Substoichiometric Tuning of the Electronic Properties of Titania
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36 MATERIALS SCIENCE↗
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A cross-sectional aeroelastic analysis and structural optimization tool for slender composite structures
A fully open-source available framework for the parametric cross-sectional analysis and design optimization of slender composite structures, such as helicopter or wind turbine blades, is presented. The framework—Structural Optimization and Aeroelastic Analysis (SONATA)—incorporates two structural solvers, the commercial tool VABS, and the novel open-source code ANBA4. SONATA also parameterizes the design inputs, postprocesses and visualizes the results, and generates the structural inputs to a variety of aeroelastic analysis tools. It is linked to the optimization library OpenMDAO. This work presents the methodology and explains the fundamental approaches of SONATA. Structural characteristics were successfully verified for both VABS and ANBA4 using box beam examples from literature, thereby verifying the parametric approach to generating the topology and mesh in a cross section as well as the solver integration. The framework was furthermore exercised by analyzing and evaluating a fully resolved highly flexible wind turbine blade. Computed structural characteristics correlated between VABS and ANBA4, including off-diagonal terms. Stresses, strains, and deformations were recovered from loads derived through coupling with aeroelastic analysis. The framework, therefore, proves effective in accurately analyzing and optimizing slender composite structures on a high-fidelity level that is close to a three-dimensional finite element model.
42 ENGINEERING↗
Effect of laser melt schedule on the microstructure of additively manufactured IN718 Superalloy
Laser powder bed fusion (L-PBF) has enabled the fabrication of geometrically complex metallic structures and components that are challenging to producing using conventional manufacturing approaches. The site-specific and far from equilibrium thermal conditions of L-PBF offer the potential to facilitate multi-length scale design of structure and properties across the atomic-through macro-levels. However, L-PBF systems face scalability challenges due to throughput constraints. Laser rotary powder bed fusion (L-RPBF) systems are being investigated as a solution to enhance the deposition rates compared to conventional L-PBF. Rotary systems also offer additional flexibility for controlling the time structure of melting through laser interleaving on alternating layers. Here, in this study, IN718 test samples were printed using single-laser or interleaved dual-laser configuration in a L-RPBF system to investigates the effect of process settings and melt-interleaving on as-fabricated microstructure. The microstructural evolution, such as grain size and crystallographic texture, was assessed by determining variations in the melt-pool shapes. Laser interleaving leads to a reduction in average grain size compared to single laser by ∼ 40 % at high power (400 W) and by ∼36 % at medium power (370 W). Results presented here identify key challenge for obtaining uniform microstructures and barriers for the broader adoption of high-deposition rate L-RPBF.
Dual-laser↗
Flexible metal–gas batteries: a potential option for next-generation power accessories for wearable electronics
Flexible metal–gas batteries have become increasingly attractive for use in wearable electronics in the recent years due to their large theoretical energy density and superior adaptability to irregular geometric surfaces, such as the human body. With continuous improvements in design strategies and assembly technologies, the fabrication of various advanced flexible metal–gas batteries has been attempted. In spite of these efforts, the synchronous integration of high flexibility, safety, comfort, and high performance into flexible metal–gas batteries with specifically functionalized configurations still remains a formidable challenge. To resolve these dilemmas, the redesign of cathode catalysts, gel polymer electrolyte, and battery configurations/components has been investigated. In this paper, we review the recent technical advances together with the major dilemmas facing currently available flexible metal–gas batteries, highlighting how flexible cathodes and gel polymer electrolytes with various structures and components can affect the electrochemical performance and functionality of flexible metal–gas batteries. Flexible Zn–air, Li–O 2 /air, and Li–CO 2 batteries are mainly exemplified to elucidate their promising potential. Finally, based on our considerations, unresolved technical hurdles and future research perspectives involving flexible metal–gas batteries for wearable electronics are proposed.
25 ENERGY STORAGE↗
X‐ray scattering reveals disordered linkers and dynamic interfaces in complexes and mechanisms for DNA double‐strand break repair impacting cell and cancer biology
Abstract Evolutionary selection ensures specificity and efficiency in dynamic metastable macromolecular machines that repair DNA damage without releasing toxic and mutagenic intermediates. Here we examine non‐homologous end joining (NHEJ) as the primary conserved DNA double‐strand break (DSB) repair process in human cells. NHEJ has exemplary key roles in networks determining the development, outcome of cancer treatments by DSB‐inducing agents, generation of antibody and T‐cell receptor diversity, and innate immune response for RNA viruses. We determine mechanistic insights into NHEJ structural biochemistry focusing upon advanced small angle X‐ray scattering (SAXS) results combined with X‐ray crystallography (MX) and cryo‐electron microscopy (cryo‐EM). SAXS coupled to atomic structures enables integrated structural biology for objective quantitative assessment of conformational ensembles and assemblies in solution, intra‐molecular distances, structural similarity, functional disorder, conformational switching, and flexibility. Importantly, NHEJ complexes in solution undergo larger allosteric transitions than seen in their cryo‐EM or MX structures. In the long‐range synaptic complex, X‐ray repair cross‐complementing 4 (XRCC4) plus XRCC4‐like‐factor (XLF) form a flexible bridge and linchpin for DNA ends bound to KU heterodimer (Ku70/80) and DNA‐PKcs (DNA‐dependent protein kinase catalytic subunit). Upon binding two DNA ends, auto‐phosphorylation opens DNA‐PKcs dimer licensing NHEJ via concerted conformational transformations of XLF‐XRCC4, XLF–Ku80, and LigIV BRCT –Ku70 interfaces. Integrated structures reveal multifunctional roles for disordered linkers and modular dynamic interfaces promoting DSB end processing and alignment into the short‐range complex for ligation by LigIV. Integrated findings define dynamic assemblies fundamental to designing separation‐of‐function mutants and allosteric inhibitors targeting conformational transitions in multifunctional complexes.
59 BASIC BIOLOGICAL SCIENCES↗
Unique Structural Features Relate to Evolutionary Adaptation of Cytochrome P450 in the Abyssal Zone
Cytochromes P450 (CYPs) form one of the largest enzyme superfamilies, with similar structural folds yet biological functions varying from synthesis of physiologically essential compounds to metabolism of myriad xenobiotics. Sterol 14α-demethylases (CYP51s) represent a very special P450 family, regarded as a possible evolutionary progenitor for all currently existing P450s. In metazoans CYP51 is critical for the biosynthesis of sterols including cholesterol. Here we determined the crystal structures of ligand-free CYP51s from the abyssal fish Coryphaenoides armatus and human-. Comparative sequence–structure–function analysis revealed specific structural elements that imply elevated conformational flexibility, uncovering a molecular basis for faster catalytic rates, lower substrate selectivity, and intrinsic resistance to inhibition. In addition, the C. armatus structure displayed a large-scale repositioning of structural segments that, in vivo, are immersed in the endoplasmic reticulum membrane and border the substrate entrance (the FG arm, >20 Å, and the β4 hairpin, >15 Å). The structural distinction of C. armatus CYP51, which is the first structurally characterized deep sea P450, suggests stronger involvement of the membrane environment in regulation of the enzyme function. We interpret this as a co-adaptation of the membrane protein structure with membrane lipid composition during evolutionary incursion to life in the deep sea.
Biochemistry & Molecular Biology↗
Flexibility in the Energy Balancing Network of Photosynthesis Enables Safe Operation under Changing Environmental Conditions
Given their ability to harness chemical energy from the sun and generate the organic compounds necessary for life, photosynthetic organisms have the unique capacity to act simultaneously as their own power and manufacturing plant. This dual capacity presents many unique challenges, chiefly that energy supply must be perfectly balanced with energy demand to prevent photodamage and allow for optimal growth. From this perspective, we discuss the energy balancing network using recent studies and a quantitative framework for calculating metabolic ATP and NAD(P)H demand using measured leaf gas exchange and assumptions of metabolic demand. We focus on exploring how the energy balancing network itself is structured to allow safe and flexible energy supply. We discuss when the energy balancing network appears to operate optimally and when it favors high capacity instead. We also present the hypothesis that the energy balancing network itself can adapt over longer time scales to a given metabolic demand and how metabolism itself may participate in this energy balancing.
59 BASIC BIOLOGICAL SCIENCES↗
Two-Dimensional and Three-Dimensional Tetrel-Arsenide Frameworks Templated by Li and Cs Cations
Two new ternary tetrel pnictide phases, Li 1.08 Ge 4.92 As 7 and Cs 0.11 Zn 0.05 Si 0.95 As, have been synthesized. Both compounds crystallize in new structure types, which demonstrate the flexibility of Ge(Si)–As layers when accommodating electropositive cations of various sizes. Li 1.08 Ge 4.92 As 7 displays a Ge-As layer motif that has not been observed in ternary Ge-As systems, while Cs 0.11 Zn 0.05 Si 0.95 As exhibits a 3D framework composed of fragments of the 2D parent-phase SiAs. For Li 1.08 Ge 4.92 As 7 , a combination of computational modeling and solid-state 7 Li MAS NMR was used to establish the correct crystal structure with one mixed occupied Ge/Li site. The compositions of the phases were confirmed through energy-dispersive X-ray spectroscopy. Transport properties and UV–Vis spectroscopy reveal both reported compounds to be semiconductors. Cs 0.11 Zn 0.05 Si 0.95 As shows high thermal stability with congruent melting at 1300 K and an exceptionally low thermal conductivity of 0.5 W m –1 K –1 at 300 K. Temperature-dependent Li-ion hopping dynamics in Li 1.08 Ge 4.92 As 7 was characterized using 7 Li solid-state NMR.
36 MATERIALS SCIENCE↗
Cryo-EM structure of the Saccharomyces cerevisiae Rpd3L histone deacetylase complex
The Rpd3L histone deacetylase (HDAC) complex is an ancient 12-subunit complex conserved in a broad range of eukaryotes that performs localized deacetylation at or near sites of recruitment by DNA-bound factors. Here we describe the cryo-EM structure of this prototypical HDAC complex that is characterized by as many as seven subunits performing scaffolding roles for the tight integration of the only catalytic subunit, Rpd3. The principal scaffolding protein, Sin3, along with Rpd3 and the histone chaperone, Ume1, are present in two copies, with each copy organized into separate lobes of an asymmetric dimeric molecular assembly. The active site of one Rpd3 is completely occluded by a leucine side chain of Rxt2, while the tips of the two lobes and the more peripherally associated subunits exhibit varying levels of flexibility and positional disorder. The structure reveals unexpected structural homology/analogy between unrelated subunits in the fungal and mammalian complexes and provides a foundation for deeper interrogations of structure, biology, and mechanism of these complexes, as well as for the discovery of HDAC complex-specific inhibitors.
59 BASIC BIOLOGICAL SCIENCES↗
A flexible class of priors for orthonormal matrices with basis function-specific structure
Statistical modeling of high-dimensional matrix-valued data motivates the use of a low-rank representation that simultaneously summarizes key characteristics of the data and enables dimension reduction. Low-rank representations commonly factor the original data into the product of orthonormal basis functions and weights, where each basis function represents an independent feature of the data. However, the basis functions in these factorizations are typically computed using algorithmic methods that cannot quantify uncertainty or account for basis function correlation structure a priori. While there exist Bayesian methods that allow for a common correlation structure across basis functions, empirical examples motivate the need for basis function-specific dependence structure. We propose a prior distribution for orthonormal matrices that can explicitly model basis function-specific structure. The prior is used within a general probabilistic model for singular value decomposition to conduct posterior inference on the basis functions while accounting for measurement error and fixed effects. We discuss how the prior specification can be used for various scenarios and demonstrate favorable model properties through synthetic data examples. Finally, we apply our method to two-meter air temperature data from the Pacific Northwest, enhancing our understanding of the Earth system’s internal variability.
97 MATHEMATICS AND COMPUTING↗
Structure-preserving numerical discretizations for domains with boundaries
This SAND report documents Exploratory Express LDRD Project 223790, "Structure-preserving numerical discretizations for domains with boundaries", which developed a method to incorporate consistent treatment of domain boundaries and arbitrary boundary conditions in discrete exterior calculus (DEC) for arbitrary polygonal (2D) and tensor-product structure prism (3D) grids. The new DEC required the development of novel discrete exterior derivatives, boundary operators, wedge products and Hodge stars. This was accomplished through the use of boundary extension and the blending of known 2D operators on the interior with 1D operators on the boundary. The Hodge star was based on the Voronoi Hodge star, and retained the limitation of a triangular circumcentric primal or dual grid along with low-order accuracy. In addition to the new DEC, two related software packages were written: one for the study of DEC operators on arbitrary polygonal and polyhedral grids using both symbolic and numerical approaches and one for a (thermal) shallow water testbed using TRiSK-type numerics. Immediately relevant (already funded, through CANGA) followup work is the development of a high-order, geometrically flexible Hodge star and structure-preserving, high-order, oscillation-limiting transport operators (using WENO) for n-forms on arbitrary 2D and 3D grids. This will provide all of the machinery required for a high-order version of TRiSK with boundaries on arbitrary 2D and tensor-product 3D grids, which is applicable to both the atmospheric (CRM in E3SM-MMF) and oceanic (MPAS-O) components of E3SM.
97 MATHEMATICS AND COMPUTING↗
Nanometer-Thick Sr 2 IrO 4 Freestanding Films for Flexible Electronics
In this article, we report the structural and optical properties of nanoscale Sr 2 IrO 4 freestanding thin-films fabricated using a water-soluble Sr 3 Al 2 O 6 layer. The coherent lattice structure, phonon modes, two-magnon Raman scattering, and optical absorption spectra of the Sr 2 IrO 4 nanomembrane are analogous to those of the layered iridate epitaxial thin-films and single crystals. Remarkably, the formation of 3-unit-cell-thick SrIrO 3 and interfacial composite layers alleviates the antiphase boundaries at the Sr 2 IrO 4 /Sr 3 Al 2 O 6 interface, resulting in structurally-robust nanomembranes. Our experimental results show that this freestanding thin-film approach of layered oxides can provide techniques for tuning or realizing unprecedented states beyond conventional thin-film methods, suggesting a pathway in achieving flexible layered-oxide electronics.
36 MATERIALS SCIENCE↗
Structured information extraction from scientific text with large language models
Extracting structured knowledge from scientific text remains a challenging task for machine learning models. Here, we present a simple approach to joint named entity recognition and relation extraction and demonstrate how pretrained large language models (GPT-3, Llama-2) can be fine-tuned to extract useful records of complex scientific knowledge. We test three representative tasks in materials chemistry: linking dopants and host materials, cataloging metal-organic frameworks, and general composition/phase/morphology/application information extraction. Records are extracted from single sentences or entire paragraphs, and the output can be returned as simple English sentences or a more structured format such as a list of JSON objects. This approach represents a simple, accessible, and highly flexible route to obtaining large databases of structured specialized scientific knowledge extracted from research papers.
96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
Predicting receptor-ligand pairing preferences in plant-microbe interfaces via molecular dynamics and machine learning
Microbiome assembly, structure, and dynamics significantly influence plant health. Secreted microbial signaling molecules initiate and mediate symbiosis by binding to structurally compatible plant receptors. For example, lipo-chitooligosaccharides (LCOs), produced by nitrogen-fixing rhizobial bacteria and various fungi, are recognized by plant lysin motif receptor-like kinases (LysM-RLKs), which activate the common symbiotic pathway. Accurately predicting these molecular interactions could reveal complementary signatures underlying the initial stages of endosymbiosis. Despite the breakthrough in protein-ligand structure prediction with deep learning-based tools, such as AlphaFold3, the large size and highly flexible nature of signaling compounds like LCOs present major challenges for detailed structural characterization and binding-affinity prediction. Typical structure-/physics-based methods of ligand virtual screening are designed for small, drug-like molecules, often rely on high-resolution, experimentally determined structures of the protein receptors, and rarely achieve sufficient sampling to obtain converged thermodynamic quantities with large ligands. In this study, we developed a hybrid molecular dynamics/machine learning (MD/ML) approach capable of predicting binding affinity rankings with high accuracy in systems involving large, flexible ligands, despite limited experimental structural information. Using coarse initial structural models, the predictions using the MD/ML workflow achieved strong alignment with experimental trends, particularly in the top-affinity tier for four legume LysM-RLKs (LYR3) binding to LCOs and a chitooligosaccharide. Furthermore, the MD-based conformation selection protocol provided critical structural insights into substrate specificity and binding mechanisms. This study demonstrates a powerful method to screen for challenging cognate ligand-receptors and advance our understanding of the molecular basis of microbial colonization in plants.
Lipo-chitooligosaccharides↗
High-entropy Li-rich layered oxide cathode for Li-ion batteries
High-entropy oxides (HEOs) are emerging as promising cathode materials for Li-ion batteries (LIBs) due to their stable solid-state phase and compositional flexibility. Herein, we investigate the structural and electrochemical properties of a novel non-equimolar high-entropy cathode material, termed high-entropy Li-rich layered oxide (HE-LLO, Li 1.15 Na 0.05 Ni 0.19 Mn 0.56 Fe 0.02 Mg 0.02 Al 0.02 O 1.97 F 0.03 ), in comparison to a pristine Li-rich layered oxide (PR-LLO, Li1.2Ni0.2Mn0.6O2). The incorporation of multiple cations (Na + , Al 3+ , Mg 2+ , Fe 3+ ) and anion (F - ) into HE-LLO introduces compositional diversity, enhancing structural stability through the entropy stabilization effect. Theoretical calculations confirm a significantly higher configurational entropy in HE-LLO compared to PRLLO, supporting its high-entropy nature. Electrochemical evaluations demonstrate that HE-LLO exhibits considerable capacity retention, preserving 76.8 % of its discharge capacity at 0.5C after 200 cycles, compared to only 36.2 % for PR-LLO. Even under high-temperature conditions, HE-LLO outperformed PR-LLO, maintaining 76.1 % of its discharge capacity after 100 cycles at 5C, while PR-LLO retained only 12.4 %. These enhancements are attributed to the improved phase reversibility and higher Li + ion diffusion coefficients of HE-LLO, validated by ex-situ characterizations using a synchrotron X-ray technique, along with density functional theory (DFT) calculations. In conclusion, these findings highlight the promise of non-equimolar HEOs as a novel design strategy for highperformance cathode materials.
25 ENERGY STORAGE↗
Room-temperature structural studies of SARS-CoV-2 protein NendoU with an X-ray free-electron laser
NendoU from SARS-CoV-2 is responsible for the virus’s ability to evade the innate immune system by cleaving the polyuridine leader sequence of antisense viral RNA. Here we report the room-temperature structure of NendoU, solved by serial femtosecond crystallography at an X-ray free-electron laser to 2.6 Å resolution. The room-temperature structure provides insight into the flexibility, dynamics, and other intrinsic properties of NendoU, with indications that the enzyme functions as an allosteric switch. Functional studies examining cleavage specificity in solution and in crystals support the uridine-purine cleavage preference, and we demonstrate that enzyme activity is fully maintained in crystal form. Optimizing the purification of NendoU and identifying suitable crystallization conditions set the benchmark for future time-resolved serial femtosecond crystallography studies. This could advance the design of antivirals with higher efficacy in treating coronaviral infections, since drugs that block allosteric conformational changes are less prone to drug resistance.
59 BASIC BIOLOGICAL SCIENCES↗
Unlocking Li superionic conductivity in face-centred cubic oxides via face-sharing configurations
Oxides with a face-centred cubic (fcc) anion sublattice are generally not considered as solid-state electrolytes as the structural framework is thought to be unfavourable for lithium (Li) superionic conduction. Here we demonstrate Li superionic conductivity in fcc-type oxides in which face-sharing Li configurations have been created through cation over-stoichiometry in rocksalt-type lattices via excess Li. We find that the face-sharing Li configurations create a novel spinel with unconventional stoichiometry and raise the energy of Li, thereby promoting fast Li-ion conduction. The over-stoichiometric Li–In–Sn–O compound exhibits a total Li superionic conductivity of 3.38 × 10 -4 S cm -1 at room temperature with a low migration barrier of 255 meV. Our work unlocks the potential of designing Li superionic conductors in a prototypical structural framework with vast chemical flexibility, providing fertile ground for discovering new solid-state electrolytes.
36 MATERIALS SCIENCE↗
OpenTurbine [SWR-23-07]
OpenTurbine is an open-source code designed for the simulation of wind turbine structural dynamics. It is a flexible multi-body dynamics solver wherein the wind turbine is modeled as a collection of beam finite elements, rigid bodies, and constraints. OpenTurbine is equipped with an application programming interface primarily designed for coupling to computational fluid dynamics codes, but it is also suited for coupling to aerodynamics solvers based on blade element momentum theory.
Sprague, MichaelA.↗