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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 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Identifying Boron Active Sites for the Oxidative Dehydrogenation of Propane

Oxidative dehydrogenation of propane (ODHP) to propylene could have a significant impact on the production of this critical chemical intermediate, if appropriate catalysts can be discovered. Recently, heterogeneous catalysts based on boron (oxides and nitrides) have been demonstrated to be promising for ODHP, but their active sites have not been conclusively identified. Here, we report that the deposition of differently sized boronic acids into the micropores of silica supports results in different distributions of surface borate species after calcination. Furthermore, these materials, in turn, display a wide range of rates in ODHP but similar selectivity, suggesting that they differ only in the numbers of active sites. Features identified by in situ Raman, IR, and magic-angle-spinning 11 B solid-state NMR spectroscopies are compared to catalyst activity. This correlation identifies the S2 borate species, a hydroxylated nonring boron, as the likely active site and provides a target for directed syntheses of future catalysts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Hypergraph Models of Biological Networks to Identify Genes Critical to Pathogenic Viral Response

Motivation: Representing biological networks as graphs is a powerful approach to reveal underlying patterns, signatures, and critical components from high-throughput biomolecular data. However, graphs do not natively capture the multi-way relationships present among genes and proteins in biological systems such as protein complexes, metabolic reactions, and signal transduction pathways. Hypergraphs are generalizations of graphs that naturally model multi-way interactions in data, and we therefore seek to understand how they can more faithfully identify, and potentially predict, complex relationships in genomic expression data sets. Results: We compiled a novel data set of transcriptional host response to pathogenic viral infections and formulated relationships between genes as a hypergraph where hyperedges are differentially expressed genes and vertices represent conditions. We find that hypergraph betweenness centrality is a superior method for identification of genes important to viral response when compared with graph centrality. Our results demonstrate the utility of using hypergraphs to represent complex biological systems, and highlight potentially interesting biological results about host response to highly pathogenic viruses.

systems biology, hypergraph, viral infection, biol↗
DOE OSTI2020

Learning from existing photovoltaic technologies to identify alternative perovskite module designs

Perovskite solar cells have now become the most efficient of all multicrystalline thin film photovoltaic technologies, reaching 25.2% in 2019. This outstanding figure of merit has only been achieved on small lab-scale devices, with significantly lower performance when processed on larger more industrially relevant substrate sizes. Perovskite modules, connecting several smaller area cells together, are commonly demonstrated with a superstrate monolithic interconnection method. However, several other module designs exist and remain largely unexplored by the perovskite community. In this work, we review and highlight those alternatives and discuss their advantages and limitations. We propose that a singulated substrate-oriented module design, using metallic substrates, could provide a quicker path to seeing highly efficient, lightweight, and flexible perovskite modules on the market, while mitigating near-term technical risks. Finally, as an experimental starting-point towards this design, we demonstrate a substrate-oriented all-perovskite 2-terminal tandem with 18% efficiency.

14 SOLAR ENERGY↗
DOE OSTI2020

The sensitive surface chemistry of Co-free, Ni-rich layered oxides: identifying experimental conditions that influence characterization results

Recent studies have suggested that Co-free, Ni-rich layered cathodes (e.g., doped LiNiO2) can provide promising battery performance for practical applications. However, these layered cathodes suffer from significant surface instability during various stages of the sample history, which generates inherent challenges for achieving stable battery performance and obtaining statistically representative characterization results. To reliably report the surface chemistry of these materials, delicate controls of stepwise sample preparation are required. In this study, we aim to reveal how the surface chemistry of LiNiO2 based materials changes with various environments, including human exhalation, sample storage, sample preparation, electrochemistry cycling, and surface doping. Our results demonstrate that the surface of these materials is highly reactive and prone to alter at various stages of sample handling and characterization. The sensitive surface could impact the interpretation of the surface chemical and structural information, including surface carbonate formation, transition metal reduction and dissolution, and surface reconstruction. Importantly, the heterogeneity of the surface degradation calls for a consolidation of nanoscale, high-resolution characterization, and ensemble-averaged methods in order to improve statistical representation. Furthermore, the doping chemistry can effectively mitigate the surface degradation and improve overall battery performance due to the enhanced surface oxygen retention. Our study highlights the necessity of strict measurements through complementary characterizations at multiple length scales to eliminate unintentional biased conclusions.

surface chemistry, Co-free Ni-rich cathodes, Istab↗
DOE OSTI2022

Leaf microscopy applications in photosynthesis research: identifying the gaps

Abstract Leaf imaging via microscopy has provided critical insights into research on photosynthesis at multiple junctures, from the early understanding of the role of stomata, through elucidating C4 photosynthesis via Kranz anatomy and chloroplast arrangement in single cells, to detailed explorations of diffusion pathways and light utilization gradients within leaves. In recent decades, the original two-dimensional (2D) explorations have begun to be visualized in three-dimensional (3D) space, revising our understanding of structure–function relationships between internal leaf anatomy and photosynthesis. In particular, advancing new technologies and analyses are providing fresh insight into the relationship between leaf cellular components and improving the ability to model net carbon fixation, water use efficiency, and metabolite turnover rate in leaves. While ground-breaking developments in imaging tools and techniques have expanded our knowledge of leaf 3D structure via high-resolution 3D and time-series images, there is a growing need for more in vivo imaging as well as metabolite imaging. However, these advances necessitate further improvement in microscopy sciences to overcome the unique challenges a green leaf poses. In this review, we discuss the available tools, techniques, challenges, and gaps for efficient in vivo leaf 3D imaging, as well as innovations to overcome these difficulties.

Plant Sciences↗
DOE OSTI2021

Identifying Periodic Variable Stars and Eclipsing Binary Systems with Long-term Las Cumbres Observatory Photometric Monitoring of ZTF J0139+5245

We present the results of our search for variable stars using the long-term Las Cumbres Observatory (LCO) monitoring of white dwarf ZTF J0139+5245 with the two 1.0 m telescope nodes located at McDonald Observatory using the Sinistro imaging instrument. In this search, we find 38 variable sources, of which 27 are newly discovered or newly classified (71%) based on comparisons with previously published catalogs, thereby increasing the number of detections in the field of view under consideration by a factor of ≈2.5. We find that the improved photometric precision per exposure due to longer exposure time for LCO images combined with the greater time sampling of LCO photometry enables us to increase the total number of detections in this field of view. Each LCO image covers a field of view of 26' × 26' and observes a region close to the Galactic plane (b = -9.°4) abundant in stars with an average stellar density of ≈8 arcmin{sup -2}. We perform aperture photometry and Fourier analysis on over 2000 stars across 1560 LCO images spanning 537 days to find 28 candidate BY Draconis variables, three candidate eclipsing binaries of type EA, and seven candidate eclipsing binaries of type EW. In assigning preliminary classifications to our detections, we demonstrate the applicability of the Gaia color–magnitude diagram as a powerful classification tool for variable-star studies.

47 OTHER INSTRUMENTATION↗
DOE OSTI2025

Identifying preferential flow from soil moisture time series: Review of methodologies

Abstract Identifying and quantifying preferential flow (PF) through soil—the rapid movement of water through spatially distinct pathways in the subsurface—is vital to understanding how the hydrologic cycle responds to climate, land cover, and anthropogenic changes. In recent decades, methods have been developed that use measured soil moisture time series to identify PF. Because they allow for continuous monitoring and are relatively easy to implement, these methods have become an important tool for recognizing when, where, and under what conditions PF occurs. The methods seek to identify a pattern or quantification that indicates the occurrence of PF. Most commonly, the chosen signature is either (1) a nonsequential response to infiltrated water, in which soil moisture responses do not occur in order of shallowest to deepest, or (2) a velocity criterion, in which newly infiltrated water is detected at depth earlier than is possible by nonpreferential flow processes. Alternative signatures have also been developed that have certain advantages but are less commonly utilized. Choosing among these possible signatures requires attention to their pertinent characteristics, including susceptibility to errors, possible bias toward false negatives or false positives, reliance on subjective judgments, and possible requirements for additional types of data. We review 77 studies that have applied such methods to highlight important information for readers who want to identify PF from soil moisture data and to inform those who aim to develop new methods or improve existing ones. Core Ideas Soil moisture data can be used to identify the occurrence of preferential flow (PF) and its initiating conditions. Various data‐analysis methods to identify PF differ in susceptibility to error, bias, and subjectivity. These methods can utilize vast amounts of data from soil moisture monitoring networks to develop understanding of when, where, and under what conditions PF occurs. Newly developed methods may lead to better accuracy and reliability, and reduce the need for subjective judgments. Plain Language Summary Preferential flow through soil occurs when a large amount of water is suddenly available, as during an intense storm. This type of flow moves rapidly through the soil in distinct narrow pathways rather than moving evenly throughout the body of soil, with major consequences for groundwater resources, ecosystems, spreading of contaminants, and other vital concerns. Methods of detecting preferential flow have been developed that utilize measurements of soil water content made by sensors installed at various depths. This measurement technology has been widely implemented, many locations now having datasets years in length, and various methods have been developed for using these to identify preferential flow. The various methods are based on different features in the soil moisture records and vary in their advantages and shortcomings. In this review, we explain and evaluate these methods, highlighting important information for their implementation to identify preferential flow from soil moisture data and for efforts to develop new methods or improve existing ones.

Nimmo, John R↗
DOE OSTI2021

A k-mer based approach for classifying viruses without taxonomy identifies viral associations in human autism and plant microbiomes

Viruses are an underrepresented taxa in the study and identification of microbiome constituents; however, they play an essential role in health, microbiome regulation, and transfer of genetic material. Only a few thousand viruses have been isolated, sequenced, and assigned a taxonomy, which limits the ability to identify and quantify viruses in the microbiome. Additionally, the vast diversity of viruses represents a challenge for classification, not only in constructing a viral taxonomy, but also in identifying similarities between a virus’ genotype and its phenotype. However, the diversity of viral sequences can be leveraged to classify their sequences in metagenomic and metatranscriptomic samples, even if they do not have a taxonomy. To identify and quantify viruses in transcriptomic and genomic samples, we developed a dynamic programming algorithm for creating a classification tree out of 715,672 metagenome viruses. To create the classification tree, we clustered proportional similarity scores generated from the k-mer profiles of each of the metagenome viruses to create a database of metagenomic viruses. The resulting Kraken2 database of the metagenomic viruses can be found here: https://www.osti.gov/biblio/1615774 and is compatible with Kraken2. We then integrated the viral classification database with databases created with genomes from NCBI for use with ParaKraken (a parallelized version of Kraken provided in Supplemental Zip 1), a metagenomic/transcriptomic classifier. To illustrate the breadth of our utility for classifying metagenome viruses, we analyzed data from a plant metagenome study identifying genotypic and compartment specific differences between two Populus genotypes in three different compartments. We also identified a significant increase in abundance of eight viral sequences in post mortem brains in a human metatranscriptome study comparing Autism Spectrum Disorder patients and controls. We also show the potential accuracy for classifying viruses by utilizing both the JGI and NCBI viral databases to identify the uniqueness of viral sequences. Finally, we validate the accuracy of viral classification with NCBI databases containing viruses with taxonomy to identify pathogenic viruses in known COVID-19 and cassava brown streak virus infection samples. Our method represents the compulsory first step in better understanding the role of viruses in the microbiome by allowing for a more complete identification of sequences without taxonomy. Better classification of viruses will improve identifying associations between viruses and their hosts as well as viruses and other microbiome members. Despite the lack of taxonomy, this database of metagenomic viruses can be used with any tool that utilizes a taxonomy, such as Kraken, for accurate classification of viruses.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Unusual modifications of protein biomarkers expressed by plasmid, prophage, and bacterial host of pathogenic Escherichia coli identified using top‐down proteomic analysis

Rationale Pathogenic bacteria often carry prophage (bacterial viruses) and plasmids (small circular pieces of DNA) that may harbor toxin, antibacterial, and antibiotic resistance genes. Proteomic characterization of pathogenic bacteria should include the identification of host proteins and proteins produced by prophage and plasmid genomes. Methods Protein biomarkers of two strains of Shiga toxin–producingEscherichia coli(STEC) were identified using antibiotic induction, matrix‐assisted laser desorption/ionization tandem time‐of‐flight (MALDI‐TOF‐TOF) tandem mass spectrometry (MS/MS) with post‐source decay (PSD), top‐down proteomic (TDP) analysis, and plasmid sequencing. Alphafold2 was also used to compare predicted in silico structures of the identified proteins to prominent fragment ions generated using MS/MS‐PSD. Strain samples were also analyzed with and without chemical reduction treatment to detect the attachment of pendant groups bound by thioester or disulfide bonds. Results Shiga toxin was detected and/or identified in both STEC strains. For the first time, we also identified the osmotically inducible protein (OsmY) whose sequence unexpectedly had two forms: a full and a truncated sequence. The truncated OsmY terminates in the middle of an α‐helix as determined by Alphafold2. A plasmid‐encoded colicin immunity protein was also identified with and without attachment of an unidentified cysteine‐bound pendant group (~307 Da). Plasmid sequencing confirmed top‐down analysis and the identification of a promoter upstream of the immunity gene that is activated by antibiotic induction, that is, SOS box. Conclusions TDP analysis, coupled with other techniques (e.g., antibiotic induction, chemical reduction, plasmid sequencing, and in silico protein modeling), is a powerful tool to identify proteins (and their modifications), including prophage‐ and plasmid‐encoded proteins, produced by pathogenic microorganisms.

Biochemistry & Molecular Biology↗
DOE OSTI2023

Genome-wide association study identifies four pan-ancestry loci for suicidal ideation in the Million Veteran Program

Suicidal ideation (SI) often precedes and predicts suicide attempt and death, is the most common suicidal phenotype and is over-represented in veterans. The genetic architecture of SI in the absence of suicide attempt (SA) is unknown, yet believed to have distinct and overlapping risk with other suicidal behaviors. We performed the first GWAS of SI without SA in the Million Veteran Program (MVP), identifying 99,814 SI cases from electronic health records without a history of SA or suicide death (SD) and 512,567 controls without SI, SA or SD. GWAS was performed separately in the four largest ancestry groups, controlling for sex, age and genetic substructure. Ancestry-specific results were combined via meta-analysis to identify pan-ancestry loci. Four genome-wide significant (GWS) loci were identified in the pan-ancestry meta-analysis with loci on chromosomes 6 and 9 associated with suicide attempt in an independent sample. Pan-ancestry gene-based analysis identified GWS associations with DRD2, DCC, FBXL19, BCL7C, CTF1, ANNK1, and EXD3. Gene-set analysis implicated synaptic and startle response pathways (q’s<0.05). European ancestry (EA) analysis identified GWS loci on chromosomes 6 and 9, as well as GWS gene associations in EXD3, DRD2, and DCC. No other ancestry-specific GWS results were identified, underscoring the need to increase representation of diverse individuals. The genetic correlation of SI and SA within MVP was high (r G = 0.87; p = 1.09e-50), as well as with post-traumatic stress disorder (PTSD; r G = 0.78; p = 1.98e-95) and major depressive disorder (MDD; r G = 0.78; p = 8.33e-83). Conditional analysis on PTSD and MDD attenuated most pan-ancestry and EA GWS signals for SI without SA to nominal significance, with the exception of EXD3 which remained GWS. Our novel findings support a polygenic and complex architecture for SI without SA which is largely shared with SA and overlaps with psychiatric conditions frequently comorbid with suicidal behaviors.

59 BASIC BIOLOGICAL SCIENCES↗