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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 1,351 records · Page 75
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Genome-Wide Discovery of G-Quadruplexes in Wheat: Distribution and Putative Functional Roles

G-quadruplexes are nucleic acid secondary structures formed by a stack of square planar G-quartets. G-quadruplexes were implicated in many biological functions including telomere maintenance, replication, transcription, and translation, in many species including humans and plants. For wheat, however, though it is one of the world’s most important staple food, no G-quadruplex studies have been reported to date. Here, we computationally identify putative G4 structures (G4s) in wheat genome for the first time and compare its distribution across the genome against five other genomes (human, maize, Arabidopsis, rice, and sorghum). We identified close to 1 million G4 motifs with a density of 76 G4s/Mb across the whole genome and 93 G4s/Mb over genic regions. Remarkably, G4s were enriched around three regions, two located on the antisense and one on the sense strand at the following positions: 1) the transcription start site (TSS) (antisense), 2) the first coding domain sequence (CDS) (antisense), and 3) the start codon (sense). Functional enrichment analysis revealed that the gene models containing G4 motifs within these peaks were associated with specific gene ontology (GO) terms, such as developmental process, localization, and cellular component organization or biogenesis. We investigated genes encoding MADS-box transcription factors and showed examples of G4 motifs within critical regulatory regions in the VRN-1 genes in wheat. Furthermore, comparison with other plants showed that monocots share a similar distribution of G4s, but Arabidopsis shows a unique G4 distribution. Our study shows for the first time the prevalence and possible functional roles of G4s in wheat.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Metagenome-assembled genome distribution and key functionality highlight importance of aerobic metabolism in Svalbard permafrost

Permafrost underlies a large portion of the land in the Northern Hemisphere. It is proposed to be an extreme habitat and home for cold-adaptive microbial communities. Upon thaw permafrost is predicted to exacerbate increasing global temperature trend, where awakening microbes decompose millennia old carbon stocks. Yet our knowledge on composition, functional potential and variance of permafrost microbiome remains limited. In this study, we conducted a deep comparative metagenomic analysis through a 2 m permafrost core from Svalbard, Norway to determine key permafrost microbiome in this climate sensitive island ecosystem. To do so, we developed comparative metagenomics methods on metagenomic-assembled genomes (MAG). We found that community composition in Svalbard soil horizons shifted markedly with depth: the dominant phylum switched from Acidobacteria and Proteobacteria in top soils (active layer) to Actinobacteria, Bacteroidetes, Chloroflexi and Proteobacteria in permafrost layers. Key metabolic potential propagated through permafrost depths revealed aerobic respiration and soil organic matter decomposition as key metabolic traits. We also found that Svalbard MAGs were enriched in genes involved in regulation of ammonium, sulfur and phosphate. Here, we provide a new perspective on how permafrost microbiome is shaped to acquire resources in competitive and limited resource conditions of deep Svalbard soils.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Taxonomic distribution of metabolic functions in bacteria associated with Trichodesmium consortia

The photosynthetic and diazotrophic cyanobacterium Trichodesmium is a key contributor to marine biogeochemical cycles in the subtropical-oligotrophic oceans. Trichodesmium form colonies that harbor a distinct microbial community in comparison to the surrounding seawater. The presence of their associated bacteria can expand Trichodesmium’s functional potential and is predicted to influence the cycling of carbon, nitrogen, phosphorus, and iron (C, N, P, and Fe). To link the bacteria associated with Trichodesmium to key functional traits and elucidate how community structure can influence nutrient cycling, we characterized Red Sea Trichodesmium colonies using metagenomics and metaproteomics. Colonies harbored bacteria that typically associate with algae and particles, such as the ubiquitous Alteromonas macleodii, but also lineages specific to Trichodesmium, such as members from the order Balneolales. The majority of associated bacteria were auxotrophic for different vitamins, indicating their dependency on vitamin production by Trichodesmium. The associated bacteria carry functional traits including siderophore biosynthesis, reduced phosphorus metabolism, and denitrification pathways. The analysis supports Trichodesmium as an active hotspot for C, N, P, Fe, and vitamin exchange. In turn, Trichodesmium may rely on associated bacteria to meet its high Fe demand as several lineages synthesize photolabile siderophores (e.g., vibrioferrin, rhizoferrin, petrobactin) which can enhance the bioavailability of particulate Fe to the entire consortium. Collectively, the results indicate that Trichodesmium colonies provide a structure where these interactions can take place. While further studies are required to clarify the exact nature of these interactions, Trichodesmium’s reliance on particle and algae-associated bacteria and the observed redundancy of key functional traits likely underpins the resilience of Trichodesmium within an ever-changing global environment.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Deep Neural Networks are Adaptive to Function Regularity and Data Distribution in Approximation and Estimation

Deep learning has exhibited remarkable results across diverse areas. To understand its success, substantial research has been directed towards its theoretical foundations. Nev- ertheless, the majority of these studies examine how well deep neural networks can model functions with uniform regularities. In this paper, we explore a different angle: how deep neural networks can adapt to varying degrees of smoothness in functions and nonuni- form data distributions across different locations and scales. More precisely, we focus on a broad class of functions defined by nonlinear tree-based approximation methods. This class encompasses a range of function types, such as functions with uniform regularities and discontinuous functions. We develop nonparametric approximation and estimation theories for this class using deep ReLU networks. Our results show that deep neural networks are adaptive to the nonuniform smoothness of functions and nonuniform data distributions at different locations and scales. We apply our results to several function classes, and derive the corresponding approximation and generalization errors. The validity of our results is demonstrated through numerical experiments.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Three-dimensional imaging of proton in basis light-front quantization

Here, we employ an effective Hamiltonian that includes the transverse and longitudinal confinement and the one-gluon exchange interaction with fixed coupling constant. By solving the eigenvalue equation in basis light-front quantization (BLFQ), we generate the light-front wavefunctions (LFWFs) for the nucleon in the valence quark Fock space. Fitting the model parameters, we obtain high quality descriptions of electromagnetic form factors and radius for proton while the results deviate somewhat from experimental data for neutron.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2021

Entropy Pair Functional Theory: Direct Entropy Evaluation Spanning Phase Transitions

We prove that, within the class of pair potential Hamiltonians, the excess entropy is a universal, temperature-independent functional of the density and pair correlation function. This result extends Henderson’s theorem, which states that the free energy is a temperature dependent functional of the density and pair correlation. The stationarity and concavity of the excess entropy functional are discussed and related to the Gibbs–Bugoliubov inequality and to the free energy. We apply the Kirkwood approximation, which is commonly used for fluids, to both fluids and solids. Approximate excess entropy functionals are developed and compared to results from thermodynamic integration. The pair functional approach gives the absolute entropy and free energy based on simulation output at a single temperature without thermodynamic integration. We argue that a functional of the type, which is strictly applicable to pair potentials, is also suitable for first principles calculation of free energies from Born–Oppenheimer molecular dynamics performed at a single temperature. In conclusion, this advancement has the potential to reduce the evaluation the free energy to a simple modification to any procedure that evaluates the energy and the pair correlation function.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2025

Adaptive Linear State Estimation for Unbalanced Distribution System

The inclusion of PMU functionality in distribution relays enables the implementation of a linear state estimator (LSE) in Distribution Systems (DS). However, the unbalanced topology and phase coupling in distribution lines necessitate modifications to the LSE formulation. Additionally, the higher fault frequency in distribution systems requires a state estimation approach that is resilient to contingencies. This work proposes an adaptive linear state estimation algorithm tailored for unbalanced distribution systems with single-phase and two-phase laterals. Furthermore, a modified Optimal PMU Placement (OPP) strategy is introduced to ensure full observability in distribution systems with single-phase and two-phase buses. To maintain adaptability to topology changes, the state estimator incorporates circuit breaker status data provided by PMUs, ensuring robust performance during topology changes triggered by faults. The performance of the algorithm is verified on the IEEE 13-bus, 34-bus, and 123-bus systems.

PMUs↗
DOE OSTI2024

Lattice QCD calculation of 𝑥-dependent meson distribution amplitudes at physical pion mass with threshold logarithm resummation

We present a lattice quantum chromodynamics (QCD) calculation of the 𝑥-dependent pion and kaon distribution amplitudes (DA) in the framework of large momentum effective theory. This calculation is performed on a fine lattice of 𝑎 = 0.076 fm at physical pion mass, with the pion boosted to 1.8 GeV and kaon boosted to 2.3 GeV. We renormalize the matrix elements in the hybrid scheme and match to Math output error with a subtraction of the leading renormalon in the Wilson-line mass. The perturbative matching is improved by resumming the large logarithms related to the small quark and gluon momenta in the soft-gluon limit. After resummation, we demonstrate that we are able to calculate a range of 𝑥 ∈[𝑥 0 ,1 − 𝑥 0 ] with 𝑥 0 = 0.25 for pion and 𝑥 0 = 0.2 for kaon with theoretical systematic errors under control. The kaon DA is shown to be slighted skewed, and narrower than pion DA. Although the 𝑥-dependence cannot be direct calculated beyond these ranges, we estimate higher moments of the pion and kaon DAs by complementing our calculation with short-distance factorization.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

Higher-order cumulants and correlation functions of proton multiplicity distributions in s N N = 3 GeV Au + Au collisions at the RHIC STAR experiment

Here, we report a measurement of cumulants and correlation functions of event-by-event proton multiplicity distributions from fixed-target Au+Au collisions at $\sqrt{s_\text{NN}}$ = 3 GeV measured by the STAR experiment. Protons are identified within the rapidity (y) and transverse momentum ($p_T$) region –0:9 < $\textit{y}$ < 0 and 0:4 < pT < 2:0 GeV/c in the center-of-mass frame. A systematic analysis of the proton cumulants and correlation functions up to sixth-order as well as the corresponding ratios as a function of the collision centrality, $p_T$, and $\textit{y}$ are presented. The effect of pileup and initial volume fluctuations on these observables and the respective corrections are discussed in detail. The results are compared to calculations from the hadronic transport UrQMD model as well as a hydrodynamic model. In the most central 5% collisions, the value of proton cumulant ratio $C_4 = C_2$ is negative, drastically different from the values observed in Au+Au collisions at higher energies. Compared to model calculations including Lattice QCD, a hadronic transport model, and a hydrodynamic model, the strong suppression in the ratio of $C_4/C_2$ at 3 GeV Au+Au collisions indicates an energy regime dominated by hadronic interactions.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2021

Characterization of zirconium carbide microspheres synthesized via internal gelation

Microspheres of zirconium carbide with grain size 40-320 nm were synthesized using internal gelation techniques and characterized by scanning electron microscopy, synchrotron X-ray diffraction, and neutron total scattering. Compared with a polycrystalline benchmark ZrC sample prepared by plasma vapor phase deposition, the microspheres display lower variance in grain size and considerably lower microstrain representative of a more homogenous internal microstructure. However, excess carbon was present in the microspheres, evident in both the X-ray and neutron diffraction data as well as a corresponding hypostoichiometric ZrC phase. Furthermore, the excess carbon phase is assumed to be pockets of carbon that remained unreacted through the combined internal gelation and subsequent carbothermic reduction synthesis process. Atomic-scale structural characterization with neutron PDF analysis confirmed the presence of localized nano-sized domains of graphite-like carbon material.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Moment preserving constrained resampling with applications to particle-in-cell methods

The Moment Preserving Constrained Resampling (MPCR) algorithm for particle resampling is introduced and applied to particle-in-cell (PIC) methods to increase simulation accuracy, reduce compute cost, and/or avoid numerical instabilities. The general algorithm partitions the system space into smaller subsets and resamples the distribution within each subset. Further, the algorithm is designed to conserve any number of particle and grid moments with a high degree of accuracy (i.e. machine accuracy). The effectiveness of MPCR is demonstrated with several numerical tests, including a use-case study in gyrokinetic fusion plasma simulations. Finally, the computational cost of MPCR is negligible compared to the cost of particle evolution in PIC methods, and the tests demonstrate that periodic particle resampling yields a significant improvement in the accuracy and stability of the results.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗
DOE OSTI2023

Future Studies of Dihadron Production in SIDIS

Spin asymmetry and cross section measurements in semi-inclusive hadroproduction grant access to a variety of parton distribution and fragmentation functions. Such measurements of dihadron production additionally constrain Dihadron Fragmentation Functions (DiFFs), and the extra degree of freedom from the second hadron facilitates access to some of the parton distribution functions. At CLAS kinematics, subleading-twist parton distributions are accessible in dihadron beam-spin and target-spin asymmetries, and a comparison of semi-inclusive scattering off a proton and a deuteron probes their flavor dependence. The future Electron-Ion Collider (EIC) with a transversely polarized proton will access several transverse-momentum dependent distributions such as Sivers and transversity. On the fragmentation side, numerous DiFFs are accessible, and their partial wave expansion probes correlations between the angular momentum of the fragmenting parton with that of the observed dihadron. Furthermore, different hadron channels probe flavor dependence in fragmentation. Together with CLAS, the EIC as well as CLAS with the proposed 22 GeV accelerator upgrade will cover a broad range of $Q^2$ and $x$, allowing for the study of evolution effects of all of these functions. This presentation will summarize the possibilities of these measurements at CLAS and at future experimental facilities.

Dilks, Christopher↗
DOE OSTI2021

Cumulants and correlation functions of net-proton, proton, and antiproton multiplicity distributions in Au+Au collisions at energies available at the BNL Relativistic Heavy Ion Collider

Here, we report a systematic measurement of cumulants, C n , for net-proton, proton, and antiproton multiplicity distributions, and correlation functions, κ n , for proton and antiproton multiplicity distributions up to the fourth order in Au+Au collisions at $\sqrt{s_{NN}}$ = 7.7, 11.5, 14.5, 19.6, 27, 39, 54.4, 62.4, and 200 GeV. The C n and κ n are presented as a function of collision energy, centrality and kinematic acceptance in rapidity, y, and transverse momentum, p T . The data were taken during the first phase of the Beam Energy Scan (BES) program (2010–2017) at the BNL Relativistic Heavy Ion Collider (RHIC) facility. The measurements are carried out at midrapidity (|y| < 0.5) and transverse momentum 0.4 < p T < 2.0 GeV/c, using the STAR detector at RHIC. We observe a nonmonotonic energy dependence ($\sqrt{s_{NN}}$ = 7.7–62.4 GeV) of the net-proton C 4 /C 2 with the significance of 3.1σ for the 0–5% central Au+Au collisions. This is consistent with the expectations of critical fluctuations in a QCD-inspired model. Thermal and transport model calculations show a monotonic variation with $\sqrt{s_{NN}}$. For the multiparticle correlation functions, we observe significant negative values for a two-particle correlation function, κ 2 , of protons and antiprotons, which are mainly due to the effects of baryon number conservation. Furthermore, it is found that the four-particle correlation function, κ 4 , of protons plays a role in determining the energy dependence of proton C 4 /C 1 below 19.6 GeV, which cannot be understood by the effect of baryon number conservation.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2021

Macroecological distributions of gene variants highlight the functional organization of soil microbial systems

Abstract The recent application of macroecological tools and concepts has made it possible to identify consistent patterns in the distribution of microbial biodiversity, which greatly improved our understanding of the microbial world at large scales. However, the distribution of microbial functions remains largely uncharted from the macroecological point of view. Here, we used macroecological models to examine how the genes encoding the functional capabilities of microorganisms are distributed within and across soil systems. Models built using functional gene array data from 818 soil microbial communities showed that the occupancy-frequency distributions of genes were bimodal in every studied site, and that their rank-abundance distributions were best described by a lognormal model. In addition, the relationships between gene occupancy and abundance were positive in all sites. This allowed us to identify genes with high abundance and ubiquitous distribution (core) and genes with low abundance and limited spatial distribution (satellites), and to show that they encode different sets of microbial traits. Common genes encode microbial traits related to the main biogeochemical cycles (C, N, P and S) while rare genes encode traits related to adaptation to environmental stresses, such as nutrient limitation, resistance to heavy metals and degradation of xenobiotics. Overall, this study characterized for the first time the distribution of microbial functional genes within soil systems, and highlight the interest of macroecological models for understanding the functional organization of microbial systems across spatial scales.

59 BASIC BIOLOGICAL SCIENCES↗