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At least 1,225 records · Page 68

Spectral Element Applications in Complex Nuclear Reactor Geometries: Tet-to-Hex Meshing

The spectral element code Nek5000 is an open-source, higher-order computational fluid dynamics code developed at Argonne National Laboratory. It is designed to solve incompressible Navier-Stokes equations, but it also has a low-Mach-number approximation feature available. Large eddy simulation is approached by explicit filtering of the velocity field (and other fields) to mimic the effect of dissipation due to the unresolved scale. The computational domain is decomposed into second-order hexahedral elements that conform to the boundaries. However, generating a high-quality pure-hexahedral mesh can be challenging for some problems. For simple geometries, traditional blocking methods can be used to decompose the domain into smaller blocks to generate a so-called structural mesh. A structural mesh can maintain good orthogonality but can have a highly skewed mesh to conform to the geometry, as well as unnecessary refinement in the far field. Moreover, for geometries with relative complexity, blocking the geometry becomes impossible. To address these issues, we adopted a let-to-hex strategy to generate a pure hexahedral mesh for Nek5000. First, we generate a pure tetrahedral mesh for the geometry; then we divide one tetrahedral element into four hexahedral elements. A pure tetrahedral mesh could be easily generated for complex geometries by using many current meshing codes. In this paper, we use the commercial codes ANSYS meshing and ANSYSICEM to generate the pure tetrahedral mesh and then convert it to a pure hexahedral mesh. Boundary layers are extruded in ANSYSICEM to maintain near-wall resolution.

ANSYS ICEM↗

Light sources with bias tunable spectrum based on van der Waals interface transistors

Light-emitting electronic devices are ubiquitous in key areas of current technology, such as data communications, solid-state lighting, displays, and optical interconnects. Controlling the spectrum of the emitted light electrically, by simply acting on the device bias conditions, is an important goal with potential technological repercussions. However, identifying a material platform enabling broad electrical tuning of the spectrum of electroluminescent devices remains challenging. Here, we propose light-emitting field-effect transistors based on van der Waals interfaces of atomically thin semiconductors as a promising class of devices to achieve this goal. We demonstrate that large spectral changes in room-temperature electroluminescence can be controlled both at the device assembly stage –by suitably selecting the material forming the interfaces– and on-chip, by changing the bias to modify the device operation point. Even though the precise relation between device bias and kinetics of the radiative transitions remains to be understood, our experiments show that the physical mechanism responsible for light emission is robust, making these devices compatible with simple large areas device production methods.

36 MATERIALS SCIENCE↗

Accurate prediction of terahertz spectra of molecular crystals of fentanyl and its analogs

Fentanyl is a potent synthetic opioid pain reliever with a high bioavailability that can be used as prescription anesthetic. Rapid identification via non-contact methods of both known and emerging opioid substances in the fentanyl family help identify the substances and enable rapid medical attention. We apply PBEh-3c method to identify vibrational normal modes from 0.01 to 3 THz in solid fentanyl and its selected analogs. The molecular structure of each fentanyl analog and unique arrangement of H-bonds and dispersion interactions significantly change crystal packing and is subsequently reflected in the THz spectrum. Further, the study of THz spectra of a series of stereoisomers shows that small changes in molecular structure results in distinct crystal packing and significantly alters THz spectra as well. We discuss spectral features of synthetic opioids with higher potency than conventional fentanyl such as ohmefentanyl and sufentanil and discover the pattern of THz spectra of fentanyl analogs.

42 ENGINEERING↗

Ultrafast nano-imaging and nano-spectroscopy

Ultrafast pump–probe nano-imaging combines scanning probe-based optical near-field microscopy with ultrafast spectroscopy to enable imaging with deep sub-wavelength spatial resolution, femtosecond temporal resolution and simultaneous spectral resolution. Ultrafast nano-imaging has gained increased attention for its ability to provide far-from-equilibrium excitation and excited-state contrast. With coherent and nonlinear probing, coupled electron, spin and lattice dynamics on elementary timescale and length scale can be resolved. Through nano-movies, ultrafast nano-imaging visualizes correlated quantum dynamics underlying the properties of solid-state materials, semiconductors, molecular electronic, photonic, photovoltaic and other functional materials. With nanometre spatial resolution, this method probes elementary dynamic processes across multiple length scales that are otherwise obscured in conventional ultrafast spectroscopy in which heterogeneities are spatially averaged. Furthermore, this Primer describes the theoretical background and experimental implementation of ultrafast nano-imaging; signal interpretation and modelling; representative examples and a perspective for the future development of the field.

Microscopy↗

Laser-spectroscopy testbed for impurity monitoring in liquid metal-cooled fast reactors

A significant challenge in sodium-cooled fast reactors is controlling impurities, in particular oxygen impurities, within the sodium coolant, as they can accelerate corrosion and indicate leaks. Optical methods offer the potential to rapidly detect small concentrations of both gaseous and metal impurities that accelerate corrosion, plug coolant channels, and lead to increased activation of isotopes in the coolant. We present the design and performance of an apparatus designed to enable the application of multiple optical analytical techniques, such as laser-induced breakdown spectroscopy, to detect elemental impurities in the sodium melt with high sensitivity. Here, we experimentally demonstrate the detection of characteristic sodium and oxygen spectral lines in liquid sodium, which sets the stage for the optimization of its analytical sensitivity. A robust sensor of this type integrated with the sodium cooling loop has the potential to significantly improve the safety and operational efficiency of generation IV nuclear reactors.

47 OTHER INSTRUMENTATION↗

Where did the tumor start? An inverse solver with sparse localization for tumor growth models

In this work, we present a numerical scheme for solving an inverse problem for parameter estimation in tumor growth models for glioblastomas, a form of aggressive primary brain tumor. The growth model is a reaction–diffusion partial differential equation (PDE) for the tumor concentration. We use a PDE-constrained optimization formulation for the inverse problem. The unknown parameters are the reaction coefficient (proliferation), the diffusion coefficient (infiltration), and the initial condition field for the tumor PDE. Segmentation of magnetic resonance imaging (MRI) scans drive the inverse problem where segmented tumor regions serve as partial observations of the tumor concentration. Like most cases in clinical practice, we use data from a single time snapshot. Moreover, the precise time relative to the initiation of the tumor is unknown, which poses an additional difficulty for inversion. We perform a frozen-coefficient spectral analysis and show that the inverse problem is severely ill-posed. We introduce a biophysically motivated regularization on the structure and magnitude of the tumor initial condition. In particular, we assume that the tumor starts at a few locations (enforced with a sparsity constraint on the initial condition of the tumor) and that the initial condition magnitude in the maximum norm is equal to one. We solve the resulting optimization problem using an inexact quasi-Newton method combined with a compressive sampling algorithm for the sparsity constraint. Our implementation uses PETSc and AccFFT libraries. We conduct numerical experiments on synthetic and clinical images to highlight the improved performance of our solver over a previously existing solver that uses standard two-norm regularization for the calibration parameters. The existing solver is unable to localize the initial condition. Our new solver can localize the initial condition and recover infiltration and proliferation. In clinical datasets (for which the ground truth is unknown), our solver results in qualitatively different solutions compared to the two-norm regularized solver.

97 MATHEMATICS AND COMPUTING↗

Penetration Through Slots in Overmoded Cavities

A resonant cavity undergoes three distinct behaviors with increasing frequency: 1) fundamental modes, localized in frequency with well defined modal distribution; 2) undermoded region, where modes are still separated, but are sufficiently perturbed by small imperfections that their spectral positions (and distributions) are statistical in nature; and 3) overmoded region, where modes overlap, field distributions follow stochastic distributions, and the slot acts as if in free space. Understanding the penetration through slots in the overmoded region is of great interest, and is the focus of this article. Since full-wave solvers may not be able to provide a timely answer for very high frequencies due to a lack of memory and/or computation resources, we develop bounding methods to estimate worst-case average and maximum fields within the cavity. Finally, after discussing the bounding formulation, we compare its results to full-wave simulations at the first, second, and third resonance supported by the slot in the case of a cylindrical cavity. Note that the bounding formulation indicates that results are nearly independent of cavity shape: only the cavity volume, frequency, and cavity quality factor affect the overmoded region, making this formulation a powerful tool to assess electromagnetic interference and electromagnetic compatibility effects within cavities.

overmoded cavity↗

Expanding the range of the resolvable strain from distributed fiber optic sensors using a local adaptive reference approach

Optical frequency domain reflectometry (OFDR) is a spectral measurement technique in which shifts in the local Rayleigh backscatter spectra can be used to perform distributed temperature or strain measurements relative to a reference measurement using ordinary single-mode optical fibers. Here, we demonstrate a data processing methodology for improving the resolvable range of temperature and strain by adaptively varying the reference measurement position by position, based on the time evolution of the local optical intensities and the correlation between the reference and active measurements. These methods nearly double the resolvable range of temperature and strain compared with that achieved using the traditional static reference approach.

47 OTHER INSTRUMENTATION↗

Seismic Spatial Gradients and Machine Learning-Based Classifiers for Explosion Monitoring (LDRD 218327)

This final report summarizes the work completed under the Laboratory Directed Research and Development (LDRD) project “Seismic Spatial Gradients as a Machine Learning-Based Classifier for Explosion Monitoring.” The overarching goal of the project was to explore the efficacy of using machine learning-based classification algorithms where the input data are the spatial gradient of the seismic wavefield collected at a single point on the Earth’s surface. The methods that I describe here are in direct contrast to conventional methods of seismic discrimination which typically rely on a spatially extended network of instruments and physics-based wavefield attributes such as, for example, the ratio between $\textit{P}$ and $\textit{S}$ waves. Rather, we use the spatial gradient of the seismic wavefield observed at a single point on the Earth’s surface and data processing approaches inspired by the machine learning community. We tested two algorithms, a neural network and a modified version of principal component analysis termed Spectrally Filtered Principal Component Analysis (SFPCA). To test these algorithms, we first conducted a series of numerical tests using synthetic data and then conducted a small-scale controlled field experiment. The tests using synthetic data showed that both algorithms had high success rates on gradiometric data, even when simulated noise was added to the signal. Furthermore, we found that using seismic spatial gradients increased the performance of our discrimination algorithms when compared to using just the traditional translational motion seismic data. The tests with field data also showed a high degree of discriminative success.

58 GEOSCIENCES↗

Results from a multi-laboratory ocean metaproteomic intercomparison: effects of LC-MS acquisition and data analysis procedures

Metaproteomics is an increasingly popular methodology that provides information regarding the metabolic functions of specific microbial taxa and has potential for contributing to ocean ecology and biogeochemical studies. A blinded multi-laboratory intercomparison was conducted to assess comparability and reproducibility of taxonomic and functional results and their sensitivity to methodological variables. Euphotic zone samples from the Bermuda Atlantic Time-series Study (BATS) in the North Atlantic Ocean collected by in situ pumps and the autonomous underwater vehicle (AUV) Clio were distributed with a paired metagenome, and one-dimensional (1D) liquid chromatographic data-dependent acquisition mass spectrometry analysis was stipulated. Analysis of mass spectra from seven laboratories through a common bioinformatic pipeline identified a shared set of 1056 proteins from 1395 shared peptide constituents. Quantitative analyses showed good reproducibility: pairwise regressions of spectral counts between laboratories yielded R 2 values averaged 0.62±0.11, and a Sørensen similarity analysis of the top 1000 proteins revealed 70 %–80 % similarity between laboratory groups. Taxonomic and functional assignments showed good coherence between technical replicates and different laboratories. A bioinformatic intercomparison study, involving 10 laboratories using eight software packages, successfully identified thousands of peptides within the complex metaproteomic datasets, demonstrating the utility of these software tools for ocean metaproteomic research. Lessons learned and potential improvements in methods were described. Future efforts could examine reproducibility in deeper metaproteomes, examine accuracy in targeted absolute quantitation analyses, and develop standards for data output formats to improve data interoperability. Together, these results demonstrate the reproducibility of metaproteomic analyses and their suitability for microbial oceanography research, including integration into global-scale ocean surveys and ocean biogeochemical models.

59 BASIC BIOLOGICAL SCIENCES↗

Evidence for Trapping-Induced Nonlinear Frequency Shifts in Langmuir Waves Driven via Stimulated Raman Scattering

Thomson scattering is used to detect the spectra of Langmuir waves driven through the backward stimulated Raman scattering process in a diffraction limited laser focal spot. Measured Langmuir wave spectral frequencies are found to vary in time and have broadened spectral power, consistent with a nonlinear frequency shift of the driven Langmuir wave due to electron-trapping. Broadening of the Langmuir wave spectral power is observed to decrease in time, consistent with measured variations in the frequency shift of the driven Langmuir waves. Furthermore, the observed spectral broadening is consistent with the temporally short (ps), bursty nature of backward stimulated Raman scattered light observed in simulations that cannot be resolved by the Thomson scattering diagnostic. Comparison of the broadened spectrum with time integrated spectra from two-dimensional particle-in-cell simulations shows favorable comparison in the broadened spectral widths, supporting the supposition of electron-trapping induced, nonlinear shifting of daughter Langmuir wave frequencies.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Efficient Mn 2+ Doping in Non-Stoichiometric Cesium Lead Bromide Perovskite Quantum Dots

Doping magnetic transition metal ions (e.g., Mn 2+ ) into colloidal quantum dots endows novel optical and magnetic properties to the host materials. CsPbBr 3 quantum dots (QDs) are emerging light-emitting materials with high structural and chemical flexibility in the visible spectral regime. However, efficiently doping Mn 2+ ions in CsPbBr 3 QDs remains challenging, especially when size confinement and ensemble uniformity are needed for understanding the underexplored exciton-dopant exchange interaction. Here, we introduce a doping mechanism based on electrostatic surface Mn 2+ adsorption that enables efficient Mn 2+ incorporation in strongly confined CsPbBr 3 QDs. The resultant QDs are found to have a Cs-deficient stoichiometry compared to their undoped counterparts. A redox reaction-based purification method was developed to remove Mn 2+ cations that are tightly adsorbed on the surface to determine the concentration of lattice-incorporated Mn 2+ . Our synthesis enables a Mn 2+ doping/alloying concentration of up to ∼44% with a Mn 2+ photoluminescence efficiency exceeding 90%. This allows for the determination of the intrinsic exciton-to-dopant energy transfer rate.

Hidayatova, Lamia [Univ. of Oklahoma, Norman, OK (↗

AXIOM Unfold 0.7.0, Users Manual

The AXIOM-Unfold application is a computational code for performing spectral unfolds along with uncertainty quantification of the photon spectrum. While this code was principally designed for spectral unfolds on the Saturn source, it is also relevant to other radiation sources such as Pithon. This code is a component of the AXIOM project which was undertaken in order to measure the time-resolved spectrum of the Saturn source; to support this, the AXIOM-Unfold code is able to process time-dependent dose measurements in order to obtain a time-resolved spectrum. This manual contains a full description of the algorithms used by the method. The code features are fully documented along with several worked examples.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Quantum sensing effect of electron tunneling in DQD/analyte complex

We investigate electron tunneling between quantum dots and molecules to propose a quantum sensor. This sensor consists of double quantum dots (DQD) with energy levels specifically tailored to mirror those of the target analyte. By analyzing the spectral distribution of electron localizations in the DQD system, we can delineate the analyte’s spectrum and deduce its composition by comparing it with a reference sample. To understand electron tunneling dynamics within the DQD/analyte complex, we performed three-dimensional computational modeling applying the effective potential approach to the InAs/GaAs heterostructure. In this modeling, we mimicked the analyte spectrum by utilizing a quantum well characterized by a quasi-discrete spectrum. Our calculations reveal the inherent potential of utilizing this method as a highly sensitive and selective sensor.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Semi-analytic spectral fitting: simultaneously modelling the mass accumulation and chemical evolution in MaNGA spiral galaxies

We develop a novel semi-analytic spectral fitting approach to quantify the star formation histories (SFHs) and chemical enrichment histories (ChEHs) of individual galaxies. We construct simple yet general chemical evolution models that account for gas inflow and outflow processes as well as star formation, to investigate the evolution of merger-free star-forming systems. These models are fitted directly to galaxies’ absorption-line spectra, while their emission lines are used to constrain current gas phase metallicity and star formation rate. We apply this method to spiral galaxies selected from the SDSS-IV Mapping Nearby Galaxies at Apache Point Observatory survey. By fitting the co-added absorption-line spectra for each galaxy, and using the emission-line constraints on present-day metallicity and star formation, we reconstruct both the SFHs and the ChEHs for all objects in the sample. We can use these reconstructions to obtain archaeological measures of derived correlations such as the mass–metallicity relation at any redshift, which compare favourably with direct observations. We find that both the SFHs and ChEHs have strong mass dependence: massive galaxies accumulate their stellar masses and become enriched earlier. This mass dependence causes the observed flattening of the mass–metallicity relation at lower redshifts. The model also reproduces the observed gas-to-stellar mass ratio and its mass dependence. Moreover, we are able to determine that more massive galaxies have earlier gas infall times and shorter infall time-scales, and that the early chemical enrichment of low-mass galaxies is suppressed by strong outflows, while outflows are not very significant in massive galaxies.

79 ASTRONOMY AND ASTROPHYSICS↗

Abundance of Major Cell Wall Components in Natural Variants and Pedigrees of Populus trichocarpa

The rapid analysis of biopolymers including lignin and sugars in lignocellulosic biomass cell walls is essential for the analysis of the large sample populations needed for identifying heritable genetic variation in biomass feedstocks for biofuels and bioproducts. In this study, we reported the analysis of cell wall lignin content, syringyl/guaiacyl (S/G) ratio, as well as glucose and xylose content by high-throughput pyrolysis-molecular beam mass spectrometry (py-MBMS) for >3,600 samples derived from hundreds of accessions of Populus trichocarpa from natural populations, as well as pedigrees constructed from 14 parents (7 × 7). Partial Least Squares (PLS) regression models were built from the samples of known sugar composition previously determined by hydrolysis followed by nuclear magnetic resonance (NMR) analysis. Key spectral features positively correlated with glucose content consisted of m/z 126, 98, and 69, among others, deriving from pyrolyzates such as hydroxymethylfurfural, maltol, and other sugar-derived species. Xylose content positively correlated primarily with many lignin-derived ions and to a lesser degree with m/z 114, deriving from a lactone produced from xylose pyrolysis. Models were capable of predicting glucose and xylose contents with an average error of less than 4%, and accuracy was significantly improved over previously used methods. The differences in the models constructed from the two sample sets varied in training sample number, but the genetic and compositional uniformity of the pedigree set could be a potential driver in the slightly better performance of that model in comparison with the natural variants. Broad-sense heritability of glucose and xylose composition using these data was 0.32 and 0.34, respectively. In summary, we have demonstrated the use of a single high-throughput method to predict sugar and lignin composition in thousands of poplar samples to estimate the heritability and phenotypic plasticity of traits necessary to develop optimized feedstocks for bioenergy applications.

09 BIOMASS FUELS↗

Impacts on product quality attributes of monoclonal antibodies produced in CHO cell bioreactor cultures during intentional mycoplasma contamination events

Abstract A mycoplasma contamination event in a biomanufacturing facility can result in costly cleanups and potential drug shortages. Mycoplasma may survive in mammalian cell cultures with only subtle changes to the culture and penetrate the standard 0.2‐µm filters used in the clarification of harvested cell culture fluid. Previously, we reported a study regarding the ability of Mycoplasma arginini to persist in a single‐use, perfusion rocking bioreactor system containing a Chinese hamster ovary (CHO) DG44 cell line expressing a model monoclonal immunoglobulin G 1 (IgG1) antibody. Our previous work showed that M. arginini affects CHO cell growth profile, viability, nutrient consumption, oxygen use, and waste production at varying timepoints after M. arginini introduction to the culture. Careful evaluation of certain identified process parameters over time may be used to indicate mycoplasma contamination in CHO cell cultures in a bioreactor before detection from a traditional method. In this report, we studied the changes in the IgG1 product quality produced by CHO cells considered to be induced by the M. arginini contamination events. We observed changes in critical quality attributes correlated with the duration of contamination, including increased acidic charge variants and high mannose species, which were further modeled using principal component analysis to explore the relationships among M. arginini contamination, CHO cell growth and metabolites, and IgG1 product quality attributes. Finally, partial least square models using NIR spectral data were used to establish predictions of high levels (≥10 4 colony‐forming unit [CFU/ml]) of M. arginini contamination, but prediction of levels below 10 4 CFU/ml were not reliable. Contamination of CHO cells with M. arginini resulted in significant reduction of antibody product quality, highlighting the importance of rapid microbiological testing and mycoplasma testing during particularly long upstream bioprocesses to ensure product safety and quality.

60 APPLIED LIFE SCIENCES↗