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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 361 records · Page 20
All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

Protein structure prediction guided by crosslinking restraints – A systematic evaluation of the impact of the crosslinking spacer length

Recent development of high-resolution mass spectrometry (MS) instruments enables chemical crosslinking (XL) to become a high-throughput method for obtaining structural information about proteins. Restraints derived from XL-MS experiments have been used successfully for structure refinement and protein–protein docking. However, one formidable question is under which circumstances XL-MS data might be sufficient to determine a protein’s tertiary structure de novo? Answering this question will not only include understanding the impact of XL-MS data on sampling and scoring within a de novo protein structure prediction algorithm, it must also determine an optimal crosslinker type and length for protein structure determination. While a longer crosslinker will yield more restraints, the value of each restraint for protein structure prediction decreases as the restraint is consistent with a larger conformational space. In this study, the number of crosslinks and their discriminative power was systematically analyzed in silico on a set of 2055 non-redundant protein folds considering Lys–Lys, Lys–Asp, Lys–Glu, Cys–Cys, and Arg–Arg reactive crosslinkers between 1 and 60 Å. Depending on the protein size a heuristic was developed that determines the optimal crosslinker length. Next, simulated restraints of variable length were used to de novo predict the tertiary structure of fifteen proteins using the BCL::Fold algorithm. The results demonstrate that a distinct crosslinker length exists for which information content for de novo protein structure prediction is maximized. The sampling accuracy improves on average by 1.0 Å and up to 2.2 Å in the most prominent example. XL-MS restraints enable consistently an improved selection of native-like models with an average enrichment of 2.1.

Biochemistry & Molecular Biology↗
DOE OSTI2021

Hybrid-Lipid Bilayers Induce n -Alkyl-Chain Order in Reversed-Phase Chromatographic Surfaces, Impacting their Shape Selectivity for Aromatic Hydrocarbon Partitioning

Shape selectivity is important in reversed-phase liquid chromatographic separations, where stationary phases are capable of separating geometric isomers, thereby resolving solutes based on their three-dimensional structure or shape rather than other chemical differences. Numerous chromatographic studies have been carried out using n-alkyl-chain-modified columns to understand how molecular shape affects retention. For polycyclic aromatic hydrocarbons (PAHs), it was found that planar compounds were selectively retained over non-planar structures of comparable molecular weight on surfaces with longer n-alkyl chains, higher chain-density, or at lower temperatures, where selectivity likely arises with greater ordering of the n-alkyl chains. A limitation of these studies, however, is the small range of chain ordering that can be achieved and lack of a direct measure of the n-alkyl-chain order of the stationary phases. In this work, we employ a C 18 stationary phase modified with a monolayer of phospholipid as a means of significantly varying the n-alkyl chain order. These hybrid-supported lipid bilayers, which have previously been employed as membrane-like stationary phases for measuring lipophilicity, provide a unique approach to control n-alkyl chain ordering by varying the acyl chain length and degree of unsaturation of the phospholipid modifier. The degree of alkyl-chain order of the resulting modified surfaces is determined from the ratio of trans- versus gauche-conformers, measured in situ within individual porous particles by confocal Raman microscopy. This methodology was also used to assess the affinity of these surfaces for planar versus non-planar PAH molecules. The retention selectivity for the planar versus non-planar compounds, thus determined, was found to vary significantly and systematically with the degree of order of the acyl/alkyl chains in the hybrid-supported lipid bilayers. Furthermore, the investigation also demonstrates the utility of confocal Raman microscopy for interrogating the impact of solute partitioning on stationary-phase structure within porous chromatographic particles.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Impact of D1-V185 on the Water Molecules That Facilitate O 2 Formation by the Catalytic Mn 4 CaO 5 Cluster in Photosystem II

The oxidations of the O 2 -evolving Mn 4 CaO 5 cluster in Photosystem II are coupled to the release of protons to the thylakoid lumen via one or more proton egress pathways. These pathways are comprised of extensive networks of hydrogen-bonded water molecules and amino acid side chains. The hydrophobic residue, D1-V185, is adjacent to numerous water molecules in one of these pathways. The D1-V185N mutation dramatically slows O–O bond formation. This impairment has been attributed to a disruption of the hydrogen-bonded water molecules that are crucial for proton egress or whose rearrangement is required for catalysis. In this study, Fourier transform infrared spectroscopy was employed to characterize the impact of the D1-V185N mutation on the carboxylate groups and water molecules that form a network of hydrogen bonds in this putative proton egress pathway. By analyzing carboxylate stretching modes, carbonyl stretching modes of hydrogen-bonded carboxylic acids, O–H stretching modes of hydrogen-bonded water molecules, and D–O–D bending modes, we obtain evidence that the D1-V185N mutation perturbs the extensive network of hydrogen bonds that extends from Y Z to D1-D61 to a greater extent than any mutation yet examined but does not alter the water molecules that interact directly with D1-D61. The mutation also alters the environments of the carboxylate groups whose pK a values change in response to the S 1 to S 2 and S 2 to S 3 transitions. Lastly, the mutation alters the environment of the water molecule whose bending mode vanishes during the S 2 to S 3 transition, consistent with assigning the Ca 2+ -bound W3 as the water molecule that deprotonates and joins oxo bridge O5 during the S 2 to S 3 transition, possibly as the second substrate water molecule for O 2 formation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Expansion of the Petroleum Refinery Life Cycle Inventory Model (PRELIM) to Support Characterization of a Full Suite of Commonly Tracked Impact Potentials

This study updates the Petroleum Refinery Life Cycle Inventory Model (PRELIM) to provide a more complete gate-to-gate life cycle inventory and to allow for the calculation of a full suite of impact potentials commonly used in life cycle assessment (LCA) studies. We updated the model to add criteria air pollutants, hazardous air pollutants, releases to water, releases to land, and managed wastes reflecting 2014 reported releases and waste management practices using data from the U.S. Environmental Protection Agency Greenhouse Gas Reporting Program, National Emissions Inventory, Discharge Monitoring Reports, and Toxic Release Inventory together with process unit capacities and fuel consumption data from the U.S. Energy Information Administration (U.S. EIA). The expanded version of PRELIM offers users a reliable, transparent, and streamlined tool for estimating the effect of changes in petroleum refineries on LCIA results in the context of policy analysis.

Source record↗
DOE OSTI2022

Inter-Leaflet Phospholipid Exchange Impacts the Ligand Density Available for Protein Binding at Supported Lipid Bilayers

Phospholipid bilayers formed at solid-liquid interfaces have garnered interest as mimics of cell-membranes to model association reactions of proteins with lipid-bilayer-tethered ligands. Despite the importance of understanding how ligand density in a lipid bilayer impacts the protein-ligand association response, relating the ligand-modified lipid fraction to the absolute density of solution-accessible ligands in a lipid bilayer remains a challenge in interfacial quantitative analysis. In this work, confocal-Raman microscopy is employed to quantify the association of anti-biotin IgG with a small fraction of biotinylated lipids dispersed in either gel-phase or liquid-crystalline supported lipid bilayers, deposited on the interior surfaces of wide-pore silica surfaces. We examine the question whether inter-leaflet lipid translocation contributes to the population of solution-accessible biotin ligands on the distal leaflet of a supported lipid bilayer by comparing their protein accumulation response with ligands dispersed in lipid monolayers on nitrile-derivatized silica surfaces. The binding of antibody to biotin ligands dispersed in gel-phase bilayers exhibited an equivalent biotin-coverage response as the accumulation of IgG onto gel-phase monolayers, indicating that gel-phase bilayer symmetry was preserved. This result contrasts with the ~60% greater anti-biotin capture observed at fluid-phase bilayers compared to fluid-phase monolayers prepared at equivalent biotin fractions. This enhanced protein capture is attributed to biotin-capped lipids being transferred from the surface-associated proximal leaflet of the bilayer to the solution-exposed distal leaflet by the inter-leaflet exchange or lipid flip-flop, a facile process in fluid-phase supported lipid bilayers. Here, the results suggest caution in interpreting the results of quantitative studies of protein binding to lipid-tethered ligands dispersed in fluid-phase phospholipid bilayers.

36 MATERIALS SCIENCE↗
DOE OSTI2014

Biomass Feedstocks for Renewable Fuel Production: A review of the impacts of feedstock and pretreatment on the yield and product distribution of fast pyrolysis bio-oils and vapors

Renewable transportation fuels from biomass have the potential to substantially reduce greenhouse gas emissions and diversify global fuel supplies. Thermal conversion by fast pyrolysis converts up to 75% of the starting plant material (and its energy content) to a bio-oil intermediate suitable for upgrading to motor fuel. Woody biomass, by far the most widely-used and researched material, is generally preferred in thermochemical processes due to its low ash content and high quality bio-oil produced. However, the availability and cost of biomass resources, e.g. forest residues, agricultural residues, or dedicated energy crops, vary greatly by region and will be key determinates in the overall economic feasibility of a pyrolysis-to-fuel process. Formulation or blending of various feedstocks, combined with thermal and/or chemical pretreatment, could facilitate a consistent, high-volume, lower-cost biomass supply to an emerging biofuels industry. However, the impact of biomass type and pretreatment conditions on bio-oil yield and quality, and the potential process implications, are not well understood. This literature review summarizes the current state of knowledge regarding the effect of feedstock and pretreatments on the yield, product distribution, and upgradability of bio-oil.

09 BIOMASS FUELS↗
DOE OSTI2018

Impacts of oxo interactions within actinyl metal organic materials: highlight on thermal expansion behaviour

Physical properties of actinyl materials are influenced by the presence of oxo functional groups. Herein, we report large thermal expansion coefficients for a uranyl metal organic nanotube that switch from positive to negative upon dehydration. Finally, different behaviour is observed in the neptunyl system due to variations in the oxo interactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

The impact of laser plasma interactions on three-dimensional drive symmetry in inertial confinement fusion implosions

Achieving symmetric hohlraum radiation drive is an important aspect of indirectly driven inertial confinement fusion experiments. However, when experimentally delivered laser powers deviate from ideal conditions, the resultant radiation field can become asymmetric. Two situations in which this may arise are random uncorrelated fluctuations, in as-delivered laser power and laser beams that do not participate in the implosion (either intentionally or unintentionally). Furthermore, laser plasma interactions in the hohlraum obfuscate the connection between laser powers and radiation drive. To study the effect of these situations on drive symmetry, we develop a simplified model for crossed-beam energy transfer, laser backscatter, and plasma absorption that can be used in conjunction with view factor calculations to expediently translate laser powers into three-dimensional capsule flux symmetries. We find that crossed-beam energy transfer can alter both the statistical properties of uncorrelated laser fluctuations and the impact of missing laser beams on radiation symmetry. A method is proposed to mitigate the effects of missing laser beams.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2015

Differential cross sections for electron-impact vibrational-excitation of tetrahydrofuran at intermediate impact energies

We report differential cross sections (DCSs) for electron-impact vibrational-excitation of tetrahydrofuran, at intermediate incident electron energies (15-50 eV) and over the 10°-90° scattered electron angular range. These measurements extend the available DCS data for vibrational excitation for this species, which have previously been obtained at lower incident electron energies (≤20 eV). Where possible, our data are compared to the earlier measurements in the overlapping energy ranges. Here, quite good agreement was generally observed where the measurements overlapped.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2011

Impact of surface imperfections on the Casimir force for lenses of centimeter-size curvature radii

The impact of imperfections, which are always present on surfaces of lenses with centimeter-size curvature radii, on the Casimir force in the lens-plate geometry is investigated. It is shown that the commonly used formulation of the proximity force approximation is inapplicable for spherical lenses with surface imperfections, such as bubbles and pits. More general expressions for the Casimir force are derived that take surface imperfections into account. Using these expressions, we show that surface imperfections can both increase and decrease the magnitude of the Casimir force up to a few tens percent when compared with the case of a perfectly spherical lens. We demonstrate that the Casimir force between a perfectly spherical lens and a plate described by the Drude model can be made approximately equal to the force between a sphere with some surface imperfection and a plate described by the plasma model, and vice versa. In the case of a metallic sphere and a semiconductor plate, approximately the same Casimir forces are obtained for four different descriptions of charge carriers in the semiconductor if appropriate surface imperfections on the lens surface are present. The conclusion is made that there is a fundamental problem in the interpretation of measurement data for the Casimir force using spherical lenses of centimeter-size radii.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗