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At least 271 records · Page 15

Structural Basis of Clostridium perfringens Enterotoxin Activation and Oligomerization by Trypsin

Clostridium perfringens enterotoxin (CpE) is a β-pore forming toxin that disrupts gastrointestinal homeostasis in mammals by binding membrane protein receptors called claudins. Although structures of CpE fragments bound to claudins have been determined, the mechanisms that trigger CpE activation and oligomerization that lead to the formation of cytotoxic β-pores remain undetermined. Proteolysis of CpE in the gut by trypsin has been shown to play a role in this and subsequent cytotoxicity processes. Here, we report solution structures of full-length and trypsinized CpE using small-angle X-ray scattering (SAXS) and crystal structures of trypsinized CpE and its C-terminal claudin-binding domain (cCpE) using X-ray crystallography. Mass spectrometry and SAXS uncover that removal of the CpE N-terminus by trypsin alters the CpE structure to expose areas that are normally unexposed. Crystal structures of trypsinized CpE and cCpE reveal unique dimer interfaces that could serve as oligomerization sites. Moreover, comparisons of these structures to existing ones predict the functional implications of oligomerization in the contexts of cell receptor binding and β-pore formation. This study sheds light on trypsin’s role in altering CpE structure to activate its function via inducing oligomerization on its path toward cytotoxic β-pore formation. Its findings can incite new approaches to inhibit CpE-based cytotoxicity with oligomer-disrupting therapeutics.

59 BASIC BIOLOGICAL SCIENCES↗

Shear strength measurements and hydrostatic compression of rhenium diboride under high pressures

Shear strength measurements have been carried out on rhenium diboride, ReB 2 , to a pressure of 74 GPa using a Radial X-ray Diffraction (R-XRD) technique in a diamond anvil cell using platinum as an internal x-ray pressure standard. The R-XRD result has provided a unique insight into the deformation of hexagonal crystal lattice under non-hydrostatic compression and variation of shear strength with increasing pressure. From R-XRD data, we have estimated hydrostatic component of compression to determine an equation of state of rhenium diboride yielding a bulk modulus of K 0 = 366 ± 25 GPa with a pressure derivative $K^{'}_{0}$ = 4.3 ± 0.5 in good agreement with hydrostatic density functional theory calculations. Here, the average lower bound of shear strength (τ) from various diffraction planes was then calculated using the measured interplanar d-spacing (d m ) and hydrostatic component of d-spacing (d p ) to be shown to approach 6.7 ± 0.4 GPa at 70 GPa. Our results show that the anisotropic compression effects observed in ReB 2 under hydrostatic compression are correlated to electronic structure changes under compression as predicted by theoretical calculations.

36 MATERIALS SCIENCE↗

Structural basis for the calmodulin-mediated activation of eukaryotic elongation factor 2 kinase

Translation is a tightly regulated process that ensures optimal protein quality and enables adaptation to energy/nutrient availability. The α-kinase eukaryotic elongation factor 2 kinase (eEF-2K), a key regulator of translation, specifically phosphorylates the guanosine triphosphatase eEF-2, thereby reducing its affinity for the ribosome and suppressing the elongation phase of protein synthesis. eEF-2K activation requires calmodulin binding and autophosphorylation at the primary stimulatory site, T348. Biochemical studies predict a calmodulin-mediated activation mechanism for eEF-2K distinct from other calmodulin-dependent kinases. Here, we resolve the atomic details of this mechanism through a 2.3-Å crystal structure of the heterodimeric complex of calmodulin and the functional core of eEF-2K (eEF-2K TR ). This structure, which represents the activated T348-phosphorylated state of eEF-2K TR , highlights an intimate association of the kinase with the calmodulin C-lobe, creating an “activation spine” that connects its amino-terminal calmodulin-targeting motif to its active site through a conserved regulatory element.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Materializing rival ground states in the barlowite family of kagome magnets: quantum spin liquid, spin ordered, and valence bond crystal states

The spin- 1 2 kagome antiferromagnet is considered an ideal host for a quantum spin liquid ground state. We find that when the bonds of the kagome lattice are modulated with a periodic pattern, new quantum ground states emerge. Newly synthesized crystalline barlowite (Cu 4 (OH) 6 FBr) and Zn-substituted barlowite demonstrate the delicate interplay between singlet states and spin order on the spin- 1 2 kagome lattice. Comprehensive structural measurements demonstrate that our new variant of barlowite maintains hexagonal symmetry at low temperatures with an arrangement of distorted and undistorted kagome triangles, for which numerical simulations predict a pinwheel va- lence bond crystal (VBC) state instead of a quantum spin liquid (QSL). The presence of interlayer spins eventually leads to an interesting pinwheel q=0 magnetic order. Partially Zn-substituted bar- lowite (Cu 3.44 Zn 0.56 (OH) 6 FBr) has an ideal kagome lattice and shows QSL behavior, indicating a surprising robustness of the QSL against interlayer impurities. The magnetic susceptibility is simi- lar to that of herbertsmithite, even though the Cu 2+ impurities are above the percolation threshold for the interlayer lattice and they couple more strongly to the nearest kagome moment. This system is a unique playground displaying QSL, VBC, and spin order, furthering our understanding of these highly competitive quantum states.

36 MATERIALS SCIENCE↗

Superconductivity up to 243 K in the yttrium-hydrogen system under high pressure

The discovery of superconducting H 3 S with a critical temperature T c ~200 K opened a door to room temperature superconductivity and stimulated further extensive studies of hydrogen-rich compounds stabilized by high pressure. Here, we report a comprehensive study of the yttrium-hydrogen system with the highest predicted T c s among binary compounds and discuss the contradictions between different theoretical calculations and experimental data. We synthesized yttrium hydrides with the compositions of YH 3 , YH 4 , YH 6 and YH 9 in a diamond anvil cell and studied their crystal structures, electrical and magnetic transport properties, and isotopic effects. We found superconductivity in the Im-3m YH 6 and P6 3 /mmc YH 9 phases with maximal T c s of ~220 K at 183 GPa and ~243 K at 201 GPa, respectively. Fm-3m YH 10 with the highest predicted T c > 300 K was not observed in our experiments, and instead, YH 9 was found to be the hydrogen-richest yttrium hydride in the studied pressure and temperature range up to record 410 GPa and 2250 K.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

An In-situ and Direct Confirmation of Super-Planckian Thermal Radiation Emitted From a Metallic Photonic-Crystal at Optical Wavelengths

Planck’s law predicts the distribution of radiation energy, color and intensity, emitted from a hot object at thermal equilibrium. The Law also sets the upper limit of radiation intensity, the blackbody limit. Recent experiments reveal that micro-structured tungsten can exhibit significant deviation from the blackbody spectrum. However, whether thermal radiation with weak non-equilibrium pumping can exceed the blackbody limit in the far field remains un-answered experimentally. Here, we compare thermal radiation from a micro-cavity/tungsten photonic crystal (W-PC) and a blackbody, which are both measured from the same sample and also in-situ. We show that thermal radiation can exceed the blackbody limit by >8 times at λ=1.7 μm resonant wavelength in the far-field. Our observation is consistent with a recent calculation by Wang and John performed for a 2D W-PC filament. This finding is attributed to non-equilibrium excitation of localized surface plasmon resonances coupled to nonlinear oscillators and the propagation of the electromagnetic waves through non-linear Bloch waves of the W-PC structure. This discovery could help create super-intense narrow band thermal light sources and even an infrared emitter with a laser-like input-output characteristic.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

X-ray Diffraction Studies of Single-Crystal Materials for Broad Battery Applications

Single-crystal materials have attracted growing interest in battery research due to their well-defined crystallographic orientation, absence of grain boundaries, and enhanced mechanical and electrochemical stability. This Review provides a comprehensive overview of recent advances in the synthesis, structural evolution, and performance optimization of single-crystal electrodes and solid electrolytes. Particular focus is placed on the application of advanced X-ray diffraction (XRD) techniques, including operando synchrotron diffraction, reciprocal space mapping, and Bragg coherent diffraction imaging, which have enabled in-depth investigations of lattice strain, cation disorder, phase transitions, and defect formation. Representative case studies across Ni-rich layered oxides, spinel-type cathodes, and garnet-based electrolytes are examined to highlight the structural features unique to single crystals. Additionally, the synergistic integration of XRD with machine learning, tomography, and spectroscopy is discussed as a powerful direction for real-time analysis and predictive modeling. Furthermore, these insights provide critical guidance for the rational design of high-performance single-crystal materials in lithium, sodium, and solid-state battery systems.

25 ENERGY STORAGE↗

A crystal plasticity finite element method modeling of Zircaloy with hydride phases based on scanning electron micrographs

This work developed a microstructure-based finite element model to predict the stress state of alloys with second phase inclusions. Quantitative microstructural details extracted from scanning electron microscopy (SEM) images were used to generate heterogeneous microstructures including the morphology and spatial distribution of hydrides. Generation of digital microstructure was achieved through two steps of tessellations using software Neper and Matlab. The process is demonstrated using an example of Zircaloy material with secondary phases of hydrides dispersed within and stress-strain response of Zircaloy containing hydrides was predicted. The constitutive material model for Zircaloy in this study was based on crystal plasticity theory which considers the hexagonal close-packed (HCP) atomic structure of Zircaloy material. The hydrides were modeled as isotropic elasto-plastic material. A parametric study had been conducted to understand the effect of volume fraction, and lamellae thickness of the hydride phase on the mechanical properties of the overall material. Results can help designers to alter the manufacturing process to obtain the enhanced mechanical properties for components used in nuclear applications made by Zircaloy material.

Kulkarni, Shank S.↗

LDRD conclusion poster - Synthesizing Heterometallic Uranium Single Crystals to Understand the Influence of the Secondary Metals on Uranyl Axial Bond Strength

Understanding how transition metals influenced the chemistry of lanthanide and actinide (f-element) materials is critical for advancing separation technologies, materials design, and coordination chemistry. This project examined how incorporating first-row transition metals affected the structural and spectroscopic properties of f-element coordination polymers. In uranium(VI)-based systems synthesized with 2,6-pyridinedicarboxylic acid (PDC) ligands, single-crystal X-ray diffraction and Raman spectroscopy revealed that the presence of transition metals shortened the uranyl axial bond and induced a blue shift in its symmetric stretching vibration—evidence of increased bond strength. Electronic structure analysis, including Density of States (DOS) calculations using density functional theory (DFT), revealed altered orbital overlaps and highlighted the role of transition metal d-orbitals in modulating bonding. Raman modes were modeled using truncated structural fragments in collaboration with the University of Notre Dame, and although the predicted frequencies were lower than experimental values, they remained within expected ranges. In parallel, similar experiments with cerium (Ce) in the presence of cobalt (Co) and PDC demonstrated multi-step single-crystal-to-single-crystal transformations—behavior not observed in the uranium systems. Initial products included light yellow, orange, and polycrystalline materials. Single-crystal X-ray diffraction studies, conducted in collaboration with the Colorado School of Mines, identified the yellow phase as monometallic Ce(PDC)2(H2O)2·4H2O and the orange phase as heterometallic Ce2Co(PDC)4(H2O)6. After standing in solution for one week, both phases fully transformed into a dark yellow crystalline phase, [Ce3(PDC)5(H2O)8].6(H2O). Remarkably, this transformation was reversible—disturbing the equilibrium by removing some crystals caused reversion to the initial Ce(PDC)2(H2O)2·4H2O phase, highlighting dynamic behavior. All three structures were previously unreported. Solid-state UV-visible and Raman spectroscopy further distinguished these phases, revealing ligand-to-metal charge transfer involving Ce and characteristic d–d transitions from Co(II). The precise mechanism driving these transformations remained unclear; however, pH-dependent experiments confirmed that the transformation did not occur when the pH decreased. Overall, the project demonstrated that transition metals could be employed to tune bonding interactions, structural dimensionality, and optical properties in f-element materials, establishing new pathways for designing functional heterometallic systems. The work resulted in several novel structural discoveries and fostered productive collaborations with the University of Notre Dame and the Colorado School of Mines.

37 - INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL C↗

Phase Diagrams and Piezoelectric Properties of Wurtzite Al1-x-yScxGdyN Heterostructural Alloys

Ternary nitride alloys based on wurtzite AlN are a promising platform to realize functional materials, particularly ferroelectrics and optical emitters, that can smoothly integrate with conventional microelectronics. Here, a strategic design is presented to enable multifunctional materials by substituting multiple elements into AlN to create quaternary nitride alloys. By combining computational predictions and combinatorial thin film synthesis, the phase diagram of these quaternary Al-Sc-Gd-N alloys (or pseudo-ternary heterostructural AlN-ScN-GdN alloys) is successfully predicted as a function of effective temperature, and we experimentally grow Al1-x-xScxGdyN thin films for the first time. It is revealed that Al1-x-xScxGdyN crystallizes in a wurtzite-derived structure for X + y <~ 0.35, consistent with the calculated phase diagram. The computational investigation explores whether co-substitution induces cooperative effects on these alloys' piezoelectric and ferroelectric properties, finding that it is beneficial for reducing the polarization switching barrier. We calculate that Al1-x-xScxGdyN thin films should display ferroelectric switching. This is supported by our experimental measurements of a high optical bandgap, enhanced piezoelectric coefficient, and a change in the calculated polarization switching mechanism, and we achieve preliminary ferroelectric switching that experimentally realizes the prediction. Overall, our work sets the foundation toward quaternary wurtzite-nitride-based multifunctional materials, including piezoelectrics, ferroelectrics, and possibly even multiferroics.

36 MATERIALS SCIENCE↗

Effect of loading path on grain misorientation and geometrically necessary dislocation density in polycrystalline aluminum under reciprocating shear

Solid phase processing (SPP) is a promising alloy fabrication technique to produce fine and homogeneous grain structures for high-performance alloys. However, there is very limited modeling capability to understand and predict the grain refinement during SPP. In this work, the crystal plasticity theory was used to study elastic-plastic deformation in polycrystalline aluminums under large shear deformation. Two approaches, kernel averaged misorientation (KAM) and grain reference orientation deviation (GROD), were used to assess the grain misorientations. The geometrically necessary dislocation (GND) density was computed with the plastic strain rate. The deformation simulations were carried out under two loading conditions to investigate the effect of loading paths on the evolutions of grain misorientation and GND density. The results show that the regions with high misorientation and GND density first appear near grain boundaries. These regions then extend toward interior grains. The loading path affects dislocation system activation and dislocation recovery, hence dislocation evolution and misorientation. In conclusion, both two- and three-dimensional simulations showed that the spatial and temporal evolutions of GROD, KAM, and GND density in are closely correlated, which indicates they all can be used as criteria of grain refinement or recrystallization.

36 MATERIALS SCIENCE↗

Perovskite design principles for efficient microwave dry reforming with noble metal free catalysts

Microwave absorbing catalysts have the potential to electrify high-temperature thermal reactions such as the dry reforming of methane process (DRM: CO 2 + CH 4 → 2CO + 2 H 2 ). However, microwave catalysts present unique challenges due to their dual requirements of maintaining microwave absorption in both oxidative and reductive environments and stability across a range of temperatures in inherently non-isothermal reactors. Here, catalyst candidates from the La 0.8 Sr 0.2 CoO 3 -La 0.8 Sr 0.2 NiO 3 -La 0.8 Sr 0.2 MnO 3 perovskite systems were screened (28 total) to identify promising microwave catalysts free of noble metals for dry reforming methane. The best performing candidates met two main criteria. First, they occurred at crystal phase boundaries, giving rise to a pseudocubic perovskite structure. The combined use of Goldschmidt tolerance factor and octahedral tolerance factors appeared to be suitable for predicting pseudocubic perovskites. Second, they provided a balance of reducible metal sites with an irreducible metal oxide support. The best performing catalyst was found to exsolve Ni-Co alloy particles as active sites for the DRM reaction which offered superior resistance to coking for excellent reforming efficiency and stability.

42 ENGINEERING↗

Data-Driven Constitutive Model for the Inelastic Response of Metals: Application to 316H Steel

Here, predictions of the mechanical response of structural elements are conditioned by the accuracy of constitutive models used at the engineering length-scale. In this regard, a prospect of mechanistic crystal-plasticity-based constitutive models is that they could be used for extrapolation beyond regimes in which they are calibrated. However, their use for assessing the performance of a component is computationally onerous. To address this limitation, a new approach is proposed whereby a surrogate constitutive model (SM) of the inelastic response of 316H steel is derived from a mechanistic crystal plasticity-based polycrystal model tracking the evolution of dislocation densities on all slip systems. The latter is used to generate a database of the expected plastic response and dislocation content evolution associated with several instances of creep loading. From the database, a SM is developed. It relies on the use of orthogonal polynomial regression to describe the evolution of the dislocation content. The SM is then validated against predictions of the dead load creep response given by the polycrystal model across a range of temperatures and stresses. When the SM is used to predict the response of 316H during complex non monotonic loading, extrapolating to new loading conditions, it is found that predictions compare particularly well against those from the physics-based polycrystal model.

36 MATERIALS SCIENCE↗

Development of Predictive Model for Accurate Rupture Time from Multi-Axial Creep in Alloy 709 with Physics-Based Simulations

A physics-based model is developed to predict multiaxial creep behavior in Alloy 709 (A709), an advanced austenitic stainless steel intended for high-temperature applications such as Sodium Fast Reactors (SFRs). Compared to conventional stainless steels like 316H, A709 offers superior high-temperature performance; however, comprehensive data on its multiaxial creep response remain limited. To address this gap, a crystal plasticity finite element (CPFE) framework is used to simulate the deformation and failure mechanisms of A709 under multiaxial loading conditions. The model incorporates an extended Hu-Cocks dislocation creep formulation that accounts for precipitation effects, along with the Sham–Needleman model to capture grain boundary cavitation-driven failure. These advanced constitutive models enable a detailed understanding of the interplay between microstructural evolution and macroscopic creep response. Furthermore, the study evaluates the predictive accuracy of various effective stress measures in estimating creep rupture life, leveraging simulated multiaxial creep data. The findings provide critical insights into the applicability of different stress measures for engineering design and life prediction of A709 components operating under complex loading conditions. This work contributes to improving the reliability of high-temperature structural components by advancing predictive modeling capabilities for advanced austenitic steels.

Alloy 709↗

RCSB Protein Data Bank: supporting research and education worldwide through explorations of experimentally determined and computationally predicted atomic level 3D biostructures

The Protein Data Bank (PDB) was established as the first open-access digital data resource in biology and medicine in 1971 with seven X-ray crystal structures of proteins. Today, the PDB houses >210 000 experimentally determined, atomic level, 3D structures of proteins and nucleic acids as well as their complexes with one another and small molecules ( e.g. approved drugs, enzyme cofactors). These data provide insights into fundamental biology, biomedicine, bioenergy and biotechnology. They proved particularly important for understanding the SARS-CoV-2 global pandemic. The US-funded Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) and other members of the Worldwide Protein Data Bank (wwPDB) partnership jointly manage the PDB archive and support >60 000 `data depositors' (structural biologists) around the world. wwPDB ensures the quality and integrity of the data in the ever-expanding PDB archive and supports global open access without limitations on data usage. The RCSB PDB research-focused web portal at https://www.rcsb.org/ (RCSB.org) supports millions of users worldwide, representing a broad range of expertise and interests. In addition to retrieving 3D structure data, PDB `data consumers' access comparative data and external annotations, such as information about disease-causing point mutations and genetic variations. RCSB.org also provides access to >1 000 000 computed structure models (CSMs) generated using artificial intelligence/machine-learning methods. To avoid doubt, the provenance and reliability of experimentally determined PDB structures and CSMs are identified. Related training materials are available to support users in their RCSB.org explorations.

59 BASIC BIOLOGICAL SCIENCES↗

Atomic cooperation in enhancing magnetism: (Fe, Cu)-doped CeCo 5

Developing permanent magnet alloys with decreased critical elements (e.g., Nd, Dy, and Co) requires identifying compositions and structures with uniaxial magneto-crystalline anisotropy energy (MAE), large magnetization, and a high ferromagnetic transition temperature (Curie temperature - T C ). One approach to minimizing the critical elements in potential permanent magnet alloys is to use overly produced Ce, which is less critical. Furthermore, reducing Co content in RCo 5 (R = Rare Earth) alloys is necessary since Co is also a critical element. An obvious choice for decreasing Co content is a substitution with non-critical Fe. However, the Fe is not stable in the lattice due to the reduced number of d -electrons. Concomitant substitution of Cu stabilizes Fe substitution. Employing first-principles electronic structure theory, we identify the weakly localized nature of cobalt in CeCo 5 , which causes high uniaxial magnetic anisotropy of ~10 MJ/m 3 . In contrast, substituted Cu delocalizes the Co’s 3 d -states, resulting in lower anisotropy. Calculations show that 10% Cu can stabilize 20% Fe subsituted for Co, which significantly enhances magnetic moment in the Ce (Co, Fe, Cu) 5 . We report this prediction is in good agreement with a single-crystal experiment in which the optimal composition was identified to be 15% of Fe and 12% Cu. The competitive non-equivalent Co sites preferred by Cu and Fe, a unique electronic structure including exchange and crystal field splitting, and rigid band shift variation are borne by 3 d states of Co, Fe, and Cu around the Fermi level, all play an essential role in tuning the magnetic properties.

36 MATERIALS SCIENCE↗

Using machine-learning to understand complex microstructural effects on the mechanical behavior of Ti-6Al-4V alloys

Structural materials properties are highly dependent on their microstructure. Their microstructure is in turn affected by multiple fabrication and thermo-mechanical treatment parameters, all of which conform a highly-dimensional parametric space with often hidden correlations that are difficult to extract by experimentation alone. This is particularly true for alloys of the dual-phase Ti-6Al-4V family, with their greatly complex and rich microstructures, which combine several intrinsic length scales associated with multiple grain and subgrain structures, grains with different crystal lattices (α and β phases), and complex chemistry. In this paper we use a comprehensive set of machine learning techniques to develop predictive tools relating the yield strength and hardening rate of these alloys to a set of input parameters covering extensive ranges. The data generator is a finite-element crystal plasticity model for polycrystal deformation that takes into account slip anisotropy and employs standard dislocation evolution models for the α and β phases of Ti-based alloys. Our dataset includes over two thousand independent simulations and is used to train the machine learning models, which are then used to establish correlations between microstructural parameters and the alloys’ mechanical response. Our results point to the most influential parameters affecting yield strength and hardening rate, information that can then be used to guide experimental synthesis and characterization efforts to save time and resources.

36 MATERIALS SCIENCE↗

Role of Short-Range Order on Diffusion Coefficients in the Li–Mg Alloy

Li–Mg alloys are important because of their beneficial role in fostering uniform plating and stripping of lithium in all-solid-state batteries. The alloy Li x Mg 1–x forms a solid solution on the BCC crystal structure when the lithium content is greater than x ≈ 0.3. The activation barriers of lithium and magnesium exchanges with a vacancy, crucial for substitutional diffusion, are predicted to be exceptionally low and almost identical, with negligible dependence on the alloy composition. The equilibrium vacancy concentration at room temperature is predicted to be very low, and it also remains almost constant with no dependence on Mg content in the alloy (for x Li ≥ 0.5). Nevertheless, both experiments and kinetic Monte Carlo simulations indicate that the tracer diffusion coefficients decrease by almost an order of magnitude with the addition of Mg to the alloy. In this contribution, the crucial role that chemical short-range order plays in affecting the diffusion coefficients is studied. Chemical short-range order is found to increase the effective activation barrier for lithium and magnesium diffusion by making successive atomic hops with vacancies correlated.

36 MATERIALS SCIENCE↗