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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 505 records · Page 28
All sourcesNASA NTRSDOE OSTI
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 OSTI2018

Observational Relationship between Entrainment Rate and Environmental Relative Humidity and Implications for Convection Parameterization

Entrainment rate is a critical but highly uncertain quantity in convective parameterizations; especially, the effects of environmental relative humidity on entrainment rate are controversial, or even opposite, in different studies. Analysis of aircraft observations of cumuli from the RACORO and RICO field campaigns shows that entrainment rate is positively correlated with relative humidity. Physical analysis shows that higher relative humidity promotes entrainment by reducing buoyancy in the cloud cores and by weakening downdrafts near the cloud cores. The reduced buoyancy in the cloud cores and weakened downdrafts surrounding the cores further reduce updrafts in the cloud cores; the cloud cores with smaller updrafts are more significantly affected by their environment, resulting in larger entrainment rate. The relationship between entrainment rate and relative humidity is consistent with the buoyancy sorting concept widely used in convection parameterizations. The results provide reliable in situ observations to improve parameterizations of entrainment rate.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2019

Simulation of Mesoscale Cellular Convection in Marine Stratocumulus: 2. Nondrizzling Conditions

This is the second of two large-eddy simulation studies on the mechanisms of mesoscale cellular organization in drizzling (open cells) and nondrizzling marine stratocumulus (closed cells). This study uses a hard nudging approach which maintains fixed horizontal-mean temperature and humidity profiles for a well-mixed boundary layer with a constant boundary layer depth. For the case studied, closed cells develop and broaden by 32 hr to an aspect ratio of 25. Simulations show that the closed-cell mesoscale cellular convection is driven by positive feedback from cloud-induced mesoscale perturbations of longwave radiative cooling. A conceptual model for closed-cell stratocumulus as a mesoscale wavelength hydrodynamic instability in which mesoscale moist and dry anomalies spontaneously grow is presented. In simulations in which long-wavelength sinusoidal moisture anomalies are initially imposed, these anomalies evolve into amplifying closed cells. The cell structure is visualized with a compositing approach based on sorting grid columns by their mesoscale-smoothed total water path. A thermally direct mesoscale circulation pattern develops in the interior of the boundary layer with buoyant mesoscale updrafts, thicker cloud, and a slightly higher capping inversion in the moister columns. There is a mesoscale flow of above-inversion air down the slightly sloping capping inversion from the moist to the dry regions, reinforced by cloud top radiative cooling. This strengthens the mesoscale anomalies by preferentially cooling and drying the already dry regions. The sloping inversion flow is not driven as efficiently if the radiative cooling is artificially horizontally homogenized, partly disrupting this positive feedback and the resulting closed-cell development.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2019

Assessing XMT-Measurement Variability of Air-Water Interfacial Areas in Natural Porous Media

This study investigates the accuracy and reproducibility of air-water interfacial areas measured with high-resolution synchrotron X-ray microtomography (XMT). Columns packed with one of two relatively coarse-grained monodisperse granular media, glass beads or a well-sorted quartz sand, were imaged over several years, encompassing changes in acquisition equipment, improved image quality, and enhancements to image acquisition and to processing software. For the glass beads, the specific solid surface area (SSSA-XMT) of 31.6 ± 1 cm -1 determined from direct analysis of the segmented solid-phase image data is statistically identical to the independently calculated geometric smooth-sphere specific solid surface area (GSSA, 32 ± 1 cm -1 ) and to the measured SSSA (28 ± 3 cm -1 ) obtained with the N2-Brunauer, Emmett, and Teller method. The maximum specific air-water interfacial area (Amax) is 27.4 (±2) cm -1 , which compares very well to the SSSA-XMT, GSSA, and SSSA-N2-Brunauer, Emmett, and Teller values. For the sand, the SSSA-XMT (111 ± 2 cm -1 ) and GSSA (113 ± 1 cm -1 ) are similar. The mean Amax is 96 ± 5 cm -1 , which compares well to both the SSSA and the GSSA values. The XMT-SSSA values deviated from the GSSA values by 7–16% for the first four experiments but were essentially identical for the later experiments. This indicates that enhancements in image acquisition and processing improved data accuracy. The Amax values ranged from 74 cm -1 to 101 cm -1 , with a coefficient of variation (COV) of 9%. The maximum capillary interfacial area ranged from 12 cm-1 to 19 cm -1 , for a COV of 10%. The COVs for both decreased to 5–6% for the latter five experiments. These results demonstrate that XMT imaging provides accurate and reproducible measurements of total and capillary interfacial areas.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2019

Mimicking Geologic Depositional Fabrics for Multiphase Flow Experiments

A novel laboratory technique is presented for generating two-dimensional beadpacks with reproducible natural geologic sedimentary bedforms. The heterogeneous beadpacks are deposited in a 0.6 m × 0.6 m × 0.02 m glass slab chamber using a programmable two-axis linear actuator. The method takes advantage of natural mechanical sorting processes, along with the ability to program the motion of the arm, to efficiently build cross-beds and ripple laminae similar to those seen in natural water-lain clastic deposits. By using a mixture of grain sizes (200 to 800 μm diameter), depositional fabrics with multiscale heterogeneity (mm to dm) are generated. Reproducibility tests show very high correlation among multiple fabric realizations produced with similar inputs. After introducing this first-of-a-kind capability to produce depositionally realistic fabrics at scales larger than that of rock cores, a demonstrative study is presented that illustrates gravity unstable multiphase flow which is relevant in the context of CO 2 sequestration. Preliminary results highlight the dramatic impact small scale capillary heterogeneities have on multiphase immiscible displacement and can help bridge understanding between core scale experiments and reservoir scale observations.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Advancing Cross-Disciplinary Understanding of Land-Atmosphere Interactions

The evolution of disciplinary silos and increasingly narrow disciplinary boundaries have together resulted in one-sided approaches to the study of land-atmosphere interactions—a field that requires a bi-directional approach to understand the complex feedbacks and interactions that occur. The integration of surface flux and atmospheric boundary layer measurements is therefore essential to advancing our understanding. The Land-Atmosphere 2021 workshop (held virtually, June 10-11, 2021) involved almost 300 participants from around the world and promoted cross-discipline collaboration by way of talks from invited speakers, moderated discussions, breakout sessions, and a virtual poster session. The workshop focused on five main theme areas: “big picture” overview, instrumentation and remote sensing, modeling, water, and aerosols and clouds. In talks and breakout groups, there were frequent calls for more AmeriFlux sites to be instrumented for boundary layer height measurements, and for the development of some “super sites” where profiling instruments would be deployed. There was further agreement on the need for the standardization of various datasets. There was also a consensus that funding agencies need to be willing to support the sorts of large projects (including associated instrumentation) which can drive interdisciplinary work. Early-career scientists, in particular, expressed enthusiasm for working across disciplinary boundaries but noted that there need to be more financial support and training opportunities so they would be better prepared for interdisciplinary work. Investment in these career development opportunities would enable today's cohort of early-career scientists to advance the frontiers of interdisciplinary work over the next couple of decades.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Microphysical Piggybacking in the Weather Research and Forecasting Model

Abstract This paper presents incorporation of the microphysical piggybacking into the Weather Research and Forecasting (WRF) model. Microphysical piggybacking is to run a single simulation applying two microphysical schemes, the first scheme driving the simulation and the second piggybacking this simulated flow. “Driving the simulation” means that the simulated microphysical processes, affect the cloud buoyancy and thus force the simulated flow. In contrast, the piggybacking variables are advected by the simulated flow and undergo microphysical transformation, but they do not affect the simulated flow (like in prescribed flow—kinematic—simulations). The two sets of variables (driver and piggybacker) include temperature, water vapor mixing ratio, and all microphysical variables. We provide details of implementing piggybacking into the WRF model, illustrate its applications, and demonstrate the benefits of this methodology in two idealized three‐dimensional cases: (a) a squall line case applying two microphysics schemes, the Thompson bulk microphysics scheme and the University of Pécs/NCAR bin (UPNB) scheme. The piggybacking simulations revealed that the microphysics‐dynamics interaction plays a more important role than the pure microphysical size sorting effect in the transition zone formation. (b) A case of daytime shallow‐to‐deep convective development over land. This case uses the UPNB scheme and contrasts convection developing in environments with either pristine or polluted cloud condensation nuclei (CCN). The piggybacking results indicated that the increase of cloud cover and decrease of supersaturation are mainly associated with the microphysical effect of increasing CCN while the change of precipitation on the ground is also influenced by microphysics‐dynamics interactions.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2017

Impacts of chemical gradients on microbial community structure

Succession of redox processes is sometimes assumed to define a basic microbial community structure for ecosystems with oxygen gradients. In this paradigm, aerobic respiration, denitrification, fermentation and sulfate reduction proceed in a thermodynamically determined order, known as the ‘redox tower’. Here, we investigated whether redox sorting of microbial processes explains microbial community structure at low-oxygen concentrations. We subjected a diverse microbial community sampled from a coastal marine sediment to 100 days of tidal cycling in a laboratory chemostat. Oxygen gradients (both in space and time) led to the assembly of a microbial community dominated by populations that each performed aerobic and anaerobic metabolism in parallel. This was shown by metagenomics, transcriptomics, proteomics and stable isotope incubations. Effective oxygen consumption combined with the formation of microaggregates sustained the activity of oxygen-sensitive anaerobic enzymes, leading to braiding of unsorted redox processes, within and between populations. Analyses of available metagenomic data sets indicated that the same ecological strategies might also be successful in some natural ecosystems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Experimentally-validated correlation analysis reveals new anaerobic methane oxidation partnerships with consortium-level heterogeneity in diazotrophy

Abstract Archaeal anaerobic methanotrophs (“ANME”) and sulfate-reducing Deltaproteobacteria (“SRB”) form symbiotic multicellular consortia capable of anaerobic methane oxidation (AOM), and in so doing modulate methane flux from marine sediments. The specificity with which ANME associate with particular SRB partners in situ, however, is poorly understood. To characterize partnership specificity in ANME-SRB consortia, we applied the correlation inference technique SparCC to 310 16S rRNA amplicon libraries prepared from Costa Rica seep sediment samples, uncovering a strong positive correlation between ANME-2b and members of a clade of Deltaproteobacteria we termed SEEP-SRB1g. We confirmed this association by examining 16S rRNA diversity in individual ANME-SRB consortia sorted using flow cytometry and by imaging ANME-SRB consortia with fluorescence in situ hybridization (FISH) microscopy using newly-designed probes targeting the SEEP-SRB1g clade. Analysis of genome bins belonging to SEEP-SRB1g revealed the presence of a complete nifHDK operon required for diazotrophy, unusual in published genomes of ANME-associated SRB. Active expression of nifH in SEEP-SRB1g within ANME-2b—SEEP-SRB1g consortia was then demonstrated by microscopy using hybridization chain reaction (HCR-) FISH targeting nifH transcripts and diazotrophic activity was documented by FISH-nanoSIMS experiments. NanoSIMS analysis of ANME-2b—SEEP-SRB1g consortia incubated with a headspace containing CH4 and 15N2 revealed differences in cellular 15N-enrichment between the two partners that varied between individual consortia, with SEEP-SRB1g cells enriched in 15N relative to ANME-2b in one consortium and the opposite pattern observed in others, indicating both ANME-2b and SEEP-SRB1g are capable of nitrogen fixation, but with consortium-specific variation in whether the archaea or bacterial partner is the dominant diazotroph.

58 GEOSCIENCES↗
DOE OSTI2021

Host population diversity as a driver of viral infection cycle in wild populations of green sulfur bacteria with long standing virus-host interactions

Abstract Temperate phages are viruses of bacteria that can establish two types of infection: a lysogenic infection in which the virus replicates with the host cell without producing virions, and a lytic infection where the host cell is eventually destroyed, and new virions are released. While both lytic and lysogenic infections are routinely observed in the environment, the ecological and evolutionary processes regulating these viral dynamics are still not well understood, especially for uncultivated virus-host pairs. Here, we characterized the long-term dynamics of uncultivated viruses infecting green sulfur bacteria (GSB) in a model freshwater lake (Trout Bog Lake, TBL). As no GSB virus has been formally described yet, we first used two complementary approaches to identify new GSB viruses from TBL; one in vitro based on flow cytometry cell sorting, the other in silico based on CRISPR spacer sequences. We then took advantage of existing TBL metagenomes covering the 2005–2018 period to examine the interactions between GSB and their viruses across years and seasons. From our data, GSB populations in TBL were constantly associated with at least 2-8 viruses each, including both lytic and temperate phages. The dominant GSB population in particular was consistently associated with two prophages with a nearly 100% infection rate for >10 years. We illustrate with a theoretical model that such an interaction can be stable given a low, but persistent, level of prophage induction in low-diversity host populations. Overall, our data suggest that lytic and lysogenic viruses can readily co-infect the same host population, and that host strain-level diversity might be an important factor controlling virus-host dynamics including lytic/lysogeny switch.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Life history strategies among soil bacteria—dichotomy for few, continuum for many

Abstract Study of life history strategies may help predict the performance of microorganisms in nature by organizing the complexity of microbial communities into groups of organisms with similar strategies. Here, we tested the extent that one common application of life history theory, the copiotroph-oligotroph framework, could predict the relative population growth rate of bacterial taxa in soils from four different ecosystems. We measured the change of in situ relative growth rate to added glucose and ammonium using both 18O–H2O and 13C quantitative stable isotope probing to test whether bacterial taxa sorted into copiotrophic and oligotrophic groups. We saw considerable overlap in nutrient responses across most bacteria regardless of phyla, with many taxa growing slowly and few taxa that grew quickly. To define plausible life history boundaries based on in situ relative growth rates, we applied Gaussian mixture models to organisms’ joint 18O–13C signatures and found that across experimental replicates, few taxa could consistently be assigned as copiotrophs, despite their potential for fast growth. When life history classifications were assigned based on average relative growth rate at varying taxonomic levels, finer resolutions (e.g., genus level) were significantly more effective in capturing changes in nutrient response than broad taxonomic resolution (e.g., phylum level). Our results demonstrate the difficulty in generalizing bacterial life history strategies to broad lineages, and even to single organisms across a range of soils and experimental conditions. We conclude that there is a continued need for the direct measurement of microbial communities in soil to advance ecologically realistic frameworks.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Coherent diffractive imaging of microtubules using an X-ray laser

X-ray free electron lasers (XFELs) create new possibilities for structural studies of biological objects that extend beyond what is possible with synchrotron radiation. Serial femtosecond crystallography has allowed high-resolution structures to be determined from micro-meter sized crystals, whereas single particle coherent X-ray imaging requires development to extend the resolution beyond a few tens of nanometers. Here we describe an intermediate approach: the XFEL imaging of biological assemblies with helical symmetry. We collected X-ray scattering images from samples of microtubules injected across an XFEL beam using a liquid microjet, sorted these images into class averages, merged these data into a diffraction pattern extending to 2 nm resolution, and reconstructed these data into a projection image of the microtubule. Details such as the 4 nm tubulin monomer became visible in this reconstruction. These results illustrate the potential of single-molecule X-ray imaging of biological assembles with helical symmetry at room temperature.

47 OTHER INSTRUMENTATION↗
DOE OSTI2019

Probing the active fraction of soil microbiomes using BONCAT-FACS

The ability to link soil microbial diversity to soil processes requires technologies that differentiate active microbes from extracellular DNA and dormant cells. Here, we use BONCAT (bioorthogonal non-canonical amino acid tagging) to measure translationally active cells in soils. We compare the active population of two soil depths from Oak Ridge (Tennessee, USA) and find that a maximum of 25-70% of the extractable cells are active. Analysis of 16S rRNA sequences from BONCAT-positive cells recovered by fluorescence-activated cell sorting (FACS) reveals that the phylogenetic composition of the active fraction is distinct from the total population of extractable cells. Some members of the community are found to be active at both depths independently of their abundance rank, suggesting that the incubation conditions favor the activity of similar organisms. We conclude that BONCAT-FACS is effective for interrogating the active fraction of soil microbiomes in situ and provides a new approach for uncovering the links between soil processes and specific microbial groups.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Non-structural carbohydrates mediate seasonal water stress across Amazon forests

Non-structural carbohydrates (NSC) are major substrates for plant metabolism and have been implicated in mediating drought-induced tree mortality. Despite their significance, NSC dynamics in tropical forests remain little studied. We present leaf and branch NSC data for 82 Amazon canopy tree species in six sites spanning a broad precipitation gradient. During the wet season, total NSC (NSC T ) concentrations in both organs were remarkably similar across communities. However, NSC T and its soluble sugar (SS) and starch components varied much more across sites during the dry season. Notably, the proportion of leaf NSC T in the form of SS (SS:NSC T ) increased greatly in the dry season in almost all species in the driest sites, implying an important role of SS in mediating water stress in these sites. This adjustment of leaf NSC balance was not observed in tree species less-adapted to water deficit, even under exceptionally dry conditions. Thus, leaf carbon metabolism may help to explain floristic sorting across water availability gradients in Amazonia and enable better prediction of forest responses to future climate change.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Ferroelectric phase-transition frustration near a tricritical composition point

Phase transition describes a mutational behavior of matter states at a critical transition temperature or external field. Despite the phase-transition orders are well sorted by classic thermodynamic theory, ambiguous situations interposed between the first- and second-order transitions were exposed one after another. Here, we report discovery of phase-transition frustration near a tricritical composition point in ferroelectric Pb(Zr 1-x Ti x )O 3 . Our multi-scale transmission electron microscopy characterization reveals a number of geometrically frustrated microstructure features such as self-assembled hierarchical domain structure, degeneracy of mesoscale domain tetragonality and decoupled polarization-strain relationship. Associated with deviation from the classic mean-field theory, dielectric critical exponent anomalies and temperature dependent birefringence data unveil that the frustrated transition order stems from intricate competition of short-range polar orders and their decoupling to long-range lattice deformation. With supports from effective Hamiltonian Monte Carlo simulations, our findings point out a potentially universal mechanism to comprehend the abnormal critical phenomena occurring in phase-transition materials.

42 ENGINEERING↗
DOE OSTI2023

Macroevolutionary diversity of traits and genomes in the model yeast genus Saccharomyces

Species is the fundamental unit to quantify biodiversity. In recent years, the model yeast Saccharomyces cerevisiae has seen an increased number of studies related to its geographical distribution, population structure, and phenotypic diversity. However, seven additional species from the same genus have been less thoroughly studied, which has limited our understanding of the macroevolutionary events leading to the diversification of this genus over the last 20 million years. Here, we show the geographies, hosts, substrates, and phylogenetic relationships for approximately 1,800 Saccharomyces strains, covering the complete genus with unprecedented breadth and depth. We generated and analyzed complete genome sequences of 163 strains and phenotyped 128 phylogenetically diverse strains. This dataset provides insights about genetic and phenotypic diversity within and between species and populations, quantifies reticulation and incomplete lineage sorting, and demonstrates how gene flow and selection have affected traits, such as galactose metabolism. These findings elevate the genus Saccharomyces as a model to understand biodiversity and evolution in microbial eukaryotes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Competition between charge-density-wave and superconducting orders on eight-leg square Hubbard cylinders

The issue of whether d-wave superconductivity (SC) occurs in the square-lattice Hubbard model with U of order of the bandwidth has been one of the most debated issues to emerge from the study of high temperature SC. Here, we report variational results on eight-leg cylinders with next-nearest-neighbor hopping in the range $-0.5t\le t^{\prime} \le 0.25t$ with U = 8t and 12t and doped hole concentrations δ = 1/12 and 1/8. For $t^{\prime} \le 0$, the ground-state appears to be a charge-density wave (CDW) of one sort or another with SC correlations that are extremely short-ranged. In contrast, in some cases, the local magnetic order has a correlation length greater than half the cylinder width - suggestive that magnetic order might also arise in the 2D limit. For $t^{\prime} \le 0$, our results depend more strongly on boundary conditions (periodic vs antiperiodic), making it still harder to correctly guess whether SC or CDW correlations dominate in the 2D limit. These results were obtained employing matrix-product states with bond dimensions large enough that energy differences as small as 10 −3 t per site can be resolved.

materials science↗
DOE OSTI2021

An open-access database and analysis tool for perovskite solar cells based on the FAIR data principles

Large datasets are now ubiquitous as technology enables higher-throughput experiments, but rarely can a research field truly benefit from the research data generated due to inconsistent formatting, undocumented storage or improper dissemination. Here we extract all the meaningful device data from peer-reviewed papers on metal-halide perovskite solar cells published so far and make them available in a database. We collect data from over 42,400 photovoltaic devices with up to 100 parameters per device. We then develop open-source and accessible procedures to analyse the data, providing examples of insights that can be gleaned from the analysis of a large dataset. The database, graphics and analysis tools are made available to the community and will continue to evolve as an open-source initiative. This approach of extensively capturing the progress of an entire field, including sorting, interactive exploration and graphical representation of the data, will be applicable to many fields in materials science, engineering and biosciences.

14 SOLAR ENERGY↗