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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 1,063 records · Page 59
All sourcesNASA NTRSDOE OSTI
NASA NTRS1994

The speeds of coronal mass ejections in the solar wind at mid heliographic latitudes: Ulysses

Six CMEs (coronal mass ejections) have been detected in the Ulysses plasma observations poleward of S31 deg. The most striking aspect of these mid-latitude CMEs was their high speeds; the overall average speed of these CMEs was approximately 740 km/s, which was comparable to that of the rest of the solar wind at these latitudes. This average CME speed is much higher than average CME speeds observed in the solar wind in the ecliptic or in the corona close to the Sun. The evidence indicates that the CMEs were not pushed up to high speeds in interplanetary space by interaction with trailing high-speed plasma. Rather, they simply seem to have received the same basic acceleration as the rest of the solar wind at these mid-latitudes. Our results suggest that the basic acceleration process for many CMEs at all latitudes is essentially the same as for the normal solar wind. Frequently most of this acceleration must occur well beyond 6 solar radii from Sun center.

Gosling, J. T.↗
NASA NTRS1993

A computer-based training system combining virtual reality and multimedia

Training new users of complex machines is often an expensive and time-consuming process. This is particularly true for special purpose systems, such as those frequently encountered in DOE applications. This paper presents a computer-based training system intended as a partial solution to this problem. The system extends the basic virtual reality (VR) training paradigm by adding a multimedia component which may be accessed during interaction with the virtual environment. The 3D model used to create the virtual reality is also used as the primary navigation tool through the associated multimedia. This method exploits the natural mapping between a virtual world and the real world that it represents to provide a more intuitive way for the student to interact with all forms of information about the system.

Stansfield, Sharon A.↗
NASA NTRS2008

Scheme for Quantum Computing Immune to Decoherence

A constructive scheme has been devised to enable mapping of any quantum computation into a spintronic circuit in which the computation is encoded in a basis that is, in principle, immune to quantum decoherence. The scheme is implemented by an algorithm that utilizes multiple physical spins to encode each logical bit in such a way that collective errors affecting all the physical spins do not disturb the logical bit. The scheme is expected to be of use to experimenters working on spintronic implementations of quantum logic. Spintronic computing devices use quantum-mechanical spins (typically, electron spins) to encode logical bits. Bits thus encoded (denoted qubits) are potentially susceptible to errors caused by noise and decoherence. The traditional model of quantum computation is based partly on the assumption that each qubit is implemented by use of a single two-state quantum system, such as an electron or other spin-1.2 particle. It can be surprisingly difficult to achieve certain gate operations . most notably, those of arbitrary 1-qubit gates . in spintronic hardware according to this model. However, ironically, certain 2-qubit interactions (in particular, spin-spin exchange interactions) can be achieved relatively easily in spintronic hardware. Therefore, it would be fortunate if it were possible to implement any 1-qubit gate by use of a spin-spin exchange interaction. While such a direct representation is not possible, it is possible to achieve an arbitrary 1-qubit gate indirectly by means of a sequence of four spin-spin exchange interactions, which could be implemented by use of four exchange gates. Accordingly, the present scheme provides for mapping any 1-qubit gate in the logical basis into an equivalent sequence of at most four spin-spin exchange interactions in the physical (encoded) basis. The complexity of the mathematical derivation of the scheme from basic quantum principles precludes a description within this article; it must suffice to report that the derivation provides explicit constructions for finding the exchange couplings in the physical basis needed to implement any arbitrary 1-qubit gate. These constructions lead to spintronic encodings of quantum logic that are more efficient than those of a previously published scheme that utilizes a universal but fixed set of gates.

Williams, Colin↗
DOE OSTI2013

Structural Insights into Neutrophilic Migration Revealed by the Crystal Structure of the Chemokine Receptor CXCR2 in Complex with the First PDZ Domain of NHERF1

Neutrophil plays an essential role in host defense against infection, but uncontrolled neutrophilic infiltration can cause inflammation and severe epithelial damage. We recently showed that CXCR2 formed a signaling complex with NHERF1 and PLC-2, and that the formation of this complex was required for intracellular calcium mobilization and neutrophilic transepithelial migration. To uncover the structural basis of the complex formation, we report here the crystal structure of the NHERF1 PDZ1 domain in complex with the C-terminal sequence of CXCR2 at 1.16 Å resolution. The structure reveals that the CXCR2 peptide binds to PDZ1 in an extended conformation with the last four residues making specific side chain interactions. Remarkably, comparison of the structure to previously studied PDZ1 domains has allowed the identification of PDZ1 ligand-specific interactions and the mechanisms that govern PDZ1 target selection diversities. In addition, we show that CXCR2 can bind both NHERF1 PDZ1 and PDZ2 in pulldown experiments, consistent with the observation that the peptide binding pockets of these two PDZ domains are highly structurally conserved. The results of this study therefore provide structural basis for the CXCR2-mediated neutrophilic migration and could have important clinical applications in the prevention and treatment of numerous neutrophil-dependent inflammatory disorders.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Experimental and theoretical description of the process of contact laser surgery with a titanium-doped optothermal fibre converter

In an in vitro experiment simulating a surgeon’s actions in the process of contact laser surgery of soft biological tissue, the dependences of the temperature of a titanium-doped optothermal fibre converter (TOTFC) and the depths of coagulation and ablation of biological tissue on the average radiation power of a diode laser with a wavelength of 980 nm and on the speed of the converter movement along biological tissue are obtained. The structural, optical, and thermophysical models of TOTFC are discussed, as well as the thermophysical model of the interaction of a laser-heated converter with biological tissue, which takes into account the temperature dependences of the basic thermophysical parameters of the converter and biological tissue, as well as the contribution of the thickness h{sub int} of the water vapour layer between the converter and biotissue. It is shown that the proposed model allows describing the result of contact laser surgery of soft biotissue with TOTFC adequately to the experiment. (laser biophotonics)

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2014

Many-body effects on the structures and stability of Ba{sup 2+}Xe{sub n} (n = 1–39, 54) clusters

The structures and relative stabilities of mixed Ba{sup 2+}Xe{sub n} (n = 1–39, 54) clusters have been theoretically studied using basin-hopping global optimization. Analytical potential energy surfaces were constructed from ab initio or experimental data, assuming either purely additive interactions or including many-body polarization effects and the mutual contribution of self-consistent induced dipoles. For both models the stable structures are characterized by the barium cation being coated by a shell of xenon atoms, as expected from simple energetic arguments. Icosahedral packing is dominantly found, the exceptional stability of the icosahedral motif at n = 12 being further manifested at the size n = 32 where the basic icosahedron is surrounded by a dodecahedral cage, and at n = 54 where the transition to multilayer Mackay icosahedra has occurred. Interactions between induced dipoles generally tend to decrease the Xe-Xe binding, leading to different solvation patterns at small sizes but also favoring polyicosahedral growth. Besides attenuating relative energetic stability, many-body effects affect the structures by expanding the clusters by a few percents and allowing them to deform more.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS2002

Generalized interactions using virtual tools within the spring framework: cutting

We present schemes for real-time generalized mesh cutting. Starting with the a basic example, we describe the details of implementing cutting on single and multiple surface objects as well as hybrid and volumetric meshes using virtual tools with single and multiple cutting surfaces. These methods have been implemented in a robust surgical simulation environment allowing us to model procedures ranging from animal dissection to cleft lip correction.

Feedback↗
DOE OSTI2024

Probing interspecies metabolic interactions within a synthetic binary microbiome using genome-scale modeling

Metabolic interactions within a microbial community play a key role in determining the structure, function, and composition of the community. However, due to the complexity and intractability of natural microbiomes, limited knowledge is available on interspecies interactions within a community. In this work, using a binary synthetic microbiome, a methanotroph-photoautotroph (M-P) coculture, as the model system, we examined different genome-scale metabolic modeling (GEM) approaches to gain a better understanding of the metabolic interactions within the coculture, how they contribute to the enhanced growth observed in the coculture, and how they evolve over time. Using batch growth data of the model M-P coculture, we compared three GEM approaches for microbial communities. Two of the methods are existing approaches: SteadyCom, a steady state GEM, and dynamic flux balance analysis (DFBA) Lab, a dynamic GEM. We also proposed an improved dynamic GEM approach, DynamiCom, for the M-P coculture. SteadyCom can predict the metabolic interactions within the coculture but not their dynamic evolutions; DFBA Lab can predict the dynamics of the coculture but cannot identify interspecies interactions. DynamiCom was able to identify the cross-fed metabolite within the coculture, as well as predict the evolution of the interspecies interactions over time. A new dynamic GEM approach, DynamiCom, was developed for a model M-P coculture. Constrained by the predictions from a validated kinetic model, DynamiCom consistently predicted the top metabolites being exchanged in the M-P coculture, as well as the establishment of the mutualistic N-exchange between the methanotroph and cyanobacteria. The interspecies interactions and their dynamic evolution predicted by DynamiCom are supported by ample evidence in the literature on methanotroph, cyanobacteria, and other cyanobacteria-heterotroph cocultures.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Structures of CTCF–DNA complexes including all 11 zinc fingers

The CCCTC-binding factor (CTCF) binds tens of thousands of enhancers and promoters on mammalian chromosomes by means of its 11 tandem zinc finger (ZF) DNA-binding domain. In addition to the 12–15-bp CORE sequence, some of the CTCF binding sites contain 5' upstream and/or 3' downstream motifs. Here, we describe two structures for overlapping portions of human CTCF, respectively, including ZF1–ZF7 and ZF3–ZF11 in complex with DNA that incorporates the CORE sequence together with either 3' downstream or 5' upstream motifs. Like conventional tandem ZF array proteins, ZF1–ZF7 follow the right-handed twist of the DNA, with each finger occupying and recognizing one triplet of three base pairs in the DNA major groove. ZF8 plays a unique role, acting as a spacer across the DNA minor groove and positioning ZF9–ZF11 to make cross-strand contacts with DNA. We ascribe the difference between the two subgroups of ZF1–ZF7 and ZF8–ZF11 to residues at the two positions -6 and -5 within each finger, with small residues for ZF1–ZF7 and bulkier and polar/charged residues for ZF8–ZF11. ZF8 is also uniquely rich in basic amino acids, which allows salt bridges to DNA phosphates in the minor groove. Highly specific arginine–guanine and glutamine–adenine interactions, used to recognize G:C or A:T base pairs at conventional base-interacting positions of ZFs, also apply to the cross-strand interactions adopted by ZF9–ZF11. The differences between ZF1–ZF7 and ZF8–ZF11 can be rationalized structurally and may contribute to recognition of high-affinity CTCF binding sites.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Beyond microbes: Are fauna the next frontier in soil biogeochemical models?

The explicit representation of microbial communities in soil biogeochemical models is improving their projections, promoting new interdisciplinary research, and stimulating novel theoretical developments. However, microbes are the foundation of complicated soil food webs, with highly intricate and non-linear interactions among trophic groups regulating soil biogeochemical cycles. This food web includes fauna, which influence litter decomposition and the structure and activity of the microbial community. Given the early success of microbial-explicit models, should we also consider explicitly representing faunal activity and physiology in soil biogeochemistry models? Herein we explore this question, arguing that the direct effects of fauna on litter decomposition are stronger than on soil organic matter dynamics, and that fauna can have strong indirect effects on soil biogeochemical cycles by influencing microbial population dynamics, but the direction and magnitude of these effects remains too unpredictable for models used to predict global biogeochemical patterns. Given glaring gaps in our understanding of fauna-microbe interactions and how these might play out along climatic and land use gradients, we believe it remains early to explicitly represent fauna in these global-scale models. However, their incorporation into models used for conceptual exploration of food-web interactions or into ecosystem-scale models using site-specific data could provide rich theoretical breakthroughs and provide a starting point for improving model projections across scales.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

The Dark Energy Survey Data Release I

We describe the first public data release of the Dark Energy Survey, DES DR1, consisting of reduced single-epoch images, co-added images, co-added source catalogs, and associated products and services assembled over the first 3 yr of DES science operations. DES DR1 is based on optical/near-infrared imaging from 345 distinct nights (2013 August to 2016 February) by the Dark Energy Camera mounted on the 4 m Blanco telescope at the Cerro Tololo InterAmerican Observatory in Chile. We release data from the DES wide-area survey covering similar to 5000 deg(2) of the southern Galactic cap in five broad photometric bands, grizY. DES DR1 has a median delivered point-spread function of g = 1.12, r = 0.96, i = 0.88, z = 0.84, and Y = 0.'' 90 FWHM, a photometric precision of <1% in all bands, and an astrometric precision of 151 mas. The median co-added catalog depth for a 1.'' 95 diameter aperture at signal-to-noise ratio (S/N) = 10 is g = 24.33, r = 24.08, i = 23.44, z = 22.69, and Y = 21.44 mag. DES DR1 includes nearly 400 million distinct astronomical objects detected in similar to 10,000 co-add tiles of size 0.534 deg(2) produced from similar to 39,000 individual exposures. Benchmark galaxy and stellar samples contain similar to 310 million and similar to 80 million objects, respectively, following a basic object quality selection. These data are accessible through a range of interfaces, including query web clients, image cutout servers, jupyter notebooks, and an interactive co-add image visualization tool. DES DR1 constitutes the largest photometric data set to date at the achieved depth and photometric precision.

Abbott, T. M. C.↗
NASA NTRS1989

Turbulent eddy viscosity modeling in transonic shock/boundary-layer interactions

The treatment of turbulence effects on transonic shock/turbulent boundary layer interaction is addressed within the context of a triple deck approach valid for arbitrary practical Reynolds numbers between 1000 and 10 billion. The modeling of the eddy viscosity and basic turbulent boundary profile effects in each deck is examined in detail using Law-of-the-Wall/Law-of-the-Wake concepts as the foundation. Results of parametric studies showing how each of these turbulence model aspects influences typical interaction zone property distributions (wall pressure, displacement thickness and local skin friction) are presented and discussed.

Inger, G. R.↗
DOE OSTI2014

FLS2-BAK1 Extracellular Domain Interaction Sites Required for Defense Signaling Activation

Signaling initiation by receptor-like kinases (RLKs) at the plasma membrane of plant cells often requires regulatory leucine-rich repeat (LRR) RLK proteins such as SERK or BIR proteins. The present work examined how the microbe-associated molecular pattern (MAMP) receptor FLS2 builds signaling complexes with BAK1 (SERK3). We first, using in vivo methods that validate separate findings by others, demonstrated that flg22 (flagellin epitope) ligand-initiated FLS2-BAK1 extracellular domain interactions can proceed independent of intracellular domain interactions. We then explored a candidate SERK protein interaction site in the extracellular domains (ectodomains; ECDs) of the significantly different receptors FLS2, EFR (MAMP receptors), PEPR1 (damage-associated molecular pattern (DAMP) receptor), and BRI1 (hormone receptor). Repeat conservation mapping revealed a cluster of conserved solvent-exposed residues near the C-terminus of models of the folded LRR domains. However, site-directed mutagenesis of this conserved site in FLS2 did not impair FLS2-BAK1 ECD interactions, and mutations in the analogous site of EFR caused receptor maturation defects. Hence this conserved LRR C-terminal region apparently has functions other than mediating interactions with BAK1. In vivo tests of the subsequently published FLS2-flg22-BAK1 ECD co-crystal structure were then performed to functionally evaluate some of the unexpected configurations predicted by that crystal structure. In support of the crystal structure data, FLS2-BAK1 ECD interactions were no longer detected in in vivo co-immunoprecipitation experiments after site-directed mutagenesis of the FLS2 BAK1-interaction residues S554, Q530, Q627 or N674. In contrast, in vivo FLS2-mediated signaling persisted and was only minimally reduced, suggesting residual FLS2-BAK1 interaction and the limited sensitivity of co-immunoprecipitation data relative to in vivo assays for signaling outputs. However, Arabidopsis plants expressing FLS2 with the Q530A+Q627A double mutation were impaired both in detectable interaction with BAK1 and in FLS2-mediated responses, lending overall support to current models of FLS2 structure and function.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Enhanced Photo-Cross-Linking of Thymines in DNA Holliday Junction-Templated Squaraine Dimers

Programmable self-assembly of dyes using DNA templates to promote exciton delocalization in dye aggregates is gaining considerable interest. New methods to improve the rigidity of the DNA scaffold and thus the stability of the molecular dye aggregates to encourage exciton delocalization are desired. In these dye–DNA constructs, one potential way to increase the stability of the aggregates is to create an additional covalent bond via photo-cross-linking reactions between thymines in the DNA scaffold. Specifically, we report an approach to increase the yield of photo-cross-linking reaction between thymines in the core of a DNA Holliday junction while limiting the damage from UV irradiation to DNA. We investigated the effect of the distance between thymines on the photo-cross-linking reaction yields by using linkers with different lengths to tether the dyes to the DNA templates. By comprehensively evaluating the photo-cross-linking reaction yields of dye–DNA aggregates using linkers with different lengths, we conclude that interstrand thymines tend to photo-cross-link more efficiently with short linkers. A higher cross-linking yield was achieved due to the shorter intermolecular distance between thymines influenced by strong dye–dye interactions. Furthermore, our method establishes the possibility of improving the stability of DNA-scaffolded dye aggregates, thereby expanding their use in exciton-based applications such as light harvesting, nanoscale computing, quantum computing, and optoelectronics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Mineral properties, microbes, transport, and plant-input profiles control vertical distribution and age of soil carbon stocks

The role of organo-mineral interactions, microbial dynamics, and vertical plant input profiles are hypothesized to be important in controlling soil organic matter (SOM) stocks and dynamics. In this paper, to test this hypothesis, we enhanced and applied a model (Biotic and Abiotic Model of SOM – BAMS1) that represents microbial dynamics and organo-mineral interactions integrated with a multiphase reactive transport solver for variably saturated porous media. The model represents aqueous chemistry, aqueous advection and diffusion, gaseous diffusion, sorption processes, bacterial and fungal activity, and archetypal monomer- and polymer-carbon substrate groups, including dead cell wall material. This model structure is fundamentally different, and produces different SOM dynamics, than the pseudo-first order relationships that are used in most site- and global-scale terrestrial SOM models. We simulated two grasslands, a seven-site chronosequence (~3.9–240 Ky) in Northern California, and a Russian Chernozem site where soils were sampled 100 years apart. We calibrated the model's vertically-resolved soil bulk specific surface area (SBSSA) using observed bulk SOM content, and then tested the model against observed Δ 14 C profiles. The modeled microbial processes, organo-mineral interactions, and vertical aqueous transport produced realistic vertically-resolved predictions of bulk SOM content, Δ 14 C values of SOM, lignin content, and fungi-to-aerobic bacteria biomass ratios. Using sensitivity analyses, we found that vertical carbon input profiles were important controls over the Δ 14 C depth distribution. Shallower carbon input profiles lead to older carbon at depth. In addition, the SBSSA was the dominant control over the magnitude and vertical distribution of SOM stocks. Finally, the findings of this study demonstrate the value of explicitly incorporating microbial activity, sorption, and vertical transport into land models to predict SOM dynamics.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Natural soil microbiome variation affects spring foliar phenology with consequences for plant productivity and climate-driven range shifts

Identifying the potential for natural soil microbial communities to predictably affect complex plant traits is an important frontier in climate change research. Plant phenology varies with environmental and genetic factors, but few studies have examined if the soil microbiome interacts with plant population differentiation to affect phenology and ecosystem function. We compared soil microbial variation in a widespread tree species (Populus angustifolia) with different soil inoculum treatments in a common garden environment to test how the soil microbiome affects spring foliar phenology and subsequent biomass growth. We hypothesized and show that: 1) soil bacterial and fungal communities vary with tree conditioning from different populations and elevations, 2) this soil community variation influences patterns of foliar phenology and plant growth across populations and elevation gradients, and 3) transferring lower elevation plant genotypes to higher elevation soil communities delayed foliar phenology, thereby shortening the growing season and reducing annual biomass production. Our findings show the importance of plant-soil interactions that help shape the timing of tree foliar phenology and productivity. Here, these geographic patterns in plant population x microbiome interactions also broaden our understanding of how soil communities impact plant phenotypic variation across key climate change gradients, with consequences for ecosystem functioning.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2011

Analysis of the Isolated SecA DEAD Motor Suggests a Mechanism for Chemical-Mechanical Coupling

The preprotein cross-linking domain and C-terminal domains of Escherichia coli SecA were removed to create a minimal DEAD motor, SecA-DM. SecA-DM hydrolyzes ATP and has the same affinity for ADP as full-length SecA. The crystal structure of SecA-DM in complex with ADP was solved and shows the DEAD motor in a closed conformation. Comparison with the structure of the E. coli DEAD motor in an open conformation (Protein Data Bank ID 2FSI) indicates main-chain conformational changes in two critical sequences corresponding to Motif III and Motif V of the DEAD helicase family. The structures that the Motif III and Motif V sequences adopt in the DEAD motor open conformation are incompatible with the closed conformation. Therefore, when the DEAD motor makes the transition from open to closed, Motif III and Motif V are forced to change their conformations, which likely functions to regulate passage through the transition state for ATP hydrolysis. The transition state for ATP hydrolysis for the SecA DEAD motor was modeled based on the conformation of the Vasa helicase in complex with adenylyl imidodiphosphate and RNA (Protein Data Bank ID 2DB3). A mechanism for chemical-mechanical coupling emerges, where passage through the transition state for ATP hydrolysis is hindered by the conformational changes required in Motif III and Motif V, and may be promoted by binding interactions with the preprotein substrate and/or other translocase domains and subunits.

59 BASIC BIOLOGICAL SCIENCES↗