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At least 451 records · Page 25

A Parametric, Data-Driven, Non-Intrusive Reduced-Order Model Framework for Crystal Plasticity Simulations of Voids

The influence of the internal structure at micrometer length scales on the deformation of polycrystalline materials can be effectively captured using crystal plasticity finite element methods (CPFEM). However, the complexity and nonlinearity of the deformation equations CPFEM solves demand significant computational power and resources to achieve accurate predictions, limiting its broader application. To address this challenge, we have identified a reduced-order representation of the complex data in order to establish a computationally efficient reduced-order models (ROM) and drastically reduce the computational expense of CPFEM. Specifically, in this work, we developed a parametric, data-driven, and non-intrusive ROM framework for CPFEM using proper orthogonal decomposition (POD) and sparse variational Gaussian process (SVGP) regression for single-crystal microstructures under tensile loading conditions. The developed protocol enables one to compress field into a latent/low-dimensional space described by principal component analysis (PCA) via the singular value decomposition (SVD) algorithm. As a result, the high-dimensional data are reduced to a significantly smaller amount of dimensions with POD bases and POD coefficients. Furthermore, we deployed an ensemble of SVGPs—extended from the classical Gaussian process (GP) regression for scalability and handling big data—in a massively parallel manner to train and predict latent POD coefficients using known POD bases from a set of previously obtained simulations results. Lastly, using the predicted POD coefficients, we reconstructed the full-field results and showed reasonable agreement compared with the true values obtained from running CPFEM. The developed framework is validated with a set of CPFEM simulations of a single embedded void in single-crystal aluminum alloy. While the framework is broadly applicable, this work specifically focuses on single-crystal microstructures, a single load case (e.g., tensile), and a specific void geometry (spherical).

Anisotropy↗

Characterization of lignin-degrading enzyme PmdC, which catalyzes a key step in the synthesis of polymer precursor 2-pyrone-4,6-dicarboxylic acid

Pyrone-2,4-dicarboxylic acid (PDC) is a valuable polymer precursor that can be derived from the microbial degradation of lignin. The key enzyme in the microbial production of PDC is 4-carboxy-2-hydroxymuconate-6-semialdehyde (CHMS) dehydrogenase, which acts on the substrate CHMS. We present the crystal structure of CHMS dehydrogenase (PmdC from Comamonas testosteroni) bound to the cofactor NADP, shedding light on its three-dimensional architecture, and revealing residues responsible for binding NADP. Using a combination of structural homology, molecular docking, and quantum chemistry calculations, we have predicted the binding site of CHMS. Key histidine residues in a conserved sequence are identified as crucial for binding the hydroxyl group of CHMS and facilitating dehydrogenation with NADP. Mutating these histidine residues results in a loss of enzyme activity, leading to a proposed model for the enzyme's mechanism. These findings are expected to help guide efforts in protein and metabolic engineering to enhance PDC yields in biological routes to polymer feedstock synthesis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structural basis of peptidoglycan endopeptidase regulation

Most bacteria surround themselves with a cell wall, a strong meshwork consisting primarily of the polymerized aminosugar peptidoglycan (PG). PG is essential for structural maintenance of bacterial cells, and thus for viability. PG is also constantly synthesized and turned over; the latter process is mediated by PG cleavage enzymes, for example, the endopeptidases (EPs). EPs themselves are essential for growth but also promote lethal cell wall degradation after exposure to antibiotics that inhibit PG synthases (e.g., β-lactams). Thus, EPs are attractive targets for novel antibiotics and their adjuvants. However, we have a poor understanding of how these enzymes are regulated in vivo, depriving us of novel pathways for the development of such antibiotics. Here, we have solved crystal structures of the LysM/M23 family peptidase ShyA, the primary EP of the cholera pathogen Vibrio cholerae. Our data suggest that ShyA assumes two drastically different conformations: a more open form that allows for substrate binding and a closed form, which we predicted to be catalytically inactive. Mutations expected to promote the open conformation caused enhanced activity in vitro and in vivo, and these results were recapitulated in EPs from the divergent pathogens Neisseria gonorrheae and Escherichia coli. Our results suggest that LysM/M23 EPs are regulated via release of the inhibitory Domain 1 from the M23 active site, likely through conformational rearrangement in vivo.

59 BASIC BIOLOGICAL SCIENCES↗

Assessing the Sensitivity of Pourbaix Diagrams to Computational Protocols: Electrochemical Stability of Ni Oxides as a Case Study

Pourbaix diagrams stand as a useful tool in assessing and visualizing materials’ electrochemical stability and are widely used for electrocatalyst design. However, their reliability hinges on the accuracy of the chemical potentials of involved phases, which may bear uncertainties and can be significantly impacted by decision-making steps in the computational protocol. Here, this study introduces a robust sensitivity analysis framework, exemplified through a detailed examination of the computational Pourbaix diagram of Ni, the oxides of which are used as high-activity and cost-friendly catalysts for many electrochemical reactions. Quantities of interest derived from the Pourbaix diagram include the appearance and stability domain of the catalytically active Ni oxide phases along with the onset electrochemical potentials of phase transitions. These metrics can guide the design of operational conditions for Ni oxide electrocatalysts. We find that the employed DFT exchange-correlation functional has the most significant influence on the computed Pourbaix diagram. Uncertainties on crystal structures, along with their related ab initio energetics, are also found to affect the size of the phase stability domain. Higher-order coupling among input parameters is found to play a crucial role in influencing the appearance and distribution of Ni phases in the diagram. Our findings suggest a need to consider variations and uncertainties associated with the computational procedures on predicted Pourbaix diagrams for materials design.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structural Heterogeneity in Medium-Entropy AgMnSbPbTe 4 for Glassy Thermal Transport and High Thermoelectric Performance

Medium-entropy semiconductors represent a unique category of entropy-engineered materials. They possess a considerable level of randomness in atomic mixing, although this is not sufficient to conclusively achieve single-phase structure stabilization, in contrast to high-entropy materials. This introduces strong competition between the formation of different phases, which can potentially lead to structural heterogeneity. Here, in this work, we uncover endotaxial nanoprecipitates in the microscopically identified homogeneous medium-entropy semiconductor AgMnSbPbTe 4 . These nanoprecipitates initially crystallize in a cubic phase $(Fm\bar{3}m)$ within kinetically stabilized AgMnSbPbTe 4 , subsequently evolving into a thermodynamically stable monoclinic phase $(P2_1/c)$ during thermal annealing while maintaining an endotaxial relationship with the matrix lattice. This nanophase segregation and the resultant lattice mismatch at interfaces introduce strain fluctuations up to 5% at intervals of 20 nm across the entire microstructure. Within the matrix phase, atomic displacement of up to 23 pm was observed. This structural heterogeneity results in glass-like thermal transport behavior, achieving an ultralow lattice thermal conductivity κ L = 0.312 Wm –1 K –1 at 800 K, which is in accordance with the amorphous limit predicted by the Cahill model. The synergy of band convergence effect and well-maintained carrier mobility leads to a maximum ZT of 1.72 at 800 K and an average ZT avg of 1.02 over the temperature range of 300–825 K. This study highlights that the underexplored structural heterogeneity in medium-entropy semiconductors can potentially yield beneficial phenomena, such as the phonon-glass electron-crystal transport behavior in this case, which holds promise for advancing thermoelectric applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Potential Skyrmion Host Fe(IO3)3: Connecting Stereoactive Lone-Pair Electron Effects to the Dzyaloshinskii-Moriya Interaction

Magnetic skyrmions, which are topologically distinct magnetic spin textures, are gaining increased attention for their unique physical properties and potential applications in spintronic devices. Here we present a design strategy for skyrmion host candidates based on combinations of magnetic spin, asymmetric building units having stereoactive lone-pair electrons, and polar lattice symmetry. To demonstrate the viability of the proposed rational design principles, we successfully synthesized a Fe(IO 3 ) 3 polycrystalline sample and single crystals by using a new simplified low-temperature pathway, which is experimentally feasible for extending materials growth of transition metal iodates. Single crystal X-ray and powder synchrotron X-ray diffraction measurements demonstrated that Fe(IO 3 ) 3 crystallizes in the polar chiral hexagonal lattice with space group P63. The combined structural features of the macroscopic electric polarization along the c-axis stemming from the coalignment of the stereoactive lone-pairs of the IO 3 – trigonal pyramid and the magnetic Fe 3+ cation residing on the 3-fold rotation axis were selected to promote asymmetric exchange coupling. We find evidence of a predicted skyrmion phase at 14 K ≤ T ≤ 16 K and 2.5 T ≤ μ 0 H ≤ 3.2 T driven by a Dzyaloshinskii–Moriya (DM) interaction, a conclusion supported by the appreciable DM exchange and the zero-field spiral antiferromagnetic ground state of Fe(IO 3 ) 3 deduced from neutron diffraction experiments. The associated magnetic modulation wavelength of the putative skyrmions is expected to be short ~18 nm, comparable to the period of the DM-driven incommensurate order. This work links stereoactive lone-pair electron effects to enhanced DM interaction, demonstrating a new approach for chemical guidelines in the search for skyrmionic states of matter.

36 MATERIALS SCIENCE↗

Tunable and Cooperative Thermomechanical Properties of Protein-Metal-Organic Frameworks

We recently introduced protein-metal-organic frameworks (protein-MOFs) as chemically designed protein crystals, composed of ferritin nodes that predictably assemble into 3D lattices upon coordination of various metal ions and ditopic, hydrox-amate-based linkers. Owing to their unique tripartite construction, protein-MOFs possess extremely sparse lattice connectivi-ty, suggesting that they might display unusual thermomechanical properties. Leveraging the synthetic modularity of ferritin-MOFs, we investigated the temperature-dependent structural dynamics of six distinct frameworks. Our results show that the thermostabilities of ferritin-MOFs can be tuned through the metal component or the presence of crowding agents. Our stud-ies also reveal a framework that undergoes a reversible and isotropic first-order phase transition near-room temperature, corre-sponding to a 4% volumetric change within ≤1 deg C and a hysteresis window of ~10 deg C. Here, this highly cooperative crystal-to-crystal transformation, which stems from the soft crystallinity of ferritin-MOFs, illustrates the advantage of modular con-struction strategies in discovering tunable–and unpredictable–material properties.

36 MATERIALS SCIENCE↗

Distorted dislocation cores and asymmetric glide resistances in titanium

The determination of Critical Resolved Shear Stress (CRSS) in titanium for basal, prismatic, and pyramidal slip-planes without empirical constants is presented by combining Density Functional Theory (DFT) and anisotropic elasticity. A new mechanism leading to tension-compression (T-C) asymmetry in the CRSS levels has been revealed for the first time. The conditions for this asymmetry are established, involving a complex interplay between the dislocation core-structure and core-advance behavior. The three conditions for T-C asymmetry that need to be simultaneously satisfied can be summarized as: (1) a medium stacking fault width, d, (3 < d/b F < 10, where b F is the magnitude of the Burgers vector of the full dislocation), (2) an asymmetric core-structure of the extended dislocation (ξ 1 ≠ ξ 2 , where ξ 1 and ξ 2 are the core-widths of the first and second partials, respectively), and (3) intermittent motion of the partials (Δd/b F ≠ 0, where Δd is the magnitude of fluctuation in stacking fault width during intermittent motion). Pyramidal-slip in titanium satisfies all three conditions, resulting in significant T-C asymmetry. The CRSS theory considers a Wigner-Seitz (W-S) cell based domain area assigned to each lattice site for the calculations of core-energies accurately capturing the slip-plane lattice. The W-S based approach is essential due to the lower symmetry of the HCP crystal circumventing potential errors associated with the one-dimensional atomic-row approximation. Dislocation core structures are obtained for all the slip-systems in titanium showing significant distortion of the disregistry profile governing the core-advance behavior. The CRSS values predicted from the theory show agreement with the experimental CRSS levels reported in the literature.

Dislocation core↗

Phase-field-guided design of record-high piezoelectricity and discovery of simultaneous high light transparency and high piezoelectricity in relaxor ferroelectrics

Here, the phase-field method has been extensively applied to predicting the domain structures and their responses to external fields and understanding experimentally observed domain states under different electromechanical conditions in ferroelectric heterostructures. This article highlights the successful examples of phase-field applications in guiding the design of relaxor ferroelectric ceramics and crystals with record-high piezoelectricity and the discovery of simultaneous high light transparency and piezoelectricity of relaxor ferroelectric crystals for a wide range of biomedical, robotics, and optoelectronics applications.

36 MATERIALS SCIENCE↗

Undercooling of molten silicon

Droplets of uncoated molten Si(0.4-0.8 mm diameter) have been undercooled 250 C. Ge droplets of similar size have been undercooled 280 C in a B2O3 flux. The observed nucleation onset temperatures of both Si and Ge droplets are at or below the predicted amorphous phase melting temperatures T(al). The solidified structures were polycrystalline. The nucleation frequency I, calculated from the Si data (20,000/cu cm s at 240 + or - 20 C undercooling), should be an upper limit of the homogeneous nucleation frequency of the crystal phase, since it has not been established that nucleation was homogeneous in these experiments. However, this limiting I for Si indicates that homogeneous nucleation of crystal would not become appreciable in laser pulsing experiments until the liquid Si is undercooled to well below T(al).

Devaud, G.↗

Nonlinear optical properties of organic materials: A theoretical study

Replacement of electronic switching circuits in computing and telecommunication systems with purely optical devices offers the potential for extremely high throughput and compact information processing systems. The potential application of organic materials containing molecules with large nonresonant nonlinear effects in this area have triggered intensive research during the last decade. Interest on this area was due to two facts: (1) that many organic materials show nonlinearities that are orders of magnitude larger than those of conventional inorganic materials such as lithium niobate and potassium dihydrogen phosphate; and (2) that organic materials show much flexibility in terms of molecular designs. Some of the desirable characteristics that these materials should have are that they be transparent to the frequency of the incident laser and its second or third harmonic, that they have a high damage threshold, and, in the case of second-order effects, that their crystal structure or molecular orientation be accentric. Since polymeric assemblages can enhance the nonlinear response of organic molecules severalfold, efforts have been directed toward the synthesis of thin films with interpenetrating lattices of electroactive molecules. The goal of this theoretical investigation is to predict the magnitude of the molecular polarizabilities of organic molecules that could be incorporated into films. These calculations are intended to become a powerful tool to assist material scientists in screening for the best candidates for optical applications. The procedure that was developed for the present calculations is based on the static-field approach, and is a modification to the method developed by Dewar and Stewart, 1984 for calculating molecular linear polarizabilities.

Cardelino, Beatriz H.↗

Low Temperature Rhombohedral Single Crystal SiGe Epitaxy on c-plane Sapphire

Current best practice in epitaxial growth of rhombohedral SiGe onto (0001) sapphire (Al2O3) substrate surfaces requires extreme conditions to grow a single crystal SiGe film. Previous models described the sapphire surface reconstruction as the overriding factor in rhombohedral epitaxy, requiring a high temperature Al-terminated surface for high quality films. Temperatures in the 850-1100 C range were thought to be necessary to get SiGe to form coherent atomic matching between the (111) SiGe plane and the (0001) sapphire surface. Such fabrication conditions are difficult and uneconomical, hindering widespread application. This work proposes an alternative model that considers the bulk sapphire structure and determines how the SiGe film nucleates and grows. Accounting for thermal expansion effects, calculations using this new model show that both pure Ge and SiGe can form single crystal films in the 450-550 C temperature range. Experimental results confirm these predictions, where x-ray diffraction and atomic force microscopy show the films fabricated at low temperature rival the high temperature films in crystallographic and surface quality. Finally, an explanation is provided for why films of comparable high quality can be produced in either temperature range.

Duzik, Adam J.↗

Synthesis, crystal and electronic structure of the Zintl phase Ba 16 Sb 11 . A case study uncovering greater structural complexity via monoclinic distortion of the tetragonal Ca 16 Sb 11 structure type

The binary Zintl phase Ba 16 Sb 11 has been synthesized and structurally characterized. Detailed studies via single-crystal X-ray diffraction methods indicate that although Ba 16 Sb 11 appears to crystallize in the tetragonal Ca 16 Sb 11 structure type (space group $P\bar{4}2_1$m with a=13.5647(9) Å, c=12.4124(12)Å, Z=2, R 1 = 3.14%; wR 2 = 4.77%), there exists an extensive structural disorder. Some Ba 16 Sb 11 crystals were found to be monoclinic and the structure was solved and refined in space group P2 1 (a=18.3929(12) Å, b=13.5233(8) Å, c=18.3978(12) Å, β=94.6600(10)°; Z=4, R 1 =5.84 %; wR 2 =9.58 %). The latter corresponds to a 2-fold superstructure of the tetragonal one, which provides a disorder-free structural model. In both descriptions, the disordered tetragonal and the ordered monoclinic superstructure, the basic building units that make up the structure of this Ba-rich compound are pairs of face-shared square antiprisms of Ba atoms, which are centered by Sb atoms. The dimerized antiprisms are linked into parallel chains via square prisms of Ba atoms, which are also centered by Sb atoms. The Zintl concept can be applied in a straightforward manner and as result, the structure of Ba 32 Sb 22 (=2×Ba 16 Sb 11 ) can be rationalized as (Ba 2+ ) 32 (Sb 3– ) 20 [Sb 2 ] 4– . Notably, the partitioning of the valence electrons is done taking into an account the homoatomic Sb–Sb contacts (d=3.01 Å), which can be clearly distinguished in the lower symmetry space group. Electronic structure calculations of Ba 16 Sb 11 are in good accordance with the Zintl rationalization and predict a semiconductor with a band gap of 0.77 eV.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Distinctive features of fluorescence and waveguides in magnesium aluminate spinel crystals driven by structural discrepancy

Transparent polycrystalline ceramics are of significant importance for a wide range of scientific and industrial applications. Developing a deeper understanding of their thermodynamic behavior is essential for achieving their maximum output performance in technological applications. This study provides a systematic investigation into the thermal excitation-induced fluorescence kinetics and waveguide characteristics of Magnesium Aluminate Spinel (MgAl 2 O 4 ) single crystals, with a focus on the intricate relationship between structure and properties. High-temperature extreme environments through irradiation with swift heavy ions 645.0 MeV Xe and 352.8 MeV Fe ions were created; the atomic deposition energy threshold (E th ) associated with disorder morphologies was assessed between 0.91 and 0.99 eV atom –1 . The track prediction model was developed to support the theoretical prediction of track formation. Electronic energy loss (E ele ) disrupts the balance of the initial structure through the thermal spike effect, leading to the formation of absorption-related F and F + color centers. These defects enhance photoluminescence in the visible spectrum and result in an effective modulation of the intrinsic bandgap. Moreover, as ion beams penetrate into the material, the uneven damage distribution induces the formation of waveguide structures. In conclusion, these findings provide valuable insights into the fabrication of functional devices through irradiation technologies and the structural changes of MgAl 2 O 4 at high temperatures within extreme environments.

36 MATERIALS SCIENCE↗

cGAS-like receptors sense RNA and control 3'2'-cGAMP signalling in Drosophila

Cyclic GMP–AMP synthase (cGAS) is a cytosolic DNA sensor that produces the second messenger cG[2'–5']pA[3'–5']p (2'3'-cGAMP) and controls activation of innate immunity in mammalian cells. Animal genomes typically encode multiple proteins with predicted homology to cGAS, but the function of these uncharacterized enzymes is unknown. Here we show that cGAS-like receptors (cGLRs) are innate immune sensors that are capable of recognizing divergent molecular patterns and catalysing synthesis of distinct nucleotide second messenger signals. Crystal structures of human and insect cGLRs reveal a nucleotidyltransferase signalling core shared with cGAS and a diversified primary ligand-binding surface modified with notable insertions and deletions. We demonstrate that surface remodelling of cGLRs enables altered ligand specificity and used a forward biochemical screen to identify cGLR1 as a double-stranded RNA sensor in the model organism Drosophila melanogaster. We show that RNA recognition activates Drosophila cGLR1 to synthesize the novel product cG[3'–5']pA[2'–5']p (3'2'-cGAMP). A crystal structure of Drosophila stimulator of interferon genes (dSTING) in complex with 3'2'-cGAMP explains selective isomer recognition, and 3'2'-cGAMP induces an enhanced antiviral state in vivo that protects from viral infection. Similar to radiation of Toll-like receptors in pathogen immunity, our results establish cGLRs as a diverse family of metazoan pattern recognition receptors.

59 BASIC BIOLOGICAL SCIENCES↗

Crystal structure of the CoV-Y domain of SARS-CoV-2 nonstructural protein 3

Abstract Replication of the coronavirus genome starts with the formation of viral RNA-containing double-membrane vesicles (DMV) following viral entry into the host cell. The multi-domain nonstructural protein 3 (nsp3) is the largest protein encoded by the known coronavirus genome and serves as a central component of the viral replication and transcription machinery. Previous studies demonstrated that the highly-conserved C-terminal region of nsp3 is essential for subcellular membrane rearrangement, yet the underlying mechanisms remain elusive. Here we report the crystal structure of the CoV-Y domain, the most C-terminal domain of the SARS-CoV-2 nsp3, at 2.4 Å-resolution. CoV-Y adopts a previously uncharacterized V-shaped fold featuring three distinct subdomains. Sequence alignment and structure prediction suggest that this fold is likely shared by the CoV-Y domains from closely related nsp3 homologs. NMR-based fragment screening combined with molecular docking identifies surface cavities in CoV-Y for interaction with potential ligands and other nsps. These studies provide the first structural view on a complete nsp3 CoV-Y domain, and the molecular framework for understanding the architecture, assembly and function of the nsp3 C-terminal domains in coronavirus replication. Our work illuminates nsp3 as a potential target for therapeutic interventions to aid in the on-going battle against the COVID-19 pandemic and diseases caused by other coronaviruses.

36 MATERIALS SCIENCE↗

Controlling superconductivity of CeIrIn 5 microstructures by substrate selection

Superconductor/metal interfaces are usually fabricated in heterostructures that join these dissimilar materials. A conceptually different approach has recently exploited the strain sensitivity of heavy-fermion superconductors, selectively transforming regions of the crystal into the metallic state by strain gradients. The strain is generated by differential thermal contraction between the sample and the substrate. Here, we present an improved finite-element model that reliably predicts the superconducting transition temperature in CeIrIn 5 even in complex structures. Different substrates are employed to tailor the strain field into the desired shapes. Using this approach, both highly complex and strained as well as strain-free microstructures are fabricated to validate the model. This enables a high degree of control over the microscopic strain fields and forms the basis for more advanced structuring of superconductors as in Josephson junctions yet also finds natural use cases in any material class in which a modulation of the physical properties on a chip is desirable.

36 MATERIALS SCIENCE↗

Czochralski Growth and Characterization of a Compositionally Complex Rare Earth Aluminum Garnet Scintillator: (Gd 1/4 Y 1/4 Tb 1/4 Lu 1/4 ) 3 Al 5 O 12 :Ce

Compositionally complex oxides have garnered increasing interest for their enhanced phase stability and tunable functional properties, yet their development as bulk single crystal scintillators remains limited. Herein, we report the Czochralski growth and characterization of (Gd 1/4 Y 1/4 Tb 1/4 Lu 1/4 ) 3 Al 5 O 12 :Ce (GYTLAG), a compositionally complex garnet incorporating four dodecahedrally coordinated principal rare earth elements. The garnet phase was confirmed by powder and single crystal X-ray diffraction, and macroscopic defects are described. X-ray absorption near-edge structure measurements confirm the 3+ oxidation state of all rare earths and support their occupation of the same crystallographic site; white line intensity variations correlate with the anticipated segregation behavior. Elemental segregation is quantified by SEM/EDS and ICP-OES, and a linear trend was established between the segregation coefficient and the difference between each rare earth’s ionic radius (r) and the average ionic radius (AIR) of the dodecahedral site. This trend offers a predictive framework for compositional control in future REAG crystals grown by the Czochralski method. Photoluminescence and radioluminescence measurements reveal both Ce 3+ and Tb 3+ emission. Scintillation pulses exhibit four-component decay with dominant ~230 µs and ~1.2 ms components, and the light yield is estimated to be up to 43,000 ph/MeV under 137Cs γ-ray excitation. GYTLAG also demonstrates a strong radioluminescence efficiency and 50% lower afterglow at 20 ms compared to a LuAG:Ce reference, underscoring its promise for scintillator applications.

Compositionally complex oxide, high entropy oxide,↗