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Results for “structural identification”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 217 records · Page 12
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Structural and functional insights into δ-poly-L-ornithine polymer biosynthesis from Acinetobacter baumannii

Cationic homo-polyamino acid (CHPA) peptides containing isopeptide bonds of diamino acids have been identified from Actinomycetes strains. However, none has been reported from other bacteria. Here, we report a δ-poly-L-ornithine synthetase from Acinetobacter baumannii, which we name PosA. Surprisingly, structural analysis of the adenylation domain and biochemical assay shows L-ornithine as the substrate for PosA. The product from the enzymatic reaction was purified and identified as poly-L-ornithine composed of 7-12 amino acid units. Chemical labeling of the polymer confirmed the isopeptide linkage of δ-poly-L-ornithine. We examine the biological activity of chemically synthesized 12-mer δ-poly-L-ornithine, illustrating that the polymer may act as an anti-fungal agent. Structures of the isolated adenylation domain from PosA are presented with several diamino acids and biochemical assays identify important substrate binding residues. Structurally-guided genome-mining led to the identification of homologs with different substrate binding residues that could activate additional substrates. A homolog from Bdellovibrionales sp. shows modest activity with L-arginine but not with any diamino acids observed to be substrates for previously examined CHPA synthetases. Our study indicates the possibility that additional CHPAs may be produced by various microbes, supporting the further exploration of uncharacterized natural products.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Structural analysis of molten materials by a remote fiber optic Raman sensor

This study presents a novel in situ high-temperature fiber optic Raman probe that enables the study of the physical properties and structure of molten samples at temperatures up to 1400 °C. To demonstrate the functionality of the high-temperature fiber optic Raman probe, different composition mold fluxes were evaluated in this report. The Raman spectra at flux molten temperature were successfully collected and analyzed. A deconvolution algorithm was employed to identify peaks in the spectra associated with the molecular structure of the components in each sample. Here, the experimental results demonstrate that the composition-dependent Raman signal shift can be detected at high temperatures, indicating that molten materials analysis using a high-temperature Raman system shows significant promise. This flexible and reliable high-temperature Raman measurement method has great potential for various applications, such as materials development, composition and structure monitoring during high-temperature processing, chemical identification, and process monitoring in industrial production.

47 OTHER INSTRUMENTATION↗
DOE OSTI2020

Identifying Characteristics of Wildfire Towers and Troughs

Wildfire behavior is dictated by the complex interaction of numerous physical phenomena including dynamic ambient and fire-induced winds, heat transfer, aerodynamic drag on the wind by the fuel and combustion. These phenomena create complex feedback effects between the fire and its surroundings. In this study, we aim to study the mechanisms by which buoyant flame dynamics along with vortical motions and instabilities control wildfire propagation. Specifically, this study employs a suite of simulations conducted with the physics-based coupled fire-atmosphere behavior model (FIRETEC). The simulations are initialized with a fire line and the fires are allowed to propagate on a grass bed, where the fuel heights and wind conditions are varied systematically. Flow variables are extracted to identify the characteristics of the alternating counter-rotational vortices, called towers and troughs, that drive convective heat transfer and fire spread. These vortices have previously been observed in wildfires and laboratory fires, and have also been observed to arise spontaneously in FIRETEC due to the fundamental physics incorporated in the model. However, these past observations have been qualitative in nature and no quantitative studies can be found in the literature which connected these coherent structures fundamental to fire behavior with the constitutive flow variables. To that end, a variety of state variables are examined in the context of these coherent structures under various wind profile and grass height conditions. Identification of various correlated signatures and fire-atmosphere feedbacks in simulations provides a hypothesis that can be tested in future observational or experimental efforts, potentially assisting experimental design, and can aid in the interpretation of data from in situ detectors.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Restructuring and integrity of molecular catalysts in electrochemical CO 2 reduction

Electrocatalysts that start a reaction as molecules do not always end the reaction as molecules, and even when they do, they might not be molecules during catalysis. In this Perspective, we discuss knowledge learned from the study of Cu-based molecularly structured electrocatalysts––including metal coordination complexes, metal-organic frameworks, single-atom catalysts, and polymeric materials––that restructure under electrochemical CO 2 reduction reactions. Recent reports are summarized with an emphasis on the nature and significance of post-mortem and in situ characterization for the proper identification of active sites. We demonstrate that molecular and material structures determine whether electrocatalysts restructure and how they restructure, that understanding of restructuring processes can help us identify active sites for catalysis, and that this knowledge can be leveraged to design precatalysts that generate highly active catalysts under reaction conditions. In addition, we provide recommended practices for studying the integrity of heterogeneous molecular catalysts during and after CO 2 reduction reactions.

CO2 reduction↗
DOE OSTI2022

Cryo-electron Microscopy of Adeno-associated Virus

Adeno-associated virus (AAV) has a single-stranded DNA genome encapsidated in a small icosahedrally symmetric protein shell with 60 subunits. AAV is the leading delivery vector in emerging gene therapy treatments for inherited disorders, so its structure and molecular interactions with human hosts are of intense interest. A wide array of electron microscopic approaches have been used to visualize the virus and its complexes, depending on the scientific question, technology available, and amenability of the sample. Approaches range from subvolume tomographic analyses of complexes with large and flexible host proteins to detailed analysis of atomic interactions within the virus and with small ligands at resolutions as high as 1.6 Å. Analyses have led to the reclassification of glycan receptors as attachment factors, to structures with a new-found receptor protein, to identification of the epitopes of antibodies, and a new understanding of possible neutralization mechanisms. AAV is now well-enough characterized that it has also become a model system for EM methods development. Heralding a new era, cryo-EM is now also being deployed as an analytic tool in the process development and production quality control of high value pharmaceutical biologics, namely AAV vectors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

𝛽 decay of 36 Mg and 36 Al: Identification of a 𝛽-decaying isomer in 36 Al

The level structure of 36 Al has been studied via 𝛽 decay of 36 Mg at the Facility for Rare Isotope Beams (FRIB) and the National Superconducting Cyclotron Laboratory (NSCL). A long-lived isomer in 36 Al was identified which decays by 𝛽 to an excited state of 36 Si. The ground state and the isomeric state of 36 Al were found to populate different energy levels of 36 Si. Furthermore, the results from the two data sets in the present work complement each other. Configuration interaction calculations performed with the FSU shell-model Hamiltonians provide reasonable descriptions to the experimental observations and offer insight into future improvements of the theoretical interpretation.

20 ≤ A ≤ 38↗
DOE OSTI2026

Multiscale Cryo Electron Microscopy Reveals Interfacial Degradation and Stabilization in Battery Electrodes

Electrochemical interfaces are dynamic systems, evolving based on their local environment and reactant surface structures. The electrode-electrolyte interface in Li-ion batteries can be protective, limiting parasitic reactions with the electrolyte to passivate the surface [1]. Additionally, this interphase has an impact on the Li-ion transport through that layer based on its composition, bonding environment, and thickness. These parameters are challenging to collect and may vary depending on the electrode surface site investigated relative to its spatial position in a coin cell. This study will detail a multiscale cryogenic electron microscopy approach where millimeter-scale cross-sections through the coin cell batteries were made using a cryogenic stage within a fs-laser plasma focused ion beam (laser PFIB) with complementary energy dispersive X-ray spectroscopy able to detect variations in the composition at electrode interfaces [2]. Microscale cross-sectioning and lamella sample preparation of battery electrodes was conducted at the Center for Integrated Nanotechnologies using a Ga-ion focused ion beam (FIB) with air-free and cryo-transfer [3], followed by nanoscale mapping of composition and bonding within the CEI through cryo-scanning transmission electron microscopy (cryo-STEM) electron energy loss spectroscopy [4]. This multiscale approach enabled identification of millimeter-scale features of a battery stack with visualization of degradation in electrodes such as cracks in cathode particles, gas evolution, and SEI evolution; microscale interfacial characteristics, such as heterogeneity in the SEI or barrier layer and identification of electrolyte networks to the electrode surfaces; and nanoscale measurement of the CEI thickness, mapping of transition metal bonding within the cathode particles to identify loss of active materials, and identification of beneficial electrolyte additives incorporated into the CEI structure. This multiscale approach allows for a statistical understanding of the primary mechanisms and parasitic degradation pathways that impact performance by limiting the ion transport pathways within Li+ batteries.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Rietveld Refinement for Macromolecular Powder Diffraction

Powder X-ray diffraction (PXRD) has been employed extensively for the structural characterization of materials, quantitative analysis of multicomponent mixtures, phase identification, texture, and microstructural analysis. At the heart of all those lies the Rietveld method, which has revolutionized the use of powder diffraction for materials studies. Initially applied to minerals and inorganics, the Rietveld method has progressively been used for more complex materials, for instance, zeolites and pharmaceuticals. A major advance of the method came some 20 years ago, when the first protein structure was successfully refined. Because of the sheer complexity of macromolecules, several new approaches and algorithms had to be pioneered or adapted from macromolecular single-crystal diffraction experiments, thus constituting macromolecular PXRD a quite unique field of study. This review aims to provide necessary elements of theory and application of structure solution and refinement via the Rietveld method for macromolecular PXRD data. Here, practical explanations and highlighted case studies are also presented.

36 MATERIALS SCIENCE↗
DOE OSTI2025

A Model Based Approach to Extract Health Information from Textual Data

In current nuclear power plants (NPPs) a large amount of condition-based data is being generated and stored to assess and monitor component health and performance. The format of this data can be either numeric (e.g., pump vibration data) or textual (e.g., condition report which assess component health). While assessing component health from numeric data can be performed with a large variety of methods, the extraction of information from textual data still remains a challenge. Natural language processing (NLP) methods are starting to be deployed in current NPPs mainly to filter out incident reports (IRs) that are not safety related by employing supervised machine learning methods. However, these methods do not really provide the quantitative information that might be contained in IRs. This paper presents an approach to extract information from textual data (e.g., from IRs, maintenance reports) that is based on NLP data analytics methods coupled with model-based system engineer (MBSE) models. NLP methods are employed to perform syntactic and semantic analyses. Syntactic analysis analyzes the grammatical structure of a sentence; such analysis includes: part of speech (POS) tagging (i.e., identification of grammatic elements of each string - e.g., nouns, verbs), named entity recognition (i.e., identification of text entities - e.g., names, dates, events), and relation extraction (e.g., coreference resolution). On the other hand, semantic analysis is designed to analyze the logic structure of a sentence. Through a specific set of rules, our methods can identify whether a sentence contains health information of a component (e.g., degraded performance, anomaly behavior) or the causal relationship between two events (i.e., a cause-effect pair). An innovative element of our approach is that semantic analysis relies on MBSE models to identify links between textual elements. MBSE are diagrams designed to represent system and component dependencies (from both a form and functional point of view). In our approach, MBSE models emulate system engineer knowledge about component/system architecture. This paper presents in detail how the integration of NLP methods and MBSE models is performed. Few analysis examples focusing on centrifugal pumps are presented.

97 - MATHEMATICS AND COMPUTING↗
DOE OSTI2026

Deep generative learning of magnetic frustration in artificial spin ice from magnetic force microscopy images

Increasingly large datasets of microscopic images with nanoscale resolution facilitate the development of machine learning methods to identify and analyze subtle physical phenomena embedded within the images. In this work, microscopic images of honeycomb lattice spin-ice samples serve as datasets from which we automate the calculation of net magnetic moments and directional orientations of spin-ice configurations. In the first stage of our workflow, machine learning models are trained to accurately predict magnetic moments and directions within spin-ice structures. Variational Autoencoders (VAEs), an emergent unsupervised deep learning technique, are employed to generate high-quality synthetic magnetic force microscopy (MFM) images and extract latent feature representations, thereby reducing experimental and segmentation errors. The second stage of proposed methodology enables precise identification and prediction of frustrated vertices and nanomagnetic segments, effectively correlating structural and functional aspects of microscopic images. This facilitates the design of optimized spin-ice configurations with controlled frustration patterns, enabling potential on-demand synthesis.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Protein remote homology detection and structural alignment using deep learning

Exploiting sequence–structure–function relationships in biotechnology requires improved methods for aligning proteins that have low sequence similarity to previously annotated proteins. We develop two deep learning methods to address this gap, TM-Vec and DeepBLAST. TM-Vec allows searching for structure–structure similarities in large sequence databases. It is trained to accurately predict TM-scores as a metric of structural similarity directly from sequence pairs without the need for intermediate computation or solution of structures. Once structurally similar proteins have been identified, DeepBLAST can structurally align proteins using only sequence information by identifying structurally homologous regions between proteins. It outperforms traditional sequence alignment methods and performs similarly to structure-based alignment methods. We show the merits of TM-Vec and DeepBLAST on a variety of datasets, including better identification of remotely homologous proteins compared with state-of-the-art sequence alignment and structure prediction methods.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Automating Discovery of Physics-Informed Neural State Space Models via Learning and Evolution

Recent works exploring deep learning application to dynamical systems modeling have demonstrated that embedding physical priors into neural networks can yield more effective, physically-realistic, and data-efficient models. However, in the absence of complete prior knowledge of a dynamical system's physical characteristics, determining the optimal structure and optimization strategy for these models can be difficult. In this work, we explore methods for discovering neural state space dynamics models for system identification. Starting with a design space of block-oriented state space models and structured linear maps with strong physical priors, we encode these components into a model genome alongside network structure, penalty constraints, and optimization hyperparameters. Demonstrating the overall utility of the design space, we employ an asynchronous genetic search algorithm that alternates between model selection and optimization and obtains accurate physically consistent models of three physical systems: an aerodynamics body, a continuous stirred tank reactor, and a two tank interacting system.

genetic algorithms, neural architecture search, ne↗
DOE OSTI2020

Filament-induced breakdown spectroscopy with structured beams

Filament-induced ablation represents an attractive scheme for long-range material identification via optical spectroscopy. However, the delivery of laser energy to the target can be severely hindered by the stochastic nature of multiple-filamentation, ionization of ambient gas, and atmospheric turbulence. In order to mitigate some of these adverse effects, we examine the utility of beam shaping for femtosecond filament-induced breakdown spectroscopy with Gaussian and structured (Laguerre-Gaussian, Airy, and Bessel-Gaussian) beams in the nonlinear regime. Interaction of filaments with copper, zinc, and brass targets was studied by recording axially-resolved broadband emission from the filament-induced plasma. The laser-solid coupling efficacy was assessed by inferring thermodynamic parameters such as excitation temperature and electron density. While under our experimental conditions the ablation rate with Gaussian- and Laguerre-Gaussian beams is found to be similar, the Airy and Bessel-Gaussian beams offer the advantage of longitudinally extended working zones. These results provide insights into potential benefits of structuring ultrafast laser beams for standoff sensing applications.

47 OTHER INSTRUMENTATION↗
DOE OSTI2025

De novo design of D-peptide ligands: Application to influenza virus hemagglutinin

D-peptides hold great promise as therapeutics by alleviating the challenges of metabolic stability and immunogenicity in L-peptides. However, current D-peptide discovery methods are severely limited by specific size, structure, and the chemical synthesizability of their protein targets. Here, we describe a computational method for de novo design of D-peptides that bind to an epitope of interest on the target protein using Rosetta’s hotspot-centric approach. The approach comprises identifying hotspot sidechains in a functional protein–protein interaction and grafting these side chains onto much smaller structured peptide scaffolds of opposite chirality. The approach enables more facile design of D-peptides and its applicability is demonstrated by design of D-peptidic binders of influenza A virus hemagglutinin, resulting in identification of multiple D-peptide lead series. The X-ray structure of one of the leads at 2.38 Å resolution verifies the validity of the approach. This method should be generally applicable to targets with detailed structural information, independent of molecular size, and accelerate development of stable, peptide-based therapeutics.

Science & Technology - Other Topics↗
DOE OSTI2023

On the relation between the subadditivity cone and the quantum entropy cone

Given a multipartite quantum system, what are the possible ways to impose mutual independence among some subsystems, and the presence of correlations among others, such that there exists a quantum state which satisfies these demands? This question and the related notion of a pattern of marginal independence (PMI) were introduced in [1], and then argued in [2] to be central in the derivation of the holographic entropy cone. Here we continue the general information theoretic analysis of the PMIs allowed by strong subadditivity (SSA) initiated in [1]. We show how the computation of these PMIs simplifies when SSA is replaced by a weaker constraint, dubbed Klein’s condition (KC), which follows from the necessary condition for the saturation of subadditivity (SA). Formulating KC in the language of partially ordered sets, we show that the set of PMIs compatible with KC forms a lattice, and we investigate several of its structural properties. One of our main results is the identification of a specific lower dimensional face of the SA cone that contains on its boundary all the extreme rays (beyond Bell pairs) that can possibly be realized by quantum states. We verify that for four or more parties, KC is strictly weaker than SSA, but nonetheless the PMIs compatible with SSA can easily be derived from the KC-compatible ones. For the special case of 1-dimensional PMIs, we conjecture that KC and SSA are in fact equivalent. To make the presentation self-contained, we review the key ingredients from lattice theory as needed.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2025

A Robust Data-Driven Approach for Mechanical Serial Sectioning

Mechanical serial sectioning (MSS) provides detailed microstructural information across large length scales. By repeatedly removing thin layers of material and imaging the exposed surface, a 3D representation of a specimen’s internal structure can be constructed, enabling failure analysis and feature identification that are otherwise inaccessible via conventional 2D or nondestructive evaluation techniques. Achieving consistent and accurate material removal can be challenging due to system variability, requiring an experienced operator to manually adjust parameters, prolonging data collection times and necessitating post-processing routines to standardize the data. Here, to address these challenges, this paper presents the employment of a one-step model predictive control (MPC) framework tailored to a run-to-run (R2R) controller. The R2R-MPC controller automates the parameter selection process, improving the consistency of material removal through iterative feedback for disturbance rejection and accurate tracking of the target removal rate. Using a data-driven approach, the controller robustly adapts to changing material characteristics. The effectiveness of the R2R-MPC controller is demonstrated through simulation and experimental results and compared to previous data collection procedures.

3D Materials Science↗
DOE OSTI2026

Higher-order LaSDI: Reduced order modeling with multiple time derivatives

Solving complex partial differential equations (PDEs) is essential across scientific disciplines but often requires numerical models that can be prohibitively expensive in time-sensitive applications. Reduced-order models (ROMs) address this challenge by exploiting low-dimensional structure to create fast approximations. The Latent Space Dynamics Identification (LaSDI) framework has demonstrated success in learning ROMs for parameterized PDE families, but remains limited to first-order systems. Here, in this paper, we propose Higher-Order LaSDI (HLaSDI), which extends the LaSDI framework to PDEs with arbitrary order of time derivatives. This generalization significantly expands the applicability of LaSDI-based methods to systems previously outside their scope, including hyperbolic PDEs. We demonstrate HLaSDI’s accuracy and efficiency on several linear and nonlinear benchmark problems.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2026

SMEFT ATLAS: The landscape beyond the Standard Model

The Standard Model Effective Field Theory (SMEFT) based on the unbroken gauge group SU(3) 𝐶 ⊗SU(2) 𝐿 ⊗U(1) 𝑌 and containing only particles of the Standard Model (SM) has developed in the last decade to a mature field. It is the framework to be used in the energy gap from scales sufficiently higher than the electroweak scale up to the lowest energy scale at which new particles show up. We summarize the present status of this theory with a particular emphasize on its role in the indirect search for new physics (NP). While flavour physics of both quarks and leptons is the main topic of our review, we also discuss electric dipole moments, anomalous magnetic moments (𝑔−2) 𝜇,𝑒 , 𝑍-pole observables, Higgs observables and high-𝑝𝑇 scattering processes within the SMEFT. We group the observables into ten classes and list for each class the most relevant operators and the corresponding renormalization group equations (RGEs). We exhibit the correlations between different classes implied both by the operator mixing and the SU(2) 𝐿 gauge symmetry. Our main goal is to provide an insight into the complicated operator structure of this framework which hopefully will facilitate the identification of valid ultraviolet completions behind possible anomalies observed in future data. Numerous colourful charts, and 85 tables, while representing rather complicated RG evolution from the NP scale down to the electroweak scale, beautify the involved SMEFT landscape. Over 1000 references to the literature underline the importance and the popularity of this field. We discuss both top-down and bottom-up approaches as well as their interplay. This allows us eventually to present an atlas of different landscapes beyond the SM that includes heavy gauge bosons and scalars, vector-like quarks and leptons and leptoquarks.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗