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DOE OSTI2021

A Simple, Cost-Effective, and Automation-Friendly Direct PCR Approach for Bacterial Community Analysis

Understanding bacterial interactions and assembly in complex microbial communities using 16S rRNA sequencing normally requires a large experimental load. However, the current DNA extraction methods, including cell disruption and genomic DNA purification, are normally biased, costly, time-consuming, labor-intensive, and not amenable to miniaturization by droplets or 1,536-well plates due to the significant DNA loss during the purification step for tiny-volume and low-cell-density samples.

16S rRNA sequencing↗

DOE OSTI2024

A robust synthetic data generation framework for machine learning in high-resolution transmission electron microscopy (HRTEM)

Machine learning techniques are attractive options for developing highly-accurate analysis tools for nanomaterials characterization, including high-resolution transmission electron microscopy (HRTEM). However, successfully implementing such machine learning tools can be difficult due to the challenges in procuring sufficiently large, high-quality training datasets from experiments. In this work, we introduce Construction Zone, a Python package for rapid generation of complex nanoscale atomic structures which enables fast, systematic sampling of realistic nanomaterial structures and can be used as a random structure generator for large, diverse synthetic datasets. Using Construction Zone, we develop an end-to-end machine learning workflow for training neural network models to analyze experimental atomic resolution HRTEM images on the task of nanoparticle image segmentation purely with simulated databases. Further, we study the data curation process to understand how various aspects of the curated simulated data—including simulation fidelity, the distribution of atomic structures, and the distribution of imaging conditions—affect model performance across three benchmark experimental HRTEM image datasets. Using our workflow, we are able to achieve state-of-the-art segmentation performance on these experimental benchmarks and, further, we discuss robust strategies for consistently achieving high performance with machine learning in experimental settings using purely synthetic data. Construction Zone and its documentation are available at https://github.com/lerandc/construction_zone.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Influence of Ga doping on magnetic properties, magnetocaloric effect, and electronic structure of pseudobinary GdZn 1 - x Ga x ( x = 0 - 0.1 )

Here, we explore the impact of introducing IIIA-group element Ga in place of IIB-group element Zn in binary intermetallic GdZn on its magnetic and magnetocaloric properties, as well as explicate the modified electronic band structure of the compound. The magnetic transition temperature of the compound decreases with the increase of Ga concentration in GdZn 1-x ⁢Ga x ⁢(x = 0–0.1) while the crystal structure (CsCl prototype) and lattice parameters remain unchanged. Our detailed analysis of magnetization and magnetocaloric data conclusively proves that long-ranged magnetic ordering exists in the sample, despite the magnetic interaction considerably weakening with the increase of Ga. The experimental data are rationalized using both a theoretical machine-learning model and first-principle density functional theory. The electronic band structure of GdZn is manifested with some unusual complex features which gradually diminish with Ga doping and the conventional sinusoidal feature of Ruderman-Kittel-Kasuya-Yosida-type interactions also disappears. A mean-field theory model is developed and can successfully describe the overall magnetocaloric behavior of the GdZn 1-x⁢ Ga x series of samples.

36 MATERIALS SCIENCE↗

DOE OSTI2023

BuildStockQuery [SWR-23-58]

BuildStockQuery is a python library designed to simplify and streamline the process of querying massive, terabyte-scale datasets generated by ResStock(TM). ResStock (SWR-19-15) is a U.S. DOE-supported, NREL-built, national residential building energy stock model that enables a new approach to large-scale residential energy analysis across the U.S. by combining large public and private data sources, statistical sampling, detailed sub-hourly building simulations, and high-performance computing. BuildStockQuery offers an intuitive Object-Oriented Programming (OOP) interface to the ResStock output dataset allowing users to easily perform common queries and receive results in familiar pandas DataFrame format, abstracting away the need for complex SQL query. By initializing a query object with the pertinent Athena database and table names, users can easily query for various kinds of insights, for example, timeseries electricity for an end use for a given state grouped by building types.

Adhikari, Rajendra↗

DOE OSTI2020

Proposed Analytical Methods for Determining Filter Media Properties

High Efficiency Particulate Air (HEPA) filters, commonly used in nuclear filtration applications, are an integral part of the waste management processes in nuclear plants. HEPA filters are 99.97% efficient filtration devices characterized by their high resistance to air flow, or pressure drop. From theoretical models, the initial pressure drop across a clean filter is proven to be a function of the filter media fiber diameters and porosity of the media. These filter properties are relatively difficult to obtain with traditional manual methods; therefore, there is a need to develop analytical methods to find the fiber diameter and porosity to determine the pressure drop. Typically, these values can be found by substituting a calculated representative value based upon measured values, such as equivalent fiber diameter based upon a clean pressure drop. However, these values may also be directly recorded and measured by incorporating Scanning Electron Microscope (SEM) image analysis and other measurement methods to analyze the filter media and determine its physical properties without the need for media testing. DiameterJ, an open source Java plug-in, used with ImageJ, can process images of filter media taken by an SEM to find statistical data such as mean fiber diameter and porosity. To produce the raw data, SEM images of two filter media type samples are taken and segmented in DiameterJ using the traditional and statistical region merging segmentation algorithms. Manual segmentation is necessary after the initial segmentation by the algorithms as the images tend to be too complex for the algorithms to output with the necessary accuracy. However, complications exist in the manual segmentation process as these methods can be time intensive and prone to the individual bias of the user. This in turn can skew the final mean fiber diameter result, and lead to either an over or under prediction of the pressure drop. It was also discovered that the porosity data produced by DiameterJ is inaccurate, as the SEM analyzes the three-dimensional filter media by projecting its geometry onto a plane and analyzing it as a two-dimensional binary image. Thus, the porosity is artificially inflated through the segmentation process, rendering this result incorrect. Alternatively, density determination, gravimetric analysis, and thickness testing of the filter media is collectively used to determine the filter fiber porosity. Together, the SEM image analysis and analytical lab methods produce results through direct measurements which allow for the prediction of the initial pressure drop from clean filter media without the need for prior media testing to collect pressure data. By improving upon this proposed analytical method in the future, there is potential to streamline the process of finding these filter properties into a more direct methodology for determining the pressure drop across HEPA filters.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2023

Advancing Elemental and Isotopic Analysis of Uranium Mineral Inclusions: Rapid Screening via Laser-Induced Breakdown Spectroscopy and High-Resolution Laser Ablation-ICP-MS Mapping

The work presented herein employs two laser-based analytical techniques (laser-induced breakdown spectroscopy (LIBS) and laser ablation – inductively coupled plasma – mass spectrometry (LA-ICP-MS)) to spatially determine the elemental and isotopic composition of uranium bearing minerals. Uniquely, this work leverages the high-speed applicability of LIBS to “screen” the sample(s) for their elemental constituents. After determining the location of the uranium inclusions (via LIBS), high-resolution LA-ICP-MS was employed to further characterize the inclusions. The high-resolution (sub-µm) capabilities of LA-ICP-MS were able to extract important information from the uranium minerals including discerning its chemical form (e.g., finchite from carnotite, Sr- and K-bearing uranyl vanadates, respectively) as well as their 235 U/ 238 U isotopic composition. This approach, LIBS followed by LA-ICP-MS, significantly reduces the analysis time (~95 %) in comparison to employing a LA-ICP-MS only approach. Furthermore, this work presented a novel approach to analyzing inclusions via a particle/inclusion analysis tool which is commercially available within the iolite 4 software. This tool allowed for a more accurate characterization of the isotopic distribution of the inclusions, as well as allowing for rapid sizing of the inclusions. Finally, this analytical approach could readily be applied to other sample types in which the target species (e.g., µm-sized inclusions) are embedded in complex matrices (e.g., cm-sized samples).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2018

Microbiome characterization by high-throughput transfer RNA sequencing and modification analysis

Advances in high-throughput sequencing have facilitated remarkable insights into the diversity and functioning of naturally occurring microbes; however, current sequencing strategies are insufficient to reveal physiological states of microbial communities associated with protein translation dynamics. Transfer RNAs (tRNAs) are core components of protein synthesis machinery, present in all living cells, and are phylogenetically tractable, which make them ideal targets to gain physiological insights into environmental microbes. Here we report a direct sequencing approach, tRNA-seq, and a software suite, tRNA-seq-tools, to recover sequences, abundance profiles, and post-transcriptional modifications of microbial tRNA transcripts. Our analysis of cecal samples using tRNA-seq distinguishes high-fat-and low-fat-fed mice in a comparable fashion to 16S ribosomal RNA gene amplicons, and reveals taxon- and diet-dependent variations in tRNA modifications. Our results provide taxon-specific in situ insights into the dynamics of tRNA gene expression and post-transcriptional modifications within complex environmental microbiomes.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

A novel transfer learning framework for sorghum biomass prediction using UAV-based remote sensing data and genetic markers

Yield for biofuel crops is measured in terms of biomass, so measurements throughout the growing season are crucial in breeding programs, yet traditionally time- and labor-consuming since they involve destructive sampling. Modern remote sensing platforms, such as unmanned aerial vehicles (UAVs), can carry multiple sensors and collect numerous phenotypic traits with efficient, non-invasive field surveys. However, modeling the complex relationships between the observed phenotypic traits and biomass remains a challenging task, as the ground reference data are very limited for each genotype in the breeding experiment. In this study, a Long Short-Term Memory (LSTM) based Recurrent Neural Network (RNN) model is proposed for sorghum biomass prediction. The architecture is designed to exploit the time series remote sensing and weather data, as well as static genotypic information. As a large number of features have been derived from the remote sensing data, feature importance analysis is conducted to identify and remove redundant features. A strategy to extract representative information from high-dimensional genetic markers is proposed. To enhance generalization and minimize the need for ground reference data, transfer learning strategies are proposed for selecting the most informative training samples from the target domain. Consequently, a pre-trained model can be refined with limited training samples. Field experiments were conducted over a sorghum breeding trial planted in multiple years with more than 600 testcross hybrids. The results show that the proposed LSTM-based RNN model can achieve high accuracies for single year prediction. Further, with the proposed transfer learning strategies, a pre-trained model can be refined with limited training samples from the target domain and predict biomass with an accuracy comparable to that from a trained-from-scratch model for both multiple experiments within a given year and across multiple years.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Anisotropic spall failure of additively manufactured 316L stainless steel

The dynamic high strain rate tensile (spall) failure of additively manufactured (AM) materials is an area of great interest but much less understood than material failure under other loading regimes. The research presented here examines the effects of microstructure anisotropy in 316L stainless steel fabricated by laser powder bed fusion (LPBF) on its spall failure and properties. In this work, plate-on-plate impact experiments were performed using an 80-mm gas gun to investigate the spall behavior of AM fabricated sample discs with impact along the perpendicular and parallel orientations relative to build directions. Experiments were also performed on wrought 316L stainless steel as baseline material with uniform equiaxed grain microstructure for comparison with the AM material of same composition. The spall experiments involved free-surface velocity profiles measured using Photon Doppler Velocimetry (PDV) to capture the spall pull-back signals, combined with post-mortem analysis of the microstructure of soft-recovered impacted samples. In the case of AM samples, spall failure initiated preferentially at melt pool boundaries in both impact directions. The spall plane location and spall strength, however, were both heavily influenced by the orientation of the impact direction relative to the build direction in the AM samples. The spall behavior is also observed to be more complex in the samples impacted perpendicular to the build (through-thickness) direction, due in large part to the orientation of the microstructural features such as melt pool boundaries, laser scan tracks, and general grain morphology.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Editorial: Applications of spectroscopy and chemometrics in nuclear materials analysis

Optical analysis techniques, including spectroscopy and image analysis, have many advantages when applied to the study of nuclear materials. They require small sample sizes, can be performed remotely, and can be proceduralized through consistent practice. Most importantly, they provide a wealth of information by generating multivariate data. For example, ultraviolet–visible–near-infrared absorbance spectroscopy of actinides in aqueous and organic solutions is dependent on the oxidation state, anionic complexation, and temperature. These variables are important for solution-based separation processes, and sensitivity to these factors, combined with online monitoring, can drive the efficiency and control of these processes. The morphology and chemical composition of actinide particles can also provide a vital clue to the mechanisms by which the particles were formed, providing forensic information on the origins of the particles.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2019

Total Protein Analysis in Algae via Bulk Amino Acid Detection: Optimization of Amino Acid Derivatization after Hydrolysis with O -Phthalaldehyde 3-Mercaptopropionic Acid (OPA-3MPA)

The analysis of protein in algal biomass is one of the most critical areas of commercial development of algae characterization for nutritional or other high value applications. A new rapid and accurate method is required that can be widely implemented and that is free from interferences from the complex algal biomass matrix. We developed a simple spectrophotometric method for primary amino acid quantification bulk measurement in an acid hydrolyzed algal biomass preparation, as an alternative to the more labor-intensive amino HPLC acid analysis or less specific nitrogen-to-protein conversion. We have validated an O -phthalaldehyde (OPA)-based derivatization method, showing accurate and linear quantification for standard reference amino acids as well as mixtures, mimicking the amino acid complexity found in algal biomass. The presence of interferences that may be derived from the complex biomass biochemical composition was tested during the method validation phase. We document the application of a novel method of OPA derivatization with 3-mercaptopropionic acid (3MPA) to determine the total amino acid content of harvested algal biomass collected from different, controlled cultivation conditions and demonstrated a within 10% accuracy against a reference measurement of amino acid content in at least 4 species and 10 algal biomass samples, across early, mid, and late-stages of cultivation.

09 BIOMASS FUELS↗

DOE OSTI2024

Selective laser sintering and spark plasma sintering of (Zr,Nb,Ta,Ti,W)C compositionally complex carbide ceramics

Abstract Two advanced manufacturing processes, spark plasma sintering (SPS) and selective laser sintering (SLS), have been developed for synthesis of (Zr,Nb,Ta,Ti,W)C compositionally complex carbide (CCC) via reactive sintering of a powder mixture of constitute monocarbides. X‐ray diffraction analysis confirmed that the single‐phase CCC can be formed by both SPS and SLS. While a homogenous microstructure with uniform metal element distributions was developed during SPS, three‐layer microstructures with a thin TiC‐rich layer and two TaC‐rich layers along with a TiO 2 ‐rich surface layer containing W nanoparticles were formed during SLS. In addition, cellular structures with W, Zr, and Ti element segregation and dislocations on cell boundaries were observed in the SLS‐CCC sample, indicating the effect of nonequilibrium conditions on microstructure formation during laser melting followed by rapid cooling and solidification process. Compared to the SPS‐CCC sample, the SLS‐CCC showed enhanced hardness and reduced thermal conductivity, which may be related to their unique cellular structures.

36 MATERIALS SCIENCE↗

DOE OSTI2018

Solidification pattern, microstructure and texture development in Laser Powder Bed Fusion (LPBF) of Al10SiMg alloy

Highlights: • The complex solidification pattern during Laser Powder Bed Fusion of Al10SiMg alloy is explained. • The evolution of α-Al cellular network, grain structure and texture development is characterized. • The grain structure is shown to be columnar throughout the printed sample • The grains’ orientation align with that of the α-Al cells. • The size evolution of α-Al cells and grains within the scan tracks follow opposite patterns. • Utilizing of a 67° hatch angle enhances densification and promotes a more isotropically developed texture across the build. - Abstract: A comprehensive analysis of solidification patterns and microstructural development is presented for an Al10SiMg sample produced by Laser Powder Bed Fusion (LPBF). Utilizing a novel scanning strategy that involves counter-clockwise rotation of the scan vector by 67° upon completion of each layer, a relatively randomized cusp-like pattern of protruding/overlapping scan tracks has been produced along the build direction. We show that such a distribution of scan tracks, as well as enhancing densification during LPBF, reduces the overall crystallographic texture in the sample, as opposed to those normally achieved by commonly-used bidirectional or island-based scanning regimes with 90° rotation. It is shown that, under directional solidification conditions present in LPBF, the grain structure is strictly columnar throughout the sample and that the grains' orientation aligns well with that of the α-Al cells. The size evolution of cells and grains within the melt pools, however, is shown to follow opposite patterns. The cells'/grains' size distribution and texture in the sample are explained via use of analytical models of cellular solidification as well as the overall heat flow direction and local solidification conditions in relation to the LPBF processing conditions. Such a knowledge of the mechanisms upon which microstructural features evolve throughout a complex solidification process is critical for process optimization and control of mechanical properties in LPBF.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Liquid Chromatography Mass Spectrometry study of eutectic bis(2,2-dinitropropyl) acetal/formal

This study is the first attempt to document methodology development undergone using liquid chromatography tandem quadrupole time of flight mass spectrometry (LC-QTOF) to investigate degradation products of eutectic bis(2,2-dinitropropyl) acetal/formal nitroplasticizer (called NP here). Method properties investigated are: desolvation temperature (°C) and spray voltage (V) of the electrospray ionization source, and the development of an acetone system rinse to prevent any residual contamination between sample injections. Details are given on why it is essential to investigate method optimization with changes shown in MS/MS analysis in addition to MS results. Trends in MS/MS analytic results reveal important relationships between baseline and aged materials. In addition to verification of previously proposed fragments, insights offered by this newly developed methodology will also identify new degradation products and shed light on the complexity of NP degradation chemistry.

36 MATERIALS SCIENCE↗

DOE OSTI2026

Exploring the potential of using L-Band InSAR for the mapping of flooded vegetation in tropical wetlands

Wetlands play a critical role in global water and carbon cycles, yet monitoring their water extent remains difficult, particularly beneath dense vegetation. SAR-based techniques such as backscatter thresholding are limited by complex scattering mechanisms, while fully polarimetric SAR (PolSAR) data capable of detecting doublebounce scattering remain scarce. To address these challenges, this study evaluates the potential of Interferometric SAR (InSAR) for mapping water surfaces beneath vegetation, termed flooded vegetation, using the Atrato floodplain in Colombia as a case study. We develop an automated workflow combining InSAR fringe detection with local phase homogeneity analysis and random sampling of processing parameters to generate probabilistic flooded vegetation maps. Applied to ALOS PALSAR-1 L-band image pairs from 2007–2011, the workflow captures seasonal fluctuations in flooded extent ranging from 500 to 1,500 km2. Compared to other L-band SAR inundation products, the InSAR-based maps identify broader flooded areas, with ~70% agreement in pairwise comparisons. Around 84% of detections align with existing wetland inventories and seasonal changes correspond with regional hydrological indicators, including terrestrial water storage anomalies and water gauge measurements. PolSAR analysis shows that InSAR complements backscatter-based methods by detecting inundation in areas with weak double-bounce signals. These findings suggest that combining InSAR with backscatter-based methods can improve detection of flooded vegetation, which is especially relevant for the upcoming NISAR mission that will offer frequent global L-band observations.

Coastal inundation↗

DOE OSTI2025

Analysis methodology of coherent oscillations in time- and angle-resolved photoemission spectroscopy

Oscillatory signals from coherently excited phonons are regularly observed in ultrafast pump–probe experiments on condensed matter samples. Electron–phonon coupling implies that coherent phonons also modulate the electronic band structure. These oscillations can be probed with energy and momentum resolution using time- and angle-resolved photoemission spectroscopy (trARPES), which reveals the orbital dependence of the electron–phonon coupling for a specific phonon mode. However, a comprehensive analysis remains challenging when multiple coherent phonon modes couple to multiple electronic bands. Complex spectral line shapes due to strong correlations in quantum materials add to this challenge. In this work, we examine how the frequency domain representation of trARPES data facilitates a quantitative analysis of coherent oscillations of the electronic bands. Here, we investigate the frequency domain representation of the photoemission intensity and the first moment of the energy distribution curves. Both quantities provide complementary information and are able to distinguish oscillations of binding energy, linewidth, and intensity. We analyze a representative trARPES dataset of the transition metal dichalcogenide WTe 2 and construct composite spectra, which intuitively illustrate how much each electronic band is affected by a specific phonon mode. We also show how a linearly chirped probe pulse can generate extrinsic artifacts that are distinct from the intrinsic coherent phonon signal.

47 OTHER INSTRUMENTATION↗

DOE OSTI2019

The Quantum Alternating Operator Ansatz on Maximum k -Vertex Cover

The Quantum Alternating Operator Ansatz is a generalization of the Quantum Approximate Optimization Algorithm (QAOA) designed for finding approximate solutions to combinatorial optimization problems with hard constraints. In this paper, we study Maximum k-Vertex Cover under this ansatz due to its modest complexity, while still being more complex than the well studied problems of Max-Cut and Max E3-LIN2. Our approach includes (i) a performance comparison between easy-to-prepare classical states and Dicke states as starting states, (ii) a performance comparison between two XY -Hamiltonian mixing operators: the ring mixer and the complete graph mixer, (iii) an analysis of the distribution of solutions via Monte Carlo sampling, and (iv) the exploration of efficient angle selection strategies.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Exploration of signal processing methods for superconducting magnet and quench data

Quenching is the phenomenon of a superconducting magnetic material carrying current transitioning into a regular conducting material. This may cause severe and irreparable damage to the superconductor due to Joule heating. The Magnet Department at Fermi National Accelerator Laboratory (FNAL) has acquired experimental data through quench antenna arrays that are recorded when the quench is detected. These data are in terms of voltage signals that are sampled at 100kHz for several minutes. There are multiple channels and each channel provides a data set of more than 20 million observations, while there is one channel, called the trigger channel which shows the time when quench is detected. Despite some advancements that were made including machine learning, data complexity still shadows the progress. In this work, we studied a multi-resolution analysis of the quench antenna data through the Haar wavelet transform. In particular, we applied the maximally overlapped discrete w avelet transform (MODWT) of a suitable level L to the given data and then projected it onto the wavelet basis. This decomposes a given signal (Original data) $x ϵ \mathbb{R}^N$ into $L + 1$ subspaces of $\mathbb{R}^N$. One of the subspaces called the approximation, captures the trend of the signal, and the others, called the details, capture the fluctuations at different frequency bands. This decomposition provides a clear trend of the data at a suitable level and also various activities (spikes) are seen in the details of the decomposition at every level. These spikes might reveal some information about the quench under investigation but in any case, give information about magnet behavior. Also, this decomposition is seen to be very useful in removing noise present in the data due to the source or mechanism of the experiment.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗