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Results for “structural alignment”

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 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

SIMILE enables alignment of tandem mass spectra with statistical significance

Abstract Interrelating small molecules according to their aligned fragmentation spectra is central to tandem mass spectrometry-based untargeted metabolomics. Current alignment algorithms do not provide statistical significance and compounds that have multiple delocalized structural differences and therefore often fail to have their fragment ions aligned. Here we align fragmentation spectra with both statistical significance and allowance for multiple chemical differences using Significant Interrelation of MS/MS Ions via Laplacian Embedding (SIMILE). SIMILE yields spectral alignment inferred structural connections in molecular networks that are not found with cosine-based scoring algorithms. In addition, it is now possible to rank spectral alignments based on p-values in the exploration of structural relationships between compounds and enhance the chemical connectivity that can be obtained with molecular networking.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Confronting Large‐Eddy Simulations With Stereo Camera Data by Means of Reconstructed Hemispheric Cloud Size Distributions

High-resolution hemispheric camera images at a meteorological site in western Germany are used to analyze the multi-dimensional spatial characteristics of continental cumulus cloud fields, and to evaluate Large-Eddy Simulations on this aspect. Traditional non-hemispheric cloud-detecting instruments provide additional reference data. The main model-observation comparison focuses on cloud size distributions (CSDs), employing two methods: (a) directly using three-dimensional model fields, direct CSDs, and (b) using rendered hemispheric images of the model fields as produced by a camera simulator based on path-tracing. In the latter method, both the real and rendered images are used to three-dimensionally reconstruct the cloud fields, yielding hemispheric CSDs. Advantages of hemispheric comparisons over more classic approaches include (a) fair comparisons between model and data, and (b) full use of the enhanced resolutions and hemispheric spatial coverage of the camera imagery. Basic evaluation of the simulations demonstrates good agreement on thermodynamic structure and its diurnal cycle. Cloud heights and cloud cover are intercompared between the model, camera data and other instrumentation, providing insight into their structural differences. A consistent alignment is found between the hemispheric CSDs from both the model and the cameras. Power law fits reveal structurally lower exponents in hemispheric CSDs compared to non-hemispheric CSDs, which particularly caution against directly comparing hemispheric CSDs to non-hemispheric distributions. This result is robust for sample size and fitting method. These findings inform future use of hemispheric camera systems for studying cumulus cloud field morphology and model evaluation.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Massless and massive photons within basis light-front quantization

We compute the structure function, transverse momentum dependent parton distributions (TMDs), and generalized parton distributions (GPDs) for the photon from the light-front quantum electrodynamics (QED) Hamiltonian, determined for its constituent bare photon and electron-positron Fock components within the basis light-front quantization framework. While the structure function and GPDs align well with expectations, some oscillatory behavior in the TMDs emerges as a finite-basis artifact. We also compute the GPD and the corresponding structure function for the longitudinal polarization mode of the massive photon. We further study the photon mass dependence of the calculated observables. After performing nonperturbative renormalization, we obtain a good quality description of the perturbative QED properties of the photon, as well as good agreement with the experimental data for the massless photon’s structure function.

Ab initio calculations↗
DOE OSTI2021

MULTICOM2 open-source protein structure prediction system powered by deep learning and distance prediction

Protein structure prediction is an important problem in bioinformatics and has been studied for decades. However, there are still few open-source comprehensive protein structure prediction packages publicly available in the field. In this paper, we present our latest open-source protein tertiary structure prediction system—MULTICOM2, an integration of template-based modeling (TBM) and template-free modeling (FM) methods. The template-based modeling uses sequence alignment tools with deep multiple sequence alignments to search for structural templates, which are much faster and more accurate than MULTICOM1. The template-free (ab initio or de novo) modeling uses the inter-residue distances predicted by DeepDist to reconstruct tertiary structure models without using any known structure as template. In the blind CASP14 experiment, the average TM-score of the models predicted by our server predictor based on the MULTICOM2 system is 0.720 for 58 TBM (regular) domains and 0.514 for 38 FM and FM/TBM (hard) domains, indicating that MULTICOM2 is capable of predicting good tertiary structures across the board. It can predict the correct fold for 76 CASP14 domains (95% regular domains and 55% hard domains) if only one prediction is made for a domain. The success rate is increased to 3% for both regular and hard domains if five predictions are made per domain. Moreover, the prediction accuracy of the pure template-free structure modeling method on both TBM and FM targets is very close to the combination of template-based and template-free modeling methods. This demonstrates that the distance-based template-free modeling method powered by deep learning can largely replace the traditional template-based modeling method even on TBM targets that TBM methods used to dominate and therefore provides a uniform structure modeling approach to any protein. Finally, on the 38 CASP14 FM and FM/TBM hard domains, MULTICOM2 server predictors (MULTICOM-HYBRID, MULTICOM-DEEP, MULTICOM-DIST) were ranked among the top 20 automated server predictors in the CASP14 experiment. After combining multiple predictors from the same research group as one entry, MULTICOM-HYBRID was ranked no. 5. The source code of MULTICOM2 is freely available at https://github.com/multicom-toolbox/multicom/tree/multicom_v2.0 .

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Modularization of Ceramic Hollow Fiber Membrane Technology for Air Separation

This proposed project is aimed at studying high performance and economically competitive ceramic membrane technology for air separation and high-purity oxygen production using hollow fiber ceramic membrane stack and module technology. The design of the single permeate membrane is a hollow fiber substrate-supported thin tri-layer structure. Radially well-aligned micro-channels are embedded in the thick substrate and open at the inner surface of the substrate, enabling facile air/gas diffusion. The tri-layer structure of thin dense membrane layer (~ 10 µm) sandwiched by porous surface layer on either side is then built on the substrate using advanced fabrication process. The tri-layer structure design allows different materials to be used in different layers, where the materials of surface layers have high surface exchange coefficients while the material of dense layer has high bulk diffusivity. Such a synergetic combination leads to high permeation performance. The focus of the proposed project will be on membrane stack/module development using the developed single hollow fiber membranes, including: 1) fabrication and characterization of novel single hollow fiber membranes; 2) membrane stack design and assembly using fabricated single membranes; 3) stack modeling and analysis to guide membrane stack designs; 4) permeation performance testing and characterization of membrane stacks. The hollow fiber feature and simple sealing requirement enable very compact design of membrane stacks, which have excellent flexibility for further modularizations at different scales. The operations of such membrane stack and module may employ the exhaust heat from other components of Integrated Gasification Combined Cycle and oxy-combustion systems. Therefore, modularization of such an air separation membrane technology can be incorporated into the DOE’s REMS (radically engineered modular systems)-gasification skid and support the oxidant feed of an oxygen-blown REMS gasifier scaled to different ranges.

01 COAL, LIGNITE, AND PEAT↗
DOE OSTI2023

Electronic, magnetic, and structural properties of NiFeMnAl

Abstract Half-metallic Heusler compounds have been extensively studied in the recent years, both experimentally and theoretically, for potential applications in spin-based electronics. Here, we present the results of a combined theoretical and experimental study of the quaternary Heusler compound NiFeMnAl. Our calculations indicate that this material is half-metallic in the ground state and maintains its half-metallic electronic structure under a considerable range of external hydrostatic pressure and biaxial strain. NiFeMnAl crystallizes in the regular cubic Heusler structure, and exhibits ferromagnetic alignment. The practical feasibility of the proposed system is confirmed in the experimental section of this work. More specifically, a bulk ingot of NiFeMnAl was synthesized in A2 type disordered cubic structure using arc melting. It shows a high Curie temperature of about 468 K and a saturation magnetization of 2.3 μ B / f .u . The measured magnetization value is smaller than the one calculated for the ordered structure. This discrepancy is likely due to the A2 type atomic disorder, as demonstrated by our calculations. We hope that the presented results may be useful for researchers working on practical applications of spin-based electronics.

Physics↗
DOE OSTI2024

Extended interaction length laser-driven acceleration in a tunable dielectric structure

The development of long, tunable structures is critical to increasing energy gain in laser-driven dielectric accelerators (DLAs). Here we combine pulse-front-tilt illumination with slab-geometry structures assembled by precisely aligning off-the-shelf 4 mm long transmission gratings to achieve up to 200 keV energy modulation for 6 MeV injected electrons. The effective interaction length is longer than 1 mm, limited by the dephasing of the accelerated particles in the structure. The piezo-based independent mounting system for the gratings allows tuning of the gap and field distribution inside the structure. Published by the American Physical Society 2024

43 PARTICLE ACCELERATORS↗
DOE OSTI2021

Defect-free-induced Na + disordering in electrode materials

For reaching high-performance of electrode materials, it is generally believed that understanding the structure evolution and heterogeneous alignment effect is the key. Presently, a very simple and universally applicable self-healing method is investigated to prepare defect-free Prussian blue analogs (PBAs) that reach their theoretical capacity as cathode materials for sodium-ion batteries (SIBs). For direct imaging of the local structure and the dynamic process at the atomic scale, we deliver a fast ion-conductive nickel-based PBA that enables rapid Na + extraction/insertion within 3 minutes and a capacity retention of nearly 100% over 4000 cycles. This guest-ion disordered and quasi-zero-strain nonequilibrium solid–solution reaction mechanism provides an effective guarantee for realizing long-cycle life and high-rate capability electrode materials that operate via reversible two-phase transition reaction. Unconventional materials and mechanisms that enable reversible insertion/extraction of ions in low-cost metal–organic frameworks (MOFs) within minutes have implications for fast-charging devices, grid-scale energy storage applications, material discovery, and tailored modification.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Ultrastrong Ionotronic Films Showing Electrochemical Osmotic Actuation

Abstract A multifunctional soft material with high ionic and electrical conductivity, combined with high mechanical properties and the ability to change shape can enable bioinspired responsive devices and systems. The incorporation of all these characteristics in a single material is very challenging, as the improvement of one property tends to reduce other properties. Here, a nanocomposite film based on charged, high‐aspect‐ratio 1D flexible nanocellulose fibrils, and 2D Ti 3 C 2 T x MXene is presented. The self‐assembly process results in a stratified structure with the nanoparticles aligned in‐plane, providing high ionotronic conductivity and mechanical strength, as well as large water uptake. In hydrogel form with 20 wt% liquid, the electrical conductivity is over 200 S cm −1 and the in‐plane tensile strength is close to 100 MPa. This multifunctional performance results from the uniquely layered composite structure at nano‐ and mesoscales. A new type of electrical soft actuator is assembled where voltage as low as ±1 V resulted in osmotic effects and giant reversible out‐of‐plane swelling, reaching 85% strain.

Chemistry↗
DOE OSTI2020

Machine Learning Approaches for Nuclear Material Accounting Data from Irradiation and Reprocessing

We are currently exploring data analysis methods for their ability to strengthen the synthesis and evaluation of information generated within domestic and international safeguard regimes. Safeguard data typically includes rich heterogenous datasets amenable to advanced data analytics methods, such as machine learning. We have converted transactional data containing both numerical and categorical attributes from a domestic nuclear material control and accountability (NMC&A) system into a low-dimensional numerical structure via linear principal component analysis. This data representation allows for global structure discovery via cluster analysis, which can characterize the typical behavior of each of the primary types of transaction events. Furthermore, the structure of the top principal components captures the “typical behavior” of the data and is thus amenable to anomaly detection through statistical hypothesis testing. We explored this capability by generating erroneous permutations of the data and computing the Q-residual quantity increase associated with the information loss when these data are projected into the low-dimensional principal component analysis space representative of typical transactions.Future work will focus on identifying data transformations (e.g., graph networks) that more closely align with the inherent structure of these transactions to explain more salient information and disambiguate the underlying nuclear process—in this case, irradiation and reprocessing—from artifacts of NMC&A system transactional record keeping data.

Drescher, Adam↗
DOE OSTI2025

Structure of the Ecuadorian Upper Plate From a Joint Seismic‐Gravity Inversion

The Ecuadorian portion of the South American subduction zone presents an interesting case study in the structure and complex evolution of an upper plate. There are outstanding questions about its tectonic history, composition, and magmatic processes. While previous studies have employed ambient noise tomography to image the Ecuadorian upper plate, surface wave inversions alone often lack sensitivity at relevant shallow depths. This limitation can be overcome with an independent, complementary data set, such as gravity. We have jointly inverted Rayleigh wave phase velocities and Bouguer gravity anomalies to provide a more detailed seismic velocity model of the Ecuadorian upper plate. Our joint inversion has yielded several key improvements from previous models. First, we observe much shallower slow velocities beneath major basins (the Manabí, Progreso, and Gulf of Guayaquil), better aligning with expected basin structure. Second, we identify a high-velocity block beneath the entire forearc, corresponding to the Piñon Terrane, with velocities suggesting the presence of ultramafic material. Third, we highlight a new narrow swath of slow velocities beneath the Ecuadorian Andes, which closely follows the active volcanoes along the Eastern Cordillera. The extent of these slow velocities coincides with the termination of active arc volcanism and the predicted location of the subducted Carnegie Ridge. The predicted compositions for the mid to lower crust in the region preclude a purely compositional explanation for these velocities, suggesting that some level of partial melt is necessary.

Birkey, Andrew [Univ. of Delaware, Newark, DE (Uni↗
DOE OSTI2023

Transforming layered 2D mats into multiphasic 3D nanofiber scaffolds with tailored gradient features for tissue regeneration

Abstract Multiphasic scaffolds with tailored gradient features hold significant promise for tissue regeneration applications. Herein, this work reports the transformation of two‐dimensional (2D) layered fiber mats into three‐dimensional (3D) multiphasic scaffolds using a ‘solids‐of‐revolution’ inspired gas‐foaming expansion technology. These scaffolds feature precise control over fiber alignment, pore size, and regional structure. Manipulating nanofiber mat layers and Pluronic F127 concentrations allows further customization of pore size and fiber alignment within different scaffold regions. The cellular response to multiphasic scaffolds demonstrates that the number of cells migrated and proliferated onto the scaffolds is mainly dependent on the pore size rather than fiber alignment. In vivo subcutaneous implantation of multiphasic scaffolds to rats reveals substantial cell infiltration, neo tissue formation, collagen deposition, and new vessel formation within scaffolds, greatly surpassing the capabilities of traditional nanofiber mats. Histological examination indicates the importance of optimizing pore size and fiber alignment for the promotion of cell infiltration and tissue regeneration. Overall, these scaffolds have potential applications in tissue modeling, studying tissue‐tissue interactions, interface tissue engineering, and high‐throughput screening for optimized tissue regeneration.

Shahriar, S. M. Shatil↗
DOE OSTI2021

Plastic deformation mechanism of calcium-silicate hydrates determined by deviatoric-stress Raman spectroscopy

Highlights: • C-(A-)S-H samples under stress were characterized at the bond and grain level. • Small angle scattering showed that 720 MPa reduced grain thickness by 30%. • In-situ Raman showed that cross-linked C-A-S-H slips along its intralayer. • However, in-situ Raman showed that C-S-H slips along the interlayer. • In-situ Raman also showed a growth in CaCO{sub 3}, indicating fracture in both samples. Creep of the cement matrix affects the structural stability of concrete. In Portland cements, the creep is largely controlled by the binding phase calcium-(aluminum-)silicate-hydrate, or C-(A-)S-H. This phase has a lamellar structure and under deviatoric stress aligns its c-axis with the principal stress. However, the limiting resistance to this reorientation is unknown at the nanocrystalline level. Small-angle X-ray scattering shows that the lamellae thickness decreases under 100's MPa deviatoric stress. Deviatoric stress Raman spectroscopy shows that there are two ways that this break-up can occur. If the material's silicate chains are cross-linked, then strain in SiO bonds does not increase above certain stresses, indicating a relaxation adjacent to the SiO bond. If the chains are not cross-linked, then the silicate chains are broken up by rastering against each other, introducing defects. These results show that the plastic deformation of C-(A-)S-H is relevant for Portland cement creep.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Vacancy-tuned magnetism in LaMn x Sb 2

The layered AMP 2 (A = alkali-earth or rare-earth atom, M = transition metal, P = Sb, Bi) compounds are widely studied for their rich magnetism and electronic structure topology. We provide a detailed characterization of the magnetic and transport properties of LaMn x Sb 2 , an understudied member of the AMP 2 family. LaMn x Sb 2 forms with intrinsic Mn vacancies, and we demonstrate that by varying the starting ratio of La, Mn, and Sb, we can synthetically control the Mn occupancy and produce single crystals with x = 0.74 – 0.97. Magnetization and transport measurements indicate LaMn x Sb 2 has a rich temperature-composition (T–x) magnetic phase diagram with physical properties strongly influenced by the Mn occupancy. LaMn x Sb 2 orders antiferromagnetically at T 1 = 130–180 K, where T 1 increases with x. Below T 1 , the T–x phase diagram is complicated. At high x, there is a second transition T 2 that decreases in temperature as x is lowered, vanishing below x ≤ 0.85. A third, first-order, transition T 3 is detected at x ≈ 0.92, and the transition temperature increases as x is lowered, crossing above T 2 near x ≈ 0.9. On moving below x < 0.79, here we find the crystal structure changes from the P 4/nmm arrangement to an I$\bar{4}$2m structure with partially ordered Mn vacancies. The change in crystal structure results in the sudden appearance of two new low-temperature phases and a crossover between regimes of negative and positive magnetoresistance when x ≤ 0.78. Finally, we provide powder neutron diffraction for x = 0.93, and find that the high-x compositions first adopt a G-type antiferromagnetic structure with the Mn moments aligned within the ab plane, which is followed upon further cooling by a second transition to a different, noncollinear structure where the moments are rotated within the basal plane. Our results demonstrate that LaMn x Sb 2 is a highly tunable material with six unique magnetically ordered phases, depending on T and x.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

ppdx : Automated modeling of protein–protein interaction descriptors for use with machine learning

This paper describes ppdx, a python workflow tool that combines protein sequence alignment, homology modeling, and structural refinement, to compute a broad array of descriptors for characterizing protein–protein interactions. The descriptors can be used to predict various properties of interest, such as protein–protein binding affinities, or inhibitory concentrations (IC 50 ), using approaches that range from simple regression to more complex machine learning models. The software is highly modular. It supports different protocols for generating structures, and 95 descriptors can be currently computed. More protocols and descriptors can be easily added. The implementation is highly parallel and can fully exploit the available cores in a single workstation, or multiple nodes on a supercomputer, allowing many systems to be analyzed simultaneously. As an illustrative application, ppdx is used to parametrize a model that predicts the IC 50 of a set of antigens and a class of antibodies directed to the influenza hemagglutinin stalk.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Bilayer hybrid graphite anodes via freeze tape casting for extreme fast charging applications

Extreme fast charging (XFC) of lithium-ion batteries is critical for continuous market adoption of electric vehicles. However, mass transport limitations and sluggish kinetics lead to lithium plating in graphite anodes under fast charging conditions. One approach to address the mass transport limitation in graphite is to design low-tortuosity electrodes to enhance ionic transport. In this study, a bilayer hybrid structured electrode with directionally aligned channels was developed via freeze tape casting, which enables faster lithium ion diffusion through the graphite electrode. A scalable roll-to-roll process was designed in which slurry can be cast on any substrates for simple processing. Additionally, electrochemical impedance spectroscopy measurements indicated that the bilayer hybrid coating had both low tortuosity and short diffusion pathways, enabling XFC charging. Rate testing for the bilayer hybrid electrode indicated superior performance over the other coatings, exhibiting a ~20% improvement in the charge capacity compared with the conventional coating at 5C and 10 min total charging time. The bilayer hybrid electrode also demonstrated a 10% improvement in capacity retention compared with the conventional electrode after 1000 cycles at XFC conditions. This study demonstrates freeze tape casting as a scalable way to fabricate low-tortuosity electrodes for XFC applications.

25 ENERGY STORAGE↗
DOE OSTI2026

Fast solvers for tokamak fluid models with PETSc

Multigrid (MG) is widely recognized as a highly effective solver for the model problem, the Laplacian, but textbook MG fails on most problems of interest. MG methods have been applied to complex, real-world applications with careful consideration of the physical model and discretization. In this work we develop the first step in applying MG methods to science and engineering relevant magnetohydrodynamics (MHD) tokamak models in the M3D-C1 (https://m3dc1.pppl.gov) fusion energy science code. The semi-implicit time integrator in M3D-C1 is composed of many linear solves. The implicit advance of the momentum equation is the most challenging and is the focus of this work. The current production solver in M3D-C1 is a block Jacobi (BJ) preconditioner within a Krylov solver, where blocks group degrees of freedom on planes of constant toroidal coordinate. BJ convergence degrades as the number of planes increases due to the spectral properties of the matrix preconditioned with BJ. The partially magnetic field-aligned, regular toroidal grid structure in M3D-C1 is amenable to semi-coarsening geometric MG in the toroidal direction. This paper develops such a solver and demonstrates competitive performance on a runaway electron model of a SPARC (https://cfs.energy/technology/sparc) disruption, and superior robustness on a stellarator model on which the BJ solver fails to converge.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

Formation and growth of cerium (III) oxalate nanocrystals by liquid-cell transmission electron microscopy

Using rare earth elements as analogs for actinide series elements enables studying the chemistry of these radioactive materials without the inherent risks. A fundamental understanding of the nucleation and growth of actinide oxalates is crucial for processing nuclear waste. Using in-situ liquid cell TEM (LC-TEM), we show particle attachment processes occurring during the nucleation and growth of cerium oxalate. The early stages of the observed non-classical growth mechanisms have important implications for particle evolution and predictions of final particle morphology. In this work, we observed particle formation via monomer-by-monomer addition or the particle aggregation pathway depending on the selected precursor concentration. At the highest precursor concentration at a high dose rate, we observed particle alignment in a branch structure is due to the interfacial instability. It was demonstrated that in-situ LC-TEM is an invaluable tool in studying the cerium oxalate formation and ultimately a path to understanding actinide chemistry.

36 MATERIALS SCIENCE↗