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At least 1,207 records · Page 67

Inverse design of cellular structures with the targeted nonlinear mechanical response

Advanced additive manufacturing capabilities have enabled a transformational ability to create sophisticated cellular structures using diverse materials. By altering the topology of the unit cell, the mechanical behavior, such as the stress-strain response during compression, can be modulated. Nevertheless, identifying a printable topology within an enormous design space that would precisely deliver the targeted nonlinear material response is challenging. We propose a data-driven generative framework based on a conditional variational autoencoder (cVAE) architecture that can inverse design the cellular structure based on the intended nonlinear stress-strain response. Trained on a dataset of structure-property pairs, the cVAE learns a compact and expressive latent space that enables efficient mapping from targets to feasible geometries. Two inference modes are explored: (1) decoder-only generation, which enables the exploration of diverse designs conditioned solely on the desired mechanical response, and (2) encoder-decoder generation, which further allows for the incorporation of desired topologies, ensuring the generated structure conforms to both mechanical properties and to desired-topology constraints. The results demonstrate that the model can generate structurally plausible and mechanically accurate designs, with the predicted stress-strain curves closely matching the targets. Even under joint conditioning, the model effectively balances geometric fidelity and functional performance.

36 MATERIALS SCIENCE↗

Combinatorial investigation of structural and optical properties of cation-disordered ZnGeN 2

Cation-disordered ZnGeN 2 shows promise for application as a blue-green emitter in light-emitting devices, but more foundational work is necessary to understand structure–property relationships. In this work, we present a combinatorial exploration of the experimental phase space of wurtzite (cation-disordered) ZnGeN 2 using high-throughput co-sputtering. Structure, morphology and optical properties are explored as a function of cation composition and synthesis temperature. ZnGeN 2 is found to crystallize in the wurtzite structure ranging from Zn-rich to Ge-rich compositions. X-ray diffraction refinements reveal a continuous shift in cell volume with off-stoichiometry, indicating alloy-like structural behavior. Furthermore, the optical absorption of all films examined is lower in energy than the value predicted for cation-ordered ZnGeN 2 , suggesting that cation disorder is decreasing the bandgap. Additionally, the absorption threshold shifts continuously to higher energy for Ge-rich samples, consistent with bandgap shifts due to alloy-like structural behavior. Defect formation energy diagrams are calculated to help guide understanding of off-stoichiometry from a defect complex perspective. This work paves the way toward use of ZnGeN 2 as a bandgap-tunable optoelectronic semiconductor.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The ellipticity parameterization for an NFW profile: An overlooked angular structure in strong lens modeling

Galaxy-scale gravitational lenses are often modeled with two-component mass profiles where one component represents the stellar mass and the second is a Navarro Frenk White (NFW) profile representing the dark matter. Outside of the spherical case, the NFW profile is costly to implement, and so it is approximated via two different methods; ellipticity can be introduced via the lensing potential (NFWp) or via the mass by approximating the NFW profile as a sum of analytical profiles (NFWm). While the NFWp method has been the default for lensing applications, it gives a different prescription of the azimuthal structure, which we show introduces ubiquitous gradients in ellipticity and boxiness in the mass distribution rather than having a constant elliptical shape. Because an unmodeled azimuthal structure has been shown to be able to bias lens model results, we explored the degree to which this azimuthal structure that was introduced can affect the model accuracy. We constructed input profiles using composite models using both the NFWp and NFWm methods and fit these mocks with a power-law elliptical mass distribution (PEMD) model with external shear. As a measure of the accuracy of the recovered lensing potential, we calculated the value of the Hubble parameter H 0 one would determine from the lensing fit. We found that the fits to the NFWp input return H 0 values that are systematically biased by about 3% lower than the NFWm counterparts. We explored whether such an effect is attributable to the mass sheet transformation (MST) by using an MST-independent quantity, ξ 2 . We show that, as expected, the NFWm mocks are degenerate with PEMD through an MST. For the NFWp, an additional bias was found beyond the MST due to the azimuthal structure exterior to the Einstein radius. We recommend modelers use an NFWm prescription in the future, such that the azimuthal structure can be introduced explicitly rather than implicitly.

79 ASTRONOMY AND ASTROPHYSICS↗

The SRG/eROSITA All-Sky Survey: Constraints on the structure growth from cluster number counts

Recent advancements in methods used in wide-area surveys have demonstrated the reliability of the number density of galaxy clusters as a viable tool for precision cosmology. Beyond testing the current cosmological paradigm, cluster number counts can also be used to investigate the discrepancies currently affecting cosmological measurements. In particular, cosmological studies based on cosmic shear and other large-scale structure probes routinely find a value for the amplitude of the fluctuations in the universe S​ 8 = σ 8 (Ω m /0.3) 0.5 smaller than the one inferred from the primary cosmic microwave background. In this work, we investigate this tension by measuring structure evolution across cosmic time as probed by the number counts of massive halos with the first SRG/eROSITA All-Sky Survey cluster catalog in the western Galactic hemisphere, complemented with the overlapping Dark Energy Survey Year-3, Kilo-Degree Survey, and Hyper Suprime-Cam data for weak lensing mass calibration, by implementing two different parameterizations and a model-agnostic method. In the first model, we measured the cosmic linear growth index as γ = 1.19 ± 0.21, which is in tension with the standard value of γ = 0.55 but in good statistical agreement with other large-scale structure probes. The second model is a phenomenological scenario in which we rescale the linear matter power spectrum at low redshift to investigate a potential reduction of structure formation, and it provided similar results. Finally, in a third strategy, we considered a standard ΛCDM cosmology, but we separated the cluster catalog into five redshift bins, measuring the cosmological parameters in each and inferring the evolution of the structure formation, finding hints of a reduction. Interestingly, the S ​8 value inferred from the number counts of the cluster eRASS1 when we add a degree of freedom to the matter power spectrum recovers the value inferred by cosmic shear studies. The observed reduction in the growth rate or systematic uncertainties associated with various measurements may account for the discrepancy in the S 8 ​ values suggested between cosmic shear probes and eROSITA cluster number counts and Planck CMB measurements.

cosmological parameters↗

Polysulfone shock compressed above the decomposition threshold: Velocimetry and modeling of two-wave structures

Polysulfone was shock loaded to pressures of 14.6–26.2 GPa in a series of gas gun-driven plate-impact experiments measuring material response with embedded electro-magnetic particle velocity gauges and optical velocimetry. The embedded electro-magnetic particle velocity gauges did not show a distinct two-wave structure but did show rounding that suggested a reaction but not a distinct separation of the reactants and product waves. In contrast, the transmission experiments fielded with optical velocimetry, with product pressures ranging from 21.0 to 26.2 GPa, showed well-defined two-wave structures due to shock-driven chemical decomposition of the polymer to products at a higher density. Distinct two-wave structures have not previously been published in literature during polymer compression; here, we observed these two-wave structures at both the polymer/lithium fluoride and polymer/polymethylmethacrylate interfaces. Hydrodynamic simulations of the experiments were performed using a newly constructed SESAME equation of state (EOS) for the polymer, a thermochemical EOS for the decomposition products, and an Arrhenius reaction rate model for the kinetics of the reaction. Finally, simulation results also demonstrated two-wave structures but were unable to quantitatively reproduce either the embedded gauge or optical velocimetry data.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Applications of visualization technology in the structural sciences

The structural sciences are undergoing a transformation driven by advancements in visualization technologies that aid researchers in understanding and communicating experimental data from complex molecular systems. New applications of integrative structural biological and biophysical approaches add a wide variety of complementary information from a broad range of scientific disciplines. These approaches extend structural biophysical methodologies to enable research by the incorporation of a variety of data streams and utilization of tools like molecular graphics, virtual reality, and machine learning. To redefine how structural data—particularly from cryo-electron microscopy and x-ray crystallography—are fed forward for scientific exploration and communication, the advances in tools for data visualization and interpretation have been critical. By bringing molecular systems into an interactive three-dimensional space, these novel technologies enhance research workflows, facilitate structure-based drug design, and create engaging educational experiences. Taken together, these visualization innovations are essential tools for advancing the field by making concepts more accessible and compelling.

Eng, Edward T. [New York Structural Biology Center↗

Isotope effects on the structural transformation and relaxation of deeply supercooled water

Herein, we have examined the structure of supercooled liquid D 2 O as a function of temperature between 185 and 255 K using pulsed laser heating to rapidly heat and cool the sample on a nanosecond timescale. The liquid structure can be represented as a linear combination of two structural motifs, with a transition between them described by a logistic function centered at 218 K with a width of 10 K. The relaxation to a metastable state, which occurred prior to crystallization, exhibited nonexponential kinetics with a rate that was dependent on the initial structural configuration. When the temperature is scaled by the temperature of maximum density, which is an isostructural point of the isotopologues, the structural transition and the non-equilibrium relaxation kinetics of D 2 O agree remarkably well with those for H 2 O.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Thickness and temperature dependence of the atomic-scale structure of SrRuO 3 thin films

The temperature-dependent layer-resolved structure of 3 to 44 unit cell thick SrRuO 3 (SRO) films grown on Nb-doped SrTiO 3 substrates is investigated using a combination of high-resolution synchrotron x-ray diffraction and high-resolution electron microscopy to understand the role that structural distortions play in suppressing ferromagnetism in ultra-thin SRO films. The oxygen octahedral tilts and rotations and Sr displacements characteristic of the bulk orthorhombic phase are found to be strongly dependent on temperature, the film thickness, and the distance away from the film–substrate interface. For thicknesses, t, above the critical thickness for ferromagnetism (t > 3 uc), the orthorhombic distortions decrease with increasing temperature above T C . Below T C , the structure of the films remains constant due to the magneto-structural coupling observed in bulk SRO. The orthorhombic distortions are found to be suppressed in the 2–3 interfacial layers due to structural coupling with the SrTiO 3 substrate and correlate with the critical thickness for ferromagnetism in uncapped SRO films.

36 MATERIALS SCIENCE↗

SQMBox: Interfacing a semiempirical integral library to modular ab initio electronic structure enables new semiempirical methods

Ab initio and semiempirical electronic structure methods are usually implemented in separate software packages or use entirely different code paths. As a result, it can be time-consuming to transfer an established ab initio electronic structure scheme to a semiempirical Hamiltonian. Here we present an approach to unify ab initio and semiempirical electronic structure code paths based on a separation of the wavefunction ansatz and the needed matrix representations of operators. With this separation, the Hamiltonian can refer to either an ab initio or semiempirical treatment of the resulting integrals. We built a semiempirical integral library and interfaced it to the GPU-accelerated electronic structure code TeraChem. Equivalency between ab initio and semiempirical tight-binding Hamiltonian terms is assigned according to their dependence on the one-electron density matrix. The new library provides semiempirical equivalents of the Hamiltonian matrix and gradient intermediates, corresponding to those provided by the ab initio integral library. This enables the straightforward combination of semiempirical Hamiltonians with the full pre-existing ground and excited state functionality of the ab initio electronic structure code. We demonstrate the capability of this approach by combining the extended tight-binding method GFN1-xTB with both spin-restricted ensemble-referenced Kohn–Sham and complete active space methods. We also present a highly efficient GPU implementation of the semiempirical Mulliken-approximated Fock exchange. The additional computational cost for this term becomes negligible even on consumer-grade GPUs, enabling Mulliken-approximated exchange in tight-binding methods for essentially no additional cost.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structure of molten ytterbium aluminum garnet

Rare earth aluminum garnets are important materials in optical, dielectric, and thermal barrier applications. To advance the understanding of their melt processing and glass forming ability, we report the atomic structure of molten Yb 3 Al 5 O 12 over 1770–2630 K, which spans the equilibrium and supercooled liquid regimes. The melt density at T m = 2283 K is 5.50 g cm –3 , measured via silhouette imaging of electrostatically levitated drops over 1010–2420 K. Four separate structure measurements were made with aerodynamically levitated melts using x-ray and neutron diffraction with isotope substitution of Yb ( 172 Yb, 174 Yb, or nat Yb). Empirical potential structure refinement models were developed, which are in excellent agreement with the experiments. Coordination environments for Al–O are predominantly 4- and 5-coordinate, with a mean coordination of n AlO = 4.43(8), while Yb–O environments mostly range from 5- to 8-coordinate, with n YbO = 6.26(8). The cation–oxygen polyhedra are connected primarily by corner-sharing, with edge-sharing constituting up to ~1/3 of the connectivity among polyhedra with Yb or higher-coordinated Al–O. Structurally, the –Al–O– network in molten Yb 3 Al 5 O 12 appears conducive to glass formation: n OAl = 1.85(3), there are 1.86 AlO x –AlO x connections per Al atom (e.g., a mixture of Q 3 and Q 4 units), and the modal ring size is six cations. These characterize a network that is somewhat less constrained compared to SiO 2 glass, yet Yb 3 Al 5 O 12 cannot be quenched into crystal-free glass. Here, aluminum garnet compositions with larger rare earth cations do form glass, so these characterizations help reveal the structural characteristics corresponding to the limit of glass forming ability in rare earth aluminates.

36 MATERIALS SCIENCE↗

Structural and compositional complexities of hierarchical self-assembly: A hypergraph approach

Programmable self-assembly enables the construction of complex molecular, supramolecular, and crystalline architectures from well-designed building blocks. In this work, we introduce a hypergraph-based formalism, Blocks & Bonds (B&B), which generalizes classical chemical graph theory by incorporating directed and multicolored interactions, internal symmetries, and hierarchical organization. Within this framework, we develop the Structure Code (SC), a compact and versatile language for describing self-assembled architectures. We define a Kolmogorov-style structural complexity as the total information content of SC, obtained through its tokenization and Shannon information assignment. Complementing this encoding-based measure, we introduce a much simpler quantity, the compositional complexity, which depends only on the number and cumulative usage of block and bond types in the construction set. A central result of this work is a strong empirical correlation between the token-based structural complexity and the compositional complexity across all examined systems. Owing to this agreement, the compositional complexity emerges as the most practical and broadly applicable measure: it is easy to compute, requires no explicit encoding, and yet closely tracks the actual information content of structurally diverse architectures. Applications to molecular systems (ethylene glycol and glucose), DNA-origami lattices, and crystalline assemblies show that B&B hypergraphs provide a unified, scalable, and information-efficient representation of structural organization, naturally capturing symmetry, modularity, and stereochemistry. This framework establishes a quantitative foundation for complexity-aware classification and inverse design of programmable matter.

36 MATERIALS SCIENCE↗

Local structure of Sr 2 CuO 3.3 , a 95 K cuprate superconductor without CuO 2 planes

The local structure of the highly “overdoped” 95 K superconductor Sr 2 CuO 3.3 determined by Cu K X-ray absorption fine structure (XAFS) at 62 K in magnetically oriented samples shows that 1) the magnetization is perpendicular to the c axis; 2) at these levels of precision the Cu sublattice is tetragonal in agreement with the crystal structure; the O sublattice has 3) continuous -Cu-O- chains that orient perpendicular to an applied magnetic field; 4) approximately half-filled -Cu-O- chains that orient parallel to this field; 5) a substantial number of apical O vacancies; 6) O ions at some apical positions with expanded Cu-O distances; and 7) interstitial positions that imply highly displaced Sr ions. These results contradict the universally accepted features of cuprates that require intact CuO 2 planes, magnetization along the c axis, and a termination of the superconductivity when the excess charge on the CuO 2 Cu ions exceeds 0.27. These radical differences in charge and structure demonstrate that this compound constitutes a separate class of Cu-O–based superconductors in which the superconductivity originates in a different, more complicated structural unit than CuO 2 planes while retaining exceptionally high transition temperatures.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Structure of human NADK2 reveals atypical assembly and regulation of NAD kinases from animal mitochondria

All kingdoms of life produce essential nicotinamide dinucleotide NADP(H) using NAD kinases (NADKs). A panel of published NADK structures from bacteria, eukaryotic cytosol, and yeast mitochondria revealed similar tetrameric enzymes. Here, we present the 2.8-Å structure of the human mitochondrial kinase NADK2 with a bound substrate, which is an exception to this uniformity, diverging both structurally and biochemically from NADKs. We show that NADK2 harbors a unique tetramer disruptor/dimerization element, which is conserved in mitochondrial kinases of animals (EMKA) and absent from other NADKs. EMKA stabilizes the NADK2 dimer but prevents further NADK2 oligomerization by blocking the tetramerization interface. This structural change bears functional consequences and alters the activation mechanism of the enzyme. Whereas tetrameric NADKs undergo cooperative activation via oligomerization, NADK2 is a constitutively active noncooperative dimer. Thus, our data point to a unique regulation of NADP(H) synthesis in animal mitochondria achieved via structural adaptation of the NADK2 kinase.

59 BASIC BIOLOGICAL SCIENCES↗

Unveiling the complexity of nanodiamond structures

Understanding nanodiamond structures is of great scientific and practical interest. It has been a long-standing challenge to unravel the complexity underlying nanodiamond structures and to resolve the controversies surrounding their polymorphic forms. Here, we use transmission electron microscopy with high-resolution imaging, electron diffraction, multislice simulations, and other supplementary techniques to study the impacts of small sizes and defects on cubic diamond nanostructures. The experimental results show that common cubic diamond nanoparticles display the (200) forbidden reflections in their electron diffraction patterns, which makes them indistinguishable from new diamond (n-diamond). The multislice simulations demonstrate that cubic nanodiamonds smaller than 5 nm can present the d -spacing at 1.78 Å corresponding to the (200) forbidden reflections, and the relative intensity of these reflections increases as the particle size decreases. Our simulation results also reveal that defects, such as surface distortions, internal dislocations, and grain boundaries can also make the (200) forbidden reflections visible. These findings provide valuable insights into the diamond structural complexity at nanoscale, the impact of defects on nanodiamond structures, and the discovery of novel diamond structures.

36 MATERIALS SCIENCE↗

Seismic Performance of Deeply Embedded Conceptual Advanced Reactors: Three-Dimensional Nonlinear Soil-Structure Interaction Analyses

The U.S. Nuclear Regulatory Commission’s functional containment concept provides advanced nuclear power plant designers with more flexibility in terms of the civil/structural design if the appropriate set of barriers for prevention of radioactive material release exist. Some of the conceptual advanced reactor structures, without the traditional pressure boundaries of large containment structures, are proposed to be deeply embedded or buried into soil. This approach is expected to provide (1) lesser seismic demands on the structures and safety-critical structures, (2) eased regulatory efforts and overall design against other external hazards such as aircraft impact, and (3) overall cost savings. Further, one of the important aspects of assessing the technical and economic viability of deeply embedding advanced reactor buildings is to assess the seismic performance with the understanding of effects with material and geometric nonlinearities. This study investigates the seismic response of deeply embedded or buried advanced reactors by conducting three-dimensional nonlinear soil-structure interaction analyses. Although the results indicate that there is a general trend of decreased seismic response with increased embedment depths, the change in the dynamic environment with different embedment depths and the nonlinear environment under high-intensity seismic inputs may result in increased peak response at increased embedment depths.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Identifying candidate structured RNAs in CRISPR operons

Noncoding RNAs with secondary structures play important roles in CRISPR-Cas systems. Many of these structures likely remain undiscovered. We used a large-scale comparative genomics approach to predict 156 novel candidate structured RNAs from 36,111 CRISPR-Cas systems. A number of these were found to overlap with coding genes, including palindromic candidates that overlapped with a variety of Cas genes in type I and III systems. Among these 156 candidates, we identified 46 new models of CRISPR direct repeats and 1 tracrRNA. This tracrRNA model occasionally overlapped with predicted cas9 coding regions, emphasizing the importance of expanding our search windows for novel structure RNAs in coding regions. We also demonstrated that the antirepeat sequence in this tracrRNA model can be used to accurately assign thousands of predicted CRISPR arrays to type II-C systems. This study highlights the importance of unbiased identification of candidate structured RNAs across CRISPR-Cas systems.

59 BASIC BIOLOGICAL SCIENCES↗

Edgewise Structural Damping of a 2.8-MW Land-Based Wind Turbine Rotor Blade

Modern wind turbines push the predictive capabilities of state-of-the-art aero-servo-elastic tools. The existing limitations hide across the numerical tool chain and can result in serious issues, such as missing aeroelastic instabilities during the design phase. Structural damping is an input that is usually hard to estimate, but also has a major impact on the turbine behavior. In this paper, we discuss an experiment that aims to accurately quantify the structural damping characterizing the edgewise modes of modern wind turbine blades. The experiment is carried out on a 2.8-MW land-based wind turbine and features a fast yaw actuation that induces an edgewise motion on one of the three blades. The Covariant-subspace system identification (Cov-SSI) method is then used to post-process the blade root moment to estimate the short-term edgewise structural damping. Despite limitations of the Cov-SSI method, which consistently under-predicts the absolute values of damping, we observe that structural damping decreases across the first three blade edgewise modes, which is different from the stiffness-proportional damping model that assumes that structural damping increases with the modes. This paper argues that a stiffness-proportional damping model, which is implemented in most aeroelastic tools, is therefore not conservative and might hide aeroelastic instabilities that can instead appear in the field.

17 WIND ENERGY↗

Structure of active methyl-CoM reductase, Earth’s main methane producer

Summary Our work reveals the structure of the active state of Methyl-Coenzyme M Reductase (MCR), the key and rate-limiting enzyme in biological methane formation. We find large differences between the active Ni(I) and inactive Ni(II) proteins and provide insight into how nature makes and breaks the C-H bond of methane. The Ni(II)-F430 center in inactive MCR contains four planar nitrogen ligands, a lower axial glutamine oxo, and an upper axial thiolate. The Ni(I)-enzyme replaces the axial ligands with a single water. The one-electron redox change results in movement of the Ni ion and upward swing of the β-lactam ring in the tetrapyrrole coupled to a domino-like protein quake through second sphere residues, inter-subunit interactions, a substrate tunnel, affecting even the dimensions of the unit cell. These structural changes lead Ni(I)-MCR to release a charge clamp that, in the Ni(II) state, locks down substrate Coenzyme B. Determining the Ni(I)-MCR structure required development of rigorous anaerobic crystallographic techniques. Validation of the MCR redox state was accomplished by in-line and parallel spectroscopic and unit cell analyses. This structure has large implications for developing technologies to limit methane emissions and efficiently produce biofuels. Methodology described here will enhance structural biology for other oxygen-sensitive enzymes.

09 BIOMASS FUELS↗