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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 721 records · Page 40
All sourcesNASA NTRSDOE OSTI
DOE OSTI2011

Atomic-Resolution Structure of an N(5) Flavin Adduct in D-Arginine Dehydrogenase

D-Arginine dehydrogenase (DADH) catalyzes the flavin-dependent oxidative deamination of D-arginine and other D-amino acids to the corresponding imino acids. The 1.07 {angstrom} atomic-resolution structure of DADH crystallized with D-leucine unexpectedly revealed a covalent N(5) flavin adduct, instead of the expected iminoleucine product in the active site. This acyl adduct has been successfully reproduced by photoreduction of DADH in the presence of 4-methyl-2-oxopentanoic acid (ketoleucine). The iminoleucine may be released readily because of weak interactions in the binding site, in contrast to iminoarginine, converted to ketoleucine, which reacts with activated FAD to form the covalently linked acyl adduct.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Microfluidics and Metabolomics Reveal Symbiotic Bacterial–Fungal Interactions Between Mortierella elongata and Burkholderia Include Metabolite Exchange

We identified two poplar ( Populus sp.)-associated microbes, the fungus, Mortierella elongata strain AG77, and the bacterium, Burkholderia strain BT03, that mutually promote each other’s growth. Using culture assays in concert with a novel microfluidic device to generate time-lapse videos, we found growth specific media differing in pH and pre-conditioned by microbial growth led to increased fungal and bacterial growth rates. Coupling microfluidics and comparative metabolomics data results indicated that observed microbial growth stimulation involves metabolic exchange during two ordered events. The first is an emission of fungal metabolites, including organic acids used or modified by bacteria. A second signal of unknown nature is produced by bacteria which increases fungal growth rates. We find this symbiosis is initiated in part by metabolic exchange involving fungal organic acids.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

X-ray photoelectron spectroscopy of morpholinium ionic liquids: impact of a long alkyl side substituent on the cation–anion interactions

In this study, X-ray photoelectron spectroscopy is used to analyse nine morpholinium ionic liquids, which are of great interest in green chemistry because of their low toxicity and high recyclability. Here, the effect of the alkyl chain length on the aliphatic C 1s binding energy and the impact of the anion basicity on the cationic N 1s and O 1s binding energies are investigated. It is concluded that by changing the basicity of the anion, there is a more notable change in the electronic environment of the oxygen centre. The impact of a long alkyl side substituent on the cation–anion interactions is also discussed. It is observed that there is an intense charge shielding effect of the alkyl side chain in the cases of octyl and dodecyl substituents, which is reflected in the reduced Br 3d 5/2 binding energy.

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

Control over Silica Particle Growth and Particle–Biomolecule Interactions Facilitates Silica Encapsulation of Mammalian Cells with Thickness Control

Over the past 20 years, many strategies utilizing sol–gel chemistry to integrate biological cells into silica-based materials have been reported. One such strategy, Sol-Generating Chemical Vapor into Liquid (SG-CViL) deposition, shows promise as an efficient encapsulation technique due to the ability to vary the silica encapsulation morphology obtained by this process through variation of SG-CViL reaction conditions. In this report, we develop SG-CViL as a tunable, multi-purpose silica encapsulation strategy by investigating the mechanisms governing both silica particle generation and subsequent interaction with phospholipid assemblies (liposomes and living cells). Using Dynamic Light Scattering (DLS) measurements, linear and exponential silica particle growth dynamics were observed which were dependent on deposition buffer ion constituents and ion concentration. Silica particle growth followed a cluster–cluster growth mechanism at acidic pH, and a monomer-cluster growth mechanism at neutral to basic pH. Increasing silica sol aging temperature resulted in higher rates of particle growth and larger particles. DLS measurements employing PEG-coated liposomes and cationic liposomes, serving as model phospholipid assemblies, revealed that electrostatic interactions promote more stable liposome–silica interactions than hydrogen bonding and facilitate silica coating on suspension cells. However, continued silica reactivity leads to aggregation of silica-coated suspension cells, revealing the need for cell isolation to tune deposited silica thickness. As a result, utilizing these mechanistic study insights, silica was deposited onto adherent HeLa cells under biocompatible conditions with micrometer-scale control over silica thickness, minimal cell manipulation steps, and retained cell viability over several days.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Influence of Hyperfine Coupling Strain on Two-Dimensional ESEEM Spectra from I = 1/2 Nuclei

HYSCORE, a variant of two-dimensional ESEEM spectroscopy, is currently one of the most effective tools in high-resolution solid-state EPR spectroscopy. Our systematic studies of hydrogen bonds with semiquinones in 15 N-labeled proteins have previously provided us with an extensive collection of 15 N HYSCORE spectra produced by N–H…O nitrogen donors. Examination of these spectra has indicated in several cases lineshape distortions not described by available theoretical models. We were able to explain all observed artificial phenomena in the 15 N spectra of semiquinones considering a single mechanism—strain of the isotropic hyperfine interaction. In this review article, we introduce the HYSCORE experiment and the theoretical background for spectra of I = 1/2 nuclei in orientation-disordered samples. We then present a description of the observed lineshape distortions and an explanation of the hyperfine strain’s influence on the experimental spectra. In the final part of the article, we discuss (i) similar lineshape distortions found in previously published spectra from 15 N, 29 Si, 31 P, and 57 Fe nuclei that can be explained using the approach applied for the analysis of the 15 N spectra of semiquinones, and (ii) a recently published analysis of 31P spectra with a different type of lineshape distortion based on a more sophisticated method, where the strength of anisotropic coupling is correlated with the sign and value of the isotropic constant in different conformations of a Cu(II) complex.

30 DIRECT ENERGY CONVERSION↗
DOE OSTI2022

Ionic liquids for carbon capture

This article covers cutting-edge research in ionic liquid-based materials and their impact on carbon capture. Ionic liquids boast high thermal stability, low vapor pressure, and great tunability. They can be deployed as either sorbents or supported liquid membranes for carbon capture and other gas separations. Absorption of CO 2 in ionic liquids can be achieved via physisorption or chemisorption, depending on the strength of the interaction. For physisorption, both CO 2 -anion and cation–anion interactions are important factors in dictating CO 2 solubility. For chemisorption, the reactivity with CO 2 can be tuned by the basicity of the anion while the stability of the ionic liquid can be enhanced by controlling the cation. Marrying ionicity of ionic liquids with porosity leads to novel porous ionic liquids that feature unique properties for facilitating gas transport, while interfacing ionic liquids with microporous membranes allow the ions to gate the pores for selective gas transport. Further, composite materials of ionic liquids with crystalline materials such as metal–organic frameworks offer scalable heterogeneous interfaces to promote selectivity. Future opportunities include controlling the interaction with CO 2 and its transport at the charged or electrified interface with the ionic-liquid electric double layer, as well as combining CO 2 capture and conversion with ionic liquids.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Basics of Gamma Ray Detection

The objective of this training is to explain the origin of x-rays and gamma rays, gamma ray interactions with matter, detectors and electronics used in gamma ray-spectrometry, and features of a gamma-ray spectrum for nuclear material that is safeguarded.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2024

Fabricated devices for performing bacterial-fungal interaction experiments across scales

Diverse and complex microbiomes are found in virtually every environment on Earth. Bacteria and fungi often co-dominate environmental microbiomes, and there is growing recognition that bacterial-fungal interactions (BFI) have significant impacts on the functioning of their associated microbiomes, environments, and hosts. Investigating BFI in vitro remains a challenge, particularly when attempting to examine interactions at multiple scales of system complexity. Fabricated devices can provide control over both biotic composition and abiotic factors within an experiment to enable the characterization of diverse BFI phenotypes such as modulation of growth rate, production of biomolecules, and alterations to physical movements. Engineered devices ranging from microfluidic chips to simulated rhizosphere systems have been and will continue to be invaluable to BFI research, and it is anticipated that such devices will continue to be developed for diverse applications in the field. This will allow researchers to address specific questions regarding the nature of BFI and how they impact larger microbiome and environmental processes such as biogeochemical cycles, plant productivity, and overall ecosystem resilience. Devices that are currently used for experimental investigations of bacteria, fungi, and BFI are discussed herein along with some of the associated challenges and several recommendations for future device design and applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Mitigating climate change through managing constructed-microbial communities in agriculture

The importance of increasing crop production while reducing resource inputs and land-use change cannot be overstated especially in light of climate change and a human population growth projected to reach nine billion this century. Here, mutualistic plant microbe interactions offer a novel approach to enhance agricultural productivity while reducing environmental costs. In concert with other novel agronomic technologies and management, plant-microbial mutualisms could help increase crop production and reduce yield losses by improving resistance and/or resilience to edaphic, biologic, and climatic variability from both bottom-up and top-down perspectives.

54 ENVIRONMENTAL SCIENCES↗
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↗
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↗