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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 1,135 records · Page 63
All sourcesNASA NTRSDOE OSTI
DOE OSTI2012

Identification of Amino Acids that Account for Long-Range Interactions in Two Triosephosphate Isomerases from Pathogenic Trypanosomes

For a better comprehension of the structure-function relationship in proteins it is necessary to identify the amino acids that are relevant for measurable protein functions. Because of the numerous contacts that amino acids establish within proteins and the cooperative nature of their interactions, it is difficult to achieve this goal. Thus, the study of protein-ligand interactions is usually focused on local environmental structural differences. Here, using a pair of triosephosphate isomerase enzymes with extremely high homology from two different organisms, we demonstrate that the control of a seventy-fold difference in reactivity of the interface cysteine is located in several amino acids from two structurally unrelated regions that do not contact the cysteine sensitive to the sulfhydryl reagent methylmethane sulfonate, nor the residues in its immediate vicinity. The change in reactivity is due to an increase in the apparent pKa of the interface cysteine produced by the mutated residues. Our work, which involved grafting systematically portions of one protein into the other protein, revealed unsuspected and multisite long-range interactions that modulate the properties of the interface cysteines and has general implications for future studies on protein structure-function relationships.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Temporal dynamics of fibrolytic and methanogenic rumen microorganisms during in situ incubation of switchgrass determined by 16S rRNA gene profiling

The rumen microbial ecosystem is known for its biomass-degrading and methane-producing phenotype. Fermentation of recalcitrant plant material, comprised of a multitude of interwoven fibers, necessitates the synergistic activity of diverse microbial taxonomic groups that inhabit the anaerobic rumen ecosystem. Although interspecies hydrogen (H2) transfer, a process during which bacterially generated H2 is transferred to methanogenic Archaea, has obtained significant attention over the last decades, the temporal variation of the different taxa involved in in situ biomass-degradation, H2 transfer and the methanogenesis process remains to be established. Here we investigated the temporal succession of microbial taxa and its effect on fiber composition during rumen incubation using 16S rRNA amplicon sequencing. Switchgrass filled nylon bags were placed in the rumen of a cannulated cow and collected at nine time points for DNA extraction and 16S pyrotag profiling. The microbial community colonizing the air-dried and non-incubated (0 h) switchgrass was dominated by members of the Bacilli (recruiting 63% of the pyrotag reads). During in situ incubation of the switchgrass, two major shifts in the community composition were observed: Bacilli were replaced within 30 min by members belonging to the Bacteroidia and Clostridia, which recruited 34 and 25% of the 16S rRNA reads generated, respectively. A second significant shift was observed after 16 h of rumen incubation, when members of the Spirochaetes and Fibrobacteria classes became more abundant in the fiber-adherent community. During the first 30 min of rumen incubation ~13% of the switchgrass dry matter was degraded, whereas little biomass degradation appeared to have occurred between 30 min and 4 h after the switchgrass was placed in the rumen. Interestingly, methanogenic members of the Euryarchaeota (i.e., Methanobacteria) increased up to 3-fold during this period of reduced biomass-degradation, with peak abundance just before rates of dry matter degradation increased again. We hypothesize that during this period microbial-mediated fibrolysis was temporarily inhibited until H2 was metabolized into CH4 by methanogens. Collectively, our results demonstrate the importance of inter-species interactions for the biomass-degrading and methane-producing phenotype of the rumen microbiome—both microbially facilitated processes with global significance.

interspecies H2 transfer↗
DOE OSTI2022

Community Structure and Microbial Associations in Sediment-Free Methanotrophic Enrichment Cultures from a Marine Methane Seep

We report Syntrophic consortia of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB) consume large amounts of methane and serve as the foundational microorganisms in marine methane seeps. Despite their importance in the carbon cycle, research on the physiology of ANME-SRB consortia has been hampered by the slow growth and complex physicochemical environment the consortia inhabit. Here, we report successful sediment-free enrichment of ANME-SRB consortia from deep-sea methane seep sediments in the Santa Monica Basin, California. Anoxic Percoll density gradients and size-selective filtration were used to separate ANME-SRB consortia from sediment particles and single cells to accelerate the cultivation process. Over a 3-year period, a subset of the sediment-associated ANME and SRB lineages, predominantly comprised of ANME-2a/2b (“Candidatus Methanocomedenaceae”) and their syntrophic bacterial partners, SEEP-SRB1/2, adapted and grew under defined laboratory conditions. Metagenome-assembled genomes from several enrichments revealed that ANME-2a, SEEP-SRB1, and Methanococcoides in different enrichments from the same inoculum represented distinct species, whereas other coenriched microorganisms were closely related at the species level. This suggests that ANME, SRB, and Methanococcoides are more genetically diverse than other members in methane seeps. Flow cytometry sorting and sequencing of cell aggregates revealed that Methanococcoides, Anaerolineales, and SEEP-SRB1 were overrepresented in multiple ANME-2a cell aggregates relative to the bulk metagenomes, suggesting they were physically associated and possibly interacting. Overall, this study represents a successful case of selective cultivation of anaerobic slow-growing microorganisms from sediments based on their physical characteristics, introducing new opportunities for detailed genomic, physiological, biochemical, and ecological analyses. Biological anaerobic oxidation of methane (AOM) coupled with sulfate reduction represents a large methane sink in global ocean sediments. Methane consumption is carried out by syntrophic archaeal-bacterial consortia and fuels a unique ecosystem, yet the interactions in these slow-growing syntrophic consortia and with other associated community members remain poorly understood. The significance of this study is the establishment of sediment-free enrichment cultures of anaerobic methanotrophic archaea and sulfate-reducing bacteria performing AOM with sulfate using selective cultivation approaches based on size, density, and metabolism. By reconstructing microbial genomes and analyzing community composition of the enrichment cultures and cell aggregates, we shed light on the diversity of microorganisms physically associated with AOM consortia beyond the core syntrophic partners. These enrichment cultures offer simplified model systems to extend our understanding of the diversity of microbial interactions within marine methane seeps.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

The membrane QmoABC complex interacts directly with the dissimilatory adenosine 5'-phosphosulfate reductase in sulfate reducing bacteria

The adenosine 5 -phosphosulfate reductase (AprAB) is the enzyme responsible for the reduction of adenosine 5 -phosphosulfate (APS) to sulfite in the biological process of dissimilatory sulfate reduction, which is carried out by a ubiquitous group of sulfate reducing prokaryotes. The electron donor for AprAB has not been clearly identified, but was proposed to be the QmoABC membrane complex, since an aprBA–qmoABC gene cluster is found in many sulfate reducing and sulfur-oxidizing bacteria. The QmoABC complex is essential for sulfate reduction, but electron transfer between QmoABC and AprAB has not been reported. In this work we provide the first direct evidence that QmoABC and AprAB interact in Desulfovibrio spp., using co-immunoprecipitation, cross-linking FarWestern blot, tag-affinity purification, and surface plasmon resonance studies.This showed that the QmoABC–AprAB complex has a strong steady-state affinity (K D = 90 ± 3 nM), but has a transient character due to a fast dissociation rate. Far-Western blot identified QmoA as the Qmo subunit most involved in the interaction. Nevertheless, electron transfer from menaquinol analogs to APS through anaerobically purified QmoABC and AprAB could not be detected. We propose that this reaction requires the involvement of a third partner to allow electron flow driven by a reverse electron bifurcation process, i.e., electron confurcation. This process is deemed essential to allow coupling of APS reduction to chemiosmotic energy conservation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

DBSI: DNA-binding site identifier

In this study, we present the DNA-Binding Site Identifier (DBSI), a new structure-based method for predicting protein interaction sites for DNA binding. DBSI was trained and validated on a data set of 263 proteins (TRAIN-263), tested on an independent set of protein-DNA complexes (TEST-206) and data sets of 29 unbound (APO-29) and 30 bound (HOLO-30) protein structures distinct from the training data. We computed 480 candidate features for identifying protein residues that bind DNA, including new features that capture the electrostatic microenvironment within shells near the protein surface. Our iterative feature selection process identified features important in other models, as well as features unique to the DBSI model, such as a banded electrostatic feature with spatial separation comparable with the canonical width of the DNA minor groove. Validations and comparisons with established methods using a range of performance metrics clearly demonstrate the predictive advantage of DBSI, and its comparable performance on unbound (APO-29) and bound (HOLO-30) conformations demonstrates robustness to binding-induced protein conformational changes. Finally, we offer our feature data table to others for integration into their own models or for testing improved feature selection and model training strategies based on DBSI.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1988

Plasma wave observations with the Dynamics Explorer 1 spacecraft

This paper reviews the results from the plasma wave instrument on the Dynamics Explorer 1 (DE-1) spacecraft. The DE-1 spacecraft was launched on August 3, 1981, into an elliptical polar orbit with initial perigee and apogee radial distances of 1.09 and 4.65 earth radii. In the roughly six years since the launch of the spacecraft, DE-1 has provided basic new information on a wide variety of magnetospheric plasma wave phenomena. These include auroral kilometric radiation, auroral hiss, Z mode radiation, narrow-band electromagnetic emissions associated with equatorial upper hybrid waves, whistler mode emissions, wave-particle interactions stimulated by ground VLF transmitters, equatorial ion-cyclotron emissions, ion Bernstein-mode emissions, and electric field turbulence along the auroral field lines. A brief review of the basic plasma wave modes that can exist in the equatorial and polar regions of the magnetosphere is first given. After the basic terminology is established, each of the above areas of plasma wave research is discussed in detail, first by reviewing the state of knowledge at the time of the DE-1 launch, and then by describing the contribution made by DE-1 in the six years since the spacecraft was launched.

Gurnett, D. A.↗
DOE OSTI2017

Convolution Correction Factor Adjustments on Static PRA Models for Event Assessment

Current probabilistic risk assessment (PRA) models will contain cut sets that have time-constrained basic events such as switched components, recovery of failed components, and failures in time. For these cut sets that have multiple time-constrained events that interact (e.g., offsite power recover at the same time as multiple diesel generators fail to run), there is the possibility that the minimal cut set quantified result is too large. Since current PRA models typically assume that the accident scenario starts at “time zero,” the fails-to-run basic events use this starting time as the basis for their respective reliability models. Over time, the standard practice was to recognize this issue and accept it as part of the conservatism built into the event tree/fault tree PRA models. However, now that these same PRA models are being used in a regulatory forum, this conservatism needs to be addressed. Further, this issue exists not only for the baseline PRA results, but for deficiencies that have been observed or those that have the potential of occurrence, whether the deficiency is complete failure or just a degraded condition. We have found that this conservatism becomes very important when evaluating scenarios such as station blackout sequences and other loss of offsite power sequences. This paper will address the theory and implemented process used by the Systems Analysis Programs for Hands-on Integrated Reliability Evaluations (SAPHIRE) PRA software. Starting with SAPHIRE version 8, the process that was developed is to calculate a “convolution correction factor” based on three distinct calculations. The first calculation is the cut set based frequency calculated via the standard event tree/fault tree PRA model (assuming all run failures start at time equal to zero). The second calculation is to perform the exact time-constrained calculation by integrating the component failure models over the time period of interest (e.g., time to recover, a mission time). For example, this exact calculation for the case of the diesel generators is to convolve their failure models with the offsite power recovery model to obtain the exact frequency. The third calculation is to produce the convolution correction factor by dividing the exact frequency calculation by the standard cut set frequency. This convolution correction factor is then applied to the PRA cut sets in order to remove the time-constrained conservatism. The process used to obtain the convolution correction factor for the baseline PRA is important; however, in this paper we also describe what happens when there is degradation of a component or a potential deficiency. These issues become very important in order to ensure that the convolution correction factor is re-calculated correctly. If the correction factor does not get re-calculated and the same baseline convolution correction factor is used, the final analysis result could be over conservative or under conservative. This paper will discuss how these issues are addressed and provide examples on how SAPHIRE automatically makes the necessary adjustments. MathCad verification results can be computed using the provided equations and input data.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2015

Chemical Control of Plasmons in Metal Chalcogenide and Metal Oxide Nanostructures

The field of plasmonics has grown to impact a diverse set of scientific disciplines ranging from quantum optics and photovoltaics to metamaterials and medicine. Plasmonics research has traditionally focused on noble metals; however, any material with a sufficiently high carrier density can support surface plasmon modes. Recently, researchers have made great gains in the synthetic (both intrinsic and extrinsic) control over the morphology and doping of nanoscale oxides, pnictides, sulfides, and selenides. These synthetic advances have, collectively, blossomed into a new, emerging class of plasmonic metal chalcogenides that complement traditional metallic materials. Chalcogenide and oxide nanostructures expand plasmonic properties into new spectral domains and also provide a rich suite of chemical controls available to manipulate plasmons, such as particle doping, shape, and composition. As a result, new opportunities in plasmonic chalcogenide nanomaterials are highlighted in this article, showing how they may be used to fundamentally tune the interaction and localization of electromagnetic fields on semiconductor surfaces in a way that enables new horizons in basic research and energy-relevant applications.

36 MATERIALS SCIENCE↗
DOE OSTI2012

Understanding nanofluid stability through molecular simulation

We performed molecular dynamics simulations to study solvation of a nanoparticle and nanoparticle-nanoparticle interactions in an n-hexane solution. Structural signatures are barely observed between the nanoparticle and n-hexane molecules because of weak binding and steric effects. The dynamic properties of the n-hexane molecule, on the other hand, are significantly influenced by the solvated nanoparticle. The diffusion of n-hexane molecules inside the nanoparticle is significantly decreased mainly because of the loss of dimensions of translation. Because one translational degree of freedom is lost by colliding with the wall of nanoparticle, the n-hexane molecules outside the nanoparticle diffuse 30% slower than the molecules in pure solution. The computed free energy profiles illustrate that the arrangement of the nanoparticles in bulk n-hexane solution are dependent on the orientation and functional group. We found that the n-hexane solvent exerts some effects on the interactions between the solvated nanoparticles. This work was supported by the US Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences and by the Office of Energy Efficiency and Renewable Energy, Geothermal Technologies Program. Pacific Northwest National Laboratory (PNNL) is a multiprogram national laboratory operated for DOE by Battelle.

Dang, Liem X↗
DOE OSTI2011

Role of oxygen on the optical properties of borate glass doped with ZnO

Lithium tungsten borate glass (0.56-x)B{sub 2}O{sub 3}-0.4Li{sub 2}O-xZnO-0.04WO{sub 3} (0{<=}x{<=}0.1 mol%) is prepared by the melt quenching technique for photonic applications. Small relative values of ZnO are used to improve the glass optical dispersion and to probe as well the role of oxygen electronic polarizability on its optical characteristics. The spectroscopic properties of the glass are determined in a wide spectrum range (200-2500 nm) using a Fresnel-based spectrophotometric technique. Based on the Lorentz-Lorenz theory, as ZnO content increases on the expense of B{sub 2}O{sub 3} the glass molar polarizability increased due to an enhanced unshared oxide ion 2p electron density, which increases ionicity of the chemical bonds of glass. The role of oxide ion polarizability is explained in accordance with advanced measures and theories such as optical basicity, O 1s binding energy, the outer most cation binding energy in Yamashita-Kurosawa's interionic interaction parameter and Sun's average single bond strength. FT-IR measurements confirm an increase in bridging oxygen bonds, as a result of replacement of ZnO by B{sub 2}O{sub 3}, which increase the UV glass transmission window and transmittance. - Graphical abstract: O1s, Yamashita-Kurosawa's parameter and average single bond strength of charge overlapping between electronic shells are used to explain enhanced oxide ion 2p electron density, which increases refractive index of glasses. Highlights: > New borate glass for photonic application is prepared. > The dispersion property of the glass is effectively controlled using small amounts of ZnO. > ZnO is used to probe the glass structure and investigate the role of oxygen on the obtained optical properties of the glasses. > Modern theories are used to explain enhanced unshared oxide ion 2p electron density, which increases ionicity of chemical bonds of the glass.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Spatially confined protein assembly in hierarchical mesoporous metal-organic framework

Immobilization of biomolecules into porous materials could lead to significantly enhanced performance in terms of stability towards harsh reaction conditions and easier separation for their reuse. Metal-Organic Frameworks (MOFs), offering unique structural features, have emerged as a promising platform for immobilizing large biomolecules. Although many indirect methods have been used to investigate the immobilized biomolecules for diverse applications, understanding their spatial arrangement in the pores of MOFs is still preliminary due to the difficulties in directly monitoring their conformations. To gain insights into the spatial arrangement of biomolecules within the nanopores. We used in situ small-angle neutron scattering (SANS) to probe deuterated green fluorescent protein (d-GFP) entrapped in a mesoporous MOF. Our work revealed that GFP molecules are spatially arranged in adjacent nanosized cavities of MOF-919 to form “assembly” through adsorbate-adsorbate interactions across pore apertures. Our findings, therefore, lay a crucial foundation for the identification of proteins structural basics under confinement environment of MOFs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Experimental study of the S 38 excited level scheme

Information on the 38 S level scheme was expanded through experimental work utilizing a fusion-evaporation reaction and in-beam γ-ray spectroscopy. Prompt γ-ray transitions were detected by the Gamma-Ray Energy Tracking Array (GRETINA) and recoiling 38 S residues were selected by the Fragment Mass Analyzer (FMA). Tools based on machine-learning techniques were developed and deployed for the first time in order to enhance the unique selection of 38S residues and identify any associated γ-ray transitions. The new level information, including the extension of the even-spin yrast sequence through J π =8( + ), was interpreted in terms of a basic single-particle picture as well shell-model calculations which incorporated the empirically derived FSU interaction. A comparison between the properties of the yrast states in the even-Z, N = 22 isotones from Z = 14 to 20, and for 36 Si– 38 S in particular, was also presented with an emphasis on the role and influence of the neutron 1 p 3/2 orbital on the structure in the region.

20 ≤ A ≤ 38↗
DOE OSTI2018

Internal strain tunes electronic correlations on the nanoscale

In conventional metals, charge carriers basically move freely. In correlated electron materials, however, the electrons may become localized because of strong Coulomb interactions, resulting in an insulating state. Despite considerable progress in the last decades, elucidating the driving mechanisms that suppress metallic charge transport, the spatial evolution of this phase transition remains poorly understood on a microscopic scale. Here, we use cryogenic scanning near-field optical microscopy to study the metal-to-insulator transition in an electronically driven charge-ordered system with a 20-nm spatial resolution. In contrast to common mean-field considerations, we observe pronounced phase segregation with a sharp boundary between metallic and insulating regions evidencing its first-order nature. Considerable strain in the crystal spatially modulates the effective electronic correlations within a few micrometers, leading to an extended “zebra” pattern of metallic and insulating stripes. We can directly monitor the spatial strain distribution via a gradual enhancement of the optical conductivity as the energy gap is depressed. Our observations shed new light on previous analyses of correlation-driven metal-insulator transitions.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2014

Measurements of forward jet production in polarized pp collisions at √s = 500 GeV

The A{sub N }DY project at RHIC was proposed to measure the analyzing power for Drell-Yan production. Test runs took place during polarized proton operations of RHIC in 2011 and 2012 with a model of the A {sub N }DY apparatus in place. In total, an integrated luminosity of 9 pb{sup −1} with beam polarization of 50% was sampled. The primary detector components were a hadron calorimeter (HCal) that spanned the pseudorapidity interval 2.4 < η < 4.0 and a small electromagnetic calorimeter (ECal). Basic goals for A {sub N }DY test running were to establish the impact of a third interaction region on RHIC performance and to demonstrate HCal calibration. Energy scale of HCal was established using neutral pion reconstruction and checked with hadronic response. In addition, data with a trigger based on HCal energy sum were taken to study jet events. First measurements of analyzing power in the forward jet production are reported.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2016

Heat meets light on the nanoscale

We discuss the state-of-the-art and remaining challenges in the fundamental understanding and technology development for controlling light-matter interactions in nanophotonic environments in and away from thermal equilibrium. Furthermore, the topics covered range from the basics of the thermodynamics of light emission and absorption to applications in solar thermal energy generation, thermophotovoltaics, optical refrigeration, personalized cooling technologies, development of coherent incandescent light sources, and spinoptics.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2011

Input to LLE annual report

In FY2011, an LLNL/LLE/NRL team performed a Laboratory Basic Science experiment on the OMEGA EP laser system to study positron production during high intensity laser interactions with high Z targets. This experiment was a follow-on to those of April 2009 and August 2010.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2023

Towards resolving protein structures at the atomic scale using atom probe tomography

In the field of Structural Biology, Atom Probe Tomography (APT) is in the nascent stages of development wherein coarse-grained visuals of proteins have been captured. The characterization of organic samples or biomolecules through the technique is currently limited to the detection of a few dominant signatures. The problem of indecipherable characterization can inherently be traced back to multiple forms of technique-specific responses to organic samples and consequent triggers leading to organic-sample and sample-medium interactions. While it is possible for captured manifestations of protein reconstructions to seemingly appear intact from a basic visual purview, the parameter-protein associative responses throughout the structure as a direct consequence of the inherent workings of the technique (until harmonized with organic sample complexity and behavior) and field evaporation-based factors make non-aberrative atomic associations infeasible. The work focused on identifying and theorizing the (above stated and other) fundamental mechanisms that stronghold the study of intricate atomic to higher order associations in proteins through APT. Attempts at structure elucidation of the cryogenic sample under study, through indirect associations (and methods) based on other imaging techniques, further revealed the distinct and highly distortive nature at the atomic scale deterring structural tunability and thus characterization of APT based cryogenic samples under analysis. As a direct counter to the atomic scale characterization problem, by taking the experiment-specific uncertainties, and probable APT-centric organic sample-based variabilities into account, a basic result is extracted and presented. Through mass-spectrometric and computational analysis, specific individual amino acids (Sulfur-containing protein-bound amino acids) in proteins and aspects of protein structure (probable backbone fragments, partial sequence - partial backbone portions) have been identified and characterized. Under analysis considerations, a few of the simplest known and easily inferable segments that favor structural deteriorations in the reconstructions are stated. Additionally, to overcome technique-specific deterrents to the characterization of biomolecules in cryogenic sample medium, the development of a protein-labeling strategy tailored to APT is suggested.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1972

Examination of the collision force method for analyzing the responses of simple containment/deflection structures to impact by one engine rotor blade fragment

An approximate collision analysis, termed the collision-force method, was developed for studying impact-interaction of an engine rotor blade fragment with an initially circular containment ring. This collision analysis utilizes basic mass, material property, geometry, and pre-impact velocity information for the fragment, together with any one of three postulated patterns of blade deformation behavior: (1) the elastic straight blade model, (2) the elastic-plastic straight shortening blade model, and (3) the elastic-plastic curling blade model. The collision-induced forces are used to predict the resulting motions of both the blade fragment and the containment ring. Containment ring transient responses are predicted by a finite element computer code which accommodates the large deformation, elastic-plastic planar deformation behavior of simple structures such as beams and/or rings. The effects of varying the values of certain parameters in each blade-behavior model were studied. Comparisons of predictions with experimental data indicate that of the three postulated blade-behavior models, the elastic-plastic curling blade model appears to be the most plausible and satisfactory for predicting the impact-induced motions of a ductile engine rotor blade and a containment ring against which the blade impacts.

Zirin, R. M.↗