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DOE OSTI2023

The use of gas chromatography – high resolution mass spectrometry for suspect screening and non-targeted analysis of per- and polyfluoroalkyl substances

This study is a workflow development for the analysis, identification, and categorization of per- and polyfluoroalkyl substances (PFAS) using gas chromatography-high resolution mass spectrometry (GC-HRMS) with non-targeted analysis (NTA) and suspect screening techniques. The behavior of various PFAS in a GC-HRMS was studied with regards to retention indices, ionization susceptibility, fragmentation patterns, etc. A custom PFAS database was constructed from 141 diverse PFAS. The database contains mass spectra from electron ionization (EI) mode, as well as MS and MS/MS spectra from positive and negative chemical ionization (PCI and NCI, respectively) modes. Common fragments of PFAS were identified across a diverse set of 141 PFAS analyzed. A workflow for suspect screening of PFAS and partially fluorinated products of incomplete combustion/destruction (PICs/PIDs) was developed which utilized both the custom PFAS database and external databases. PFAS and other fluorinated compounds were identified in both a challenge sample (designed to test the identification workflow) and incineration samples suspected to contain PFAS and fluorinated PICs/PIDs. The challenge sample resulted in a 100% true positive rate (TPR) for PFAS which were present in the custom PFAS database. In conclusion, several fluorinated species were tentatively identified in the incineration samples using the developed workflow.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS2000

Martian Magmatic-Driven Hydrothermal Sites: Potential Sources of Energy, Water, and Life

Magmatic-driven processes and impact events dominate the geologic record of Mars. Such recorded geologic activity coupled with significant evidence of past and present-day water/ice, above and below the martian surface, indicate that hydrothermal environments certainly existed in the past and may exist today. The identification of such environments, especially long-lived magmatic-driven hydrothermal environments, provides NASA with significant target sites for future sample return missions, since they (1) could favor the development and sustenance of life, (2) may comprise a large variety of exotic mineral assemblages, and (3) could potentially contain water/ice reservoirs for future Mars-related human activities. If life developed on Mars, the fossil record would presumably be at its greatest concentration and diversity in environments where long-term energy sources and water coexisted such as at sites where long-lived, magmatic-driven hydrothermal activity occurred. These assertions are supported by terrestrial analogs. Small, single-celled creatures (prokaryotes) are vitally important in the evolution of the Earth; these prokaryotes are environmentally tough and tolerant of environmental extremes of pH, temperature, salinity, and anoxic conditions found around hydrothermal vents. In addition, there is a great ability for bacteria to survive long periods of geologic time in extreme conditions, including high temperature hydrogen sulfide and sulfur erupted from Mount St. Helens volcano. Our team of investigators is conducting a geological investigation using multiple mission-derived datasets (e.g., existing geologic map data, MOC imagery, MOLA, TES image data, geophysical data, etc.) to identify prime target sites of hydrothermal activity for future hydrological, mineralogical, and biological investigations. The identification of these sites will enhance the probability of success for future missions to Mars.

Anderson, R. C.↗

DOE OSTI2020

Search for Electron Neutrinos in Multiple Topologies with the MicroBooNE Experiment

This note presents the status of the measurement of electron neutrinos from the Fermilab Booster Neutrino Beamline (BNB) with the MicroBooNE experiment. The analysis is aimed at investigating the nature of the low energy excess of electromagnetic activity observed by the MiniBooNE experiment. The $ν_e$ event selection relies on topological and calorimetric information to characterise particles produced in these interactions, leveraging the Pandora multi-algorithm reconstruction framework as well as custom particle identification and pattern recognition tools. Results presented in this note use 5.88 × 10 20 protons on target of data collected between 2015 and 2018. These include the performance of particle identification tools for $\mu/p$ and $e/\gamma$ separation, along with electromagnetic shower calibration with the largest sample of $\pi^0$ events measured on argon. Progress towards the completion of this analysis is shown through the measurement of high-energy charged-current $ν_e$ interactions and their kinematic distributions using both inclusive (1eX) and exclusive (1$e$0$p$0$\pi$ and 1$e$N$p$0$\pi$) channels. Measurements of charged-current $ν_µ$ interactions aimed at constraining flux and cross-section systematic uncertainties are also shown. We present the analysis’ preliminary sensitivity of an electron-like signal hypothesis to the MiniBooNE excess which includes flux, cross-section, and detector systematic uncertainties.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

NASA NTRS1988

Autonomous star identification for spacecraft attitude control

Research is being conducted to enhance the Advanced Star and Target Reference Optical Scanner (ASTROS I) so that it will be able to automatically track a star and recognize the star's pointing position. Previously developed field identification algorithms, coded on a flight-scale computer, are linked to a breadboard ASTROS star tracker to calculate pointing vectors in real time. A simple graph-searching algorithm was used in an initial study to find stellar positions based on pattern recognition. Results from this study and plans for further development are presented.

Rappaport, Barry↗

DOE OSTI2024

Identification of Potent and Selective Inhibitors of Acanthamoeba : Structural Insights into Sterol 14α-Demethylase as a Key Drug Target

Acanthamoeba are free-living pathogenic protozoa that cause blinding keratitis, disseminated infection, and granulomatous amebic encephalitis, which is generally fatal. The development of efficient and safe drugs is a critical unmet need. Acanthamoeba sterol 14α-demethylase (CYP51) is an essential enzyme of the sterol biosynthetic pathway. Repurposing antifungal azoles for amoebic infections has been reported, but their inhibitory effects on Acanthamoeba CYP51 enzymatic activity have not been studied. Here, we report catalytic properties, inhibition, and structural characterization of CYP51 from Acanthamoeba castellanii. The enzyme displays a 100-fold substrate preference for obtusifoliol over lanosterol, supporting the plant-like cycloartenol-based pathway in the pathogen. The strongest inhibition was observed with voriconazole (1 h IC 50 0.45 μM), VT1598 (0.25 μM), and VT1161 (0.20 μM). The crystal structures of A. castellanii CYP51 with bound VT1161 (2.24 Å) and without an inhibitor (1.95 Å), presented here, can be used in the development of azole-based scaffolds to achieve optimal amoebicidal effectiveness.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

Identification and characterization of proteins of unknown function (PUFs) in Clostridium thermocellum DSM 1313 strains as potential genetic engineering targets

Abstract Background Mass spectrometry-based proteomics can identify and quantify thousands of proteins from individual microbial species, but a significant percentage of these proteins are unannotated and hence classified as proteins of unknown function (PUFs). Due to the difficulty in extracting meaningful metabolic information, PUFs are often overlooked or discarded during data analysis, even though they might be critically important in functional activities, in particular for metabolic engineering research. Results We optimized and employed a pipeline integrating various “guilt-by-association” (GBA) metrics, including differential expression and co-expression analyses of high-throughput mass spectrometry proteome data and phylogenetic coevolution analysis, and sequence homology-based approaches to determine putative functions for PUFs in Clostridium thermocellum . Our various analyses provided putative functional information for over 95% of the PUFs detected by mass spectrometry in a wild-type and/or an engineered strain of C. thermocellum . In particular, we validated a predicted acyltransferase PUF (WP_003519433.1) with functional activity towards 2-phenylethyl alcohol, consistent with our GBA and sequence homology-based predictions. Conclusions This work demonstrates the value of leveraging sequence homology-based annotations with empirical evidence based on the concept of GBA to broadly predict putative functions for PUFs, opening avenues to further interrogation via targeted experiments.

09 BIOMASS FUELS↗

NASA NTRS1976

A target for production of radioxenons

A liquid cesium target has been developed which allows the production and separate identification of the neutron deficient isotopes of xenon. The present report describes irradiations utilizing 34 to 41 MeV protons to produce millicurie quantities of Xe-127 and Xe-129m. At higher energies, however, the target could be used without modification to produce xenon isotopes as light as 119.

Blue, J. W.↗

DOE OSTI2023

Characterization of a platform for the gas transport, collection, and identification of fission products in the high-intensity laser environment

Recent progress in the production of laser accelerated high flux proton beams opens new possibilities for the study of fission in unique environments. To this end, we are currently pursuing the development of a platform for the swift gas transport, collection, and identification of fission products. Fission is induced in targets fixed inside a sealed chamber through which a carrier gas flows, transporting fission products to a carbon filter for collection and online spectroscopy. This has been recently demonstrated using target normal sheath accelerated protons at the PHELIX laser facility. There were large discrepancies between measured rates and those expected based on established fission yields and measured beam parameters. These discrepancies prompted a large number of tests at the Idaho Accelerator Center (IAC), where fission in uranium is induced by bremsstrahlung photons generated by 21 MeV electrons from a linear electron accelerator. Here, the results are compared to a series of models that account for the slowing of energetic fission fragments in the carrier gas and the fluid dynamics of the gas flow that transports fission products to the collection filter. Characterization of the apparatus reveals a few mechanisms that together account for a portion of the previously observed discrepancies at the PHELIX laser facility. However, additional research is necessary before high-accuracy experiments can be performed with the apparatus. Work performed under the auspices of the U.S. Department of Energy by LLNL under contract DE-AC52-07NA27344.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2022

Photo-Brook rearrangement of acyl silanes as a strategy for photoaffinity probe design

Photoaffinity labeling (PAL) is a powerful tool for the identification of non-covalent small molecule–protein interactions that are critical to drug discovery and medicinal chemistry, but this approach is limited to only a small subset of robust photocrosslinkers. The identification of new photoreactive motifs capable of covalent target capture is therefore highly desirable. Herein, we report the design, synthesis, and evaluation of a new class of PAL warheads based on the UV-triggered 1,2-photo-Brook rearrangement of acyl silanes, which hitherto have not been explored for PAL workflows. Irradiation of a series of probes in cell lysate revealed an iPr-substituted acyl silane with superior photolabeling and minimal thermal background labeling compared to other substituted acyl silanes. Further, small molecule (+)-JQ1- and rapamycin-derived iPr acyl silanes were shown to selectively label recombinant BRD4-BD1 and FKBP12, respectively, with minimal background. Together, these data highlight the untapped potential of acyl silanes as a novel, tunable scaffold for photoaffinity labeling.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

cotH Genes Are Necessary for Normal Spore Formation and Virulence in Mucor lusitanicus

Mucormycosis is an invasive fungal infection caused by certain members of the fungal order of Mucorales. The species most frequently identified as the etiological agents of mucormycosis belong to the genera Rhizopus , Lichtheimia , and Mucor . The frequency of systemic mucormycosis has been increasing, mainly because of increasing numbers of susceptible patients. Furthermore, Mucorales display intrinsic resistance to the majority of routinely used antifungal agents (e.g., echinocandins and short-tailed azoles), which limits the number of possible therapeutic options. All the above-mentioned issues urge the improvement of molecular identification methods and the discovery of new antifungal targets and strategies. Spore coat proteins (CotH) constitute a kinase family present in many pathogenic bacteria and fungi and participate in the spore formation in these organisms. Moreover, some of them can act as virulence factors being receptors of the human GRP78 protein during Rhizopus delemar-induced mucormycosis. We identified 17 cotH -like genes in the Mucor lusitanicus genome database. Successful disruption of five cotH genes in Mucor was performed using the CRISPR-Cas9 system. The CotH3 and CotH4 proteins play a role in adaptation to different temperatures as well as in developing the cell wall structure. We also show CotH4 protein is involved in spore wall formation by affecting the total chitin content and, thus, the composition of the spore wall. The role of CotH3 and CotH4 proteins in virulence was confirmed in two invertebrate models and a diabetic ketoacidosis (DKA) mouse model.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Characterization of cubic Li$_{2}$$^{100}$MoO$_4$ crystals for the CUPID experiment

The CUPID Collaboration is designing a tonne-scale, background-free detector to search for double beta decay with sufficient sensitivity to fully explore the parameter space corresponding to the inverted neutrino mass hierarchy scenario. One of the CUPID demonstrators, CUPID-Mo, has proved the potential of enriched Li$_{2}$$^{100}$MoO$_4$ crystals as suitable detectors for neutrinoless double beta decay search. In this work, we characterised cubic crystals that, compared to the cylindrical crystals used by CUPID-Mo, are more appealing for the construction of tightly packed arrays. We measured an average energy resolution of (6.7$\pm$0.6) keV FWHM in the region of interest, approaching the CUPID target of 5 keV FWHM. We assessed the identification of $\alpha$ particles with and without a reflecting foil that enhances the scintillation light collection efficiency, proving that the baseline design of CUPID already ensures a complete suppression of this $\alpha$-induced background contribution. We also used the collected data to validate a Monte Carlo simulation modelling the light collection efficiency, which will enable further optimisations of the detector.

100Mo↗

DOE OSTI2025

Calculating Methane Emissions from Offshore Facilities Using Bottom-Up Methods

With changing demands in regulation, understanding methane emissions from offshore oil and gas production infrastructure has become increasingly important. Reported emissions from facilities in the Gulf of Mexico range from zero to thousands of tons of methane per hour, but these is currently no clear understanding of how this range compares to expected emissions from normally operating facilities. To generate realistic emission estimates, we create two bottom-up models that simulate emissions from facilities operating in the Gulf of Mexico. We estimate type 1 prototypical facilities (typically unmanned, older, lower-producing platforms in shallow water with little processing equipment, compressors, or storage tanks) to emit an average of 13 kg CH 4 h −1 , which corresponds to a loss of 2.7% of the average facility production. Type 2 prototypical facilities (continuously manned, higher production and operate in deeper water with processing equipment, oil storage tanks, compressors and power generation) emit an average of 88 kg CH 4 h −1 , which corresponds to a loss of 2.5% of production. The average measured emission from type 1 facilities was 18 kg CH 4 h −1 with a median production loss estimated at 8%. The average measured emission from type 2 facilities was 36 kg CH 4 h −1 with a median production loss estimated at 2.4%. Using emission factors that consider the long-tail emission distribution partly reconciles the difference between modelled and measured emission estimates, but we suggest the current the fugitive emission estimate may be an underestimate and more data on the number and size of fugitive emissions could explain differences between the modelled and measured emission estimate. We suggest the bottom-up approach described here that uses production data coupled with facility equipment could be used to identify facilities that have abnormally large measured emissions, caused by methodological failure or larger than expected fugitive emissions, which should be targeted for further evaluation resulting in remeasurement or identification of source type so that a more accurate estimates can be made on the absolute emission.

bottom-up↗

NASA NTRS1992

Atmospheric effects on cratering efficiency

The dramatic effects of an atmosphere on impact excavation of particulate targets are investigated, with emphasis on common trends and systematic differences for contrasting target types. The observed differences are reconciled through identification of additional atmospheric effects and consideration of scaling relations. When both static (ambient) and dynamic (drag) atmospheric pressure controls crater growth, the combined factors exhibit a functional dependence consistent with the coupling-parameter exponents suggested by Holsapple and Schmidt (1987). The disturbed air mass accompanying the projectile at laboratory scales is observed to further modify cratering efficiency. The effect of projectile-atmosphere interactions depends on the degree of coupling between the air disturbance and the impactor. At very high velocities (M greater than 10), the air disturbance changes the effective impactor dimension. If the dimensionless scaling parameters can be applied to broader planetary scales, these results have implications for interpreting the size of craters on surfaces with contrasting atmospheric envelopes.

Schultz, Peter H.↗

NASA NTRS1993

Techniques used for the analysis of oculometer eye-scanning data obtained from an air traffic control display

The methodology and techniques used to collect and analyze look-point position data from a real-time ATC display-format comparison experiment are documented. That study compared the delivery precision and controller workload of three final approach spacing aid display formats. Using an oculometer, controller lookpoint position data were collected, associated with gaze objects (e.g., moving aircraft) on the ATC display, and analyzed to determine eye-scan behavior. The equipment involved and algorithms for saving, synchronizing with the ATC simulation output, and filtering the data are described. Target (gaze object) and cross-check scanning identification algorithms are also presented. Data tables are provided of total dwell times, average dwell times, and cross-check scans. Flow charts, block diagrams, file record descriptors, and source code are included. The techniques and data presented are intended to benefit researchers in other studies that incorporate non-stationary gaze objects and oculometer equipment.

Crawford, Daniel J.↗

NASA NTRS1996

(abstract) Physical Properties of 253 Mathilde from Groundbased Observations

The only physical observations which predate the identifications of 253 Mathilde as a potential flyby target of NEAR were measurements of its absolute magnitude in reflected light and thermal radiometry by IRAS. Mathilde has been revealed to be an unusual object, of a class not previously visited by a spacecraft.

Mathilde 253 IRAS albedo flyby↗

DOE OSTI2024

Calibration of the DUNE Far Detector Using Cosmic-ray Muon Events

The Deep Underground Neutrino Experiment (DUNE) aims to set new limits on parameters associated with neutrino oscillations, neutrino astrophysics, and beyond the Standard Model (SM) searches such as nucleon decay. DUNE will quantify the magnitude of CP violation in the lepton sector, and determine the neutrino mass ordering. These benefit highly from the large target mass and excellent imaging, tracking, and particle identification capabilities of Liquid Argon Time Projection Chambers (LArTPCs). Detector calibration is essential to make precise physics measurements. For instance, accurate energy reconstruction is necessary for measuring many of the aforementioned quantities with the precision required for discovering new physics and fully exploiting the capabilities of the detector. Cosmic muons are a freely available natural source of calorimetric data and can be used for calibrating various detector parameters. This thesis provides an analysis of simulated cosmic-ray muon events generated with the Muon Simulation Underground (MUSUN) generator in the DUNE horizontal drift (HD) far detector (FD). The study focuses on analysing the energy and angular distribution of various classes of muon events, as well as characterising the different particles produced by cosmic muon interactions. The analysis of π0 → 2γ events within the cosmic-ray muon sample is presented in this thesis with a detailed study of reconstructing electromagnetic showers. The π0 mass is reconstructed within the DUNE FD, yielding a value of (136 ± 7) MeV/c2. Additionally, the thesis introduces methods for dE/dx calibration using simulated and reconstructed muon tracks. A calibration constant Ccal = (5.469 ± 0.003) × 10−3 ADC × tick/e is obtained through a model-dependent calibration process, where 1 tick corresponds to 500 ns of sampling time of an ADC. Furthermore, a calibration technique is presented, demonstrating precise translation from dQ/dx to dE/dx. This calibration method is applied to stopping muons, charged pions, and protons in the DUNE FD, addressing the measurement of energy loss in the detector volume. These are important calibrations of the DUNE FD and will contribute to achieving the exciting physics goals of the experiment.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

NASA NTRS2020

Back to the Future: Surveying the Northern Hemisphere and Reprocessing the Southern TESS Data Set

TESS launched 18 April 2018 to conduct a two-year, near all-sky survey for at least 50 small, nearby exoplanets for which masses can be ascertained and whose atmospheres can be characterized by ground- and space-based follow-on observations. TESS has completed its survey of the southern hemisphere and begun its survey of the northern hemisphere, identifying >1000 candidate exoplanets and unveiling a plethora of exciting non-exoplanet astrophysics results, such as asteroseismology, asteroids, and supernova. The TESS Science Processing Operations Center (SPOC) processes the data downlinked every two weeks to generate a range of data products hosted at the Mikulski Archive for Space Telescopes (MAST). For each sector (~1 month) of observations, the SPOC calibrates the image data for both 30-min Full Frame Images (FFIs) and up to 20,000 pre-selected 2-min target star postage stamps. Data products for the 2-min targets include simple aperture photometry and systematic error-corrected flux time series. The SPOC also conducts searches for transiting exoplanets in the 2-min data for each sector and generates Data Validation time series and associated reports for each transit-like feature identified in the search. Multi-sector searches for exoplanets are conducted periodically to discover longer period planets, including those in the James Webb Continuous Viewing Zone (CVZ), which are observed for up to one year. Starting with Sector 8, scattered light from the Earth and Moon contaminated significant portions of the data in each orbit. We have developed algorithms for automated identification of the scattered light features at the individual target level. Previously, data for all stars on a CCD affected by scattered light were manually excluded. The automated flagging will allow us to retain significantly more data for stars that are not affected by the scattered light even though it is occurring elsewhere on the CCD. We also discuss enhancements to the SPOC pipeline and the newly available FFI light curves. The TESS Mission is funded by NASA's Science Mission Directorate as an Astrophysics Explorer Mission.

Jenkins, Jon M.↗

DOE OSTI2025

Sharp detection of low-dimensional structure in probability measures via dimensional logarithmic Sobolev inequalities

Identifying low-dimensional structure in high-dimensional probability measures is an essential pre-processing step for efficient sampling. To identify this structure, we approximate the target measure as a perturbation of an arbitrary reference measure along a few directions in $\mathbb{R}^{d}$. These directions are determined by minimizing an upper bound on the Kullback–Leibler (KL) divergence between the target and its approximation. Our contribution improves upon previous works by leveraging dimensional logarithmic Sobolev inequalities to refine the bound on the KL divergence. These inequalities lead to a uniformly tighter bound on the KL divergence, thereby enhancing the identification of the most significant perturbation directions. In particular, when the target and reference are both Gaussian, minimizing the resulting bound is equivalent to minimizing the KL divergence. We further demonstrate the applicability of this analysis to the squared Hellinger distance, where analogous reasoning shows that the dimensional Poincaré inequality offers improved bounds.

Bayesian inference↗