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At least 145 records · Page 8
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Probabilistic Data-Driven Sampling via Multi-Criteria Importance Analysis

Although supercomputers are becoming increasingly powerful, their components have thus far not scaled proportionately. Compute power is growing enormously and is enabling finely resolved simulations that produce never-before-seen features. However, I/O capabilities lag by orders of magnitude, which means only a fraction of the simulation data can be stored for post hoc analysis. Prespecified plans for saving features and quantities of interest do not work for features that have not been seen before. Data-driven intelligent sampling schemes are needed to detect and save important parts of the simulation while it is running. Here, we propose a novel sampling scheme that reduces the size of the data by orders-of-magnitude while still preserving important regions. The approach we develop selects points with unusual data values and high gradients. Finally, we demonstrate that our approach outperforms traditional sampling schemes on a number of tasks.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Evaluation of dried blood spot sampling for verification of exposure to chemical threat agents

Abstract Purpose Exposure to chemical threat agents (CTAs), including nerve agents, the vesicating agent sulfur mustard, and opioids, remains a significant threat to warfighter and civilian populations. Definitive analytical methods to verify exposure to CTAs require shipping refrigerated or frozen biomedical samples to reference laboratories for analysis. Logistical and financial burdens arise as the transport of biomedical samples is subject to strict restrictions and complex packaging, which, if done incorrectly, can lead to sample deterioration. The use of dried blood spot (DBS) sampling could provide operational improvements for collecting, storing, and shipping important forensic samples. Therefore, this effort focuses on developing DBS techniques with Mitra® 30-µL volumetric absorptive microsampling (VAMS®) devices for use in CTA exposure verification. Methods VAMS® devices were loaded and dried with human whole blood that was exposed to the metabolites pinacolyl methylphosphonic acid (PMPA), ethyl methylphosphonic acid (EMPA), 1,1’sulfonylbis[2-(methylsulfinyl)ethane] (SBMSE), norfentanyl, norcarfentanil, norsufentanil, and norlofentanil. Following extraction from the VAMS® devices, metabolites were detected using liquid chromatography-tandem mass spectrometry (LC–MS/MS). The methods were validated for performance by assessing sensitivity, precision, accuracy, and recovery. Results These methods were sensitive to 1 ng/mL for SBMSE, 0.5 ng/mL for PMPA, EMPA, and norfentanyl; 0.1 ng/mL for norlofentanil, and 0.05 ng/mL for norsufentanil and norcarfentanil. All methods met acceptable precision and accuracy criteria with favorable recovery. Conclusions These results demonstrated the utility of VAMS® in stabilizing human whole blood and show promise as an improved collection method for verification of exposure to various CTAs.

Toxicology↗
NASA NTRS1999

In Situ Identification of Mineral Resources with an X-Ray-Optical "Hands-Lens" Instrument

The recognition of material resources on a planetary surface requires exploration strategies not dissimilar to those employed by early field geologists who searched for ore deposits primarily from surface clues. In order to determine the location of mineral ores or other materials, it will be necessary to characterize host terranes at regional or subregional scales. This requires geographically broad surveys in which statistically significant numbers of samples are rapidly scanned from a roving platform. To enable broad-scale, yet power-conservative planetary-surface exploration, we are developing an instrument that combines x-ray diffractometry (XRD), x-ray fluorescence spectrometry (XRF), and optical capabilities; the instrument can be deployed at the end of a rover's robotic arm, without the need for sample capture or preparation. The instrument provides XRD data for identification of mineral species and lithological types; diffractometry of minerals is conducted by ascertaining the characteristic lattice parameters or "d-spacings" of mineral compounds. D-spacings of 1.4 to 25 angstroms can be determined to include the large molecular structures of hydrated minerals such as clays. The XRF data will identify elements ranging from carbon (Atomic Number = 6) to elements as heavy as barium (Atomic Number = 56). While a sample is being x-rayed, the instrument simultaneously acquires an optical image of the sample surface at magnifications from lx to at least 50x (200x being feasible, depending on the sample surface). We believe that imaging the sample is extremely important as corroborative sample-identification data (the need for this capability having been illustrated by the experience of the Pathfinder rover). Very few geologists would rely on instrument data for sample identification without having seen the sample. Visual inspection provides critical recognition data such as texture, crystallinity, granularity, porosity, vesicularity, color, lustre, opacity, and so forth. These data can immediately distinguish sedimentary from igneous rocks, for example, and can thus eliminate geochemical or mineral ambiguities arising, say between arkose and granite. It would be important to know if the clay being analyzed was part of a uniform varve deposit laid down in a quiescent lake, or the matrix of a megabreccia diamictite deposited as a catastrophic impact ejecta blanket. The unique design of the instrument, which combines Debye-Scherrer geometry with elements of standard goniometry, negates the need for sample preparation of any kind, and thus negates the need for power-hungry and mechanically-complex sampling systems that would have to chip, crush, sieve, and mount the sample for x-ray analysis. Instead, the instrument is simply rested on the sample surface of interest (like a hand lens); the device can interrogate rough rock surfaces, coarse granular material, or fine rock flour. A breadboard version of the instrument has been deployed from the robotic arm of the Marsokhod rover in field trials at NASA Ames, where large vesicular boulders were x-rayed to demonstrate the functionality of the instrument design, and the ability of such a device to comply with constraints imposed by a roving platform. Currently under development is a flight prototype concept of this instrument that will weigh 0.3 kg, using about 4500 J of energy per sample analysis. It requires about 5 min. for XRD analysis, and about 30 min. for XRF interrogation. Its small mass and rugged design make it ideal for deployment on small rovers of the type currently envisaged for the exploration of Mars (e.g., Sojourner-scale platforms). The design utilizes a monolithic P-N junction photodiode pixel array for XRD, a Si PIN photodiode/avalanche photodiode system for XRF, and an endoscopic imaging camera system unobtrusively embedded between the detectors and the x-ray source (the endoscope with its board-mounted camera can be adapted for IR light in addition to visible wavelenths. A rugged, miniature (7 cu cm) x-ray source for the instrument has already been breadboarded.

Marshall, J.↗
NASA NTRS2016

Mars Sample Thermal Control During Mars Ascent and Orbit

Although NASA has no official plans at this time for a mission to return samples from Mars, the Program Formulation Office of the Mars Exploration Program sponsors ongoing mission concept studies, systems analyses, and technology investments which explore different strategies for the potential return of samples from Mars, consistent with the charter of the program and stated priorities of the science community. Maintaining the thermal integrity of collected samples would be very important. In general, samples would be collected, sealed inside tubes, and left on the surface for later retrieval. They would then be inserted into an OS (Orbiting Sample), and carried to a Mars or Solar orbit via a MAV (Mars Ascent Vehicle). Subsequently, an Earth return vehicle would rendezvous with the OS and bring it back to Earth. During ascent from Mars, the OS could serve as the nose cone of the MAV and would be subjected to significant aerodynamic heating from the Martian atmosphere. Once the OS is released from the MAV, its external surface would be exposed to potentially several years of sunlight, eclipse, planetary IR, albedo, and space. The challenge is to ensure that these samples are kept at thermally moderate conditions to preserve their integrity in these widely different environments. Various thermal techniques have been investigated to achieve sample thermal control: use of thermal protection shields and surfaces (ablative and non-ablative) to protect them from adverse exposure to ascent heating, as well combinations of thermo-optical coatings during the orbital phase. The work described herein is part of this ongoing effort & will describe the key challenges related to the thermal control of the potential Mars samples during these phases and the corresponding schemes to overcome them.

Bhandari, Pradeep↗
NASA NTRSDate not supplied

Advances in X-ray Instruments to Support Mars Sample Return

The Mars 2020 Perseverance rover is currently collecting drill cores of ancient igneous and sedimentary rock in and around Jezero crater for potential transport to Earth. These samples from the martian surface will enable detailed mineralogical, geochemical, and petrological measurements to characterize ancient depositional and diagenetic environments, quantitatively age-date the samples, and identify the building blocks for life or evidence for life itself. Furthermore, these drill cores are especially precious because they may represent the most pristine samples from the martian surface and our best chance at identifying martian life, as future sample return missions may be conducted by humans that can introduce biological contaminants to the samples. Because of the importance of these samples, we must take great care in their handling, curation, and preliminary analyses so that they are preserved for scientific measurements for decades to come. In-situ measurements by Perseverance have identified minerals that further warrant special treatment of the returned samples. Hydrated sulfate carbonate, swelling clay minerals, and oxychlorine salts are extremely sensitive to changes in temperature and relative humidity. The structures of hydrated sulfates and oxychlorine minerals, in particular, readily change when exposed to different conditions, meaning the mineral assemblage of the as-returned samples may be lost if the samples aren’t handled properly. Characterizing the as-returned mineral assemblage, particularly of the salts, is essential for reconstructing past aqueous conditions and habitability. To characterize the as-returned mineral assemblage, the samples must be analyzed rapidly before phase changes occur and/or under controlled conditions (e.g., within a glove box). Significant recent advances in X-ray instrumentation for robotic exploration of the solar system have resulted in high-resolution miniaturized instruments that would provide mineralogical, geochemical, and petrological information on the returned martian samples without degradation of the mineral assemblage. Here, we describe a combined X-ray diffractometer/X-ray fluorescence spectrometer (XRD/XRF), an X-ray computed tomographic (XCT) instrument, and a scanned beam XRF mapping instrument that could be used in a glove box so that the martian samples remain under controlled conditions.

E. B. Rampe↗
DOE OSTI2023

Considerations for quantitative in situ X-ray powder diffraction studies of solid-state reactions

The importance of sample preparation in collecting high-fidelity powder diffraction data suitable for quantitative structure and phase analysis is well established. Such powder diffraction experiments are increasingly being appliedin situ, during reactions, to explore solid-state reactivity. When appliedin situ, X-ray diffraction is widely used to gain insight into the mechanism and kinetics, and to identify dynamic intermediate states. Here, using a model ion-exchange reaction (NaFeO 2 + LiCl → LiFeO 2 + NaCl), we show that sample preparation not only influences the fidelity of powder diffraction analysis but also impacts the observed reaction progress. Specifically, we found that the observed reaction progress can differ by ∼50% depending on the capillary sample preparation. Thus, forin situdiffraction studies of solid-state reactions, packing fraction is an important and previously unrecognized consideration that impacts reproducibility and fidelity of the reaction study.

Chemistry↗
NASA NTRS2012

The Importance of Meteorite Collections to Sample Return Missions: Past, Present, and Future Considerations

While much of the scientific community s current attention is drawn to sample return missions, it is the existing meteorite and cosmic dust collections that both provide the paradigms to be tested by these missions and the context for interpreting the results. Recent sample returns from the Stardust and Hayabusa missions provided us with new materials and insights about our Solar System history and processes. As an example, Stardust sampled CAIs among the population of cometary grains, requiring extensive and unexpected radial mixing in the early solar nebula. This finding would not have been possible, however, without extensive studies of meteoritic CAIs that established their high-temperature, inner Solar System formation. Samples returned by Stardust also revealed the first evidence of a cometary amino acid, a discovery that would not have been possible with current in situ flight instrument technology. The Hayabusa mission provided the final evidence linking ordinary chondrites and S asteroids, a hypothesis that developed from centuries of collection and laboratory and ground-based telescopic studies. In addition to these scientific findings, studies of existing meteorite collections have defined and refined the analytical techniques essential to studying returned samples. As an example, the fortuitous fall of the Allende CV3 and Murchison CM2 chondrites within months before the return of Apollo samples allowed testing of new state-of-the-art analytical facilities. The results of those studies not only prepared us to better study lunar materials, but unanticipated discoveries changed many of our concepts about the earliest history and processes of the solar nebula. This synergy between existing collections and future space exploration is certainly not limited to sample return missions. Laboratory studies confirmed the existence of meteorites from Mars and raised the provocative possibility of preservation of ancient microbial life. The laboratory studies in turn led to a new wave of Mars exploration that ultimately could lead to sample return focused on evidence for past or present life. This partnership between collections and missions will be increasingly important in the coming decades as we discover new questions to be addressed and identify targets for for both robotic and human exploration . Nowhere is this more true than in the ultimate search for the abiotic and biotic processes that produced life. Existing collections also provide the essential materials for developing and testing new analytical schemes to detect the rare markers of life and distinguish them from abiotic processes. Large collections of meteorites and the new types being identified within these collections, which come to us at a fraction of the cost of a sample return mission, will continue to shape the objectives of future missions and provide new ways of interpreting returned samples.

Welzenbach, L. C.↗
NASA NTRS2018

Maximum Sample Temperature for Mars Sample Return: A Historical Perspective

Since the first Mars Sample Return (MSR) report published by the Jet Propulsion Laboratory (JPL) in 1974 [1], a series of panels, reports, and white papers have recognized the importance of sample temperature and offered an informed sample maximum temperature (henceforth SMT) limit for returning martian samples to Earth. The Mars Sample Handling and Requirements Panel (MSHARP, 1999) stated that "[t]he main issue in sample preservation is temperature" [2]. More recently, the Mars Exploration Program Analysis Group (MEPAG)'s "Science Priorities for Mars Sample Return" report (2008), declared that "[s]ignificant loss, particularly to biological studies, occurs if samples reach +50C for three hours", whereby "scientific objectives related to life goals could be seriously compromised" [3]. By contrast, the Mars 2020 mission has adopted a SMT of +60C as spelled out in Beaty et al., 2016 [4]. Samples will be collected and then deposited on the surface in sealed tubes for possible retrieval and return to Earth. Beaty et al. [4] calculates that the samples will experience maximum temperatures of ~+30 to +60C, depending on latitude. At present, there is no mission requirement for the measurement/data logging of sample temperature during this period. We will explore the history of martian SMTs, as they have been recorded since 1974 [1], effectively representing input across multiple generations of Mars scientists. Ten separate publications present SMTs for MSR samples [1-10]. One report [10] is for a mission concept specifically designed to exclude life detection investigations, and recommended an SMT of 50C. Another did not specify a temperature, recommending "Mars ambient temperature" [5]. Of the remaining eight, SMTs are given as: -30C [1], -20C [3], 60C [4], -73 to 41C depending on sample type [6], -40C [7], -43 to 13C depending on type [2,8], and -33C [9]. If we restrict the temperatures to samples highlighted in the Mars 2020 mission goals, i.e. organics-bearing and sedimentary rocks, then the average SMT is -28+/-39C (n=8). Applying a Dixon's Q Test at P=0.05 (two-tailed), the 60C SMT [4] fails with Q=0.602 versus Qcrit=0.526. Excluding the outlier produces an average SMT of -40+/-17C (n=7). Therefore, the average SMT expressed by the Mars science community over the past 44 years (two generations) is a sample temperature no greater than -40C. The difference in chemical reaction rates between this average SMT and Beaty et al [4] can be estimated using the Arrhenius equation. Assuming a generic chemical reaction with an activation energy of 50 kJ/mol and a pre-exponential factor invariant with temperature, this reaction will proceed 2300x faster at 60C than at -40C. To illustrate the effects of the increased reaction rate, consider 10 ppb of alanine in a Mars 2020 cache, and assume that it becomes unmeasurable if it degrades to 1 ppb, as per the Mars 2020 Organic Contamination Panel contamination limits [11]. If we illustrate the effect with an arbitrary degradation rate such that the alanine will become undetectable in ten years at -40C, then the same 10 ppb alanine degrades beyond detectability in only 38 days at 60C. Further research is required to quantify expected analyte losses in the cached samples due to thermal processing.

Fries, Marc↗
NASA NTRS2024

Will MSR Samples Cached on the Martian Surface Experience Significantly Greater Thermal Degradation than Samples Retained in the Rover?

Since the first Mars Sample Return (MSR)-related report published by the Jet Propulsion Laboratory (JPL) in 1974, a series of panels, reports, and white papers have recognized the importance of sample temperature in meeting mission goals and defined a sample maximum temperature (henceforth SMT) limit. The Mars Sample Handling and Requirements Panel (MSHARP, 1999) flatly stated that “[t]he main issue in sample preservation is temperature”. The Mars Exploration Program Analysis Group (MEPAG)’s “Science Priorities for Mars Sample Return” report (2008), declared that “[s]ignificant loss, particularly to biological studies, occurs if samples reach +50°C for three hours ” whereby “scientific objectives related to life goals could be seriously compromised”. Overall, a total of seven panels, white papers, and conference reports adopted a SMT of -40±17°C to preserve samples sufficiently to confidently achieve success in studies of past or present Martian life (see more detail in [5]). In contrast, the Mars 2020 rover (M2020) mission adopted a SMT of +60°C for samples stored on the Martian surface and +50°C for samples retained inside the rover, as stated in a conference poster presented by Beaty et al., 2016. M2020 is currently collecting samples for MSR in tubes. Half of those tubes will be retained within the M2020 rover body (hereafter rover samples, or RS) and half will be deposited on the Martian surface (cached samples or CS), with a currently undetermined number of each collected up to ten years later for return to Earth. CS samples can be expected to experience significantly higher temperatures than RS samples based on their exposed location in sunlight. This work will explore differences in deleterious chemical reaction rates due to thermal environment of both tube types. The findings here should be debated openly and considered when deciding which samples to return to Earth.

M Fries↗
DOE OSTI2023

IACMI Project 4.7: Pultruded Textile Carbon Fiber for Spar Caps (Final Report)

The primary objective of this project was to demonstrate the potential to significantly reduce the cost of wind turbine blades with carbon fiber reinforced polymer (CFRP) structure. Applicability of textile carbon fibers (TCF) were evaluated for use in pultruded spar cap (SC) elements as a path to cost reduction for utility scale wind turbine blades. In earlier work for the Department of Energy (DOE) Wind Energy Technologies Office (WETO), a collaboration of Sandia National Laboratory (SNL), Oak Ridge National Laboratory (ORNL), and Montana State University has demonstrated potential for pultruded TCF to compete with infused fiberglass and commercially available carbon fiber pultruded sections for spar cap construction. In the design cases evaluated, the TCF sections fared well when compared on cost per unit composite stiffness and cost per unit composite compressive strength for those designs [1]. Both stiffness and compressive strength tend to be key factors in the design of blade composite Spar Cap which carry the bulk of the blade structural loads in bending. Spar Cap design tends to distribute largely symmetric tensile and compressive stresses to opposite sides of the spar structure, but since carbon fiber composite compressive strength is typically 20-50% lower than tensile strength, the compressive loading reaches failure levels well before the tensile loading. Stiffness is critical in containing the large tip deflection in high wind loading situations. However, materials and process development were very limited in the earlier study and the work in this project was expanded to make the comparative information more representative of what will be required in order to make further inroads towards implementation. Similar to that study, this project team confirmed that the primary materials of interest for pultruded spar cap elements should be thermoset (TS) resins reinforced by carbon fibers, utilizing as high a percentage of TCF as practical to benchmark cost and performance against commercial carbon fibers. To make the closest comparison possible and eliminate specific test article size, resin selection, and equipment/operational nuance effects, the team planned to pultrude sections with 100% commercially available carbon fiber (Panex 35 carbon fiber from Zoltek) as well as samples utilizing high fractions of TCF. The resin system chosen was based on formulations recommended by large wind industry supplier Hexion and consisted of Hexion resin RSL-4597, curing agent CCA-138, and internal mold release additive 117, along with common kaolin filler ASP400P from BASF. As commonly deployed in spar cap configurations, the team had a mold built to pultrude a rectangular spar cap element of 100mm width and 3mm thickness. The extremely limited number of samples produced for the earlier study were produced with a “generic” epoxy utilized for a variety of applications by the pultruder contracted to produce test articles for demonstration purposes. More importantly, those samples were produced at a fiber fraction only slightly over 50%. Based on feedback from our industrial advisory team for that project and strongly recommended by this project team, the consensus is that it is highly desirable to obtain fiber fractions of 65-68% for significant penetration in wind blade spar cap. Although this requirement has yet to be exhaustively confirmed in readily available information, this was established as a project goal and informally decided we needed to exceed 60% fiber fraction to gain serious industry consideration. Previous TCF pultrusion trials have been challenged by the lack of robust TCF packages, resulting in non-uniform tension across and between tows, as well as excess labor and waste for removal of interleaved paper. The non-uniform tension and associated intermingling of tows in textile acrylic fiber tows and associated difficulties created from broken filaments in carbon fiber conversion inhibit the ordered packing necessary to enhance fiber fraction elevation. (These “cross-overs” are not considered undesirable for textile applications and there is some sense that they might be advantageous for those applications). In addition to work that is ongoing at the acrylic fiber manufacturers to improve their formats, The Institute of Advanced Composites Manufacturing Innovation (IACMI) Project 6.12 (report PA16-0349-6.12-01) [2] has developed and demonstrated a more robust packaging and creeling approach that at least partially addresses these issues, thus improving control of the TCF feed into the pultrusion unit. It was hoped that these and other improvements currently being implemented would allow us to achieve fiber fractions at least approaching these fiber fraction targets. During this project, sections utilizing 100% commercially available carbon fiber reinforcement were produced as a baseline, as well as sections reinforced with about 94% TCF and the balance being commercially available fiber for comparison. The most important finding was that similar to results reported in the earlier WETO-funded project and results from tests of TCF reported at IACMI meetings, this work demonstrated that sections pultruded with TCF in an epoxy resin frequently utilized in actual spar cap production had stiffness and compressive strengths largely comparable to similar sections pultruded with a commercially available carbon fiber also frequently utilized in the wind industry. Although the amount of that data is limited, some of the tensile strength results were actually closer than would have been expected based on fiber strength results provided by the TCF and commercial fiber producers. The actual test data are reported and discussed in detail in Section 5. The pultruded sections dominated by TCF reinforcement were approximately 8-10% lower in fiber fraction than for the sections produced using commercial fiber alone, making direct comparison difficult. The COVID-19 project has provided significant insight into the current state-of-the-art with various TCF product forms. The data obtained in this project will guide the planned improvements at the precursor level, especially in attaining uniform tensioning and payout to facilitate enhanced fiber fractions and overall processability of the TCF composites. The project team is providing guidance to stakeholders concerning the attributes, needs, and potential demand for TCF in wind blade spar caps. Results achieved in this project are consistent with findings in the related work cited [1] and support this guidance and the high potential for this product type. TCF precursor-producing partners continue to express interest in enhancing their product forms and the team looks forward to working with these improved materials as they become available.

42 ENGINEERING↗
NASA NTRSDate not supplied

Interpretable Machine Learning Models for Autonomous Characterization of Analogue Ocean World Seawater Chemistry and Biosignature Potential Using Isotope Ratio Data

Background: Future missions to ocean worlds, such as Enceladus and Europa, will attempt to characterize the subsurface seawater chemistry and assess the potential for life. Such missions will be equipped with capabilities to precisely measure volatile isotopes in plumes, atmospheres, and exospheres. Motivation: While large isotopic fractionations can indicate a biological source, there are signatures resulting from abiotic geochemical processes that mimic isotopic biosignatures. While machine learning (ML) has the potential to disentangle competing effects and biotic mimicry, high-dimensional isotope ratio mass spectrometry (IRMS) data is likely to contain noise/irrelevant features and involve complex statistical interactions that make human inference and interpretation difficult. Further, ML predictions with as far-reaching implications as an extraterrestrial biosignature on an ocean world requires the use of interpretable models (i.e., not “black box” models) with physically and mathematically meaningful feature spaces along with false positive diagnostics. Methods: We use volatile CO2 IRMS data of analogue ocean world seawaters to validate an ML approach to provide biogeochemical context for biosignature detection. We employ a feature selection method called nearest-neighbor projected distance regression (NPDR) that detects statistical interactions and helps elucidate the mechanisms of the Random Forest classification models. Results: We train and validate predictive ML models on volatile CO2 IRMS data of analogue ocean world seawaters to predict major salt components (e.g., MgSO4, NaHCO3), pH, ionic strength, and the presence of biosignatures. Features derived from IRMS measurements are augmented with extracted time-series features. Our results show high test accuracy and interpretability, which is increased by interaction network visualization, sample-wise variable importance scores, and single-sample class probability estimates. We demonstrate an ML mission software solution that triggers autonomous data transmission and biogeochemical sample prediction.

geochemistry↗
NASA NTRS2005

Mineralogy and Petrology of New Antarctic Nakhlite MIL 03346

Among the approx.1300 meteorites returned from Antarctica by the 2003-2004 ANSMET expedition was a 715g nakhlite, MIL 03346, recovered from the Miller Range. Samples of this meteorite were distributed to investigators on December 16, 2004. We were allocated PTS MIL 03346,63,100. This abstract is our preliminary report on the mineralogy and petrology of this important new sample.

McKay, G.↗
DOE OSTI2022

Microbial colonization and persistence in deep fractured shales is guided by metabolic exchanges and viral predation

Background: Microbial colonization of subsurface shales following hydraulic fracturing offers the opportunity to study coupled biotic and abiotic factors that impact microbial persistence in engineered deep subsurface ecosystems. Shale formations underly much of the continental USA and display geographically distinct gradients in temperature and salinity. Complementing studies performed in eastern USA shales that contain brine-like fluids, here we coupled metagenomic and metabolomic approaches to develop the first genome-level insights into ecosystem colonization and microbial community interactions in a lower-salinity, but high-temperature western USA shale formation. Results: We collected materials used during the hydraulic fracturing process (i.e., chemicals, drill muds) paired with temporal sampling of water produced from three different hydraulically fractured wells in the STACK (Sooner Trend Anadarko Basin, Canadian and Kingfisher) shale play in OK, USA. Relative to other shale formations, our metagenomic and metabolomic analyses revealed an expanded taxonomic and metabolic diversity of microorganisms that colonize and persist in fractured shales. Importantly, temporal sampling across all three hydraulic fracturing wells traced the degradation of complex polymers from the hydraulic fracturing process to the production and consumption of organic acids that support sulfate- and thiosulfate-reducing bacteria. Furthermore, we identified 5587 viral genomes and linked many of these to the dominant, colonizing microorganisms, demonstrating the key role that viral predation plays in community dynamics within this closed, engineered system. Lastly, top-side audit sampling of different source materials enabled genome-resolved source tracking, revealing the likely sources of many key colonizing and persisting taxa in these ecosystems. Conclusions: These findings highlight the importance of resource utilization and resistance to viral predation as key traits that enable specific microbial taxa to persist across fractured shale ecosystems. We also demonstrate the importance of materials used in the hydraulic fracturing process as both a source of persisting shale microorganisms and organic substrates that likely aid in sustaining the microbial community. Moreover, we showed that different physicochemical conditions (i.e., salinity, temperature) can influence the composition and functional potential of persisting microbial communities in shale ecosystems. Together, these results expand our knowledge of microbial life in deep subsurface shales and have important ramifications for management and treatment of microbial biomass in hydraulically fractured wells.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Chapter 13: Time-of-Flight Secondary-Ion Mass Spectrometry and Atom Probe Tomography

Time-of-flight secondary-ion mass spectrometry (TOF-SIMS) and atom probe tomography (APT) have many similarities. Both detect the chemical makeup of a solid material at ppm or better sensitivity, while retaining the spatial location information from the signal. Both use a similar principle to measure a signal associated with a given charged secondary ion—the flight time it takes a secondary ion to reach the detector after it is generated. Both are destructive techniques—albeit destructive of very small volumes—because the signal measured is generated by the removal of material from the sample itself. Importantly, both techniques require ultra-high vacuum (UHV) to ensure that the secondary ions, once generated, can reach the detector without collision with other atoms in the gas phase. In the case of TOF-SIMS, the samples can vary from several mm to several inches in size, whereas for APT, the samples are cones several hundred microns in size that are prepared in a special manner (covered in detail later in the chapter). We will discuss the basic fundamentals of each technique and cover several examples of the technique applied to photovoltaic materials, which should give a good idea of the types of information one can gain from TOF-SIMS and APT and how they are complementary as they both operate at different length scales: at the hundreds of microns to hundreds of nanometer scale for TOF-SIMS and at the nanometer to a few angstroms scale for APT.

41 EE - Solar Energy Technologies Office (EE-4S)↗
NASA NTRS2023

Boninites as Mercury Lava Analogues: Geochemical and Spectral Measurements from Pillow Lavas on Cyprus Island

In the absence of Mercurian rocks or meteorites in our collections, komatiites and boninites are often proposed as the best analog rocks to Mercury lavas. However, despite previous work on the possible analogy between komatiites and Mercury rocks, similar work has not been done for boninites. In this work, we investigate the whole-rock geochemistry and visible/near-infrared (VNIR) spectroscopy of boninitic material collected at three specific areas of the Troodos Massif (Cyprus island). The objective is to evaluate if collected boninites, these along with other boninites present in the literature, can be analogous to Mercury geochemical terranes. On average, we find an unusually high MgO/SiO 2 ratio (0.68) for the boninites from the Troodos Massif compared with previous boninite analysis. This MgO/SiO 2 value is most closely related to the high-Mg regions of Mercury, while the average Al 2 O 3 /SiO 2 ratio (0.25) is consistent with the Mercurian intermediate terrain and to the Mercury’s largest pyroclastic deposit. In addition, further affinity to the high-Mg regions and the intermediate terrains of Mercury are shown in regard to Si vs. Mg, Si vs. Ca, and Si vs. Fe content for one sample in particular. We then conduct magmatic modeling on this specific sample to provide a possible parental melt composition for analogue Mercurian magmas. In conclusion, we suggest these specific locations on the Troodos Massif in Cyprus as good geochemical analogue sites for the high-Mg regions of Mercury and explain how boninites could be important benchmark samples for the chemical and spectral data expected from the BepiColombo mission.

Boninites↗
DOE OSTI2023

Recombination smooths the time-signal disrupted by latency in within-host HIV phylogenies

Within-host HIV evolution involves several features that may disrupt standard phylogenetic reconstruction. One important feature is re-activation of latently integrated provirus, which has the potential to disrupt the temporal signal, leading to variation in the branch lengths and apparent evolutionary rates in a tree. Yet, real within-host HIV phylogenies tend to show clear, ladder-like trees structured by the time of sampling. Another important feature is recombination, which violates the fundamental assumption that evolutionary history can be represented by a single bifurcating tree. Thus, recombination complicates the within-host HIV dynamic by mixing genomes and creating evolutionary loop structures that cannot be represented in bifurcating trees. In this paper, we develop a coalescent-based simulator of within-host HIV evolution that includes latency, recombination, and effective population size dynamics that allows us to study the relationship between the true, complex genealogy of within-host HIV evolution, encoded as an Ancestral Recombination Graph (ARG), and the observed phylogenetic tree. To compare our ARG results to the familiar phylogeny format, we calculate the expected bifurcating tree after decomposing the ARG into all unique site trees, their combined distance matrix, and the overall corresponding bifurcating tree. While latency and recombination separately disrupt the phylogenetic signal, remarkably, we find that recombination recovers the temporal signal of within-host HIV evolution caused by latency by mixing fragments of old, latent genomes into the contemporary population. In effect, recombination averages over extant heterogeneity, whether it stems from mixed time-signals or population bottlenecks. Further, we establish that the signals of latency and recombination can be observed in phylogenetic trees despite being an incorrect representation of the true evolutionary history. Using an Approximate Bayesian Computation method, we develop a set of statistical probes to tune our simulation model to nine longitudinally-sampled within-host HIV phylogenies. Because ARGs are exceedingly difficult to infer from real HIV data, our simulation system allows investigating effects of latency, recombination, and population size bottlenecks by matching decomposed ARGs to real data as observed in standard phylogenies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Semi-supervised Bayesian Low-shot Learning

Deep neural networks (NNs) typically outperform traditional machine learning (ML) approaches for complicated, non-linear tasks. It is expected that deep learning (DL) should offer superior performance for the important non-proliferation task of predicting explosive device configuration based upon observed optical signature, a task which human experts struggle with. However, supervised machine learning is difficult to apply in this mission space because most recorded signatures are not associated with the corresponding device description, or “truth labels.” This is challenging for NNs, which traditionally require many samples for strong performance. Semi-supervised learning (SSL), low-shot learning (LSL), and uncertainty quantification (UQ) for NNs are emerging approaches that could bridge the mission gaps of few labels and rare samples of importance. NN explainability techniques are important in gaining insight into the inferential feature importance of such a complex model. In this work, SSL, LSL, and UQ are merged into a single framework, a significant technical hurdle not previously demonstrated. Exponential Average Adversarial Training (EAAT) and Pairwise Neural Networks (PNNs) are chosen as the SSL and LSL methods of choice. Permutation feature importance (PFI) for functional data is used to provide explainability via the Variable importance Explainable Elastic Shape Analysis (VEESA) pipeline. A variety of uncertainty quantification approaches are explored: Bayesian Neural Networks (BNNs), ensemble methods, concrete dropout, and evidential deep learning. Two final approaches, one utilizing ensemble methods and one utilizing evidential learning, are constructed and compared using a well-quantified synthetic 2D dataset along with the DIRSIG Megascene.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Mass Spectral Imaging to Map Plant–Microbe Interactions

Plant–microbe interactions are of rising interest in plant sustainability, biomass production, plant biology, and systems biology. These interactions have been a challenge to detect until recent advancements in mass spectrometry imaging. Plants and microbes interact in four main regions within the plant, the rhizosphere, endosphere, phyllosphere, and spermosphere. This mini review covers the challenges within investigations of plant and microbe interactions. We highlight the importance of sample preparation and comparisons among time-of-flight secondary ion mass spectroscopy (ToF-SIMS), matrix-assisted laser desorption/ionization (MALDI), laser desorption ionization (LDI/LDPI), and desorption electrospray ionization (DESI) techniques used for the analysis of these interactions. Using mass spectral imaging (MSI) to study plants and microbes offers advantages in understanding microbe and host interactions at the molecular level with single-cell and community communication information. More research utilizing MSI has emerged in the past several years. We first introduce the principles of major MSI techniques that have been employed in the research of microorganisms. An overview of proper sample preparation methods is offered as a prerequisite for successful MSI analysis. Traditionally, dried or cryogenically prepared, frozen samples have been used; however, they do not provide a true representation of the bacterial biofilms compared to living cell analysis and chemical imaging. New developments such as microfluidic devices that can be used under a vacuum are highly desirable for the application of MSI techniques, such as ToF-SIMS, because they have a subcellular spatial resolution to map and image plant and microbe interactions, including the potential to elucidate metabolic pathways and cell-to-cell interactions. Promising results due to recent MSI advancements in the past five years are selected and highlighted. The latest developments utilizing machine learning are captured as an important outlook for maximal output using MSI to study microorganisms.

59 BASIC BIOLOGICAL SCIENCES↗