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All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Understanding the Influence of Receptive Field and Network Complexity in Neural Network-Guided TEM Image Analysis

Abstract Trained neural networks are promising tools to analyze the ever-increasing amount of scientific image data, but it is unclear how to best customize these networks for the unique features in transmission electron micrographs. Here, we systematically examine how neural network architecture choices affect how neural networks segment, or pixel-wise separate, crystalline nanoparticles from amorphous background in transmission electron microscopy (TEM) images. We focus on decoupling the influence of receptive field, or the area of the input image that contributes to the output decision, from network complexity, which dictates the number of trainable parameters. For low-resolution TEM images which rely on amplitude contrast to distinguish nanoparticles from background, we find that the receptive field does not significantly influence segmentation performance. On the other hand, for high-resolution TEM images which rely on both amplitude and phase-contrast changes to identify nanoparticles, receptive field is an important parameter for increased performance, especially in images with minimal amplitude contrast. Rather than depending on atom or nanoparticle size, the ideal receptive field seems to be inversely correlated to the degree of nanoparticle contrast in the image. Our results provide insight and guidance as to how to adapt neural networks for applications with TEM datasets.

42 ENGINEERING↗
DOE OSTI2022

Monitoring of mechanical changes in a pipe assembly with complex geometry using multi-mode acoustic signals

Guided wave ultrasonic testing has been widely used for nondestructive and long-range evaluation of diverse mechanical structures, such as pipes and plates. In general, a large number of guided wave modes exist even in the simplest geometries, and they exhibit highly dispersive characteristics. Thus, sophisticated excitation methods and elaborate modal analyses need to be implemented to excite, acquire, and process well-defined pure modes as part of such a measurement method. If the interrogated structure has complex geometry, for example, with cross-sectional variations or multiple joints, the utilization of pure modes becomes significantly more difficult. To overcome this difficulty, this paper proposes the use of multi-mode, multi-frequency guided waves for long-range inspection of structures with arbitrarily complex geometries. Furthermore, using broadband chirp signals and multi-mode time–frequency analysis in a prototypical complex pipe assembly that includes multiple pipe diameters, elbows, and flange connections, we experimentally show sensitive detection of mechanical changes (both material addition and loss). In addition, we demonstrate that the complexity of the structure can be modeled in the digital domain with sufficient detail to allow accurate numerical simulation of the acoustic response using this method.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2019

Ligand Exchange/Scrambling Study of Gold(I)-Phosphine Complexes in the Solid Phase by DESI-MS Analysis

Only a few analytical techniques are available for the characterization of mechanochemical synthetic reaction products. We demonstrate here that DESI-MS is a powerful technique for this purpose, combining the selectivity of MS-based assays with the simplicity and in situ analysis capability of ambient ionization methods. In this work, we report that auranofin, a gold-based drug, and its precursor triethylphosphine gold(I) chloride undergo a complex array of ligand exchange/scrambling reactions with thiol-containing amino acids in the solid state. The products were readily characterized by DESI-MS analysis from the solid-phase reaction, clearly exhibiting ligand exchange and scrambling, with independent confirmation by solid state {sup 13}C-NMR. The thioglucose and triethylphosphine moieties exchanged with cysteine and its derivatives, whereas the glutathione replaced 2,3,4,6-tetra-O-acetyl-β-1-D-glucopyranose only. It was concluded that ligand exchange and scrambling reactions can be carried out in the solid state, and some of the unique products reported in this study can be conveniently prepared through mechanochemical synthesis in good yields (> 98%), as demonstrated by synthesis of (L-cysteinato-S)-triethylphosphine gold(I) from triethylphosphine gold(I) chloride and L-cysteine. .

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Novel data analysis method for obtaining better performance from a complex 3D-printed collimator

Additively manufactured scattered beam collimators are increasingly being employed to boost the sample to cell peak signal ratio in high pressure neutron diffraction studies because of manufacturing versatility and performance improvements. We study how the measured diffraction pattern is affected by the presence of a collimator downstream of the sample, and develop a novel protocol that provides more effective background rejection. This protocol takes into account critical performance-determinants that were identified in this study, namely: (i) effectively identifying the collimator pattern on the detector; (ii) understanding the dependence of this pattern on sample and cell composition; and (iii) accurately identifying and differentiating the different regions of the pattern on the detector based on the dependency of the cell or sample and finally (iv) resolving the intensities at regions of the detector where neutrons scattered from the sample are preferentially represented, in order to boost the sample to cell peak signal ratio. Application of this novel analysis protocol is shown to increase the collimator performance over the traditional method.

3D printing↗
DOE OSTI2025

Analysis of Bis(trifluoromethylsulfonyl)imide Interactions with Metal Cations Through a Chemical Informatics Approach

Nominally weakly coordinating anions are useful for modulating the solubility and chemical properties of metal complexes, but identification and analysis of the systematics of the interactions of anions with cationic metal complexes has not received the attention it deserves. Here, a chemical informatics approach is demonstrated for identifying and quantitatively analyzing the ways that the bis(trifluoromethylsulfonyl)imide anion (TFSI) can interact with metal-containing species. An open access computer program (PyCIFTer) was developed to facilitate large-scale structural analysis of TFSI-containing species by utilization of experimental atomic coordinate data from single-crystal X-ray diffraction (XRD) studies obtained from the Cambridge Structural Database (CSD). PyCIFTer establishes a three-dimensional vector space from the raw atomic coordinates, generating acyclic, undirected graphs that are used to rapidly analyze the structural properties (bond lengths and angles) of TFSI in individual structures in sequential/batch fashion. The structures are sorted by PyCIFTer into groups based on pre-set and chemically sensible criteria, affording a comprehensive and systematic view of TFSI structural chemistry. This approach avoids tedious one-at-a-time interrogation of structures, a prospect unreasonable in this case, and many others of contemporary chemical relevance; there were over 1500 structures in the CSD containing TFSI as of November 2024. The results demonstrate that TFSI only rarely binds to cations in the solid state, favoring the formation of species in which TFSI is found in cations’ outer coordination spheres. The prospect of applying PyCIFTer to other moieties is also discussed. PyCIFTer is also schematically compared to the commercial CSD Python application programming interface (API). Taken together, this work demonstrates the usefulness of modular workflows for sequential/batch analysis of structural data from XRD, an approach that appears poised to accelerate the translation of legacy structural results into new chemical insights and hypotheses.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Topological Data Analysis for Particulate Gels

Soft gels, formed via the self-assembly of particulate materials, exhibit intricate multiscale structures that provide them with flexibility and resilience when subjected to external stresses. Here, this work combines particle simulations and topological data analysis (TDA) to characterize the complex multiscale structure of soft gels. Our TDA analysis focuses on the use of the Euler characteristic, which is an interpretable and computationally scalable topological descriptor that is combined with filtration operations to obtain information on the geometric (local) and topological (global) structure of soft gels. We reduce the topological information obtained with TDA using principal component analysis (PCA) and show that this provides an informative low-dimensional representation of the gel structure. We use the proposed computational framework to investigate the influence of gel preparation (e.g., quench rate, volume fraction) on soft gel structure and to explore dynamic deformations that emerge under oscillatory shear in various response regimes (linear, nonlinear, and flow). Our analysis provides evidence of the existence of hierarchical structures in soft gels, which are not easily identifiable otherwise. Moreover, our analysis reveals direct correlations between topological changes of the gel structure under deformation and mechanical phenomena distinctive of gel materials, such as stiffening and yielding. In summary, we show that TDA facilitates the mathematical representation, quantification, and analysis of soft gel structures, extending traditional network analysis methods to capture both local and global organization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Effect of Aging and Demand for Reliability Analysis of Degrading Components

According to the U.S Energy Information Administration (EIA), the U.S fossil fuel share of energy consumption in 2015 was 67%. Furthermore, the Ecotricity UK report based on the CIA World Factbook states that with the current rate of consumption of fossil fuels, petroleum would run out by 2052, natural gas by 2060, and coal by 2088. No fossil fuel will remain by the next century. Besides the limited reserves of fossil fuel, massive consumption of fossil fuel also raises concerns about global warming and pollution. Therefore, there has been a growing interest in reducing fossil fuel consumption in the energy structure and in increasing the proportion of clean energy. Renewable energy (e.g. wind, solar) has the potential for distributed generation. However, the availability for renewable energy fluctuates and is uncontrollable. Therefore, additional energy sources need to be coupled with renewable energy to produce a stable electricity generation profile. Nuclear energy can serve this purpose as it is a clean energy source, has low greenhouse gas emission and possesses high power density and baseload power supply with low fuel cost. It is desirable to develop a hybrid energy system that combines both renewable energy and nuclear energy to meet low carbon emission goals and to utilize renewable energy. Such a nuclear hybrid energy system, consisting of different energy subsystems such as nuclear, solar, and wind, involves frequent switching between different energy subsystems. Since the primary loop in a nuclear power plant generates constant heat, the turbine bypass line in the secondary loop is required to switch frequently to meet the gap in the energy demand and that generated by the renewables. The increased usage of the turbine bypass system is considered to be the major difference between a nuclear hybrid energy system and a traditional nuclear power plant. Reliability analysis for designing such a complex system involves both high level fault propagation analysis at the conceptual design stage and low level failure prediction for specific components. The main focus of this summary to derive a degradation model of hardware components which can later help in the high level fault propagation analysis. The degradation model is a low level failure mode model that combines the effects of natural aging and frequent switching. The model can be used for predicting components' failure due to specific failure modes. The results can serve as indicators for conducting repair actions and maintenance to minimize Operation and Maintenance (O and M) costs. (authors)

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2020

Development of Direct Injection/Ionization Mass Spectrometry Methods for Whole Molecule Characterization

The objective of this work is to adapt ambient ionization mass spectrometry (AMS) techniques for the rapid analysis of intact uranium complexes, stable strontium, cerium, and explosive compounds. The methods used were “soft ionization” techniques, which facilitate the detection of whole molecule complexes. The soft ionization mass spectrometry (MS) techniques that were investigated include paper spray ionization (PSI), matrix-assisted ionization (MAI), electrospray ionization (ESI) and direct analysis in real time (DART). For the first time, PSI-MS methods were successfully developed for whole molecule uranium-containing analytes (uranyl acetate, uranyl nitrate, and uranyl-tributylphosphate complexes). This was also the first demonstration of uranium complex detection and characterization and one of the few examples of inorganic analysis using MAI techniques. Proof of concept experiments also putatively identified matrix-derived ions and ion complexes that have not previously been described in the literature. Additionally, PSI-MS on cotton swipe samples doped with a multi-element standard containing μg levels of U, Bi, Pb, Cd, Fe, and Zn were directly analyzed without purification, representing a major improvement over existing methods. Both PSI and MAI methods demonstrated limits of detection (LODs) in the 10 - 100’s ng for various uranyl species within a range of 10’s ppm - 100’s ppb, dependent on analytical method and analyte species. AMS methods were also developed for other inorganics, including Ce and Sr, and organic explosive residues to address specific challenges in environmental monitoring and forensics. Further refinement and qualification of the AMS techniques developed within this effort would lead to significant cost reduction and timeliness by facilitating the triage and queueing of samples for subsequent more sensitive and time-consuming analyses.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2015

STAR FORMATION ACROSS THE W3 COMPLEX

We present a multi-wavelength analysis of the history of star formation in the W3 complex. Using deep, near-infrared ground-based images combined with images obtained with Spitzer and Chandra observatories, we identified and classified young embedded sources. We identified the principal clusters in the complex and determined their structure and extension. We constructed extinction-limited samples for five principal clusters and constructed K-band luminosity functions that we compare with those of artificial clusters with varying ages. This analysis provided mean ages and possible age spreads for the clusters. We found that IC 1795, the centermost cluster of the complex, still hosts a large fraction of young sources with circumstellar disks. This indicates that star formation was active in IC 1795 as recently as 2 Myr ago, simultaneous to the star-forming activity in the flanking embedded clusters, W3-Main and W3(OH). A comparison with carbon monoxide emission maps indicates strong velocity gradients in the gas clumps hosting W3-Main and W3(OH) and shows small receding clumps of gas at IC 1795, suggestive of rapid gas removal (faster than the T Tauri timescale) in the cluster-forming regions. We discuss one possible scenario for the progression of cluster formation in the W3 complex. We propose that early processes of gas collapse in the main structure of the complex could have defined the progression of cluster formation across the complex with relatively small age differences from one group to another. However, triggering effects could act as catalysts for enhanced efficiency of formation at a local level, in agreement with previous studies.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Ground and excited electronic structures of electride and alkalide units: The cases of Metal-Tren, -Azacryptand, and -TriPip222 complexes

A systematic electronic structure analysis was conducted for M(L) n molecular electrides and their corresponding alkalide units M(L) n @M' (M/M' = Na, K; L = Tren, Azacryptand, TriPip222; n = 1, 2). All complexes belong to the “superalkali” category due to their low ionization potentials. The saturated molecular electrides display M+(L) n - form with a greatly diffuse quasispherical electron cloud. They were identified as “superatoms” considering the contours of populating atomic-type molecular orbitals. The observed superatomic Aufbau order of M(Tren) 2 is 1S, 1P, 1D, 1F, 2S, 2P, and 1G and it is consistent with those of M(Azacryptand) and M(TriPip222) up to the analyzed 1F level. Their excitation energies decrease gradually moving from M(Tren) 2 to M(Azacryptand) and to M(TriPip222). The studied alkalide complexes carry [M(L) n ] + @M' - ionic structure and their dissociation energies vary in the sequence of K(L) n @Na > Na(L) n @Na > K(L) n @K > Na(L) n @K. Similar to molecular electrides, the anions of alkalide units occupy electrons in diffuse Rydberg-like orbitals. In this work, excited states of [M(L) n @M'] 0/+/- and their trends are also analyzed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Active attenuation of a trailing vortex inspired by a parabolized stability analysis

Designing effective control for complex three-dimensional flow fields proves to be non-trivial. Often, intuitive control strategies lead to suboptimal control. To navigate the control space, we use a linear parabolized stability analysis to guide the design of a control scheme for a trailing vortex flow field aft of a NACA0012 half-wing at an angle of attack $\unicode[STIX]{x1D6FC}=5^{\circ }$ and a chord-based Reynolds number $Re=1000$ . The stability results show that the unstable mode with the smallest growth rate (fifth wake mode) provides a pathway to excite a vortex instability, whereas the principal unstable mode does not. Inspired by this finding, we perform direct numerical simulations that excite each mode with body forces matching the shape function from the stability analysis. Furthermore, relative to the uncontrolled case, the controlled flows show increased attenuation of circulation and peak streamwise vorticity, with the fifth-mode-based control set-up outperforming the principal-mode-based set-up. From these results, we conclude that a rudimentary linear stability analysis can provide key insights into the underlying physics and help engineers design effective physics-based flow control strategies.

42 ENGINEERING↗
DOE OSTI2017

Surface-Induced Dissociation of Protein Complexes in a Hybrid Fourier Transform Ion Cyclotron Resonance Mass Spectrometer

Mass spectrometry continues to develop as a valuable tool in the analysis of proteins and protein complexes. In protein complex mass spectrometry studies, surface-induced dissociation (SID) has been successfully applied in quadrupole time-of-flight (Q-TOF) instruments. SID provides structural information on non-covalent protein complexes that is complementary to other techniques. However, the mass resolution of Q-TOF instruments can limit the information that can be obtained for protein complexes by SID. Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) provides ultrahigh resolution and ultrahigh mass accuracy measurements. In this study, an SID device was designed and successfully installed in a hybrid FT-ICR instrument in place of the standard gas collision cell. The SID-FT-ICR platform has been tested with several protein complex systems (homooligomers, a heterooligomer, and a protein-ligand complex, ranging from 53 kDa to 85 kDa), and the results are consistent with data previously acquired on Q-TOF platforms, matching predictions from known protein interface information. SID fragments with the same m/z but different charge states are well-resolved based on distinct spacing between adjacent isotope peaks, and the addition of metal cations and ligands can also be isotopically resolved with the ultrahigh mass resolution available in FT-ICR.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2018

Experimental and Theoretical Comparison of Transition-Metal and Actinide Tetravalent Schiff Base Coordination Complexes

A series of homoleptic tetravalent transition-metal and actinide Schiff-base coordination complexes, ML 2 {M = Zr, Hf, Th, U; L = N,N'-bis[(4,4'-diethylamino)salicylidene]-1,2-phenylenediamine}, have been synthesized that feature a rigid phenyl backbone. These complexes create the opportunity for comparing a series of complexes containing metal cations in the formal IV+ oxidation state by structural, spectroscopic, and theoretical analysis that also incorporate the previously reported Ce(IV) and Pu(IV) analogues. X-ray crystallographic analysis reveals that all complexes are isomorphous and feature a co-facial ligand geometry. TD-DFT and other quantum mechanical methods were used to explore bonding differences across between the complexes, and resulting calculated absorbance spectra for ML 2 are in good agreement with the experimental data. The computational results also suggest that U(IV) and Pu(IV) analogs have more covalent character in their bonding than found with the other metal cations reported here.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

ZEM: Integrated Framework for Real-Time Data and Model Analyses for Robust Environmental Management Decision Making - 16438

Typically environmental management (EM) problems require analysis of large and complex data sets originating from concurrent data streams with different data collection frequencies and pedigree. These big data sets require on-the-fly analysis, assimilation and integration into a series of models with different complexity for various types of model-based analyses. This is needed to provide fast iterative model analyses based on the latest available data to guide decision-making. Furthermore, the data and model are associated with uncertainties. The uncertainties are probabilistic (e.g. measurement errors) and non-probabilistic (unknowns, e.g. alternative conceptual models characterizing site conditions). To address all of these issues, we have developed an integrated framework for real-time data and model analyses for environmental decision-making called ZEM. The framework allows for seamless and on-the-fly integration of data and modeling results for robust and scientifically-defensible decision-making applying advanced decision analyses tools such as Bayesian-Information-Gap Decision Theory (BIG-DT). The framework also includes advanced methods for optimization that are capable of dealing with a large number of unknown model parameters, and surrogate (reduced order) modeling capabilities based on support vector regression techniques. The framework is predominantly coded in Julia, a state-of-the-art high-performance programing language (http://julialang.org) and incorporates the MADS computational tools (Model Analysis and Decision Support; http://mads.lanl.gov). We demonstrate the application of ZEM for data and model analyses at the LANL Chromium site. The ZEM framework will be released as open-source code and can be applied to any environmental management site. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2024

Tetranuclear Polypyridylruthenium(II) Complexes as Selective Nucleic Acid Stains for Flow Cytometric Analysis of Monocytic and Epithelial Lung Carcinoma Large Extracellular Vesicles

Selective staining of extracellular vesicles (EVs) is a major challenge for diagnostic and therapeutic applications. Herein, the EV labeling properties of a new class of tetranuclear polypyridylruthenium(II) complexes, Rubb7-TNL and Rubb7-TL, as phosphorescent stains are described. These new stains have many advantages over standard stains to detect and characterize EVs, including: high specificity for EV staining versus cell staining; high phosphorescence yields; photostability; and a lack of leaching from EVs until incorporation with target cells. As an example of their utility, large EVs released from control (basal) or lipopolysaccharide (LPS)-stimulated THP-1 monocytic leukemia cells were studied as a model of immune system EVs released during bacterial infection. Key findings from EV staining combined with flow cytometry were as follows: (i) LPS-stimulated THP-1 cells generated significantly larger and more numerous large EVs, as compared with those from unstimulated cells; (ii) EVs retained native EV physical properties after staining; and (iii) the new stains selectively differentiated intact large EVs from artificial liposomes, which are models of cell membrane fragments or other lipid-containing debris, as well as distinguished two distinct subpopulations of monocytic EVs within the same experiment, as a result of biochemical differences between unstimulated and LPS-stimulated monocytes. Comparatively, the staining patterns of A549 epithelial lung carcinoma-derived EVs closely resembled those of THP-1 cell line-derived EVs, which highlighted similarities in their selective staining despite their distinct cellular origins. This is consistent with the hypothesis that these new phosphorescent stains target RNA within the EVs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Evaluating Cryo–TEM Reconstruction Accuracy of Self–Assembled Polymer Nanostructures

Cryogenic transmission electron microscopy (cryo–TEM) combined with single particle analysis (SPA) is an emerging imaging approach for soft materials. However, the accuracy of SPA–reconstructed nanostructures, particularly those formed by synthetic polymers, remains uncertain due to potential packing heterogeneity of the nanostructures. In this study, the combination of molecular dynamics (MD) simulations and image simulations is utilized to validate the accuracy of cryo–TEM 3D reconstructions of self–assembled polypeptoid fibril nanostructures. Using CryoSPARC software, image simulations, 2D classifications, ab initio reconstructions, and homogenous refinements are performed. By comparing the results with atomic models, the recovery of molecular details is assessed, heterogeneous structures are identified, and the influence of extraction location on the reconstructions is evaluated. In conclusion, these findings confirm the fidelity of single particle analysis in accurately resolving complex structural characteristics and heterogeneous structures, exhibiting its potential as a valuable tool for detailed structural analysis of synthetic polymers and soft materials.

36 MATERIALS SCIENCE↗