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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 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

A quantum algorithm to efficiently sample from interfering binary trees

Quantum computers provide an opportunity to efficiently sample from probability distributions that include non-trivial interference effects between amplitudes. Using a simple process wherein all possible state histories can be specified by a binary tree, we construct an explicit quantum algorithm that runs in polynomial time to sample from the process once. The corresponding naive Markov Chain algorithm does not produce the correct probability distribution and an explicit classical calculation of the full distribution requires exponentially many operations. Finally, the problem can be reduced to a system of two qubits with repeated measurements, shedding light on a quantum-inspired efficient classical algorithm.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Decision-tree structures utilizing a phase-transition material

The rich internal physics due to competing electronic phases present in phase-transition materials such as VO2 offer the potential for compact building block design for emerging non-von Neumann computing technologies. Here, based on the relaxation dynamics of an insulator-metal phase transition, we demonstrate experimentally a decision-tree classifier embedded within a single volatile resistive switching device. The tree is constructed by the combination of the voltage pulse and relaxation time and can adapt to different tasks. We use machine learning to analyze the relaxation process, enabling a predictive voltage-relaxation time phase diagram for the electrical resistance state. Classification of the etiology of the chronic cough is presented as a proof-of-principle use case. Further, our approach can be generalized to broader classes of solid-state and solid-liquid interfacial systems that demonstrate a variety of phase relaxations.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Momentum shift and on-shell constructible massive amplitudes

We construct tree-level amplitude for massive particles using on-shell recursion relations based on two classes of momentum shifts: an all-line transverse shift that deforms momentum by its transverse polarization vector, and a massive Britto-Cachazo-Feng-Witten-type shift. We illustrate that these shifts allow us to correctly calculate four-point and five-point amplitudes in massive QED, without an ambiguity associated with the contact terms that may arise from a simple “gluing” of lower-point on-shell amplitudes. We discuss various aspects and applicability of the two shifts, including the large-z behavior and complexity scaling. We show that there exists a “good” all-line transverse shift for all possible little group configurations of the external particles, which can be extended to a broader class of theories with massive particles such as massive QCD and theories with massive spin-1 particles. The massive Britto-Cachazo-Feng-Witten-type shift enjoys more simplicity, but a “good” shift does not exist for all the spin states due to the specific choice of spin axis.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2021

Optimization and Augmentation for Data Parallel Contour Trees

Contour trees are used for topological data analysis in scientific visualization. While originally computed with serial algorithms, recent work has introduced a vector-parallel algorithm. Furthermore, this algorithm is relatively slow for fully augmented contour trees which are needed for many practical data analysis tasks. We therefore introduce a representation called the hyperstructure that enables efficient searches through the contour tree and use it to construct a fully augmented contour tree in data parallel, with performance on average 6 times faster than the state-of-the-art parallel algorithm in the TTK topological toolkit.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2018

Classification of Complete Proteomes of Different Organisms and Protein Sets Based on Their Protein Distributions in Terms of Some Key Attributes of Proteins

The existence of complete genome sequences makes it important to develop different approaches for classification of large-scale data sets and to make extraction of biological insights easier. Here, we propose an approach for classification of complete proteomes/protein sets based on protein distributions on some basic attributes. We demonstrate the usefulness of this approach by determining protein distributions in terms of two attributes: protein lengths and protein intrinsic disorder contents (ID). The protein distributions based on L and ID are surveyed for representative proteome organisms and protein sets from the three domains of life. The two-dimensional maps (designated as fingerprints here) from the protein distribution densities in the LD space defined by ln( L ) and ID are then constructed. The fingerprints for different organisms and protein sets are found to be distinct with each other, and they can therefore be used for comparative studies. As a test case, phylogenetic trees have been constructed based on the protein distribution densities in the fingerprints of proteomes of organisms without performing any protein sequence comparison and alignments. The phylogenetic trees generated are biologically meaningful, demonstrating that the protein distributions in the LD space may serve as unique phylogenetic signals of the organisms at the proteome level.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Poplar: a phylogenomics pipeline

Motivation Generating phylogenomic trees from the genomic data is essential in understanding biological systems. Each step of this complex process has received extensive attention and has been significantly streamlined over the years. Given the public availability of data, obtaining genomes for a wide selection of species is straightforward. However, analyzing that data to generate a phylogenomic tree is a multistep process with legitimate scientific and technical challenges, often requiring a significant input from a domain-area scientist. Results We present Poplar, a new, streamlined computational pipeline, to address the computational logistical issues that arise when constructing the phylogenomic trees. It provides a framework that runs state-of-the-art software for essential steps in the phylogenomic pipeline, beginning from a genome with or without an annotation, and resulting in a species tree. Running Poplar requires no external databases. In the execution, it enables parallelism for execution for clusters and cloud computing. The trees generated by Poplar match closely with state-of-the-art published trees. The usage and performance of Poplar is far simpler and quicker than manually running a phylogenomic pipeline. Availability and implementation Freely available on GitHub at https://github.com/sandialabs/poplar. Implemented using Python and supported on Linux.

Koning, Elizabeth [Sandia National Laboratories (S↗
DOE OSTI2018

Tensor networks, p -adic fields, and algebraic curves: arithmetic and the AdS 3 /CFT 2 correspondence

One of the many remarkable properties of conformal field theory in two dimensions is its connection to algebraic geometry. Since every compact Riemann surface is a projective algebraic curve, many constructions of interest in physics (which a priori depend on the analytic structure of the spacetime) can be formulated in purely algebraic language. This opens the door to interesting generalizations, obtained by taking another choice of field: for instance, the p-adics. Herein, we generalize the $\mathrm{AdS} / \mathrm{CFT}$ correspondence according to this principle; the result is a formulation of holography in which the bulk geometry is discrete—the Bruhat–Tits tree for $\mathrm{PGL} (2, \mathbb{Q}_p)$—but the group of bulk isometries nonetheless agrees with that of boundary conformal transformations and is not broken by discretization. We anticipate that this forms the natural geometric setting for tensor networks that have been proposed as models of bulk reconstruction via quantum error correcting codes; in certain cases, geodesics in the Bruhat–Tits tree reproduce those constructed using quantum error correction. Other aspects of holography also hold: Standard holographic results for massive free scalar fields in a fixed background carry over to the tree, whose vertical direction can be interpreted as a renormalization-group scale for modes in the boundary $\mathrm{CFT}$. Higher-genus bulk geometries (the $\mathrm{BTZ}$ black hole and its generalizations) can be understood straightforwardly in our setting, and the Ryu–Takayanagi formula for the entanglement entropy appears naturally

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Host-region parameters for an adjustable model for crustal earthquakes to facilitate the implementation of the backbone approach to building ground-motion logic trees in probabilistic seismic hazard analysis

The backbone approach to constructing a ground-motion logic tree for probabilistic seismic hazard analysis (PSHA) can address shortcomings in the traditional approach of populating the branches with multiple existing, or potentially modified, ground-motion models (GMMs) by rendering more transparent the relationship between branch weights and the resulting distribution of predicted accelerations. To capture epistemic uncertainty in a tractable manner, there are benefits in building the logic tree through the application of successive adjustments for differences in source, path, and site characteristics between the host region of the selected backbone GMM and the target region for which the PSHA is being conducted. The implementation of this approach is facilitated by selecting a backbone GMM that is amenable to such host-to-target adjustments for individual source, path, and site characteristics. The NGA-West2 GMM of Chiou and Youngs (CY14) has been identified as a highly adaptable model for crustal seismicity that is well suited to such adjustments. Rather than using generic source, path, and site characteristics assumed appropriate for the host region, the final suite of adjusted GMMs for the target region will be better constrained if the host-region parameters are defined specifically on the basis of their compatibility with the CY14 backbone GMM. To this end, making use of a recently developed crustal shear-wave velocity profile consistent with CY14, we present an inversion of the model to estimate the key source and path parameters, namely the stress parameter and the anelastic attenuation. With these outputs, the effort in constructing a ground-motion logic tree for any PSHA dealing with crustal seismicity can be focused primarily on the estimation of the target-region characteristics and their associated uncertainties. The inversion procedure can also be adapted for any application in which different constraints might be relevant.

Stafford, Peter J.↗
DOE OSTI2021

Optimal decision trees for categorical data via integer programming

Decision trees have been a very popular class of predictive models for decades due to their interpretability and good performance on categorical features. However, they are not always robust and tend to overfit the data. Additionally, if allowed to grow large, they lose interpretability. In this paper, we present a mixed integer programming formulation to construct optimal decision trees of a prespecified size. We take the special structure of categorical features into account and allow combinatorial decisions (based on subsets of values of features) at each node. Our approach can also handle numerical features via thresholding. Here we show that very good accuracy can be achieved with small trees using moderately-sized training sets. The optimization problems we solve are tractable with modern solvers.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2018

Regional surname affinity: A spatial network approach

Abstract Objective We investigate surname affinities among areas of modern‐day China, by constructing a spatial network, and making community detection. It reports a geographical genealogy of the Chinese population that is result of population origins, historical migrations, and societal evolutions. Materials and methods We acquire data from the census records supplied by China's National Citizen Identity Information System, including the surname and regional information of 1.28 billion registered Chinese citizens. We propose a multilayer minimum spanning tree (MMST) to construct a spatial network based on the matrix of isonymic distances, which is often used to characterize the dissimilarity of surname structure among areas. We use the fast unfolding algorithm to detect network communities. Results We obtain a 10‐layer MMST network of 362 prefecture nodes and 3,610 edges derived from the matrix of the Euclidean distances among these areas. These prefectures are divided into eight groups in the spatial network via community detection. We measure the partition by comparing the inter‐distances and intra‐distances of the communities and obtain meaningful regional ethnicity classification. Discussion The visualization of the resulting communities on the map indicates that the prefectures in the same community are usually geographically adjacent. The formation of this partition is influenced by geographical factors, historic migrations, trade and economic factors, as well as isolation of culture and language. The MMST algorithm proves to be effective in geo‐genealogy and ethnicity classification for it retains essential information about surname affinity and highlights the geographical consanguinity of the population.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Phylogenomics and diversification of Sordariomycetes

The Sordariomycetes is a specious, morphologically diverse, and widely distributed class of the phylum Ascomycota that forms a well-supported clade diverged from Leotiomycetes. Aside from their ecological significance as plant and human pathogens, saprobes, endophytes, and fungicolous taxa, species of Sordariomycetes produces a wide range of chemically novel and diverse metabolites used in important fields. Recent phylogenetic analyses derived from a small number of genes have considerably increased our understanding of the family, order, and subclass relationships within Sordariomycetes, but several important groups have not been resolved well. In addition, there are various paraphyletic or polyphyletic groups. Moreover, the criteria used to establish higher ranks remain highly variable across different studies. Therefore, the taxonomy of Sordariomycetes is in constant flux, remains poorly understood, and is subject to much controversy. Here, for the first time, we have assembled a phylogenetic dataset containing 638 genomes representing the 156 genera, 50 families, and 17 orders and 5 subclasses of Sordariomycetes. This data set is based on 1124 genes and results in a well-resolved phylogenomic tree. We further constructed an evolutionary timeline of Sordariomycetes diversification based on the genomic data sets. Our divergence time estimate results are inconsistent with previous studies, suggesting estimates of node ages are less precise and varied. Based on these results, we discuss the higher ranks of Sordariomycetes and empirically propose an unprecedented taxonomic framework for the class.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

When can we detect lianas from space? Toward a mechanistic understanding of liana‐infested forest optics

Abstract Lianas, woody vines acting as structural parasites of trees, have profound effects on the composition and structure of tropical forests, impacting tree growth, mortality, and forest succession. Remote sensing could offer a powerful tool for quantifying the scale of liana infestation, provided the availability of robust detection methods. We analyze the consistency and global geographic specificity of spectral signals—reflectance across wavelengths—from liana‐infested tree crowns and forest stands, examining the underlying mechanisms of these signals. We compiled a uniquely comprehensive database, including leaf reflectance spectra from 5424 leaves, fine‐scale airborne reflectance data from 999 liana‐infested canopies, and coarse‐scale satellite reflectance data covering 775 ha of liana‐infested forest stands. To unravel the mechanisms of the liana spectral signal, we applied mechanistic radiative transfer models across scales, establishing a synthesis of the relative importance of different mechanisms, which we corroborate with field data on liana leaf chemistry and canopy structure. We find a consistent liana spectral signal at canopy and stand scales across globally distributed sites. This signature mainly arises at the canopy level due to direct effects of more horizontal leaf angles, resulting in a larger projected leaf area, and indirect effects from increased light scattering in the near and short‐wave infrared regions, linked to lianas' less costly leaf construction compared with trees on average. The existence of a consistent global spectral signal for lianas suggests that large‐scale quantification of liana infestation is feasible. However, because the traits responsible for the liana canopy‐reflectance signal are not exclusive to lianas, accurate large‐scale detection requires rigorously validated remote sensing methods. Our models highlight challenges in automated detection, such as potential misidentification due to leaf phenology, tree life history, topography, and climate, especially where the scale of liana infestation is less than a single remote sensing pixel. The observed cross‐site patterns also prompt ecological questions about lianas' adaptive similarities in optical traits across environments, indicating possible convergent evolution due to shared constraints on leaf biochemical and structural traits.

Environmental Sciences & Ecology↗
DOE OSTI2017

Phylogenetic relationships and phylogeography of relevant lineages within the complex Campanulaceae family in Macaronesia

Abstract Macaronesia has long been recognized as a natural model for studying evolutionary processes in plant diversification. Several studies have attempted to focus on single lineages, and few have covered the diversification of a family across all the archipelagos. We used a comprehensive sample to clarify the phylogenetic relationships and the biogeographic history of the Macaronesian Campanulaceae. Hypotheses related to the colonization of these archipelagos will be used to examine the diversification patterns of different lineages. We sequenced the ITS region and six cp DNA markers ( atpB , matK , petD , rbcL , trnL‐F , and psbA‐trnH ) from 10 Campanulaceae species, including seven endemic species in Macaronesia. The phylogeny of these taxa was reconstructed using maximum parsimony, maximum likelihood, and Bayesian inference. To study the relationships within each lineage, haplotype networks were calculated using NeighborNet and TCS algorithms. Moreover, data were combined with fossil information to construct time‐calibrated trees for the Macaronesian Campanulaceae species. The phylogenetic analyses are largely congruent with current taxon circumscriptions, and all the endemic genera formed monophyletic clades, namely Azorina in Azores; Musschia in Madeira; and Campanula in Cape Verde. The Azorina clade and the Cape Verde endemic Campanula may share a common ancestor in North Africa, and the divergence was dated ca. 12.3 million years ago (Mya). The divergence of the Musschia clade began in the Pliocene ca. 3.4 Mya. Moreover, several examples of intraspecific variation were revealed among the native species with a clear geographic structured patterns, suggesting that cryptic diversity might exist within the native Macaronesian Campanulaceae when compared to the close mainland taxa (e.g., Campanula erinus , Trachelium caeruleum ), but additional studies are needed to support the molecular data. This study highlights the power of combining data (e.g., phylogeny and divergence times, with species distribution data) for testing diversification hypotheses within the unique Macaronesian flora, providing useful information for future conservation efforts.

Menezes, Tiago↗
DOE OSTI2026

Gauged soft recursion: on-shell construction of Goldstone-gauge amplitudes

We present a new on-shell recursion relation for scattering amplitudes involving Nambu-Goldstone bosons with a gauged unbroken symmetry. A central challenge is that gauge interactions break Adler’s zero condition for charged scalars, invalidating the standard soft recursion. To overcome this, we introduce a “gauged soft recursion” that leverages the soft theorems of the gauge bosons themselves, combined with a novel decomposition of amplitudes into gauge-invariant components where Adler’s zero is partially restored. The formalism, which also incorporates internal gauge bosons via angular momentum constraints, enables the systematic construction of tree-level amplitudes with arbitrary numbers of Goldstone bosons and gauge bosons in both Abelian and non-Abelian theories, as we demonstrate with explicit examples.

Chiral Lagrangian↗
DOE OSTI2019

Comparative genomics and transcriptomics analysis reveals evolution patterns of selection in the Salix phylogeny

Background: Willows are widely distributed in the northern hemisphere and have good adaptability to different living environment. The increasing of genome and transcriptome data provides a chance for comparative analysis to study the evolution patterns with the different origin and geographical distributions in the Salix phylogeny. Results: Transcript sequences of 10 Salicaceae species were downloaded from public databases. All pairwise of orthologues were identified by comparative analysis in these species, from which we constructed a phylogenetic tree and estimated the rate of diverse. Divergence times were estimated in the 10 Salicaceae using comparative transcriptomic analysis. All of the fast-evolving positive selection sequences were identified, and some cold-, drought-, light-, universal-, and heat- resistance genes were discovered. Conclusions: The divergence time of subgenus Vetrix and Salix was about 17.6–16.0 Mya during the period of Middle Miocene Climate Transition (21–14 Mya). Subgenus Vetrix diverged to migratory and resident groups when the climate changed to the cool and dry trend by 14 Mya. Cold- and light- stress genes were involved in positive selection among the resident Vetrix, and which would help them to adapt the cooling stage. Universal- stress genes exhibited positive selection among the migratory group and subgenus Salix. These data are useful for comprehending the adaptive evolution and speciation in the Salix lineage.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Genome collection processing for “Conserved upper thermal limits and small safety margins in soil copiotrophic bacteria”

We extracted the genomic DNA of 400 randomly selected isolates using a Quick-DNA Microprep Kit (Zymo Research D3020) according to the manufacturer’s protocol. We then submitted the extracted gDNA samples for short-read Illumina sequencing (200 Mbp) at SeqCoast Genomics (Portsmouth, NH, USA). After preprocessing the sequences using Trimmommatic (Bolger et al. 2014), we assembled the genomes using SPADES (Bankevich et al. 2012) and checked the quality of each assembly using QUAST (Gurevich et al. 2013). We processed the genome assemblies using a KBase (v1.4.0) pipeline (Allen et al. 2017; Arkin et al. 2018). Briefly, we used DRAM (v0.1.2) with default settings to annotate the genome assemblies. We then evaluated genome quality and possible contamination levels using CheckM (v1.0.18) (Parks et al. 2015) and retained genomes with completeness above 98% and contamination below 5% (n = 354), following the authors' guidelines. We then obtained taxonomic assignments for all remaining isolates using the Genome Taxonomy Database tool GTDB-Tk (v2.3.2, database version r214) (Chaumeil et al. 2019). We constructed a phylogenetic tree using the tool SpeciesTree (v2.2.0). We then trimmed the tree (using Trim SpeciesTree to GenomeSet- v1.4.0), retaining only tips within our collection with measured thermal performance.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Variation in Sphingomonas traits across habitats and phylogenetic clades

Whether microbes show habitat preferences is a fundamental question in microbial ecology. If different microbial lineages have distinct traits, those lineages may occur more frequently in habitats where their traits are advantageous. Sphingomonas is an ideal bacterial clade in which to investigate how habitat preference relates to traits because these bacteria inhabit diverse environments and hosts. Here we downloaded 440 publicly available Sphingomonas genomes, assigned them to habitats based on isolation source, and examined their phylogenetic relationships. We sought to address whether: (1) there is a relationship between Sphingomonas habitat and phylogeny, and (2) whether there is a phylogenetic correlation between key, genome-based traits and habitat preference. We hypothesized that Sphingomonas strains from similar habitats would cluster together in phylogenetic clades, and key traits that improve fitness in specific environments should correlate with habitat. Genome-based traits were categorized into the Y-A-S trait-based framework for high growth yield, resource acquisition, and stress tolerance. We selected 252 high quality genomes and constructed a phylogenetic tree with 12 well-defined clades based on an alignment of 404 core genes. Sphingomonas strains from the same habitat clustered together within the same clades, and strains within clades shared similar clusters of accessory genes. Additionally, key genome-based trait frequencies varied across habitats. We conclude that Sphingomonas gene content reflects habitat preference. This knowledge of how environment and host relate to phylogeny may also help with future functional predictions about Sphingomonas and facilitate applications in bioremediation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Unveiling the Arsenal of Apple Bitter Rot Fungi: Comparative Genomics Identifies Candidate Effectors, CAZymes, and Biosynthetic Gene Clusters in Colletotrichum Species

The bitter rot of apple is caused by Colletotrichum spp. and is a serious pre-harvest disease that can manifest in postharvest losses on harvested fruit. In this study, we obtained genome sequences from four different species, C. chrysophilum, C. noveboracense, C. nupharicola, and C. fioriniae, that infect apple and cause diseases on other fruits, vegetables, and flowers. Our genomic data were obtained from isolates/species that have not yet been sequenced and represent geographic-specific regions. Genome sequencing allowed for the construction of phylogenetic trees, which corroborated the overall concordance observed in prior MLST studies. Bioinformatic pipelines were used to discover CAZyme, effector, and secondary metabolic (SM) gene clusters in all nine Colletotrichum isolates. We found redundancy and a high level of similarity across species regarding CAZyme classes and predicted cytoplastic and apoplastic effectors. SM gene clusters displayed the most diversity in type and the most common cluster was one that encodes genes involved in the production of alternapyrone. Our study provides a solid platform to identify targets for functional studies that underpin pathogenicity, virulence, and/or quiescence that can be targeted for the development of new control strategies. With these new genomics resources, exploration via omics-based technologies using these isolates will help ascertain the biological underpinnings of their widespread success and observed geographic dominance in specific areas throughout the country.

59 BASIC BIOLOGICAL SCIENCES↗