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At least 1,549 records · Page 86

How to correct relative voxel scale factors for calculations of vector-difference Fourier maps in cryo-EM

The atomic coordinates derived from cryo-electron microscopy (cryo-EM) maps can be inaccurate when the voxel scaling factors are not properly calibrated. Here, we describe a method for correcting relative voxel scaling factors between pairs of cryo-EM maps for the same or similar structures that are expanded or contracted relative to each other. We find that the correction of scaling factors reduces the amplitude differences of Fourier-inverted structure factors from voxel-rescaled maps by up to 20–30%, as shown by two cryo-EM maps of the SARS-CoV-2 spike protein measured at pH 4.0 and pH 8.0. This allows for the calculation of the difference map after properly scaling, revealing differences between the two structures for individual amino acid residues. Unexpectedly, the analysis uncovers two previously overlooked differences of amino acid residues in structures and their local structural changes. Furthermore, we demonstrate the method as applied to two cryo-EM maps of monomeric apo-photosystem II from the cyanobacteria Synechocystis sp. PCC 6803 and Thermosynechococcus elongatus. The resulting difference maps reveal many changes in the peripheral transmembrane PsbX subunit between the two species.

59 BASIC BIOLOGICAL SCIENCES↗

Fabrication, thermal analysis, and heavy ion irradiation resistance of epoxy matrix nanocomposites loaded with silane-functionalized ceria nanoparticles

This paper describes a detailed understanding of how nanofillers function as radiation barriers within the polymer matrix, and how their effectiveness is impacted by factors such as composition, size, loading, surface chemistry, and dispersion. Here, we designed a comprehensive investigation of heavy ion irradiation resistance in epoxy matrix composites loaded with surface-modified ceria nanofillers, utilizing tandem computational and experimental methods to elucidate radiolytic damage processes and relate them to chemical and structural changes observed through thermal analysis, vibrational spectroscopy, and electron microscopy. A detailed mechanistic examination supported by FTIR spectroscopy data identified the bisphenol A moiety as a primary target for degradation reactions. Results of computational modeling by the Stopping Range of Ions in Matter (SRIM) Monte Carlo simulation were in good agreement with damage analysis from surface and cross-sectional SEM imaging. All metrics indicated that ceria nanofillers reduce the damage area in polymer nanocomposites, and that nanofiller loading and homogeneity of dispersion are key to effective damage prevention. The results of this study represent a significant pathway for engineered irradiation tolerance in a diverse array of polymer nanocomposite materials. Numerous areas of materials science can benefit from utilizing this facile and effective method to extend the reliability of polymer materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Modal dynamics and flutter analysis of floating offshore vertical axis wind turbines

Floating platforms provide vertical axis wind turbines (VAWTs) significant advantages over offshore horizontal axis wind turbines, which has led to increased research interest in offshore VAWT technology. Here, this paper examines dynamic stability of floating VAWTs and presents structural dynamic and aero-elastic flutter analysis of utility-scale 5 MW floating VAWTs by coupling a rotor finite element model with a linearized model for the floating system. The coupled floating VAWT model is utilized to study the effects of tower height, number of blades, blade tapering scheme, and impacts of the floating platform on modal properties and flutter. The study provides important new results and guidance to floating VAWT designers: (1) tower height increase leads to lower tower frequencies more prone to resonance, (2) by moving from land-based foundations to a floating TLP foundation, tower-mode frequency is increased significantly (by 49%–68%) which mitigates resonance and increases the flutter RPM (154% increase), (3) increasing the number of blades reduces the tower mode frequencies for both land-based and floating configuration, and (4) blade chord tapering can have a significant impact on increasing the tower mode flutter RPM. Further, analysis of low-frequency rigid body modes shows a safe, higher flutter RPM relative to the operating RPM.

17 WIND ENERGY↗

Computationally Guided Investigation of the Optical Spectra of Pure β-UO 3

Single-phase β-UO 3 is synthesized by flash heating UO 2 (NO 3 )·6H 2 O in air to 450 °C and annealing for 60 h under the same conditions. For the first time, we report the Raman spectra of pure β-UO 3 . To facilitate the assignment of Raman and infrared vibrational modes, we use density functional theory with density functional perturbation theory. By employing a novel analysis scheme that includes the mode frequencies as well as a quantitative analysis of the mode eigenvectors, we assign the observed spectral features to individual chemical modes. In particular, the density functional theory optimized structure, observed Raman spectrum, and eigenvector analysis suggest the presence of four crystallographically distinct uranyl ions, one more than has previously been suggested.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Remarkably Weak Anisotropy in Thermal Conductivity of Two-Dimensional Hybrid Perovskite Butylammonium Lead Iodide Crystals

Two-dimensional (2D) hybrid organic-inorganic perovskites consisting of alternating organic and inorganic layers are a new class of layered structures. They have attracted increasing interest for photovoltaic, optoelectronic, and thermoelectric applications, where knowing their thermal transport properties is critical. In this study, we carry out both experimental and computational studies on thermal transport properties of 2 D butylammonium lead iodide crystals and find their thermal conductivity is ultralow (below 0.3 W m( -1 ) K -1 ) with very weak anisotropy (around 1.5) among layered crystals. Further analysis reveals that the unique structure with the preferential alignment of organic chains and complicated energy landscape leads to moderately smaller phonon lifetimes in the out-of-plane direction and comparable phonon group velocities in in-plane and out-of-plane directions. These new findings may guide the future design of novel hybrid materials with desired thermal conductivity for various applications.

2D hybrid perovskite↗

Expanding the genomic encyclopedia of Actinobacteria with 824 isolate reference genomes

The phylum Actinobacteria includes important human pathogens like Mycobacterium tuberculosis and Corynebacterium diphtheriae and renowned producers of secondary metabolites of commercial interest, yet only a small part of its diversity is represented by sequenced genomes. Here, we present 824 actinobacterial isolate genomes in the context of a phylum-wide analysis of 6,700 genomes including public isolates and metagenome-assembled genomes (MAGs). We estimate that only 30%–50% of projected actinobacterial phylogenetic diversity possesses genomic representation via isolates and MAGs. A comparison of gene functions reveals novel determinants of host-microbe interaction as well as environment-specific adaptations such as potential antimicrobial peptides. We identify plasmids and prophages across isolates and uncover extensive prophage diversity structured mainly by host taxonomy. Analysis of >80,000 biosynthetic gene clusters reveals that horizontal gene transfer and gene loss shape secondary metabolite repertoire across taxa. Our observations illustrate the essential role of and need for high-quality isolate genome sequences.

59 BASIC BIOLOGICAL SCIENCES↗

Extracting structural motifs from pair distribution function data of nanostructures using explainable machine learning

Characterization of material structure with X-ray or neutron scattering using e.g. Pair Distribution Function (PDF) analysis most often rely on refining a structure model against an experimental dataset. However, identifying a suitable model is often a bottleneck. Recently, automated approaches have made it possible to test thousands of models for each dataset, but these methods are computationally expensive and analysing the output, i.e. extracting structural information from the resulting fits in a meaningful way, is challenging. Our Machine Learning based Motif Extractor (ML-MotEx) trains an ML algorithm on thousands of fits, and uses SHAP (SHapley Additive exPlanation) values to identify which model features are important for the fit quality. We use the method for 4 different chemical systems, including disordered nanomaterials and clusters. ML-MotEx opens for a type of modelling where each feature in a model is assigned an importance value for the fit quality based on explainable ML.

36 MATERIALS SCIENCE↗

Ultra diffuse galaxies in the MATLAS low-to-moderate density fields

Recent advances in deep dedicated imaging surveys over the past decade have uncovered a surprisingly large number of extremely faint low surface brightness galaxies with large physical sizes called ultra diffuse galaxies (UDGs) in clusters and, more recently, in lower density environments. As part of the Mass Assembly of early-Type GaLAxies with their fine Structures (MATLAS) survey, a deep imaging large program at the Canada-France-Hawaii Telescope (CFHT), our team has identified 2210 dwarf galaxies, 59 (~3%) of which qualify as UDGs. Averaging over the survey area, we find ~0.4 UDG per square degree. They are found in a range of low to moderate density environments, although 61% of the sample fall within the virial radii of groups. Based on a detailed analysis of their photometric and structural properties, we find that the MATLAS UDGs do not show significant differences from the traditional dwarfs, except from the predefined size and surface brightness cut. Their median color is as red as the one measured in galaxy clusters, albeit with a narrower color range. The majority of the UDGs are visually classified as dwarf ellipticals with log stellar masses of ~6.5 – 8.7. The fraction of nucleated UDGs (~34%) is roughly the same as the nucleated fraction of the traditional dwarfs. Only five (~8%) UDGs show signs of tidal disruption and only two are tidal dwarf galaxy candidates. A study of globular cluster (GC) candidates selected in the CFHT images finds no evidence of a higher GC specific frequency S N for UDGs than for classical dwarfs, contrary to what is found in most clusters. The UDG halo-to-stellar mass ratio distribution, as estimated from the GC counts, peaks at roughly the same value as for the traditional dwarfs, but spans the smaller range of ~10 – 2000. Finally, we interpret these results to mean that the large majority of the field-to-group UDGs do not have a different formation scenario than traditional dwarfs.

79 ASTRONOMY AND ASTROPHYSICS↗

Improving luminescence response in ZnGeN 2 /GaN superlattices: defect reduction through composition control

Abstract Color-mixed (cm) light-emitting diodes (LEDs) are theoretically the most efficient white light emitters, projected to improve white light luminous efficacy by 34% compared to incumbent phosphor converted LEDs. Since white light technology is pervasive and essential, small improvements in LED technology can result in energy savings. However, cm-LEDs are not yet realized due to poor efficacy in green and amber emitting materials, a spectral region colloquially referred to as the Green Gap. ZnGeN 2 is nearly isostructural and closely lattice-matched to GaN and can be heteroepitaxially integrated with existing GaN devices; ZnGeN 2 /GaN hybrid structures are theorized to emit green (~530 nn) light with a spontaneous emission rate 4.6–4.9 times higher than traditional InGaN LEDs when incorporated into III-N LED structures. In this report we demonstrate the molecular beam epitaxy (MBE) growth of GaN and ZnGeN 2 superlattices, an important step towards realizing multiple quantum well structures required for efficient LEDs. Elemental analysis, including atom probe tomography, shows that Ga and Ge are observed in both ZnGeN 2 and GaN layers, degrading the structural uniformity. The lack of elemental abruptness also leads to increased defect luminescence and reabsorption of band edge luminescence. The source of unintentional Ga distributed throughout the ZnGeN 2 layers was identified as excess flux escaping from around the closed MBE shutter. The source of unintentional Ge, which tended to incorporate as a single delta-doped layer in GaN, was identified as Ge riding along the cyclical metal-rich Ga adlayer used for high quality GaN, incorporating during subsequent nitrogen-rich growth step. Modifying the growth strategy results in improved structural quality, elemental abruptness, and luminescence response. This realization of structurally and elementally abrupt interfaces demonstrates the potential of heteroepitaxially integrated binary and ternary nitrides for energy-relevant devices.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Dynamical Components Analysis (DCA) v1.0.0

Dynamical Components Analysis is a Python implementation of the method described in "Unsupervised discovery of temporal structure in noisy data with dynamical components analysis". It implements the method as well as related data analysis functions.

Livezey, Jesse↗

Dynamical Components Analysis (DCA) v1.0.0

Dynamical Components Analysis is a Python implementation of the method described in "Unsupervised discovery of temporal structure in noisy data with dynamical components analysis". It implements the method as well as related data analysis functions.

Livezey, Jesse↗

Measuring the Energy Consumption and Efficiency of Deep Neural Networks: An Empirical Analysis and Design Recommendations

Addressing the "Red-AI" trend of rising energy consumption by large-scale neural networks, this study investigates the measured energy consumption of training various fully connected neural network architectures. We introduce the BUTTER-E dataset, an augmentation to the BUTTER Empirical Deep Learning dataset, containing energy consumption and performance data from 41,129 individual experimental runs spanning 30,582 distinct configurations: 13 datasets, 20 sizes (trainable parameters), 8 "shapes", and 14 depths on both CPUs and GPUs using node-level watt-meters. This dataset reveals the complex relationship between dataset size, network structure, and energy use. Our analysis uncovers a surprising, hardware-mediated non-linear relationship between energy efficiency and network design, challenging the assumption that reducing the number of parameters or FLOPs is the best way to achieve greater energy efficiency. We propose a straightforward and effective energy model that accounts for network size, computing, and memory hierarchy. Highlighting the need for cache-considerate algorithm development, we suggest a codesign approach to energy efficient network, algorithm, and hardware design. This work contributes to the fields of sustainable computing and Green AI, offering practical guidance for creating more energy-efficient neural networks and promoting sustainable AI.

97 MATHEMATICS AND COMPUTING↗

Comparative Studies of Optoelectrical Properties of Prominent PV Materials: Halide Perovskite, CdTe, and GaAs

We compare three representative high performance PV materials: halide perovskite MAPbI3, CdTe, and GaAs, in terms of photoluminescence (PL) efficiency, PL lineshape, carrier diffusion, and surface recombination and passivation, over multiple orders of photo-excitation density or carrier density appropriate for different applications. An analytic model is used to describe the excitation density dependence of PL intensity and extract the internal PL efficiency and multiple pertinent recombination parameters. A PL imaging technique is used to obtain carrier diffusion length without using a PL quencher, thus, free of unintended influence beyond pure diffusion. Our results show that perovskite samples tend to exhibit lower Shockley-Read-Hall (SRH) recombination rate in both bulk and surface, thus higher PL efficiency than the inorganic counterparts, particularly under low excitation density, even with no or preliminary surface passivation. PL lineshape and diffusion analysis indicate that there is considerable structural disordering in the perovskite materials, and thus photo-generated carriers are not in global thermal equilibrium, which in turn suppresses the nonradiative recombination. This study suggests that relatively low point-defect density, less detrimental surface recombination, and moderate structural disordering contribute to the high PV efficiency in the perovskite. This comparative photovoltaics study provides more insights into the fundamental material science and the search for optimal device designs by learning from different technologies.

14 SOLAR ENERGY↗

Topochemical Oxidation of Ruddlesden–Popper Nickelates Reveals Distinct Structural Family: Oxygen-Intercalated Layered Perovskites

Layered perovskites─including the Dion–Jacobson, Ruddlesden–Popper, and Aurivillius families─exhibit a wide range of correlated electron phenomena, from high-temperature superconductivity to multiferroicity. Here, in this study, we report a new family of layered perovskites realized through topochemical oxidation of La n+1 Ni n O 3n+1+δ (n = 1–4) Ruddlesden–Popper nickelate thin films. Postgrowth ozone annealing induces a substantial c-axis expansion─17.8% for La 2 NiO 4+δ (n = 1)─that monotonically decreases with increasing n. Surface synchrotron X-ray diffraction and coherent Bragg rod analysis (COBRA) reveal that this structural expansion arises from the intercalation of approximately δ ≈ 0.7–1.0 oxygen atoms into interstitial sites within the rock salt spacer layers, far exceeding the previous record of δ ≈ 0.3 for any Ruddlesden–Popper oxide. These oxygen-intercalated phases form a new class of layered perovskites with a spacer layer composition intermediate between the Ruddlesden–Popper and Aurivillius phases. Furthermore, oxygen intercalation induces metallicity, enhances nickel–oxygen hybridization, and suppresses oxygen octahedral rotations, a feature associated with high-temperature superconductivity in Ruddlesden–Popper nickelates. Our work establishes topochemical oxidation as a powerful approach to accessing highly oxidized, metastable phases across a broad range of layered oxide systems, offering new platforms to engineer electronic properties via intercalation chemistry.

Ferenc Segedin, Dan [Harvard Univ., Cambridge, MA ↗

Extended Donnan-Manning theory for selective ion partition and transport in ion exchange membrane

The use of ion exchange membranes (IEMs) for electrochemical ion-ion separation leverages the selectivity of the IEMs toward like-charged species via valence difference and/or other ion membrane interactions. A mechanistic model that relates selectivity with membrane structural and chemical properties is lacking in the literature. Here, in this study, we extend the Manning’s counter-ion condensation model for describing ion partition and ion mobility inside IEMs to mixed salts scenarios. We evaluate the extended Donnan-Manning model against experimental data from literature and compare the performance the Donnan-Manning model to that of the ideal Donnan model and the Donnan-Affinity model. Our analysis shows that, despite its structural complexity, the Donnan-Manning model has less fitting parameters than the Donnan-Affinity model and generally outperforms the two other models in predicting counter-ion and co-ion partition. With the assumption of a higher mobility of condensed ions than that of uncondensed ions, the generalized Manning’s model can also predict counter-ion mobility selectivity for cation exchange membranes, but its performance for predicting mobility selectivity for anion exchange membranes is still unsatisfactory.

42 ENGINEERING↗

The cosmological analysis of the SDSS/BOSS data from the Effective Field Theory of Large-Scale Structure

The Effective Field Theory of Large-Scale Structure is a formalism that allows us to predict the clustering of Cosmological Large-Scale Structure in the mildly non-linear regime in an accurate and reliable way. In this paper, after validating our technique against several sets of numerical simulations, we perform the analysis for the cosmological parameters of the DR12 BOSS data. We assume Λ CDM, a fixed value of the baryon/dark-matter ratio, Ω b /Ω c , and of the tilt of the primordial power spectrum, n s , and no significant input from numerical simulations. By using the one-loop power spectrum multipoles, we measure the primordial amplitude of the power spectrum, A s , the abundance of matter, Ω m , and the Hubble parameter, H 0 , {to about 13% , 3.2% and 3.2% respectively, obtaining ln (10 10 A s )=2.72± 0.13 , 0Ω m =0.309± 0.01 , H 0 =68.5± 2.2 km/(s Mpc) at 68% confidence level. If we then add a CMB prior on the sound horizon, the error bar on H 0 is reduced to 1.6% .} These results are a substantial qualitative and quantitative improvement with respect to former analyses, and suggest that the EFTofLSS is a powerful instrument to extract cosmological information from Large-Scale Structure.

79 ASTRONOMY AND ASTROPHYSICS↗

Ytterbium ion trap quantum computing: The current state-of-the-art

In this work, we present an overview of contemporary quantum computing with ytterbium ion traps, placing the emphasis on industry implementations. We provide brief, concrete descriptions of various key features, such as trap loading, electronic structure, qubit function, gates, error analysis, and benchmarking. We focus on the underlying science and current technologies to provide readers with a holistic picture of available techniques for using ytterbium in contemporary ion trap designs.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗