Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “Diversion”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 181 records · Page 10
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Genome-resolved metagenomics reveals site-specific diversity of episymbiotic CPR bacteria and DPANN archaea in groundwater ecosystems

Abstract Candidate phyla radiation (CPR) bacteria and DPANN archaea are unisolated, small-celled symbionts that are often detected in groundwater. The effects of groundwater geochemistry on the abundance, distribution, taxonomic diversity and host association of CPR bacteria and DPANN archaea has not been studied. Here, we performed genome-resolved metagenomic analysis of one agricultural and seven pristine groundwater microbial communities and recovered 746 CPR and DPANN genomes in total. The pristine sites, which serve as local sources of drinking water, contained up to 31% CPR bacteria and 4% DPANN archaea. We observed little species-level overlap of metagenome-assembled genomes (MAGs) across the groundwater sites, indicating that CPR and DPANN communities may be differentiated according to physicochemical conditions and host populations. Cryogenic transmission electron microscopy imaging and genomic analyses enabled us to identify CPR and DPANN lineages that reproducibly attach to host cells and showed that the growth of CPR bacteria seems to be stimulated by attachment to host-cell surfaces. Our analysis reveals site-specific diversity of CPR bacteria and DPANN archaea that coexist with diverse hosts in groundwater aquifers. Given that CPR and DPANN organisms have been identified in human microbiomes and their presence is correlated with diseases such as periodontitis, our findings are relevant to considerations of drinking water quality and human health.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Viromics approaches for the study of viral diversity and ecology in microbiomes

Viruses are found across all ecosystems and infect every type of organism on Earth. Traditional culture-based methods have proven insufficient to explore this viral diversity at scale, driving the development of viromics, the sequence-based analysis of uncultivated viruses. Viromics approaches have been particularly useful for studying viruses of microorganisms, which can act as crucial regulators of microbiomes across ecosystems. They have already revealed the broad geographic distribution of viral communities and are progressively uncovering the expansive genetic and functional diversity of the global virome. Moving forward, large-scale viral ecogenomics studies combined with new experimental and computational approaches to identify virus activity and host interactions will enable a more complete characterization of global viral diversity and its effects.

Ecology↗
DOE OSTI2021

Diversity-oriented synthesis of polymer membranes with ion solvation cages

Microporous polymers feature shape-persistent free volume elements (FVEs), which are permeated by small molecules and ions when used as membranes for chemical separations, water purification, fuel cells, and batteries. It remains a significant challenge to identify FVEs with analyte specificity, due to difficulties in generating microporous polymer libraries with sufficient diversity for screening their properties. Here, we describe a diversity-oriented synthetic (DOS) strategy for microporous polymer membranes from which we identified those whose FVEs serve as solid solvation cages for lithium ions (Li + ). Furthermore, key elements of our strategy included diversification of bis(catechol)-type monomers via multi-component Mannich reactions to introduce Li+-coordinating functionality within individual FVEs, topology-enforcing polymerizations for generating macromolecular skeletal diversity for networking FVEs into different pore architectures, and several classes of on-polymer reactions for diversifying pore geometries and dielectric properties. Lead candidate polymer membranes featuring explicit ion solvation cages exhibited both higher ionic conductivity and higher cation transference number than control membranes where FVEs were aspecific, which indicates conventional bounds for membrane permeability and selectivity for ion transport can be overcome.4 These advantages are tied to enhanced Li + partitioning from the electrolyte when the cages are present, higher diffusion barriers for anions within the pores, and network-enforced restrictions on the number of solvent molecules bound to Li+ by comparison to the bulk electrolyte, which reduces the effective mass of the working ion. Such membranes show promise as anode-stabilizing interlayers in high-voltage lithium-metal batteries for electric mobility.

42 ENGINEERING↗
DOE OSTI2025

Exploring prokaryotic diversity in permafrost-affected soils of Ladakh’s Changthang region and its geochemical drivers

Global warming due to climate change has substantial impact on high-altitude permafrost affected soils. This raises a serious concern that the microbial degradation of sequestered carbon can result in alteration of the biogeochemical cycles. Therefore, the characterization of permafrost affected soil microbiomes, especially of unexplored high-altitude, low oxygen arid region, is important for predicting their response to climate change. This study presents the first report of the bacterial diversity of permafrost-affected soils in the Changthang region of Ladakh. The relationship between soil pH, organic carbon, electrical conductivity, and available micronutrients with the microbial diversity was investigated. Amplicon sequencing of permafrost affected soil samples from Jukti and Tsokar showed that Proteobacteria and Actinobacteria were the dominant phyla in all samples. The genera Brevitalea, Chthoniobacter, Sphingomonas, Hydrogenispora, Clostridium, Gaiella, Gemmatimonas were relatively abundant in the Jukti samples whereas the genera Thiocapsa, Actinotalea, Syntrophotalea, Antracticibcterium, Luteolibacter, Nitrospirillum dominated the Tsokar sample. Correlation analyses highlighted the influence of soil geochemical parameters on the bacterial community structure. PCoA analyses showed that the bacterial beta diversity varied significantly between the sampling locations (PERMANOVA test (F-value: 2.3316; R 2 = 0.466, p = 0.001) and similar results were also obtained while comparing genus abundance data using the ANOSIM test (R = 0.345, p = 0.007).

16S rRNA↗
DOE OSTI2020

Whole-proteome tree of life suggests a deep burst of organism diversity

An organism tree of life (organism ToL) is a conceptual and metaphorical tree to capture a simplified narrative of the evolutionary course and kinship among the extant organisms. Such a tree cannot be experimentally validated but may be reconstructed based on characteristics associated with the organisms. Since the whole-genome sequence of an organism is, at present, the most comprehensive descriptor of the organism, a whole-genome sequence-based ToL can be an empirically derivable surrogate for the organism ToL. However, experimentally determining the whole-genome sequences of many diverse organisms was practically impossible until recently. We have constructed three types of ToLs for diversely sampled organisms using the sequences of whole genome, of whole transcriptome, and of whole proteome. Of the three, whole-proteome sequence-based ToL (whole-proteome ToL), constructed by applying information theory-based feature frequency profile method, an “alignment-free” method, gave the most topologically stable ToL. Here, we describe the main features of a whole-proteome ToL for 4,023 species with known complete or almost complete genome sequences on grouping and kinship among the groups at deep evolutionary levels. The ToL reveals 1) all extant organisms of this study can be grouped into 2 “Supergroups,” 6 “Major Groups,” or 35+ “Groups”; 2) the order of emergence of the “founders” of all of the groups may be assigned on an evolutionary progression scale; 3) all of the founders of the groups have emerged in a “deep burst” at the very beginning period near the root of the ToL—an explosive birth of life’s diversity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Constraining the oxygen requirements for modern microbial eukaryote diversity

Eukaryotes originated prior to the establishment of modern marine oxygen (O 2 ) levels. According to the body fossil and lipid biomarker records, modern (crown) microbial eukaryote lineages began diversifying in the ocean no later than ~800 Ma. While it has long been predicted that increasing atmospheric O 2 levels facilitated the early diversification of microbial eukaryotes, the O 2 levels needed to permit this diversification remain unconstrained. Using time-resolved geochemical parameter and gene sequence information from a model marine oxygen minimum zone spanning a range of dissolved O 2 levels and redox states, we show that microbial eukaryote taxonomic richness and phylogenetic diversity remain the same until O 2 declines to around 2 to 3% of present atmospheric levels, below which these diversity metrics become significantly reduced. Our observations suggest that increasing O 2 would have only directly promoted early crown-eukaryote diversity if atmospheric O 2 was below 2 to 3% of modern levels when crown-eukaryotes originated and then later met or surpassed this range as crown-eukaryotes diversified. If atmospheric O 2 was already consistently at or above 2 to 3% of modern levels by the time that crown-eukaryotes originated, then the subsequent diversification of modern microbial eukaryotes was not directly driven by atmospheric oxygenation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Utilizing a Virtual Sodium-Cooled Fast Reactor Digital Twin to Aid in Diversion Pathway Analysis for International Safeguards Applications

We report digital twin technology has the potential to improve the effectiveness of international safeguards inspectors by providing a tool which can: first, perform an accurate diversion path analysis, identify their indicators, and required sensors to detect them; and second, monitor facilities in real-time using critical data streams that benefit from this safeguards-by-design approach. Safeguards inspectors are required to visit facilities and verify the nuclear material to ensure no diversion has taken place and detect misuse of the facility; however, this analysis and verification effort is time consuming, and with limited funding it is imperative that time spent at a nuclear facility is focused on key areas. A virtual digital twin of three prototypic sodium fast reactors was developed, where diversion and misuse scenarios were explored to determine how a digital twin could provide inspectors with an understanding of how proliferation may occur and where the most likely areas for proliferation would be. For each of the three reactors, an optimization algorithm was able to find core designs which would be difficult to detect via sensors alone; however, the use of a machine learning adapter provided by the digital twin was able to show general trends in where proliferation as likely to take place.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2021

Advancing a toolkit of diverse futures approaches for global environmental assessments

Global Environmental Assessments (GEAs) support national and international policy making for sustainable development. They rely on quantitative scenarios produced by Integrated Assessment Models (IAMs) to assess alternative futures. IAM-based scenarios can provide a coherent assessment framework that integrates different subsystems and their interactions. However, these top-down approaches have limited ability to represent key local dynamics, unexpected events, or the role of diverse actors. Other methods, including participatory scenarios, can help co-create narratives that emphasize diverse contents with clear links to existing decision-making. However, these bottom-up approaches provide only limited insight into global processes and are not constrained by measurable parameters. In our review, we identify four key challenges for current GEA scenarios: surprise, scale, diversity and imagination. We illustrate how these challenges can be overcome by combining top-down and bottom-up scenario approaches and conclude with a call to action for future research to take on this trans-disciplinary challenge.

Pereira, Laura M.↗
DOE OSTI2025

Pollinator habitat in solar facilities has potential to support high diversity of bee species

Conversion of agricultural and degraded lands to solar energy production provides opportunities to support diverse bee communities—and their pollination services—by creating habitat at solar facilities. Habitat restoration for bees at solar facilities follows the general principle of installing a diverse flowering plant community and assuming bees will come. However, selecting seed mixes for solar facilities is challenging because selected plants need to establish in the unique abiotic conditions of solar facilities and not interfere with solar energy production (tall plants may shade panels). Recent research tested commercially available and bespoke pollinator mixes for establishment success in Minnesota solar facilities and identified 14 forb species that established successfully over three years of the experiment. We ask an important follow-up question: how many native bee species, and which bee species, are these 14 plant species capable of supporting? We used a plant-bee interaction data set from Minnesota to calculate the number of bee species that would be supported by the 14 plant species for the duration of their flight seasons using a published bee species richness function. We found 122 unique bee species (24% of Minnesota diversity) may be supported for their entire flight seasons by the 14 focal plants.

14 SOLAR ENERGY↗
DOE OSTI2025

D–MOPH–25: diverse MOF–molecule pairs for Henry’s constants prediction

Computational methods like grand-canonical Monte Carlo simulations and machine learning (ML) have accelerated metal–organic frameworks (MOF) exploration but are typically limited to a narrow range of adsorbates due to data availability and force field constraints. In this study, we introduce a dataset of diverse MOF–molecule pairs for Henry’s constant prediction, D–MOPH–25, which systematically explores a diverse chemical space by combining 113 molecular adsorbates with over 5000 MOF structures through an active learning process. D–MOPH–25 constitutes the most diverse adsorbate dataset used in any ML study of molecular adsorption in MOFs to date. Our workflow builds a benchmark for predicting Henry’s constants at 300 K, leveraging conformal prediction for uncertainty quantification. Assessment through Shannon entropy and uniform manifold approximation and projection confirms the comprehensiveness of D–MOPH–25 while highlighting the importance of robust classification to filter out unphysical data points in regression tasks. Although future enhancements in model architecture and sampling criteria could improve predictive performance, our dataset already spans the target space using only 2.31% of total possibilities. This comprehensive dataset facilitates assessment of model generalizability across adsorbate species and can establish a foundation for high-throughput MOF screening and ML-driven separation processes.

active learning↗
DOE OSTI2024

Genetic and Functional Diversity Help Explain Pathogenic, Weakly Pathogenic, and Commensal Lifestyles in the Genus Xanthomonas

The genus Xanthomonas has been primarily studied for pathogenic interactions with plants. However, besides host and tissue-specific pathogenic strains, this genus also comprises nonpathogenic strains isolated from a broad range of hosts, sometimes in association with pathogenic strains, and other environments, including rainwater. Based on their incapacity or limited capacity to cause symptoms on the host of isolation, nonpathogenic xanthomonads can be further characterized as commensal and weakly pathogenic. This study aimed to understand the diversity and evolution of nonpathogenic xanthomonads compared to their pathogenic counterparts based on their cooccurrence and phylogenetic relationship and to identify genomic traits that form the basis of a life history framework that groups xanthomonads by ecological strategies. We sequenced genomes of 83 strains spanning the genus phylogeny and identified eight novel species, indicating unexplored diversity. While some nonpathogenic species have experienced a recent loss of a type III secretion system, specifically the hrp2 cluster, we observed an apparent lack of association of the hrp2 cluster with lifestyles of diverse species. We performed association analysis on a large data set of 337 Xanthomonas strains to explain how xanthomonads may have established association with the plants across the continuum of lifestyles from commensals to weak pathogens to pathogens. Presence of distinct transcriptional regulators, distinct nutrient utilization and assimilation genes, transcriptional regulators, and chemotaxis genes may explain lifestyle-specific adaptations of xanthomonads.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Genomic Analysis Enlightens Agaricales Lifestyle Evolution and Increasing Peroxidase Diversity

Abstract As actors of global carbon cycle, Agaricomycetes (Basidiomycota) have developed complex enzymatic machineries that allow them to decompose all plant polymers, including lignin. Among them, saprotrophic Agaricales are characterized by an unparalleled diversity of habitats and lifestyles. Comparative analysis of 52 Agaricomycetes genomes (14 of them sequenced de novo) reveals that Agaricales possess a large diversity of hydrolytic and oxidative enzymes for lignocellulose decay. Based on the gene families with the predicted highest evolutionary rates—namely cellulose-binding CBM1, glycoside hydrolase GH43, lytic polysaccharide monooxygenase AA9, class-II peroxidases, glucose–methanol–choline oxidase/dehydrogenases, laccases, and unspecific peroxygenases—we reconstructed the lifestyles of the ancestors that led to the extant lignocellulose-decomposing Agaricomycetes. The changes in the enzymatic toolkit of ancestral Agaricales are correlated with the evolution of their ability to grow not only on wood but also on leaf litter and decayed wood, with grass-litter decomposers as the most recent eco-physiological group. In this context, the above families were analyzed in detail in connection with lifestyle diversity. Peroxidases appear as a central component of the enzymatic toolkit of saprotrophic Agaricomycetes, consistent with their essential role in lignin degradation and high evolutionary rates. This includes not only expansions/losses in peroxidase genes common to other basidiomycetes but also the widespread presence in Agaricales (and Russulales) of new peroxidases types not found in wood-rotting Polyporales, and other Agaricomycetes orders. Therefore, we analyzed the peroxidase evolution in Agaricomycetes by ancestral-sequence reconstruction revealing several major evolutionary pathways and mapped the appearance of the different enzyme types in a time-calibrated species tree.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Analysis of intraspecies diversity reveals a subset of highly variable plant immune receptors and predicts their binding sites

The evolution of recognition specificities by the immune system depends on the generation of receptor diversity and on connecting the binding of new antigens with the initiation of downstream signaling. In plant immunity, the innate Nucleotide-Binding Leucine-Rich Repeat (NLR) receptor family enables antigen binding and immune signaling. In this study, we surveyed the NLR complements of 62 ecotypes of Arabidopsis thaliana and 54 lines of Brachypodium distachyon and identified a limited number of NLR subfamilies that show high allelic diversity. We show that the predicted specificity-determining residues cluster on the surfaces of Leucine-Rich Repeat domains, but the locations of the clusters vary among NLR subfamilies. By comparing NLR phylogeny, allelic diversity, and known functions of the Arabidopsis NLRs, we formulate a hypothesis for the emergence of direct and indirect pathogen-sensing receptors and of the autoimmune NLRs. These findings reveal the recurring patterns of evolution of innate immunity and can inform NLR engineering efforts.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Genome organization and botanical diversity

Abstract The rich diversity of angiosperms, both the planet's dominant flora and the cornerstone of agriculture, is integrally intertwined with a distinctive evolutionary history. Here, we explore the interplay between angiosperm genome organization and botanical diversity, empowered by genomic approaches ranging from genetic linkage mapping to analysis of gene regulation. Commonality in the genetic hardware of plants has enabled robust comparative genomics that has provided a broad picture of angiosperm evolution and implicated both general processes and specific elements in contributing to botanical diversity. We argue that the hardware of plant genomes—both in content and in dynamics—has been shaped by selection for rather substantial differences in gene regulation between plants and animals such as maize and human, organisms of comparable genome size and gene number. Their distinctive genome content and dynamics may reflect in part the indeterminate development of plants that puts strikingly different demands on gene regulation than in animals. Repeated polyploidization of plant genomes and multiplication of individual genes together with extensive rearrangement and differential retention provide rich raw material for selection of morphological and/or physiological variations conferring fitness in specific niches, whether natural or artificial. These findings exemplify the burgeoning information available to employ in increasing knowledge of plant biology and in modifying selected plants to better meet human needs.

Biochemistry & Molecular Biology↗
DOE OSTI2021

Natural diversity provides a broad spectrum of cyanobacteriochrome-based diguanylate cyclases

Cyanobacteriochromes (CBCRs) are spectrally diverse photosensors from cyanobacteria distantly related to phytochromes that exploit photoisomerization of linear tetrapyrrole (bilin) chromophores to regulate associated signaling output domains. Unlike phytochromes, a single CBCR domain is sufficient for photoperception. CBCR domains that regulate the production or degradation of cyclic nucleotide second messengers are becoming increasingly well characterized. Furthermore, cyclic di-guanosine monophosphate (c-di-GMP) is a widespread small-molecule regulator of bacterial motility, developmental transitions, and biofilm formation whose biosynthesis is regulated by CBCRs coupled to GGDEF (diguanylate cyclase) output domains. In this study, we compare the properties of diverse CBCR-GGDEF proteins with those of synthetic CBCR-GGDEF chimeras. Our investigation shows that natural diversity generates promising candidates for robust, broad spectrum optogenetic applications in live cells. Since light quality is constantly changing during plant development as upper leaves begin to shade lower leaves—affecting elongation growth, initiation of flowering, and responses to pathogens, these studies presage application of CBCR-GGDEF sensors to regulate orthogonal, c-di-GMP-regulated circuits in agronomically important plants for robust mitigation of such deleterious responses under natural growing conditions in the field.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Quancorde: Boosting fidelity with Quantum Canary Ordered Diverse Ensembles

On today's noisy imperfect quantum devices, execution fidelity tends to collapse dramatically for most applications beyond a handful of qubits. It is therefore imperative to employ novel techniques that can boost quantum fidelity in new ways. Here, this paper aims to boost quantum fidelity with Clifford canary circuits by proposing Quancorde: Quantum Canary Ordered Diverse Ensembles, a fundamentally newapproach to identifying the correct outcomes of extremely low-fidelity quantum applications. It is based on the key idea of diversity in quantum devices - variations in noise sources, make each (portion of a) device unique, and therefore, their impact on an application's fidelity, also unique. Quancorde utilizes Clifford canary circuits (which are classically simulable, but also resemble the target application structure and thus suffer similar structural noise impact) to order a diverse ensemble of devices or qubits/mappings approximately along the direction of increasing fidelity of the target application. Quancorde then estimates the correlation of the ensemble-wide probabilities of each output string of the application, with the canary ensemble ordering, and uses this correlation to weight the application's noisy probability distribution. The correct application outcomes are expected to have higher correlation with the canary ensemble order, and thus their probabilities are boosted in this process. Doing so, Quancorde improves the fidelity of evaluated quantum applications by a mean of 8.9x/4.2x (wrt. different baselines) and up to a maximum of 34x.

clifford↗
DOE OSTI2022

Optimizing Error-Bounded Lossy Compression for Scientific Data With Diverse Constraints

Vast volumes of data are produced by today's scientific simulations and advanced instruments. These data cannot be stored and transferred efficiently because of limited I/O bandwidth, network speed, and storage capacity. Error-bounded lossy compression can be an effective method for addressing these issues: not only can it significantly reduce data size, but it can also control the data distortion based on user-defined error bounds. In practice, many scientific applications have specific requirements or constraints for lossy compression, in order to guarantee that the reconstructed data are valid for post hoc analysis. For example, some datasets contain irrelevant data that should be isolated in particular and users often have intuition regarding value ranges, geospatial regions, and other data subsets that are crucial for subsequent analysis. Existing state-of-the-art error-bounded lossy compressors, however, do not consider these constraints during compression, resulting in inferior compression ratios with respect to user's post hoc analysis, due to the fact that the data itself provides little or no value for post hoc analysis. In this work we address this issue by proposing an optimized framework that can preserve diverse constraints during the error-bounded lossy compression, e.g., cleaning the irrelevant data, efficiently preserving different precision for multiple value intervals, and allowing users to set diverse precision over both regular and irregular regions. We perform our evaluation on a supercomputer with up to 2,100 cores. Experiments with six real-world applications show that our proposed diverse constraints based error-bounded lossy compressor can obtain a higher visual quality or data fidelity on reconstructed data with the same or even higher compression ratios compared with the traditional state-of-the-art compressor SZ. Furthermore, our experiments also demonstrate very good scalability in compression performance compared with the I/O throughput of the parallel file system.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Nonlinear drought plasticity reveals intraspecific diversity in a dominant grass species

Abstract Intraspecific diversity of dominant species in native plant communities can modulate ecosystem function under both optimal and stressful conditions. Yet, few genotype by environment interaction studies quantify differences in the shape of plasticity functions or phenotypic breakpoints across genotypes in natural populations. Using three genotypes with a history of drought selection, we performed a greenhouse study on the dominant tallgrass prairie species Andropogon gerardii . We investigated phenotypic plasticity and recovery differences among genotypes across a water availability gradient, measuring growth‐related, instantaneous and cumulative phenotypes. To further understand genotype by environment effects, we quantified plasticity functions and breakpoints among genotypes. Like other studies, we found strong evidence for phenotypic and plasticity differences among genotypes. However, we also found nonlinear plasticity functions and breakpoints were common across phenotypes, especially relative growth rates, biomass allocation and root architecture. Drought selected genotypes were also more likely to flower during recovery, but all genotypes were resilient to drought across treatments. We demonstrate that plasticity functions may help explain intraspecific diversity, patterns of selection and nonlinear community responses to more variable rainfall within an experimental population. In particular, plasticity functions can help disentangle drought/variability tolerance versus acquisitive strategies. A better understanding of intraspecific diversity in this grass species will provide more mechanistic insight into its ability to buffer ecosystem changes and provide resiliency in the tallgrass prairie under future droughts. A free Plain Language Summary can be found within the Supporting Information of this article.

Hoffman, Ava M.↗