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All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Detection of active and latent infections with microfluidic devices and systems thereof

The present invention relates to methods of detecting one or more targets of interest in a sample. In one instance, the target can be correlated to an active infection (e.g., by a virus and/or a bacterium). Methods can include treating the sample with a dissociation agent, thereby releasing the target of interest for more accurate detection (e.g., by use of a sedimentation-based centrifugal microfluidic devices). Also described herein are microfluidic devices and systems for use with a dissociation agent.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Finding quadruply imaged quasars with machine learning – I. Methods

ABSTRACT Strongly lensed quadruply imaged quasars (quads) are extraordinary objects. They are very rare in the sky and yet they provide unique information about a wide range of topics, including the expansion history and the composition of the Universe, the distribution of stars and dark matter in galaxies, the host galaxies of quasars, and the stellar initial mass function. Finding them in astronomical images is a classic ‘needle in a haystack’ problem, as they are outnumbered by other (contaminant) sources by many orders of magnitude. To solve this problem, we develop state-of-the-art deep learning methods and train them on realistic simulated quads based on real images of galaxies taken from the Dark Energy Survey, with realistic source and deflector models, including the chromatic effects of microlensing. The performance of the best methods on a mixture of simulated and real objects is excellent, yielding area under the receiver operating curve in the range of 0.86–0.89. Recall is close to 100 per cent down to total magnitude i ∼ 21 indicating high completeness, while precision declines from 85 per cent to 70 per cent in the range i ∼ 17–21. The methods are extremely fast: training on 2 million samples takes 20 h on a GPU machine, and 108 multiband cut-outs can be evaluated per GPU-hour. The speed and performance of the method pave the way to apply it to large samples of astronomical sources, bypassing the need for photometric pre-selection that is likely to be a major cause of incompleteness in current samples of known quads.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

BEACON—automated aberration correction for scanning transmission electron microscopy using Bayesian optimization

Aberration correction is an important aspect of modern high-resolution scanning transmission electron microscopy. Most methods of aligning aberration correctors require specialized sample regions and are unsuitable for fine-tuning aberrations without interrupting on-going experiments. Here, we present an automated method of correcting first- and second-order aberrations called BEACON, which uses Bayesian optimization of the normalized image variance to efficiently determine the optimal corrector settings. We demonstrate its use on gold nanoparticles and a hafnium dioxide thin film showing its versatility in nano- and atomic-scale experiments. BEACON can correct all first- and second-order aberrations simultaneously to achieve an initial alignment and first- and second-order aberrations independently for fine alignment. Ptychographic reconstructions are used to demonstrate an improvement in probe shape and a reduction in the target aberration.

techniques and instrumentation↗
DOE OSTI2025

Single-shot in-line x-ray phase-contrast imaging of void-shockwave interactions in fusion energy materials

Recent breakthroughs in nuclear fusion, specifically the report of reactions exceeding scientific breakeven at the National Ignition Facility (NIF), highlight the potential of inertial fusion energy (IFE) as a sustainable and virtually limitless energy source. However, further progress in IFE requires characterization of defects in ablator materials and how they affect fuel capsule compression. Voids within the ablator can degrade energy yield, but their impact on the density distribution has primarily been studied through simulations, with limited high-resolution experimental validation. To address this, we used the x-ray free-electron laser (XFEL) at the matter in extreme conditions (MECs) instrument at the Linac coherent light source (LCLS) to capture 2D x-ray phase-contrast (XPC) images of a void-bearing sample with a composition similar to inertial confinement fusion (ICF) ablators. By driving a compressive shockwave through the sample using MEC's long-pulse laser system, we analyzed how voids influence shockwave propagation and density distribution during compression. To quantify this impact, we extracted phase information using two phase retrieval algorithms. First, we applied the contrast transfer function (CTF) method, paired with Tikhonov regularization and a fast optimization approach to generate an initial phase estimate. We then refined the result using a projected gradient descent (PGD) method that works directly with the sample's refractive index. Comparing these results with radiation adaptive grid Eulerian (xRAGE) radiation hydrodynamic simulations enables identification of model validation needs or improvements. By calculating phase maps in situ, it becomes possible to reconstruct areal density maps, improving understanding of laser-capsule interactions and advancing IFE research.

Hodge, D. S. [Colorado State Univ., Fort Collins, ↗
DOE OSTI2023

DeepThermo: Deep Learning Accelerated Parallel Monte Carlo Sampling for Thermodynamics Evaluation of High Entropy Alloys

Since the introduction of Metropolis Monte Carlo (MC) sampling, it and its variants have become standard tools used for thermodynamics evaluations of physical systems. However, a long-standing problem that hinders the effectiveness and efficiency of MC sampling is the lack of a generic method (a.k.a. MC proposal) to update the system configurations. Consequently, current practices are not scalable. Here we propose a parallel MC sampling framework for thermodynamics evaluation—DeepThermo. By using deep learning–based MC proposals that can globally update the system configurations, we show that DeepThermo can effectively evaluate the phase transition behaviors of high entropy alloys, which have an astronomical configuration space. For the first time, we directly evaluate a density of states expanding over a range of ~e 10,000 for a real material. We also demonstrate DeepThermo’s performance and scalability up to 3,000 GPUs on both NVIDIA V100 and AMD MI250X-based supercomputers.

Yin, Junqi↗
DOE OSTI2024

Maximum a posteriori Ly α estimator (MAPLE): band power and covariance estimation of the 3D Ly α forest power spectrum

We present a novel maximum a posteriori estimator to jointly estimate band powers and the covariance of the three-dimensional power spectrum (P3D) of Ly $\alpha$ forest flux fluctuations, called MAPLE. Our Wiener-filter based algorithm reconstructs a window-deconvolved P3D in the presence of complex survey geometries typical for Ly $\alpha$ surveys that are sparsely sampled transverse to and densely sampled along the line of sight. We demonstrate our method on idealized Gaussian random fields with two selection functions: (i) a sparse sampling of 30 background sources per square degree designed to emulate the current Dark Energy Spectroscopic Instrument; (ii) a dense sampling of 900 background sources per square degree emulating the upcoming Prime Focus Spectrograph Galaxy Evolution Survey. Our proof-of-principle shows promise, especially since the algorithm can be extended to marginalize jointly over nuisance parameters and contaminants, i.e. offsets introduced by continuum fitting. Our code is implemented in JAX and is publicly available on GitHub.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Propagating sample variance uncertainties in redshift calibration: simulations, theory, and application to the COSMOS2015 data

ABSTRACT Cosmological analyses of galaxy surveys rely on knowledge of the redshift distribution of their galaxy sample. This is usually derived from a spectroscopic and/or many-band photometric calibrator survey of a small patch of sky. The uncertainties in the redshift distribution of the calibrator sample include a contribution from shot noise, or Poisson sampling errors, but, given the small volume they probe, they are dominated by sample variance introduced by large-scale structures. Redshift uncertainties have been shown to constitute one of the leading contributions to systematic uncertainties in cosmological inferences from weak lensing and galaxy clustering, and hence they must be propagated through the analyses. In this work, we study the effects of sample variance on small-area redshift surveys, from theory to simulations to the COSMOS2015 data set. We present a three-step Dirichlet method of resampling a given survey-based redshift calibration distribution to enable the propagation of both shot noise and sample variance uncertainties. The method can accommodate different levels of prior confidence on different redshift sources. This method can be applied to any calibration sample with known redshifts and phenotypes (i.e. cells in a self-organizing map, or some other way of discretizing photometric space), and provides a simple way of propagating prior redshift uncertainties into cosmological analyses. As a worked example, we apply the full scheme to the COSMOS2015 data set, for which we also present a new, principled SOM algorithm designed to handle noisy photometric data. We make available a catalogue of the resulting resamplings of the COSMOS2015 galaxies.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Analysis of Glycolate in Radioactive Waste by Ion Chromatography (IC) and Proton Nuclear Magnetic Resonance (H NMR)

Here, in preparation for implementing the Nitric-Glycolic (NG) acid flowsheet for the Savannah River Site (SRS) Liquid Waste System (LWS), analytical methods for determining glycolate at low concentration, below 20 mg/L in radioactive samples, were developed to support system management and safety. To accommodate the wide range of LWS matrix conditions, two alternative methods were developed, refined, and demonstrated for glycolate analysis in radioactive waste samples: ion chromatography (IC) and a proton nuclear magnetic resonance (H NMR). Investigators validated IC and H NMR methods for glycolate analysis, defined the range of applicability, and demonstrated key supporting analytical protocols. The deployed IC method is applicable in low to moderate ionic strength samples and requires sample pretreatment using a Dionex OnGuard II H + cartridge. The deployed H NMR method is more labor intensive but provides options for a broader range of matrices. Based on the results, high quality glycolate analysis of the Defense Waste Processing Facility (DWPF) condensate in Tank 22 is feasible by IC down to approximately 12 mg/L. Using H NMR, glycolate may be determined to 8 mg/L or lower depending on the run time with the potential for broader applicability of the method to higher ionic strength conditions in other tanks of the SRS LWS.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2022

A high-throughput skim-sequencing approach for genotyping, dosage estimation and identifying translocations

The development of next-generation sequencing (NGS) enabled a shift from array-based genotyping to directly sequencing genomic libraries for high-throughput genotyping. Even though whole-genome sequencing was initially too costly for routine analysis in large populations such as breeding or genetic studies, continued advancements in genome sequencing and bioinformatics have provided the opportunity to capitalize on whole-genome information. As new sequencing platforms can routinely provide high-quality sequencing data for sufficient genome coverage to genotype various breeding populations, a limitation comes in the time and cost of library construction when multiplexing a large number of samples. Here we describe a high-throughput whole-genome skim-sequencing (skim-seq) approach that can be utilized for a broad range of genotyping and genomic characterization. Using optimized low-volume Illumina Nextera chemistry, we developed a skim-seq method and combined up to 960 samples in one multiplex library using dual index barcoding. With the dual-index barcoding, the number of samples for multiplexing can be adjusted depending on the amount of data required, and could be extended to 3,072 samples or more. Panels of doubled haploid wheat lines ( Triticum aestivum , CDC Stanley x CDC Landmark), wheat-barley ( T . aestivum x Hordeum vulgare ) and wheat-wheatgrass ( Triticum durum x Thinopyrum intermedium ) introgression lines as well as known monosomic wheat stocks were genotyped using the skim-seq approach. Bioinformatics pipelines were developed for various applications where sequencing coverage ranged from 1 × down to 0.01 × per sample. Using reference genomes, we detected chromosome dosage, identified aneuploidy, and karyotyped introgression lines from the skim-seq data. Leveraging the recent advancements in genome sequencing, skim-seq provides an effective and low-cost tool for routine genotyping and genetic analysis, which can track and identify introgressions and genomic regions of interest in genetics research and applied breeding programs.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Bioconversion and quantification of humic substances from low rank coals using indigenous fungal isolates

The major portion of coals around the world belongs to lignitic origin, and burning of these Low Rank Coals (LRCs) not only produces energy, but also release harmful gases into the environment. On the other hand, coal is a mega source of fossilized carbon compounds that can be utilized in diverse range of carbon/organic industries. Biosolubilization is one of the safest and economical way to consume these LRCs for the harvest of humic and fulvic acids for industrial applications. Present studies deal with solubilization of coal samples from five different mines of Punjab, Pakistan by indigenously isolated fungus. From a number of indigenously isolated fungal isolates, an isolate NF-2 was selected based on its solubilization potential on solid Sabouraud medium. The intensity of coal biosolubilization was found maximum for coal sample B-1 (59%) and lowest for sample B-26 (17.2%) with 5% (w/v) pulp density at 28 ± 2°C. Humification index value (A 4 /A 6 ) for biosolubilized products of coal sample B-1 was found 6.18 which was much higher than the A 4 /A 6 value (4.27) of commercially available standard humic acid. Biosolubilized products from coal sample B-1 was found maximum with 8681 mg/L humic acid concentration as determined by standard curve method. FTIR and FE-SEM analyses of sample B-1 treated with NF-2 confirmed the structural break down and solubilization of coal. Molecular identification of fungal isolate NF-2 showed 100% similarity to Aspergillus flavus. Here, this work paves the way to utilize lignitic coals for the environment friendly and low-cost production of humic acids by fungal biosolubilization as an alternate to chemical methods.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Systems and methods for active learning from sparse training data

A method for active learning using sparse training data can include training a machine learning model using less than ten first training data points to generate a candidate machine learning model. The method can include performing a Monte Carlo process to sample one or more first outputs of the candidate machine learning model. The method can include testing the one or more first outputs to determine if each of the one or more first outputs satisfy a respective convergence condition. The method can include, responsive to at least one first output not satisfying the respective convergence condition, training the candidate machine learning model using at least one second training data point corresponding to the at least one first output. The method can include, responsive to the one or more first outputs each satisfying the respective convergence condition, outputting the candidate machine learning model.

Sankaranarayanan, Subramanian↗
DOE OSTI2021

Deciphering the source of primary biological aerosol particles: a pollen case study

Primary biological aerosol particles (PBAPs) are microscopic solids suspended in the atmosphere emitted by biological systems and play critical roles in the atmosphere and at the atmosphere-biosphere interface, impacting human health, climate, and the ecosystem function. Understanding the sources of PBAPs is necessary to decipher the mechanistic interactions between aerosols, climate, and distinct ecosystem components. However, the detection of specific PBAPs in complex ambient aerosol samples is challenging. We performed metabolomics analyses of pollen from three pollinating tree species and ambient samples collected during the peak pollination period of each species. Random Forest and sPLS-DA machine learning methods were employed to evaluate whether metabolic signatures of ambient samples can reveal the source of the main pollen particles present in the atmosphere. Our results suggest that atmospheric eco-metabolomics techniques combined with sophisticated statistical methods can decipher the origin of abundant PBAPs from complex ambient samples. Developing complete libraries containing high-resolution metabolomic fingerprints of the major PBAPs present in the atmosphere would significantly advance future research to accurately understand the role of PBAPs in the atmosphere, ecosystems and human health.

Rivas-Ubach, Albert↗
DOE OSTI2023

IsoMatchMS : Open-Source Software for Automated Annotation and Visualization of High Resolution MALDI-MS Spectra

Due to its speed, accuracy, and adaptability to various sample types, matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) has become a popular method to identify molecular isotope profiles from biological samples. Often MALDI-MS data do not include tandem MS fragmentation data, and thus the identification of compounds in samples requires external databases so that the accurate mass of detected signals can be matched to known molecular compounds. Most relevant MALDI-MS software tools developed to confirm compound identifications are focused on small molecules (e.g., metabolites, lipids) and cannot be easily adapted to protein data due to their more complex isotopic distributions. Here, we present an R package called IsoMatchMS for the automated annotation of MALDI-MS data for multiple datatypes: intact proteins, peptides, and glycans. This tool accepts already derived molecular formulas or, for proteomics applications, can derive molecular formulas from a list of input peptides or proteins including proteins with post-translational modifications. In conclusion, visualization of all matched isotopic profiles is provided in a highly accessible HTML format called a trelliscope display, which allows users to filter and sort by several parameters such as match scores and the number of peaks matched. IsoMatchMS simplifies the annotation and visualization of MALDI-MS data for downstream analyses.

47 OTHER INSTRUMENTATION↗
DOE OSTI2021

Direct determination of cellulosic glucan content in starch-containing samples

A simple and highly selective analytical procedure is presented for the determination of cellulosic glucan content in samples that contain both cellulose and starch. This method eliminates the unacceptably large compounding errors of current two-measurement methods. If both starch and cellulose are present before analytical hydrolysis, both will be hydrolyzed to glucose causing bias and inaccuracy in the method. To prevent this interference, the removal of starch prior to cellulosic quantification is crucial. The method presented here is a concise in-series procedure with minimal measurements, eliminating large compounding errors. Sample preparation consists of a starch extraction employing enzymatic hydrolysis followed by a simple filtration and wash. The samples are then subjected to a two-stage acid hydrolysis. The concentration of glucose is determined by ion exchange high-performance liquid chromatography with a Pb 2+ column and a refractive index detector. The cellulosic glucan content is calculated based on the initial dry weight of the starting material. Data for the native biomass materials studied show excellent reproducibility, with coefficients of variance of 3.0% or less associated with the method. This selectivity for cellulosic glucan by the procedure was validated with several analytical techniques such as liquid chromatography coupled with mass spectrometry (LC–MS), Raman spectroscopy, and nuclear magnetic resonance.

09 BIOMASS FUELS↗
DOE OSTI2021

Aerosol jet printed 3 omega sensors for thermal conductivity measurement

The 3 omega (3ω) method is a trusted technique for measuring thermal conductivity—a fundamental material property of critical importance in a broad range of applications. However, traditional 3ω sensor processing requires some form of physical vapor deposition, such as metal evaporation or sputtering. These 3ω sensor deposition techniques limit the materials and sample sizes applicable to the 3ω method. This work demonstrates an aerosol jet printing method to directly print silver 3ω sensors that yield accurate temperature-dependent measurement up to 300 °C on materials with thermal conductivity ranging from 1 to 150 W/m K. The interrelationship between printed sensor geometry, sensor thermal stability, and applicability to the 3ω method is examined. Thermal conductivity measurement with 3ω sensors conventionally sintered at 300 °C agrees to independent laser flash measurement within 4% from room temperature to 150 °C. An unconventional rapid high-temperature sintering method is shown to produce sensors that agree within 3% of the laser flash measurements from room temperature to 300 °C. The rapid sintering profiles also reduced the sensor–substrate thermal boundary resistance of the printed sensors by as much as 88%. The direct printing of 3ω sensors creates opportunities for measurement of thermal transport properties in applications previously inapplicable to the 3ω method.

47 OTHER INSTRUMENTATION↗
DOE OSTI2026

Absorber Clamp for Microcalorimeter Decay Energy Spectrometry

Microcalorimeter Decay Energy Spectrometry (DES) is of interest to nuclear safeguards due to its ability to provide high precision isotopic compositions of nanogram-to microgram-scale samples of Pu and U and related daughter products. The DES method is able to record decay energy of each alpha-decay event in a sample that is embedded in a metal matrix (absorber) and thermally linked to a microcalorimeter detector. This work optimizes the DES technique used to thermally link the absorber and microcalorimeter detector element to allow for more rapid assembly and to increase detector performance and operating life. Optimized attachment methods are crucial for enhancing the viability of DES in high-sample-throughput facilities, such as those that support international nuclear safeguards measurements. Here, in this study, we designed and implemented a pressure-based absorber clamp and evaluated the performance of this new attachment method relative to pressed indium bond attachment. Results using the absorber clamp demonstrate a streamlined detector assembly procedure that minimizes accidental damage to detectors, as well as increasing detector pulse speeds by 57%. Spectral comparison shows the clamp preserves detector performance relative to indium attachment.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2024

Validation of the stochastic inversion algorithm for acoustic travel-time tomography: a large eddy simulation study

Acoustic tomography (AT) is explored as a remote sensing technique to obtain instantaneous snapshots of temperature and velocity fluctuations for wind energy applications. This study integrates Large Eddy Simulation (LES) with the Stochastic Inversion (SI) method to validate the algorithm’s capacity for accurate reconstruction of atmospheric fluctuations. The initial findings demonstrate the efficacy of the method in accurately capturing the predominant flow structures. Normalized L2 error evaluations further inform the algorithm’s precision, with errors accentuated in less sampled peripheral regions. The results underscore the method’s promise as a non-intrusive observational tool, with ongoing development poised to improve its precision and reliability.

17 WIND ENERGY↗
DOE OSTI2024

Constraining Cosmology with Simulation-based inference and Optical Galaxy Cluster Abundance

We test the robustness of simulation-based inference (SBI) in the context of cosmological parameter estimation from galaxy cluster counts and masses in simulated optical datasets. We construct ``simulations'' using analytical models for the galaxy cluster halo mass function (HMF) and for the observed richness (number of observed member galaxies) to train and test the SBI method. We compare the SBI parameter posterior samples to those from an MCMC analysis that uses the same analytical models to construct predictions of the observed data vector. The two methods exhibit comparable performance, with reliable constraints derived for the primary cosmological parameters, ($\Omega_m$ and $\sigma_8$), and richness-mass relation parameters. We also perform out-of-domain tests with observables constructed from galaxy cluster-sized halos in the Quijote simulations. Again, the SBI and MCMC results have comparable posteriors, with similar uncertainties and biases. Unsurprisingly, upon evaluating the SBI method on thousands of simulated data vectors that span the parameter space, SBI exhibits worsened posterior calibration metrics in the out-of-domain application. We note that such calibration tests with MCMC is less computationally feasible and highlight the potential use of SBI to stress-test limitations of analytical models, such as in the use for constructing models for inference with MCMC.

79 ASTRONOMY AND ASTROPHYSICS↗