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At least 199 records · Page 11

Irradiation-induced chemical disordering in ceramics: The case of SiC

Chemical disordering is one feature of damage that occurs in irradiation environments and is common in ceramic compounds. This paper reviews irradiation-induced chemical disordering in SiC-based materials at elevated temperatures. Here the results were obtained using advanced analytical tools to characterize atomistic defects and to evaluate the chemistry of defect clusters and homonuclear bond structures. Finally, this paper demonstrates that chemical disordering is crucial to understanding microstructural stability and establishing a mechanistic modeling of microstructural evolution of irradiated SiC.

36 MATERIALS SCIENCE↗

Studies on the structure and the magnetic properties of high-entropy spinel oxide (MgMnFeCoNi)Al 2 O 4

The study of high-entropy materials has attracted enormous interest since they could show new functional properties that are not observed in their related parent phases. Here, we report single crystal growth, structure, thermal transport, and magnetic property studies on a novel high-entropy oxide with the spinel structure (MgMnFeCoNi)Al 2 O 4 . We have successfully grown high-quality single crystals of this high-entropy oxide using the optical floating zone growth technique for the first time. The sample was confirmed to be a phase pure high-entropy oxide using x-ray diffraction and energy-dispersive spectroscopy. Through magnetization measurements, we found (MgMnFeCoNi)Al 2 O 4 exhibits a cluster spin glass state, though the parent phases show either antiferromagnetic ordering or spin glass states. Furthermore, we also found that (MgMnFeCoNi)Al 2 O 4 has much greater thermal expansion than its CoAl 2 O 4 parent compound using high resolution neutron Larmor diffraction. We further investigated the structure of this high-entropy material via Raman spectroscopy and extended x-ray absorption fine structure spectroscopy (EXAFS) measurements. From Raman spectroscopy measurements, we observed (MgMnFeCoNi)Al 2 O 4 to display a combination of the active Raman modes in its parent compounds with the modes shifted and significantly broadened. This result, together with the varying bond lengths probed by EXAFS, reveals severe local lattice distortions in this high-entropy phase. Additionally, we found a substantial decrease in thermal conductivity and suppression of the low temperature thermal conductivity peak in (MgMnFeCoNi)Al 2 O 4 , consistent with the increased lattice defects and strain. These findings advance the understanding of the dependence of thermal expansion and transport on the lattice distortions in high-entropy materials.

36 MATERIALS SCIENCE↗

Atomic cluster expansion potential for large scale simulations of hydrocarbons under shock compression

We present an Atomic Cluster Expansion (ACE) machine learned potential developed for high-fidelity atomistic simulations of hydrocarbons, targeting pressures and temperatures near and above supercritical fluid regimes for molecular fluids. A diverse set of stoichiometries were covered in training, including 1:0 (pure carbon), 1:4 (methane), and 1:1 (benzene), and rich bonding environments sampled at supercritical temperatures, hydrogen rich, reactive mixtures where metastable stoichiometries arise, including 1:2 (ethylene) and 1:3 (ethane). A high-fidelity training database was constructed by performing large-scale quantum molecular dynamic simulations [density functional theory (DFT) MD] of diamond, graphite, methane, and benzene. A novel approach to selecting structures from DFT MD is also presented, which allows for the rapid selection of unique DFT MD frames from complex trajectories. Comparisons to DFT and experimental data demonstrate that the presented ACE potential accurately reproduces isotherms, carbon melting curves, radial distribution functions, and shock Hugoniots for carbon and hydrocarbon systems for pressures up to 100 GPa and temperatures up to 6000 K for hydrocarbon systems and up to 9000 K for pure carbon systems. This work delivers a potential that can be used for accurate, large-scale simulations of shocked hydrocarbons and demonstrates a methodology for fitting and validating machine learning interatomic potentials to complex molecular environments, which can be applied to energetic materials in future works.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Formation of short-range magnetic order and avoided ferromagnetic quantum criticality in pressurized LaCrGe 3

LaCrGe 3 has attracted attention as a paradigm example of the avoidance of ferromagnetic (FM) quantum criticality in an itinerant magnet. In this work, we combined thermodynamic (specific heat and thermal expansion), transport, x-ray, and neutron scattering as well as μSR measurements to obtain insights on the temperature-pressure phase diagram of LaCrGe 3 . Consistent with previous studies of the phase diagram by transport measurements, our thermodynamic data shows clearly that the FM transition at T FM changes its character from second order to first order when it is suppressed to low temperatures by pressure. In addition, previous studies demonstrated that for high pressures a new phase occurs below T 2 , which was proposed to be a long-wavelength antiferromagnetic state (AFM q ). In this paper, we provide evidence from our thermodynamic data that this phase transition is preceded by yet another phase transition at T 1 >T 2 . Our μSR data indicate that full magnetic volume fraction is only established below T 2 , but that this magnetism is characterized by a short correlation length. Within the experimental resolution, our neutron-scattering data is not able to identify any magnetic Bragg peaks. Overall, the microscopic magnetic data is therefore consistent with the formation of FM clusters in the proximity of the avoided FM quantum critical point in LaCrGe 3 . This conclusion is at odds with the previous proposal of AFM q order and raises questions on the role of disorder in this stochiometric compound.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

The Effects of Compounded Model Size Reductions on Adversarial Robustness

Recent advances in Edge AI and Tiny Machine Learning (TinyML) have enabled the deployment of machine learning models on resource-constrained environments. However, deploying these models on edge devices, such as micro-controllers, requires significant model footprint reduction through a variety of techniques such as quantization, pruning, and clustering. While these optimization methods offer considerable advantages, they potentially introduce AI-related security vulnerabilities, particularly concerning model robustness with respect to adversarial AI attacks. Prior research has extensively examined the impact of quantization on adversarial robustness; however, the effects of alternative reduction techniques and their combinations remain understudied. This paper investigates the impact of model size reduction techniques on adversarial robustness, when applied individually and combined. We utilized Fast Gradient Sign Method (FGSM) and Projected Gradient Descent (PGD) attacks to generate adversarial perturbations for both training and testing data, and then evaluated the models' accuracy under adversarial training conditions. Our findings revealed that reduction techniques generally diminished robustness; although, combining techniques was not found to make robustness any worse than when applied individually. Moreover, specific techniques can potentially enhance resistance to small size perturbations. This research provides insights into the trade-offs between model size reduction and security, establishing a foundation for future investigations into improving adversarial training techniques and methodologies for maintaining robustness while preserving memory footprint benefits.

Austria, Phillipe [ORNL] (ORCID:0000000236223973)↗

Reproducibility of calculations on Li species with correlation-consistent basis sets

Here we have found that two different basis set series, both labeled cc-pVxZ, are widely available and widely used for calculation on Li compounds such that calculations that should be the same are different, causing a reproducibility problem. Here we study the magnitude of the disagreement of these nominally-the-same basis sets for wave function and density functional calculations of Li clusters. We find deviations among the basis sets of as large as 22 millihartrees. In most cases one obtains lower energies with the noncanonical choices. Therefore, it is important to specify which version of the basis set is used for calculations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Targeting transcription factors through an IMiD independent zinc finger domain

Abstract Immunomodulatory imide drugs (IMiDs) degrade specific C2H2 zinc finger degrons in transcription factors, making them effective against certain cancers. SALL4, a cancer driver, contains seven C2H2 zinc fingers in three clusters, including an IMiD degron in zinc finger cluster one (ZFC1). Surprisingly, IMiDs do not inhibit the growth of SALL4-expressing cancer cells. To overcome this limit, we focused on a non-IMiD domain, SALL4 zinc finger cluster four (ZFC4). By combining ZFC4-DNA crystal structure and an in silico docking algorithm, in conjunction with cell viability assays, we screened several chemical libraries against a potentially druggable binding pocket, leading to the discovery of SH6, a compound that selectively targets SALL4-expressing cancer cells. Mechanistic studies revealed that SH6 degrades SALL4 protein through the CUL4A/CRBN pathway, while deletion of ZFC4 abolished this activity. Moreover, SH6 treatment led to a significant 87% tumor growth inhibition of SALL4+ patient-derived xenografts and demonstrated good bioavailability in pharmacokinetic studies. In summary, these studies represent a new approach for IMiD independent drug discovery targeting C2H2 transcription factors such as SALL4 in cancer.

Liu, Bee Hui↗

Kuramoto synchronization of quantum tunneling polarons for describing the dynamic structure in cuprate superconductors

A major open topic in cuprates is the interplay between the lattice and electronic dynamics and the importance of their coupling to the mechanism of high-temperature superconductivity (HTSC). As evidenced by extended x-ray absorption fine structure (EXAFS) experiments, anharmonic structural effects are correlated with the charge dynamics and the transition to a superconducting phase in different HTSC compounds. Here, in this paper, we describe how structural anharmonic effects can be coupled to electronic and lattice dynamics in cuprate systems by performing the exact diagonalization of a prototype anharmonic many-body Hamiltonian on a relevant 6-atom cluster and show that the EXAFS results can be understood as a Kuramoto synchronization transition between coupled internal quantum tunneling of polarons associated with the two-site distribution of the copper–apical oxygen (Cu-O ap ) pair in the dynamic structure. The transition is driven by the anharmonicity of the lattice vibrations and promotes the pumping of charge, initially stored at the apical oxygen reservoirs, into the copper-oxide plane. Simultaneously, a finite projection of the internal quantum tunneling polaron extends to the copper–planar oxygen (Cu-O pl ) pair. All these findings allow an interpretation based on an effective quantum-mechanical triple-well potential associated with the oxygen sites of the 6-atom cluster, which accurately represents the phase synchronization of apical oxygens and lattice-assisted charge transfer to the CuO 2 plane.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Fire Induced Rock Spalls as Long-Term Traps for Ash

Severe fires accelerate rock weathering by spalling and exfoliation, creating abundant peels, flakes or spalls. In the following years, these spalls serve as physical traps which accommodate fine particles of dust, ash, organic matter, etc. We searched for traces of ash trapped under the spalls, after four major fires: 1989, 2005, 2010 and 2015 in Israel. Samples were collected beneath the spalls that formed on the rock outcrops, and in the immediate vicinity above and below them. Three laboratory analyses were performed: pH, EC and color. Five mineral/organic compounds were measured across the Mid-Infrared (MIR) spectral region at diffuse reflectance infrared Fourier transform mode: Hydroxylapatite (HAp), charcoal, organic carbon, montmorillonite and kaolinite. Several statistical analyses were performed: MANOVA, PCA and silhouette analysis on K-means clustering. The results show evidence of ash trapped under the spalls formed during the 2005 and 2010 fires, 6 to 11 years after the fires. Charcoal presence is evident, as well as increased amounts of HAp and organic carbon. In the exposed soil above or below the burned rock outcrop, these values are lower. Negligible amounts of ash were measured 27 years after the fire. In the 2015 burned outcrop, large amounts of charcoal were found above and below the outcrop, but not under the spalls. It seems that on the carbonate slopes of Israel and under Mediterranean climate, the time required for spalls to begin functioning as traps is longer than one rainy season, while ash traces are preserved in these traps for a period of two-three decades.

ash↗

Direct conversion of methane to aromatics and hydrogen via a heterogeneous trimetallic synergistic catalyst

Abstract Non-oxidative methane dehydro-aromatization reaction can co-produce hydrogen and benzene effectively on a molybdenum-zeolite based thermochemical catalyst, which is a very promising approach for natural-gas upgrading. However, the low methane conversion and aromatics selectivity and weak durability restrain the realistic application for industry. Here, a mechanism for enhancing catalysis activity on methane activation and carbon-carbon bond coupling has been found to promote conversion and selectivity simultaneously by adding platinum–bismuth alloy cluster to form a trimetallic catalyst on zeolite (Pt-Bi/Mo/ZSM-5). This bimetallic alloy cluster has synergistic interaction with molybdenum: the formed CH 3 * from Mo 2 C on the external surface of zeolite can efficiently move on for C-C coupling on the surface of Pt-Bi particle to produce C 2 compounds, which are the key intermediates of oligomerization. This pathway is parallel with the catalysis on Mo inside the cage. This catalyst demonstrated 18.7% methane conversion and 69.4% benzene selectivity at 710 °C. With 95% methane/5% nitrogen feedstock, it exhibited robust stability with slow deactivation rate of 9.3% after 2 h and instant recovery of 98.6% activity after regeneration in hydrogen. The enhanced catalytic activity is strongly associated with synergistic interaction with Mo and ligand effects of alloys by extensive mechanism studies and DFT calculation.

03 NATURAL GAS↗

Ferromagnetic Cr 4 PtGa 17 : A Half-Heusler-Type Compound with a Breathing Pyrochlore Lattice

Here, we describe the crystal structure and elementary magnetic properties of a previously unreported ternary intermetallic compound, Cr 4 PtGa 17 , which crystallizes in a rhombohedral unit cell in the noncentrosymmetric space group R3m. The crystal structure is closely related to those of XYZ half-Heusler compounds, where X, Y, and Z are reported to be single elements only, occupying three different face-centered-cubic sublattices. The new material, Cr 4 PtGa 17 , can be most straightforwardly illustrated by writing the formula as (PtGa 2 )(Cr 4 Ga 14 )Ga (X = PtGa 2 , Y = Cr 4 Ga 14 , Z = Ga); that is, the X and Y sites are occupied by clusters instead of single elements. The magnetic Cr occupies a breathing pyrochlore lattice. Ferromagnetic ordering is found below T C ~ 61 K, by both neutron diffraction and magnetometer studies, with a small, saturated moment of ~0.25 μ B /Cr observed at 2 K, making Cr 4 PtGa 17 the first ferromagnetically ordered material with a breathing pyrochlore lattice. A magnetoresistance of ~140% was observed at 2 K. DFT calculations suggest that the material has a nearly half-metallic electronic structure. The new material, Cr 4 PtGa 17 , the first realization of both a half-Heusler-type structure and a breathing pyrochlore lattice, might pave a new way to achieve novel types of half-Heusler compounds.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Paramagnon dispersion and damping in doped Na x Ca 2 – x CuO 2 Cl 2

Here, using resonant inelastic x-ray scattering, we measure the paramagnon dispersion and damping of undoped, antiferromagnetic Ca 2 CuO 2 Cl 2 as well as doped, superconducting Na x Ca 2–x CuO 2 Cl 2 . Our estimation of the spin-exchange parameter and width of the paramagnon peak at the zone boundary X=(0.5, 0) confirms that no simple relation can be drawn between these parameters and the critical temperature T c . Consistently with other cuprate compounds, we show that upon doping there is a slight softening at (0.25,0) but not at the zone boundary X. In combination with these measurements we perform calculations of the dynamical spin structure factor of the one-band Hubbard model using cluster dynamical mean-field theory. The calculations are in excellent agreement with the experiment in the undoped case, both in terms of energy position and width. While the increase in width is also captured upon doping, the dynamical spin structure factor shows a sizable softening at X, which provides insightful information on the length-scale of the spin fluctuations in doped cuprates.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Investigation of the Cyanothece nitrogenase cluster in Synechocystis : a blueprint for engineering nitrogen-fixing photoautotrophs

ABSTRACT The nitrogenase gene cluster of unicellular diazotrophic cyanobacteria, such asCyanothece, is frequently selected by nature for nitrogen-fixing partnerships with eukaryotic phototrophs. The essential cluster components that confer an advantage in such partnerships remain underexplored. To use this cluster for the development of synthetic, phototrophic nitrogen-fixing systems, a thorough and systematic analysis of its constituent genes is necessary. An initial effort to assess the possibility of engineering this cluster into non-diazotrophic phototrophs led to the generation of aSynechocystis6803 strain with significant nitrogenase activity. In the current study, a refactoring approach was taken to determine the dispensability of the non-structural genes in the cluster and define a minimal gene set for constructing a functional nitrogenase for phototrophs. Using a bottom-up strategy, thenifgenes fromCyanothece51142 were re-organized to form new operons. The genes were then seamlessly removed to determine their essentiality in the nitrogen fixation process. We demonstrate that besides the structural genesnifHDK,nifBSUENPVZTXW, as well ashesAB, are important for optimal nitrogenase function in a phototroph. We also show that optimal expression of these genes is crucial for efficient nitrogenase activity. Our findings provide a solid foundation for generating synthetic systems that will facilitate solar-powered conversion of atmospheric nitrogen into nitrogen-rich compounds, a stride toward a greener world. IMPORTANCE Integrating nitrogen fixation genes into various photosynthetic organisms is an exciting strategy for converting atmospheric nitrogen into nitrogen-rich products in a green and energy-efficient way. In order to facilitate this process, it is essential that we understand the fundamentals of the functioning of a prokaryotic nitrogen-fixing machinery in a non-diazotrophic, photoautotrophic cell. This study examines a nitrogenase gene cluster that has been naturally selected on multiple occasions for a nitrogen-fixing partnership by eukaryotic photoautotrophs and provides a basic blueprint for designing a photosynthetic organism with nitrogen-fixing ability.

Microbiology↗

Synthase-selected sorting approach identifies a beta-lactone synthase in a nudibranch symbiotic bacterium

Background - Nudibranchs comprise a group of > 6000 marine soft-bodied mollusk species known to use secondary metabolites (natural products) for chemical defense. The full diversity of these metabolites and whether symbiotic microbes are responsible for their synthesis remains unexplored. Another issue in searching for undiscovered natural products is that computational analysis of genomes of uncultured microbes can result in detection of novel biosynthetic gene clusters; however, their in vivo functionality is not guaranteed which limits further exploration of their pharmaceutical or industrial potential. To overcome these challenges, we used a fluorescent pantetheine probe, which produces a fluorescent CoA-analog employed in biosynthesis of secondary metabolites, to label and capture bacterial symbionts actively producing these compounds in the mantle of the nudibranch Doriopsilla fulva. Results - We recovered the genome of Candidatus Doriopsillibacter californiensis from the Ca. Tethybacterales order, an uncultured lineage of sponge symbionts not found in nudibranchs previously. It forms part of the core skin microbiome of D. fulva and is nearly absent in its internal organs. We showed that crude extracts of D. fulva contained secondary metabolites that were consistent with the presence of a beta-lactone encoded in Ca. D. californiensis genome. Beta-lactones represent an underexplored group of secondary metabolites with pharmaceutical potential that have not been reported in nudibranchs previously. Conclusions - Altogether, this study shows how probe-based, targeted sorting approaches can capture bacterial symbionts producing secondary metabolites in vivo.

59 BASIC BIOLOGICAL SCIENCES↗

A hybrid Monte Carlo study of bond-stretching electron–phonon interactions and charge order in BaBiO3

Abstract The relationship between electron–phonon ( e -ph) interactions and charge-density-wave (CDW) order in the bismuthate family of high-temperature superconductors remains unresolved. We address this question using nonperturbative hybrid Monte Carlo calculations for the parent compound BaBiO 3 . Our model includes the Bi 6 s and O 2 p σ orbitals and coupling to the Bi-O bond-stretching branch of optical phonons via modulations of the Bi-O hopping integral. We simulate three-dimensional clusters of up to 4000 orbitals, with input model parameters taken from ab initio electronic structure calculations and a phonon energy ℏΩ 0 = 60 meV. Our results demonstrate that the coupling to the bond-stretching modes is sufficient to reproduce the CDW transition in this system, despite a relatively small dimensionless coupling. We also find that the transition deviates from the weak-coupling Peierls’ picture. This work demonstrates that off-diagonal e -ph interactions in orbital space are vital in establishing the bismuthate phase diagram.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Discovery of an Antarctic Ascidian-Associated Uncultivated Verrucomicrobia with Antimelanoma Palmerolide Biosynthetic Potential

The Antarctic marine ecosystem harbors a wealth of biological and chemical innovation that has risen in concert over millennia since the isolation of the continent and formation of the Antarctic circumpolar current. Scientific inquiry into the novelty of marine natural products produced by Antarctic benthic invertebrates led to the discovery of a bioactive macrolide, palmerolide A, that has specific activity against melanoma and holds considerable promise as an anticancer therapeutic. While this compound was isolated from the Antarctic ascidian Synoicum adareanum, its biosynthesis has since been hypothesized to be microbially mediated, given structural similarities to microbially produced hybrid nonribosomal peptide-polyketide macrolides. Here, we describe a metagenome-enabled investigation aimed at identifying the biosynthetic gene cluster (BGC) and palmerolide A-producing organism. A 74-kbp candidate BGC encoding the multimodular enzymatic machinery (hybrid type I-trans-AT polyketide synthase-nonribosomal peptide synthetase and tailoring functional domains) was identified and found to harbor key features predicted as necessary for palmerolide A biosynthesis. Surveys of ascidian microbiome samples targeting the candidate BGC revealed a high correlation between palmerolide gene targets and a single 16S rRNA gene variant (R = 0.83 to 0.99). Through repeated rounds of metagenome sequencing followed by binning contigs into metagenome-assembled genomes, we were able to retrieve a nearly complete genome (10 contigs) of the BGC-producing organism, a novel verrucomicrobium within the Opitutaceae family that we propose here as “Candidatus Synoicihabitans palmerolidicus.” The refined genome assembly harbors five highly similar BGC copies, along with structural and functional features that shed light on the host-associated nature of this unique bacterium.

59 BASIC BIOLOGICAL SCIENCES↗

Section-level genome sequencing and comparative genomics of Aspergillus sections Cavernicolus and Usti.

The genus Aspergillus is diverse, including species of industrial importance, human pathogens, plant pests, and model organisms. Aspergillus includes species from sections Usti and Cavernicolus, which until recently were joined in section Usti, but have now been proposed to be non-monophyletic and were split by section Nidulantes, Aenei and Raperi. To learn more about these sections, we have sequenced the genomes of 13 Aspergillus species from section Cavernicolus (A. cavernicola, A. californicus, and A. egyptiacus), section Usti (A. carlsbadensis, A. germanicus, A. granulosus, A. heterothallicus, A. insuetus, A. keveii, A. lucknowensis, A. pseudodeflectus and A. pseudoustus), and section Nidulantes (A. quadrilineatus, previously A. tetrazonus). We compared these genomes with 16 additional species from Aspergillus to explore their genetic diversity, based on their genome content, repeat-induced point mutations (RIPs), transposable elements, carbohydrate-active enzyme (CAZyme) profile, growth on plant polysaccharides, and secondary metabolite gene clusters (SMGCs). All analyses support the split of section Usti and provide additional insights: Analyses of genes found only in single species show that these constitute genes which appear to be involved in adaptation to new carbon sources, regulation to fit new niches, and bioactive compounds for competitive advantages, suggesting that these support species differentiation in Aspergillus species. Sections Usti and Cavernicolus have mainly unique SMGCs. Section Usti contains very large and information-rich genomes, an expansion partially driven by CAZymes, as section Usti contains the most CAZyme-rich species seen in genus Aspergillus. Section Usti is clearly an underutilized source of plant biomass degraders and shows great potential as industrial enzyme producers. Citation: Nybo JL, Vesth TC, Theobald S, Frisvad JC, Larsen TO, Kjaerboelling I, Rothschild-Mancinelli K, Lyhne EK, Barry K, Clum A, Yoshinaga Y, Ledsgaard L, Daum C, Lipzen A, Kuo A, Riley R, Mondo S, LaButti K, Haridas S, Pangalinan J, Salamov AA, Simmons BA, Magnuson JK, Chen J, Drula E, Henrissat B, Wiebenga A, Lubbers RJM, Müller A, dos Santos Gomes AC, Mäkelä MR, Stajich JE, Grigoriev IV, Mortensen UH, de Vries RP, Baker SE, Andersen MR (2025). Section-level genome sequencing and comparative genomics of Aspergillus sections Cavernicolus and Usti. Studies in Mycology 111: 101-114. doi: 10.3114/sim.2025.111.03.

59 BASIC BIOLOGICAL SCIENCES↗