. Energy efficiency measures resulting in an additional 400 PJ per year of primary fuels savings and close to 1,700 GWh per year of electricity savings, and an associated 24 million metric tonnes of CO 2 emission reductions are not cost-effective given the same assumption with respect to fuel prices and electricity emissions factors. Compared to the modeled energy requirements for the U.S. petroleum refining sector, the cost effective potential represents a 40% reduction in fuel consumption and a 2% reduction in electricity consumption. The non-cost-effective potential represents an additional 13% reduction in fuel consumption and an additional 7% reduction in electricity consumption. The relative energy reduction potentials are mu ch higher for fuel consumption than electricity consumption largely in part because fuel is the primary energy consumption type in the refineries. Moreover, many cost effective fuel savings measures would increase electricity consumption. The model also has the potential to be used to examine the costs and benefits of the other CO 2 mitigation options, such as combined heat and power (CHP), carbon capture, and the potential introduction of biomass feedstocks. However, these options are not addressed in this report as this report is focused on developing the modeling methodology and assessing fuels savings measures. These opportunities to further reduce refinery sector CO 2 emissions and are recommended for further research and analysis.

25 ENERGY STORAGE↗

An evaluation of the E3SMv1 Arctic ocean and sea-ice regionally refined model

The Energy Exascale Earth System Model (E3SM) is a state-of-the-science Earth system model (ESM) with the ability to focus horizontal resolution of its multiple components in specific areas. Regionally refined global ESMs are motivated by the need to explicitly resolve, rather than parameterize, relevant physics within the regions of refined resolution, while offering significant computational cost savings relative to the respective cost of configurations with high-resolution (HR) everywhere on the globe. In this paper, we document results from the first Arctic regionally refined E3SM configuration for the ocean and sea-ice components (E3SM-Arctic-OSI), while employing data-based atmosphere, land, and hydrology components. Our aim is an improved representation of the Arctic coupled ocean and sea-ice state, its variability and trends, and the exchanges of mass and property fluxes between the Arctic and the sub-Arctic. We find that E3SM-Arctic-OSI increases the realism of simulated Arctic ocean and sea-ice conditions compared to a similar low-resolution E3SM simulation without the Arctic regional refinement in ocean and sea-ice components (E3SM-LR-OSI). In particular, exchanges through the main Arctic gateways are greatly improved with respect to E3SM-LR-OSI. Other aspects, such as the Arctic freshwater content variability and sea-ice trends, are also satisfactorily simulated. Yet, other features, such as the upper-ocean stratification and the sea-ice thickness distribution, need further improvements, involving either more advanced parameterizations, model tuning, or additional grid refinements. Overall, E3SM-Arctic-OSI offers an improved representation of the Arctic system relative to E3SM-LR-OSI, at a fraction (15 %) of the computational cost of comparable global high-resolution configurations, while permitting exchanges with the lower-latitude oceans that cannot be directly accounted for in Arctic regional models.

54 ENVIRONMENTAL SCIENCES↗

Polycrystalline silicon study: Low-cost silicon refining technology prospects and semiconductor-grade polycrystalline silicon availability through 1988

Photovoltaic arrays that convert solar energy into electrical energy can become a cost effective bulk energy generation alternative, provided that an adequate supply of low cost materials is available. One of the key requirements for economic photovoltaic cells is reasonably priced silicon. At present, the photovoltaic industry is dependent upon polycrystalline silicon refined by the Siemens process primarily for integrated circuits, power devices, and discrete semiconductor devices. This dependency is expected to continue until the DOE sponsored low cost silicon refining technology developments have matured to the point where they are in commercial use. The photovoltaic industry can then develop its own source of supply. Silicon material availability and market pricing projections through 1988 are updated based on data collected early in 1984. The silicon refining industry plans to meet the increasing demands of the semiconductor device and photovoltaic product industries are overviewed. In addition, the DOE sponsored technology research for producing low cost polycrystalline silicon, probabilistic cost analysis for the two most promising production processes for achieving the DOE cost goals, and the impacts of the DOE photovoltaics program silicon refining research upon the commercial polycrystalline silicon refining industry are addressed.

Costogue, E. N.↗