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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 703 records · Page 39
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Ecosystem consequences of a nitrogen-fixing proto-organelle

Microscale symbioses can be critical to ecosystem functions, but the mechanisms of these interactions in nature are often cryptic. Here, we use a combination of stable isotope imaging and tracing to reveal carbon (C) and nitrogen (N) exchanges among three symbiotic primary producers that fuel a salmon-bearing river food web. Bulk isotope analysis, nanoSIMS (secondary ion mass spectrometry) isotope imaging, and density centrifugation for quantitative stable isotope probing enabled quantification of organism-specific C- and N-fixation rates from the subcellular scale to the ecosystem. After winters with riverbed-scouring floods, the macroalga Cladophora glomerata uses nutrients in spring runoff to grow streamers up to 10 m long. During summer flow recession, riverine N concentrations wane and Cladophora becomes densely epiphytized by three species of Epithemia, diatoms with N-fixing endosymbionts (proto-organelles) descended from a free-living Crocosphaera cyanobacterium. Over summertime epiphyte succession on Cladophora, N-fixation rates increased as Epithemia spp. became dominant, Cladophora C-fixation declined to near zero, and Epithemia C-fixation increased. Carbon transfer to caddisflies grazing on Cladophora with high densities of Epithemia was 10-fold higher than C transfer to caddisflies grazing Cladophora with low Epithemia loads. In response to demand for N, Epithemia allocates high levels of newly fixed C to its endosymbiont. Consequently, these endosymbionts have the highest rates of C and N accumulation of any taxon in this tripartite symbiosis during the biologically productive season and can produce one of the highest areal rates of N-fixation reported in any river ecosystem.

Marks, Jane C. [Northern Arizona Univ., Flagstaff,↗
DOE OSTI2012

KOLMOGOROV VECTORIAL LAW FOR SOLAR WIND TURBULENCE

We investigate a class of axisymmetric magnetohydrodynamic turbulence which satisfies the exact relation for third-order Elsaesser structure functions. Following the critical balance conjecture, we assume the existence of a power-law relation between correlation length scales along and transverse to the local mean magnetic field direction. The flow direction of the vector third-order moments F{sup {+-}} is then along axisymmetric concave/convex surfaces, the axis of symmetry being given by the mean magnetic field. Under this consideration, the vector F{sup {+-}} satisfies a simple Kolmogorov law which depends on the anisotropic parameter a{sup {+-}}, which measures the concavity of the surfaces. A comparison with recent in situ multispacecraft solar wind observations is made; it is concluded that the underlying turbulence is very likely convex. A discussion is given about the physical meaning of such an anisotropy.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2019

Experimental and synthetic measurements of polarized synchrotron emission from runaway electrons in Alcator C-Mod

This paper presents the first experimental analysis of polarized synchrotron emission from relativistic runaway electrons (REs) in a tokamak plasma. Importantly, we show that the polarization information of synchrotron radiation can be used to diagnose spatially-localized RE pitch angle distributions. Synchrotron-producing REs were generated during low density, Ohmic, diverted plasma discharges in the Alcator C-Mod tokamak. The ten-channel motional Stark effect diagnostic was used to measure spatial profiles of the polarization angle θ pol and the fraction f pol of detected light that was linearly-polarized. Spatial transitions in θ pol of 90° —from horizontal to vertical polarization and vice versa—are observed in experimental data and are well-explained by the gyro-motion of REs and high directionality of synchrotron radiation. Here polarized synchrotron emission is modeled with the synthetic diagnostic Soft; its output Green's (or detector response) functions reveal a critical RE pitch angle at which θ pol flips by 90° and f pol is minimal. Using Soft, we determine the dominant RE pitch angle which reproduces measured θ pol and f pol values. The spatiotemporal evolutions of θ pol and f pol are explored in detail for one C-Mod discharge. For channels viewing REs near the magnetic axis and flux surfaces q = 1 and 4/3, disagreements between synthetic and experimental signals suggest that the sawtooth instability may be influencing RE dynamics. Furthermore, other sources of pitch angle scattering, not considered in this analysis, could help explain discrepancies between simulation and experiment.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2015

Implementation of a multi-threaded framework for large-scale scientific applications

The CMS experiment has recently completed the development of a multi-threaded capable application framework. In this paper, we will discuss the design, implementation and application of this framework to production applications in CMS. For the 2015 LHC run, this functionality is particularly critical for both our online and offline production applications, which depend on faster turn-around times and a reduced memory footprint relative to before. These applications are complex codes, each including a large number of physics-driven algorithms. While the framework is capable of running a mix of thread-safe and 'legacy' modules, algorithms running in our production applications need to be thread-safe for optimal use of this multi-threaded framework at a large scale. Towards this end, we discuss the types of changes, which were necessary for our algorithms to achieve good performance of our multithreaded applications in a full-scale application. Lastly performance numbers for what has been achieved for the 2015 run are presented.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Crystal structure of an Escherichia coli Hfq Core (residues 2–69)–DNA complex reveals multifunctional nucleic acid binding sites

Hfq regulates bacterial gene expression post-transcriptionally by binding small RNAs and their target mRNAs, facilitating sRNA-mRNA annealing, typically resulting in translation inhibition and RNA turnover. Hfq is also found in the nucleoid and binds double-stranded (ds) DNA with a slight preference for A-tracts. Here, we present the crystal structure of the Escherichia coli Hfq Core bound to a 30 bp DNA, containing three 6 bp A-tracts. Although previously postulated to bind to the ‘distal’ face, three statistically disordered double stranded DNA molecules bind across the proximal face of the Hfq hexamer as parallel, straight rods with B-DNA like conformational properties. One DNA duplex spans the diameter of the hexamer and passes over the uridine-binding proximal-face pore, whereas the remaining DNA duplexes interact with the rims and serve as bridges between adjacent hexamers. Binding is sequence-independent with residues N13, R16, R17 and Q41 interacting exclusively with the DNA backbone. Atomic force microscopy data support the sequence-independent nature of the Hfq-DNA interaction and a role for Hfq in DNA compaction and nucleoid architecture. Our structure and nucleic acid-binding studies also provide insight into the mechanism of sequence-independent binding of Hfq to dsRNA stems, a function that is critical for proper riboregulation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Mechanisms of in-plane magnetic anisotropy in superconducting NbSe 2

Here we present a unifying picture of the magnetic in-plane anisotropies of two-dimensional superconductors based on transition metal dichalcogenides. The symmetry considerations are first applied to constrain the form of the conductivity tensor. We hence conclude that the twofold periodicity of transport distinct from the planar Hall-related contributions requires a tensor perturbation. At the same time, the sixfold periodic variation of the critical field results from the Rashba spin-orbit coupling on a hexagonal lattice. We have considered the effect of a weak tensor perturbation on the critical field, gap function, and magnetoconductivity. The latter is studied using the time-dependent Ginzburg-Landau phenomenology. The common origin of the π periodicity in transport and thermodynamics properties is identified. The scheme constructed here is applied to describe the existing theoretical scenarios from a unified point of view. This allows us to single out the differences and similarities between the suggested approaches.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Epitaxial graphene-encapsulated surface reconstruction of Ge(110)

Understanding and engineering the properties of crystalline surfaces has been critical in achieving functional electronics at the nanoscale. Employing scanning tunneling microscopy, surface x-ray diffraction, and high-resolution x-ray reflectivity experiments, we present a thorough study of epitaxial graphene (EG)/Ge(110) and report a Ge(110) "6 x 2" reconstruction stabilized by the presence of epitaxial graphene unseen in group-IV semiconductor surfaces. As a result, X-ray studies reveal that graphene resides atop the surface reconstruction with a 0.34 nm van der Waals (vdW) gap and provides protection from ambient degradation.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Structure of a fungal form of aspartate-semialdehyde dehydrogenase from Aspergillus fumigatus

Aspartate-semialdehyde dehydrogenase (ASADH) functions at a critical junction in the aspartate biosynthetic pathway and represents a validated target for antimicrobial drug design. This enzyme catalyzes the NADPH-dependent reductive dephosphorylation of β-aspartyl phosphate to produce the key intermediate aspartate semialdehyde. The absence of this entire pathway in humans and other mammals will allow the selective targeting of pathogenic microorganisms for antimicrobial development. Here, the X-ray structure of a new form of ASADH from the pathogenic fungal species Aspergillus fumigatus has been determined. The overall structure of this enzyme is similar to those of its bacterial orthologs, but there are some critical differences both in biological assembly and in secondary-structural features that can potentially be exploited for the development of species-selective drugs with selective toxicity against infectious fungal organisms.

Dahal, Gopal P.↗
DOE OSTI2023

High-throughput identification of spin-photon interfaces in silicon

Color centers in host semiconductors are prime candidates as spin-photon interfaces for quantum applications. Finding an optimal spin-photon interface in silicon would move quantum information technologies toward a mature semiconducting host. However, the space of possible charged defects is vast, making the identification of candidates from experiments alone extremely challenging. Here, we use high-throughput first-principles computational screening to identify spin-photon interfaces among more than 1000 charged defects in silicon. The use of a single-shot hybrid functional approach is critical in enabling the screening of many quantum defects with a reasonable accuracy. We identify three promising spin-photon interfaces as potential bright emitters in the telecom band: Ti$^+_i$, Fe$^0_i$, and Ru$^0_i$. These candidates are excited through defect-bound excitons, stressing the importance of such defects in silicon for telecom band operations. Our work paves the way to further large-scale computational screening for quantum defects in semiconductors.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2019

De novo design of tunable, pH-driven conformational changes

The ability of naturally occurring proteins to change conformation in response to environmental changes is critical to biological function. Although there have been advances in the de novo design of stable proteins with a single, deep free-energy minimum, the design of conformational switches remains challenging. We present a general strategy to design pH-responsive protein conformational changes by precisely preorganizing histidine residues in buried hydrogen-bond networks. We design homotrimers and heterodimers that are stable above pH 6.5 but undergo cooperative, large-scale conformational changes when the pH is lowered and electrostatic and steric repulsion builds up as the network histidine residues become protonated. The transition pH and cooperativity can be controlled through the number of histidine-containing networks and the strength of the surrounding hydrophobic interactions. Upon disassembly, the designed proteins disrupt lipid membranes both in vitro and after being endocytosed in mammalian cells. Our results demonstrate that environmentally triggered conformational changes can now be programmed by de novo protein design.

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

Geometric deep learning of RNA structure

RNA molecules adopt three-dimensional structures that are critical to their function and of interest in drug discovery. Few RNA structures are known, however, and predicting them computationally has proven challenging. We introduce a machine learning approach that enables identification of accurate structural models without assumptions about their defining characteristics, despite being trained with only 18 known RNA structures. The resulting scoring function, the Atomic Rotationally Equivariant Scorer (ARES), substantially outperforms previous methods and consistently produces the best results in community-wide blind RNA structure prediction challenges. By learning effectively even from a small amount of data, our approach overcomes a major limitation of standard deep neural networks. Because it uses only atomic coordinates as inputs and incorporates no RNA-specific information, this approach is applicable to diverse problems in structural biology, chemistry, materials science, and beyond.

Townshend, Raphael J. L.↗
DOE OSTI2019

Elucidating Syntrophic Butyrate-Degrading Populations in Anaerobic Digesters Using Stable-Isotope-Informed Genome-Resolved Metagenomics

Linking the genomic content of uncultivated microbes to their metabolic functions remains a critical challenge in microbial ecology. Resolving this challenge has implications for improving our management of key microbial interactions in biotechnologies such as anaerobic digestion, which relies on slow-growing syntrophic and methanogenic communities to produce renewable methane from organic waste. In this study, we combined DNA stable-isotope probing (SIP) with genome-centric metagenomics to recover the genomes of populations enriched in 13 C after growing on [ 13 C]butyrate. Differential abundance analysis of recovered genomic bins across the SIP metagenomes identified two metagenome-assembled genomes (MAGs) that were significantly enriched in heavy [ 13 C]DNA. Phylogenomic analysis assigned one MAG to the genus Syntrophomonas and the other MAG to the genus Methanothrix. Metabolic reconstruction of the annotated genomes showed that the Syntrophomonas genome encoded all the enzymes for beta-oxidizing butyrate, as well as several mechanisms for interspecies electron transfer via electron transfer flavoproteins, hydrogenases, and formate dehydrogenases. The Syntrophomonas genome shared low average nucleotide identity (<95%) with any cultured representative species, indicating that it is a novel species that plays a significant role in syntrophic butyrate degradation within anaerobic digesters. The Methanothrix genome contained the complete pathway for acetoclastic methanogenesis, indicating that it was enriched in 13 C from syntrophic acetate transfer. This study demonstrates the potential of stable-isotope-informed genome-resolved metagenomics to identify in situ interspecies metabolic cooperation within syntrophic consortia important to anaerobic waste treatment as well as global carbon cycling.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

High-Order Multi-Material ALE Hydrodynamics

Here, we present a new approach for multi-material arbitrary Lagrangian--Eulerian (ALE) hydrodynamics simulations based on high-order finite elements posed on high-order curvilinear meshes. The method builds on and extends our previous work in the Lagrangian and remap phases of ALE, and depends critically on a functional perspective that enables subzonal physics and material modeling. Curvilinear mesh relaxation is based on node movement, which is determined through the solution of an elliptic equation. The remap phase is posed in terms of advecting state variables between two meshes over a fictitious time interval. The resulting advection equation is solved by a discontinuous Galerkin (DG) formulation, combined with a customized Flux Corrected Transport (FCT) type algorithm. Because conservative fields are remapped, additional synchronization steps are introduced to preserve bounds with respect to primal fields. These steps include modification of the low-order FCT solutions, definition of conservative FCT fluxes based on primal field bounds, and monotone transitions between primal and conservative fields.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2019

Towards a CAN IDS Based on a Neural Network Data Field Predictor

Modern vehicles contain a few controller area networks (CANs), which allow scores of on-board electronic control units (ECUs) to communicate messages critical to vehicle functions and driver safety. CAN provides a lightweight and reliable broadcast protocol but is bereft of security features. As evidenced by many recent research works, CAN exploits are possible both remotely and with direct access, fueling a growing CAN intrusion detection system (IDS) body of research. A challenge for pioneering vehicle-agnostic IDSs is that passenger vehicles' CAN message encodings are proprietary, defined and held secret by original equipment manufacturers (OEMs). Targeting detection of next-generation attacks, in which messages are sent from the expected ECU at the expected time but with malicious content, researchers are now seeking to leverage "CAN data models'', which predict future CAN messages and use prediction error to identify anomalous, hopefully malicious CAN messages. Yet, current works model CAN signals post-translation, i.e., after applying OEM-donated or reverse-engineered translations from raw data. We present initial IDS results testing deep neural networks used to predict CAN data at the bit level, targeting IDS capabilities that avoiding reverse engineering proprietary encodings. Our results suggest the method is promising for data with signals exhibiting dependence on previous or concurrent inputs.

Pawelec, Krzysztof↗
DOE OSTI2011

High-Energy X-Ray Diffraction Analysis Tool

The functionality of heRXD includes the following: distance and angular calibration and viewing flat-panel detector images used for X-ray diffraction; image (polar) rebinning or "caking"; line position fitting in powder diffraction images; image segmentation or "blob finding"; crystal orentation indesing; and lattice vector refinement. These functionalities encompass a critical set analyzing teh data for high-energy diffraction measurements that are currently performed at synchrotron sources such as the Advanced Photon Source (APS). The software design modular and open source under LGPL. The intent is to provide a common framework and graphical user interface that has the ability to utillize internal as well as external subroutines to provide various optins for performing the fuctionalities listed above. The software will initially be deployed at several national user facilities--including APS, ALS, and CHESS--and then made available for download using a hosting service such as sourceforge.

Source record↗
DOE OSTI2017

Dereplication, Aggregation and Scoring Tool (DAS Tool) v1.0

Communities of uncultivated microbes are critical to ecosystem function and microorganism health, and a key objective of metagenomic studies is to analyze organism-specific metabolic pathways and reconstruct community interaction networks. This requires accurate assignment of genes to genomes, yet existing binning methods often fail to predict a reasonable number of genomes and report many bins of low quality and completeness. Furthermore, the performance of existing algorithms varies between samples and biotypes. Here, we present a dereplication, aggregation and scoring strategy, DAS Tool, that combines the strengths of a flexible set of established binning algorithms. DAS Tools applied to a constructed community generated more accurate bins than any automated method. Further, when applied to samples of different complexity, including soil, natural oil seeps, and the human gut, DAS Tool recovered substantially more near-complete genomes than any single binning method alone. Included were three genomes from a novel lineage . The ability to reconstruct many near-complete genomes from metagenomics data will greatly advance genome-centric analyses of ecosystems.

SIEBER, CHRISTIAN↗
DOE OSTI2013

Loss of the Arabidopsis thaliana P 4 -ATPase ALA3 Reduces Adaptability to Temperature Stresses and Impairs Vegetative, Pollen, and Ovule Development

Members of the P 4 subfamily of P-type ATPases are thought to help create asymmetry in lipid bilayers by flipping specific lipids between the leaflets of a membrane. This asymmetry is believed to be central to the formation of vesicles in the secretory and endocytic pathways. In Arabidopsis thaliana, a P 4 -ATPase associated with the trans-Golgi network (ALA3) was previously reported to be important for vegetative growth and reproductive success. Here we show that multiple phenotypes for ala3 knockouts are sensitive to growth conditions. For example, ala3 rosette size was observed to be dependent upon both temperature and soil, and varied between 40% and 80% that of wild-type under different conditions. We also demonstrate that ala3 mutants have reduced fecundity resulting from a combination of decreased ovule production and pollen tube growth defects. In-vitro pollen tube growth assays showed that ala3 pollen germinated ~2 h slower than wild-type and had approximately 2-fold reductions in both maximal growth rate and overall length. In genetic crosses under conditions of hot days and cold nights, pollen fitness was reduced by at least 90-fold; from ~18% transmission efficiency (unstressed) to less than 0.2% (stressed). Together, these results support a model in which ALA3 functions to modify endomembranes in multiple cell types, enabling structural changes, or signaling functions that are critical in plants for normal development and adaptation to varied growth environments.

59 BASIC BIOLOGICAL SCIENCES↗