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At least 1,153 records · Page 64

REDI – Readiness Engine for Data Integration

The Readiness Engine for Data Integration (REDI) is an open-source framework for automating, standardizing, and assessing the process of preparing scientific data for AI training. REDI implements a five-stage pipeline (ingest, preprocess, transform, structure, output) with per-stage provenance instrumentation via Flowcept, domain-aware transformation logic (PII anonymization, regridding, graph encoding, and more), and built-in readiness assessment and validation modes. REDI has been evaluated across climate, proteomics, materials science, and nuclear fusion datasets, demonstrating near-ideal parallel scaling to 100 nodes on OLCF's Frontier system. REDI is deployable as an agent-callable skill in coding environments such as Claude Code and OpenAI Codex, and is complemented by SetGo for FAIR compliance and catalog publication.

Brewer, Wesley [Oak Ridge National Laboratory (ORN↗

Isolation and characterization of IgG3 glycan-targeting antibodies with exceptional cross-reactivity for diverse viral families

Broadly reactive antibodies that target sequence-diverse antigens are of interest for vaccine design and monoclonal antibody therapeutic development because they can protect against multiple strains of a virus and provide a barrier to evolution of escape mutants. Using LIBRA-seq (linking B cell receptor to antigen specificity through sequencing) data for the B cell repertoire of an individual chronically infected with human immunodeficiency virus type 1 (HIV-1), we identified a lineage of IgG3 antibodies predicted to bind to HIV-1 Envelope (Env) and influenza A Hemagglutinin (HA). Two lineage members, antibodies 2526 and 546, were confirmed to bind to a large panel of diverse antigens, including several strains of HIV-1 Env, influenza HA, coronavirus (CoV) spike, hepatitis C virus (HCV) E protein, Nipah virus (NiV) F protein, and Langya virus (LayV) F protein. We found that both antibodies bind to complex glycans on the antigenic surfaces. Antibody 2526 targets the stem region of influenza HA and the N-terminal domain (NTD) region of SARS-CoV-2 spike. A crystal structure of 2526 Fab bound to mannose revealed the presence of a glycan-binding pocket on the light chain. Antibody 2526 cross-reacted with antigens from multiple pathogens and displayed no signs of autoreactivity. These features distinguish antibody 2526 from previously described glycan-reactive antibodies. Further study of this antibody class may aid in the selection and engineering of broadly reactive antibody therapeutics and can inform the development of effective vaccines with exceptional breadth of pathogen coverage.

Microbiology↗

User Guide: A Curated Dataset of Regional Meteor Events with Simultaneous Optical and Infrasound Observations

This user guide supports a curated dataset of 71 meteor events recorded between 2006 and 2011 in Southwestern Ontario, Canada. Each event was simultaneously observed by ground-based optical cameras and an infrasound array, providing a rare opportunity to examine meteor trajectories and acoustic signals from the same atmospheric entry events. The dataset includes raw and processed optical data, meteor trajectories, photometric light curves, infrasound waveforms, and atmospheric specifications relevant for acoustic modeling. The archive is structured to support reproducible research in meteor physics, atmospheric acoustics, and shock wave analysis. It is organized following transparent file naming conventions and structured folders to facilitate scientific reuse, comparison, and integration across research domains. The dataset is freely available on Zenodo, doi: 10.5281/zenodo.15868512.

54 ENVIRONMENTAL SCIENCES↗

Portable Parallel Algorithms and Frameworks for Exascale Graph Analytics

Graphs (or networks) are a tool used to model the interactions among various entities. Efficiently processing large graphs has recently attracted significant attention due to the applications of graphs in various domains, such as biology, chemistry, and cyber-security. Analyzing the structure and properties of these graphs is an important component of many scientific computing pipelines. With the explosion in the volume of data, graphs have become very large and can contain hundreds of billions of vertices and trillions of edges. Therefore, it is crucial to develop high-performance methods to enable graph analysis to be done quickly and energy-efficiently. Furthermore, these solutions should be highly parallel in order to take advantage of modern parallel machines. However, designing efficient solutions is not enough. With the wide variety of computing environments available, each with different programmability and performance characteristics, it is necessary to develop solutions that are portable in terms of both performance (i.e., provide theoretical guarantees) and programmability (i.e., provide high level abstractions).

97 MATHEMATICS AND COMPUTING↗

CyTRICS™ Assessment Report: Whole Home Battery Applications

This report examines the software supply chain security posture of mobile applications developed for consumer whole-house battery and energy-management products. While these applications are not currently integrated with critical infrastructure, their growing role in connected energy domain spaces underscores the importance of understanding the external dependencies, permission structures, and runtime behaviors that could introduce systemic risk; particularly, if adoption expands into more critical environments.

25 ENERGY STORAGE↗

Learning a general model of single phase flow in complex 3D porous media

Modeling effective transport properties of 3D porous media, such as permeability, at multiple scales is challenging as a result of the combined complexity of the pore structures and fluid physics—in particular, confinement effects which vary across the nanoscale to the microscale. While numerical simulation is possible, the computational cost is prohibitive for realistic domains, which are large and complex. Although machine learning (ML) models have been proposed to circumvent simulation, none so far has simultaneously accounted for heterogeneous 3D structures, fluid confinement effects, and multiple simulation resolutions. By utilizing numerous computer science techniques to improve the scalability of training, we have for the first time developed a general flow model that accounts for the pore-structure and corresponding physical phenomena at scales from Angstrom to the micrometer. Using synthetic computational domains for training, our ML model exhibits strong performance (R 2 = 0.9) when tested on extremely diverse real domains at multiple scales.

36 MATERIALS SCIENCE↗

Learning a General Model of Single Phase Flow in Complex 3D Porous Media

Modeling effective transport properties of 3D porous media, such as permeability, at multiple scales is challenging as a result of the combined complexity of the pore structures and fluid physics—in particular, confinement effects which vary across the nanoscale to the microscale. While numerical simulation is possible, the computational cost is prohibitive for realistic domains, which are large and complex. Although machine learning (ML) models have been proposed to circumvent simulation, none so far has simultaneously accounted for heterogeneous 3D structures, fluid confinement effects, and multiple simulation resolutions. By utilizing numerous computer science techniques to improve the scalability of training, we have for the first time developed a general flow model that accounts for the pore-structure and corresponding physical phenomena at scales from Angstrom to the micrometer. Using synthetic computational domains for training, our ML model exhibits strong performance (R 2 = 0.9) when tested on extremely diverse real domains at multiple scales.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Skyrmion lattice formation and destruction mechanisms probed with TR-SANS

Magnetic skyrmions are topologically protected, nanoscale whirls of the spin configuration that tend to form hexagonally ordered arrays. As a topologically non-trivial structure, the nucleation and annihilation of the skyrmion, as well as the interaction between skyrmions, varies from conventional magnetic systems. Recent works have suggested that the ordering kinetics in these materials occur over millisecond or longer timescales, which is unusually slow for magnetic dynamics. The current work investigates the skyrmion ordering kinetics, particularly during lattice formation and destruction, using time-resolved small angle neutron scattering (TR-SANS). Evaluating the time-resolved structure and intensity of the neutron diffraction pattern reveals the evolving real-space structure of the skyrmion lattice and the timeframe of the formation. Measurements were performed on three prototypical skyrmion materials: MnSi, (Fe,Co)Si, and Cu 2 OSeO 3 . To probe lattice formation and destruction kinetics, the systems were prepared in the stable skyrmion state, and then a square-wave magnetic field modulation was applied. The measurements show that the skyrmions quickly form ordered domains, with a significant distribution in lattice parameters, which then converge to the final structure; the results confirm the slow kinetics, with formation times between 10 ms and 99 ms. Comparisons are made between the measured formation times and the fundamental material properties, suggesting the ordering temperature, saturation magnetization and magnetocrystalline anisotropy may be driving the timeframes. Micromagnetic simulations were also performed and support a scaling of the kinetics with sample volume, a behavior which is caused by the reconciling of misaligned domains.

Liyanage, W. L. N. C.↗

Poling thin-film x-cut lithium niobate for quasi-phase matching with sub-micrometer periodicity

Quasi-phase-matched grating structures in lithium niobate waveguides with sub-micrometer periodicities will benefit the development of short-wavelength nonlinear optical devices. Here, we report on the reproducible formation of periodically poled domains in x-cut single-crystalline thin-film lithium niobate with periodicities as short as 600 nm. Shaped single-voltage poling pulses were applied to electrode structures that were fabricated by a combination of electron-beam and direct-writing laser lithography. Evidence of successful poling with good quality was obtained through second-harmonic microscopy and piezoresponse force microscopy imaging. For the sub-micrometer period structures, we observed patterns with a double periodicity formed by domain interactions and features with sizes <200 nm.

Zhao, Jie (ORCID:0000000306230125)↗

A structural analysis of ordered Cs3Sb films grown on single crystal graphene and silicon carbide substrates

Alkali antimonides are well established as high efficiency, low intrinsic emittance photocathodes for accelerators and photon detectors. However, conventionally grown alkali antimonide films are polycrystalline with surface disorder and roughness that can limit achievable beam brightness. Ordering the crystalline structure of alkali antimonides has the potential to deliver higher brightness electron beams by reducing surface disorder and enabling the engineering of material properties at the level of atomic layers. In this report, we demonstrate the growth of ordered Cs3Sb films on single crystal substrates 3C-SiC and graphene-coated 4H-SiC using pulsed laser deposition and conventional thermal evaporation growth techniques. The crystalline structures of the Cs3Sb films were examined using reflection high energy electron diffraction and x-ray diffraction diagnostics, while film thickness and roughness estimates were made using x-ray reflectivity. With these tools, we observed ordered domains in less than 10 nm thick films with quantum efficiencies greater than 1% at 530 nm. Moreover, we identify structural features such as Laue oscillations indicative of highly ordered films. We found that Cs3Sb films grew with flat, fiber-textured surfaces on 3C-SiC and with multiple ordered domains and sub-nanometer surface roughness on graphene-coated 4H-SiC under our growth conditions. We identify the crystallographic orientations of Cs3Sb grown on graphene-coated 4H-SiC substrates and discuss the significance of examining the crystal structure of these films for growing epitaxial heterostructures in future experiments.

36 MATERIALS SCIENCE↗

2D Reconstruction of Magnetotail Electron Diffusion Region Measured by MMS

Models for collisionless magnetic reconnection in near-Earth space are distinctly characterized as 2D or 3D. In 2D kinetic models, the frozen-in law for the electron fluid is usually broken by laminar dynamics involving structures set by the electron orbit size, while in 3D models the width of the electron diffusion region is broadened by turbulent effects. We present an analysis of in situ spacecraft observations from the Earth's magnetotail of a fortuitous encounter with an active reconnection region, mapping the observations onto a 2D spatial domain. While the event likely was perturbed by low-frequency 3D dynamics, the structure of the electron diffusion region remains consistent with results from a 2D kinetic simulation. As such, the event represents a unique validation of 2D kinetic, and laminar reconnection models.

79 ASTRONOMY AND ASTROPHYSICS↗

Origin of Unusual Acidity and Li+ Diffusivity in a Series of Water-in-Salt Electrolytes.

Superconcentrated aqueous electrolytes ("water-in-salt" electrolytes, or WiSEs) enable various aqueous battery chemistries beyond the voltage limits imposed by the Pourbaix diagram of water. However, their detailed structural and transport properties remain unexplored and could be better understood through added studies. Here, we report on our observations of strong acidity (pH 2.4) induced by lithium bis(trifluoromethane sulfonyl)imide (LiTFSI) at superconcentration (at 20 mol/kg). Multiple nuclear magnetic resonance (NMR) and pulsed-field gradient (PFG) diffusion NMR experiments, density functional theory (DFT) calculations, and molecular dynamics (MD) simulations reveal that such acidity originates from the formation of nanometric ion-rich structures. The experimental and simulation results indicate the separation of water-rich and ion-rich domains at salt concentrations >= 5 m and the acidity arising therefrom is due to deprotonation of water molecules in the ion-rich domains. As such, the ion-rich domain is composed of hydrophobic -CF3 (of TFSI-) and hydrophilic hydroxyl (OH-) groups. At 20 m concentration, the tortuosity and radius of water diffusion channels are estimated to be similar to 10 and similar to 1 nm, respectively, which are close to values obtained from hydrated Nafion membranes that also have hydrophobic polytetrafluoroethylene (PTFE) backbones and hydrophilic channels consisting of SO3- ion cluster networks providing for the transport of ions and water. Thus, we have discovered the structural similarity between WiSE and hydrated Nafion membranes on the nanometer scale.

Han, Kee Sung↗

Visualizing the Internal Nanocrystallinity of Calcite Due to Nonclassical Crystallization by 3D Coherent X–Ray Diffraction Imaging

The internal crystallinity of calcite is investigated for samples synthesized using two approaches: precipitation from solution and the ammonium carbonate diffusion method. Scanning electron microscopy (SEM) analyses reveal that the calcite products precipitated using both approaches have a well–defined rhombohedron shape, consistent with the euhedral crystal habit of the mineral. The internal structure of these calcite crystals is characterized using Bragg coherent diffraction imaging (BCDI) to determine the 3D electron density and the atomic displacement field. BCDI reconstructions for crystals synthesized using the ammonium carbonate diffusion approach have the expected euhedral shape, with internal strain fields and few internal defects. In contrast, the crystals synthesized by precipitation from solution have very complex external shapes and defective internal structures, presenting null electron density regions and pronounced displacement field distributions. These heterogeneities are interpreted as multiple crystalline domains, created by a nonclassical crystallization mechanism, where smaller nanoparticles coalescence into the final euhedral particles. The combined use of SEM, X–ray diffraction (XRD), and BCDI allows for structurally differentiating calcite crystals grown with different approaches, opening new opportunities to understand how grain boundaries and internal defects alter calcite reactivity.

36 MATERIALS SCIENCE↗

Microstructure Anisotropy Effects on Fracture and Fatigue Mechanisms in Shape Memory Alloy Martensites

The chief scientific object was to investigate the fatigue and fracture mechanisms in NiTi shape memory alloys, in the presence of stress concentrating factors such as micro-pores and notches. In particular, the interactions between structure (factors related to the geometry of the specimen, such as holes, pores and notches) and microstructure (related to properties of the material such as grains, secondary phases, twins) in influencing the inelastic deformation, leading up to fracture in NiTi was examined. Primarily, there were two major thrusts. The first thrust focused on fracture behavior in Shape Memory Alloys where the high crystal symmetry cubic phase transformed into the low symmetry phase during deformation and propagation of cracks. This thrust revealed the interplay between size of micro-pores, size of grains and grain orientations in determining the resistance to crack growth, during cyclic tensile deformation of porous-like NiTi specimens. The role of secondary phases (impurities of Ti, often formed during fabrication) were also shown to induce local inelastic deformation gradients during tensile deformation and reduce overall extent of deformation. The second thrust focused on the fatigue and fracture behavior in the low crystal symmetry martensite phase. Unlike high symmetry phases, characterization of deformation in low symmetry phases such as martensitic NiTi has been challenging, due to a hierarchical microstructure spanning from nanoscale twins to the macroscale, a highly anisotropic microstructure stemming from the low crystal symmetry and a multitude of inelastic mechanisms for deformation. Thus, advanced X-ray techniques such as 3D high-energy diffraction microscopy and x-ray micro-Laue diffraction and spectroscopy were used in conjunction with traditional techniques such as SEM and TEM to understand the inelastic deformation in the martensite phase in NiTi, in the presence of notches. This thrust revealed a stark difference in deformation mechanisms based on the nature of stress: regions near the notch experience a highly triaxial stress while those far away experience a uniaxial stress. Additionally, while regions close to the notch were shown to deform locally by amorphization/nanocrystallization, ultimately leading to fracture, regions far away from the notch deformed in a more traditional manner, with detwinning and twin reorientation the primary mechanisms of deformation. More importantly, this thrust revealed that in the presence of structural factors such as notches, the traditional picture of reorientation (coalescence) of nanoscale martensite twins into increasingly larger domains with increased loading does not hold true, even up to fracture of the specimen. These conclusions will inform the modeling and understanding of deformation behavior of specimens, where structure and microstructure coexist and interact.

36 MATERIALS SCIENCE↗

Molecular recognition requires dimerization of a VHH antibody

Camelid heavy-chain-only antibodies are a unique class of antibody that possesses only a single variable domain (termed VHH) for antigen recognition. Despite their apparent canonical mechanism of target recognition, where a single VHH domain binds a single target, an anti-caffeine VHH has been observed to possess 2:1 stoichiometry. Here, the structure of the anti-caffeine VHH/caffeine complex enabled the generation and biophysical analysis of variants that were used to better understand the role of VHH homodimerization in caffeine recognition. VHH interface mutants and caffeine analogs, which were examined to probe the mechanism of caffeine binding, suggested caffeine recognition is only possible with the VHH dimer species. Correspondingly, in the absence of caffeine, the anti-caffeine VHH was found to form a dimer with a dimerization constant comparable to that observed with VH:VL domains in conventional antibody systems, which was most stable near physiological temperature. While the VHH:VHH dimer structure (at 1.13 Å resolution) is reminiscent of conventional VH:VL heterodimers, the homodimeric VHH possesses a smaller angle of domain interaction, as well as a larger amount of apolar surface area burial. To test the general hypothesis that the short complementarity-determining region-3 (CDR3) may help drive VHH:VHH homodimerization, an anti-picloram VHH domain containing a short CDR3 was generated and characterized, which revealed it also existed as dimer species in solution. These results suggest homodimer-driven recognition may represent a more common method of VHH ligand recognition, opening opportunities for novel VHH homodimer affinity reagents and helping to guide their use in chemically induced dimerization applications.

60 APPLIED LIFE SCIENCES↗

Conformational and oligomeric states of SPOP from small-angle X-ray scattering and molecular dynamics simulations

Speckle-type POZ protein (SPOP) is a substrate adaptor in the ubiquitin proteasome system, and plays important roles in cell-cycle control, development, and cancer pathogenesis. SPOP forms linear higher-order oligomers following an isodesmic self-association model. Oligomerization is essential for SPOP’s multivalent interactions with substrates, which facilitate phase separation and localization to biomolecular condensates. Structural characterization of SPOP in its oligomeric state and in solution is, however, challenging due to the inherent conformational and compositional heterogeneity of the oligomeric species. Here, we develop an approach to simultaneously and self-consistently characterize the conformational ensemble and the distribution of oligomeric states of SPOP by combining small-angle X-ray scattering (SAXS) and molecular dynamics (MD) simulations. We build initial conformational ensembles of SPOP oligomers using coarse-grained molecular dynamics simulations, and use a Bayesian/maximum entropy approach to refine the ensembles, along with the distribution of oligomeric states, against a concentration series of SAXS experiments. Our results suggest that SPOP oligomers behave as rigid, helical structures in solution, and that a flexible linker region allows SPOP’s substrate-binding domains to extend away from the core of the oligomers. Additionally, our results are in good agreement with previous characterization of the isodesmic self-association of SPOP. In the future, the approach presented here can be extended to other systems to simultaneously characterize structural heterogeneity and self-assembly.

59 BASIC BIOLOGICAL SCIENCES↗

N-Glycolylneuraminic Acid Binding of Avian and Equine H7 Influenza A Viruses

Influenza A viruses (IAV) initiate infection by binding to glycans with terminal sialic acids on the cell surface. Hosts of IAV variably express two major forms of sialic acid, N-acetylneuraminic acid (NeuAc) and N-glycolylneuraminic acid (NeuGc). NeuGc is produced in most mammals, including horses and pigs, but is absent in humans, ferrets, and birds. The only known naturally occurring IAV that exclusively bind NeuGc are extinct highly pathogenic equine H7N7 viruses. We determined the crystal structure of a representative equine H7 hemagglutinin (HA) in complex with NeuGc and observed high similarity in the receptor-binding domain with an avian H7 HA. To determine the molecular basis for NeuAc and NeuGc specificity, we performed systematic mutational analyses, based on the structural insights, on two distant avian H7 HAs and an H15 HA. We found that the A135E mutation is key for binding α2,3-linked NeuGc but does not abolish NeuAc binding. The additional mutations S128T, I130V, T189A, and K193R converted the specificity from NeuAc to NeuGc. We investigated the residues at positions 128, 130, 135, 189, and 193 in a phylogenetic analysis of avian and equine H7 HAs. This analysis revealed a clear distinction between equine and avian residues. The highest variability was observed at key position 135, of which only the equine glutamic acid led to NeuGc binding. These results demonstrate that genetically distinct H7 and H15 HAs can be switched from NeuAc to NeuGc binding and vice versa after the introduction of several mutations, providing insights into the adaptation of H7 viruses to NeuGc receptors.

59 BASIC BIOLOGICAL SCIENCES↗