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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 379 records · Page 21
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DOE OSTI2018

Cations Modulate Actin Bundle Mechanics, Assembly Dynamics, and Structure

Actin bundles are key factors in the mechanical support and dynamic reorganization of the cytoskeleton. High concentrations of multivalent counterions promote bundle formation through electrostatic attraction between actin filaments that are negatively charged polyelectrolytes. In this study, we evaluate how physiologically relevant divalent cations affect the mechanical, dynamic, and structural properties of actin bundles. Using a combination of total internal reflection fluorescence microscopy, transmission electron microscopy, and dynamic light scattering, we demonstrate that divalent cations modulate bundle stiffness, length distribution, and lateral growth. Molecular dynamics simulations of an all-atom model of the actin bundle reveal specific actin residues coordinate cation-binding sites that promote the bundle formation. Finally, our work suggests that specific cation interactions may play a fundamental role in the assembly, structure, and mechanical properties of actin bundles.

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

Density Functional Theory Investigation of the NiO@Graphene Composite as a Urea Oxidation Catalyst in the Alkaline Electrolyte

Developing efficient and low-cost urea oxidation reaction (UOR) catalysts is a promising but still challenging task for environment and energy conversion technologies such as wastewater remediation and urea electrolysis. In this work, NiO nanoparticles that incorporated graphene as the NiO@Graphene composite were constructed to study the UOR process in terms of density functional theory. The single-atom model, which differed from the previous heterojunction model, was employed for the adsorption/desorption of urea and CO 2 in the alkaline media. As demonstrated from the calculated results, NiO@Graphene prefers to adsorb the hydroxyl group than urea in the initial stage due to the stronger adsorption energy of the hydroxyl group. After NiOOH@Graphene was formed in the alkaline electrolyte, it presents excellent desorption energy of CO 2 in the rate-determining step. Electronic density difference and the d band center diagram further confirmed that the Ni(III) species is the most favorable site for urea oxidation while facilitating charge transfer between urea and NiO@Graphene. Moreover, graphene provides a large surface for the incorporation of NiO nanoparticles, enhancing the electron transfer between NiOOH and graphene and promoting the mass transport in the alkaline electrolyte. Notably, this work provides theoretical guidance for the electrochemical urea oxidation work.

25 ENERGY STORAGE↗
DOE OSTI2018

Many Body Effects and Icosahedral Order in Superlattice Self-Assembly

Here, we elucidate how nanocrystals “bond” to form ordered structures. For that purpose we consider nanocrystal configurations consisting of regular polygons and polyhedra, which are the motifs that constitute single component and binary nanocrystal superlattices, and simulate them using united atom models. We compute the free energy and quantify many body effects, i.e., those that cannot be accounted for by pair potential (two-body) interactions, further showing that they arise from coalescing vortices of capping ligands. We find that such vortex textures exist for configurations with local coordination number ≤6. For higher coordination numbers, vortices are expelled and nanocrystals arrange in configurations with tetrahedral or icosahedral order. We provide explicit formulas for the optimal separations between nanocrystals, which correspond to the minima of the free energies. Our results quantitatively explain the structure of superlattice nanocrystals as reported in experiments and reveal how packing arguments, extended to include soft components, predict ordered nanocrystal aggregation.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2016

Crystal structure of the human sterol transporter ABCG5/ABCG8

ATP binding cassette (ABC) transporters play critical roles in maintaining sterol balance in higher eukaryotes. The ABCG5/ABCG8 heterodimer (G5G8) mediates excretion of neutral sterols in liver and intestines. Mutations disrupting G5G8 cause sitosterolaemia, a disorder characterized by sterol accumulation and premature atherosclerosis. Here we use crystallization in lipid bilayers to determine the X-ray structure of human G5G8 in a nucleotide-free state at 3.9 Å resolution, generating the first atomic model of an ABC sterol transporter. The structure reveals a new transmembrane fold that is present in a large and functionally diverse superfamily of ABC transporters. Here, the transmembrane domains are coupled to the nucleotide-binding sites by networks of interactions that differ between the active and inactive ATPases, reflecting the catalytic asymmetry of the transporter. The G5G8 structure provides a mechanistic framework for understanding sterol transport and the disruptive effects of mutations causing sitosterolaemia.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Solar abundance ratios of the iron-peak elements in the Perseus cluster

The metal abundance of the hot plasma that permeates galaxy clusters represents the accumulation of heavy elements produced by billions of supernovae1. Therefore, X-ray spectroscopy of the intracluster medium provides an opportunity to investigate the nature of supernova explosions integrated over cosmic time. In particular, the abundance of the iron-peak elements (chromium, manganese, iron and nickel) is key to understanding how the progenitors of typical type Ia supernovae evolve and explode2–6. Recent X-ray studies of the intracluster medium found that the abundance ratios of these elements differ substantially from those seen in the Sun, suggesting differences between the nature of type Ia supernovae in the clusters and in the Milky Way. However, because the K-shell transition lines of chromium and manganese are weak and those of iron and nickel are very close in photon energy, highresolution spectroscopy is required for an accurate determination of the abundances of these elements. Here in this paper we report observations of the Perseus cluster, with statistically significant detections of the resonance emission from chromium, manganese and nickel. Our measurements, combined with the latest atomic models, reveal that these elements have near-solar abundance ratios with respect to iron, in contrast to previous claims. Comparison between our results and modern nucleosynthesis calculations disfavours the hypothesis that type Ia supernova progenitors are exclusively white dwarfs with masses well below the Chandrasekhar limit (about 1.4 times the mass of the Sun). The observed abundance pattern of the iron-peak elements can be explained by taking into account a combination of near- and sub-Chandrasekhar-mass type Ia supernova systems, adding to the mounting evidence that both progenitor types make a substantial contribution to cosmic chemical enrichment.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2015

X-ray structure determination using low-resolution electron microscopy maps for molecular replacement

Structures of multi-subunit macromolecular machines are primarily determined by either electron microscopy (EM) or X-ray crystallography. In many cases, a structure for a complex can be obtained at low resolution (at a coarse level of detail) with EM and at higher resolution (with finer detail) by X-ray crystallography. The integration of these two structural techniques is becoming increasingly important for generating atomic models of macromolecular complexes. A low-resolution EM image can be a powerful tool for obtaining the "phase" information that is missing from an X-ray crystallography experiment, however integration of EM and X-ray diffraction data has been technically challenging. Here we show a step-by-step protocol that explains how low-resolution EM maps can be placed in the crystallographic unit cell by molecular replacement, and how initial phases computed from the placed EM density are extended to high resolution by averaging maps over non-crystallographic symmetry. As the resolution gap between EM and Xray crystallography continues to narrow, the use of EM maps to help with X-ray crystal structure determination, as described in this protocol, will become increasingly effective.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

3D structure and in situ arrangements of CatSper channel in the sperm flagellum

The sperm calcium channel CatSper plays a central role in successful fertilization as a primary Ca 2+ gateway. Here, we applied cryo-electron tomography to visualize the higher-order organization of the native CatSper complex in intact mammalian sperm. The repeating CatSper units form long zigzag-rows along mouse and human sperm flagella. Above each tetrameric channel pore, most of the extracellular domains form a canopy that interconnects to a zigzag-shaped roof. Murine CatSper contains an additional wing-structure connected to the tetrameric channel. The intracellular domains link two neighboring channels to a diagonal array, suggesting a dimer formation. Fitting of an atomic model of isolated monomeric CatSper to the in situ map reveals supramolecular interactions and assembly of the CatSper complex. Loss of EFCAB9-CATSPERζ alters the architecture and interactions of the channels, resulting in fragmentation and misalignment of the zigzag-rows and disruption of flagellar movement in Efcab9 -/- sperm. This work offers unique insights into the structural basis for understanding CatSper regulation of sperm motility.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Atomic-level structural correlations across the morphotropic phase boundary of a ferroelectric solid solution: xBiMg 1/2 Ti 1/2 O 3 -(1$-$x)PbTiO 3

Revelation of unequivocal structural information at the atomic level for complex systems is uniquely important for deeper and generic understanding of the structure property connections and a key challenge in materials science. Here in this paper we report an experimental study of the local structure by applying total elastic scattering and Raman scattering analyses to an important non-relaxor ferroelectric solid solution exhibiting the so-called composition-induced morphotropic phase boundary (MPB), where concomitant enhancement of physical properties have been detected. The powerful combination of static and dynamic structural probes enabled us to derive direct correspondence between the atomic-level structural correlations and reported properties. The atomic pair distribution functions obtained from the neutron total scattering experiments were analysed through big-box atom-modelling implementing reverse Monte Carlo method, from which distributions of magnitudes and directions of off-centred cationic displacements were extracted. We found that an enhanced randomness of the displacement-directions for all ferroelectrically active cations combined with a strong dynamical coupling between the A- and B-site cations of the perovskite structure, can explain the abrupt amplification of piezoelectric response of the system near MPB. Finally, altogether this provides a more fundamental basis in inferring structure-property connections in similar systems including important implications in designing novel and bespoke materials.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Ultraintense, ultrashort pulse X-ray scattering in small molecules

In this work, we examine X-ray scattering from an isolated organic molecule from the linear to nonlinear absorptive regime. In the nonlinear regime, we explore the importance of both the coherent and incoherent channels and observe the onset of nonlinear behavior as a function of pulse duration and energy. In the linear regime, we test the sensitivity of the scattering signal to molecular bonding and electronic correlation via calculations using the independent atom model (IAM), Hartree–Fock (HF) and density functional theory (DFT). Finally, we describe how coherent X-ray scattering can be used to directly visualize femtosecond charge transfer and dissociation within a single molecule undergoing X-ray multiphoton absorption.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Experimentally informed structure optimization of amorphous TiO 2 films grown by atomic layer deposition

Amorphous titanium dioxide TiO 2 (a-TiO 2 ) has been widely studied, particularly as a protective coating layer on semiconductors to prevent corrosion and promote electron–hole conduction in photoelectrochemical reactions. The stability and longevity of a-TiO 2 is strongly affected by the thickness and structural heterogeneity, implying that understanding the structure properties of a-TiO 2 is crucial for improving the performance. This study characterized the structural and electronic properties of a-TiO 2 thin films (~17 nm) grown on Si by atomic layer deposition (ALD). Fluctuation spectra V(k) and angular correlation functions were determined with 4-dimensional scanning transmission electron microscopy (4D-STEM), which revealed the distinctive medium-range ordering in the a-TiO 2 film. A realistic atomic model of a-TiO 2 was established guided by the medium-range ordering and the previously reported short-range ordering of a-TiO 2 film, as well as the interatomic potential. The structure was optimized by the StructOpt code using a genetic algorithm that simultaneously minimizes energy and maximizes the match to experimental short- and medium-range ordering. The StructOpt a-TiO 2 model presents improved agreements with the medium-range ordering and the k-space location of the dominant 2-fold angular correlations compared with a traditional melt-quenched model. The electronic structure of the StructOpt a-TiO 2 model was studied by ab initio calculations and compared to the crystalline phases and experimental results. Finally, this work uncovered the medium-range ordering in a-TiO 2 thin films and provided a realistic a-TiO 2 structure model for further investigation of structure–property relationships and materials design. In addition, the improved multi-objective optimization package StructOpt was provided for structure determination of complex materials guided by experiments and simulations.

36 MATERIALS SCIENCE↗
DOE OSTI2014

Positron interactions with water–total elastic, total inelastic, and elastic differential cross section measurements

Utilising a high-resolution, trap-based positron beam, we have measured both elastic and inelastic scattering of positrons from water vapour. The measurements comprise differential elastic, total elastic, and total inelastic (not including positronium formation) absolute cross sections. The energy range investigated is from 1 eV to 60 eV. Comparison with theory is made with both R-Matrix and distorted wave calculations, and with our own application of the Independent Atom Model for positron interactions.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2014

Molecular-dynamics simulations of thin polyisoprene films confined between amorphous silica substrates

Constant temperature–constant pressure (NpT) molecular-dynamics computer simulations have been carried out for the united-atom model of a non-crosslinked (1,4) cis-polyisoprene (PI) melt confined between two amorphous, fully coordinated silica surfaces. The Lennard-Jones 12-6 potential was implemented to describe the polymer–silica interactions. The thickness H of the produced PI–silica film has been varied in a wide range, 1 < H/R{sub g} < 8, where R{sub g} is the individual PI chain radius of gyration measured under the imposed confinement. After a thorough equilibration, the PI film stratified structure and polymer segmental dynamics have been studied. The chain structure in the middle of the films resembles that in a corresponding bulk, but the polymer-density profile shows a pronounced ordering of the polymer segments in the vicinity of silica surfaces; this ordering disappears toward the film middles. Tremendous slowing down of the polymer segmental dynamics has been observed in the film surface layers, with the segmental relaxation more than 150 times slower as compared to that in a PI bulk. This effect increases with decreasing the polymer-film thickness. The segmental relaxation in the PI film middles shows additional relaxation process which is absent in a PI bulk. Even though there are fast relaxation processes in the film middle, its overall relaxation is slower as compared to that in a bulk sample. The interpretation of the results in terms of polymer glassy bridges has been discussed.

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

Comparative studies of optical and elastic properties of ZrO{sub 2} thin films prepared under normal and oblique incidence deposition geometries

Oblique angle deposited optical thin films have attracted recent researcher’s interest because of their attractive optical, micro-structural, mechanical properties and more importantly because of their great potential in achieving tunability in refractive index. These properties in turn make it important in case of designing different optical devices. In the present work, ZrO{sub 2} thin films have been deposited on fused silica substrate by electron beam evaporation technique in normal as well as oblique angle deposition configurations. Optical properties, especially refractive index of the films have been estimated by fitting the measured transmission spectra with suitable theoretical dispersion models. Atomic force microscopy has been employed to characterize morphological properties of samples. The elastic properties of both the films are estimated by Atomic Force Acoustic Microscopy, a new and highly sensitive technique for thin films.

36 MATERIALS SCIENCE↗
DOE OSTI2014

Elastic scattering of low-energy electrons by 1,4-dioxane

We report calculated cross sections for elastic collisions of low-energy-electrons with 1,4-dioxane. Our calculations employed the Schwinger multichannel method with pseudopotentials and were carried out in the static-exchange and static-exchange plus polarization approximations for energies up to 30 eV. Our results show the presence of three shape resonances belonging to the B{sub u}, A{sub u}, and B{sub g} symmetries and located at 7.0 eV, 8.4 eV, and 9.8 eV, respectively. We also report the presence of a Ramsauer-Townsend minimum located at around 0.05 eV. We compare our calculated cross sections with experimental data and R-matrix and independent atom model along with the additivity rule corrected by using screening coefficients theoretical results for 1,4-dioxane obtained by Palihawadana et al. [J. Chem. Phys. 139, 014308 (2013)]. The agreement between the present and the R-matrix theoretical calculations of Palihawadana et al. is relatively good at energies below 10 eV. Our calculated differential cross sections agree well with the experimental data, showing only some discrepancies at higher energies.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2015

Thin film lubrication of hexadecane confined by iron and iron oxide surfaces: A crucial role of surface structure

A comparative analysis of thin film lubrication of hexadecane between different iron and its oxide surfaces has been carried out using classical molecular dynamic simulation. An ab initio force-field, COMPASS, was applied for n-hexadecane using explicit atom model. An effective potential derived from density functional theory calculation was utilized for the interfacial interaction between hexadecane and the tribo-surfaces. A quantitative surface parameterization was introduced to investigate the influence of surface properties on the structure, rheological properties, and tribological performance of the lubricant. The results show that although the wall-fluid attraction of hexadecane on pure iron surfaces is significantly stronger than its oxides, there is a considerable reduction of shear stress of confined n-hexadecane film between Fe(100) and Fe(110) surfaces compared with FeO(110), FeO(111), Fe{sub 2}O{sub 3}(001), and Fe{sub 2}O{sub 3}(012). It was found that, in thin film lubrication of hexadecane between smooth iron and iron oxide surfaces, the surface corrugation plays a role more important than the wall-fluid adhesion strength.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Integral elastic, electronic-state, ionization, and total cross sections for electron scattering with furfural

We report absolute experimental integral cross sections (ICSs) for electron impact excitation of bands of electronic-states in furfural, for incident electron energies in the range 20–250 eV. Wherever possible, those results are compared to corresponding excitation cross sections in the structurally similar species furan, as previously reported by da Costa et al. [Phys. Rev. A 85, 062706 (2012)] and Regeta and Allan [Phys. Rev. A 91, 012707 (2015)]. Generally, very good agreement is found. In addition, ICSs calculated with our independent atom model (IAM) with screening corrected additivity rule (SCAR) formalism, extended to account for interference (I) terms that arise due to the multi-centre nature of the scattering problem, are also reported. The sum of those ICSs gives the IAM-SCAR+I total cross section for electron–furfural scattering. Where possible, those calculated IAM-SCAR+I ICS results are compared against corresponding results from the present measurements with an acceptable level of accord being obtained. Similarly, but only for the band I and band II excited electronic states, we also present results from our Schwinger multichannel method with pseudopotentials calculations. Those results are found to be in good qualitative accord with the present experimental ICSs. Finally, with a view to assembling a complete cross section data base for furfural, some binary-encounter-Bethe-level total ionization cross sections for this collision system are presented.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Temperature of maximum density and excess thermodynamics of aqueous mixtures of methanol

In this work, we present a study of representative excess thermodynamic properties of aqueous mixtures of methanol over the complete concentration range, based on extensive computer simulation calculations. In addition to test various existing united atom model potentials, we have developed a new force-field which accurately reproduces the excess thermodynamics of this system. Moreover, we have paid particular attention to the behavior of the temperature of maximum density (TMD) in dilute methanol mixtures. The presence of a temperature of maximum density is one of the essential anomalies exhibited by water. This anomalous behavior is modified in a non-monotonous fashion by the presence of fully miscible solutes that partly disrupt the hydrogen bond network of water, such as methanol (and other short chain alcohols). In order to obtain a better insight into the phenomenology of the changes in the TMD of water induced by small amounts of methanol, we have performed a new series of experimental measurements and computer simulations using various force fields. We observe that none of the force-fields tested capture the non-monotonous concentration dependence of the TMD for highly diluted methanol solutions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Anomalous properties and the liquid-liquid phase transition in gallium

A group of materials including water and silicon exhibit many anomalous behaviors, e.g., density anomaly and diffusivity anomaly (increase upon compression). These materials are hypothesized to have a liquid-liquid phase transition (LLPT) and the critical fluctuation in the vicinity of the liquid-liquid critical point is considered as the origin of different anomalies. Liquid gallium was also reported to have a LLPT, yet whether it shows similar water-like anomalies is not yet studied. Using molecular dynamics simulations on a modified embedded-atom model, we study the thermodynamic, dynamic, and structural properties of liquid gallium as well as its LLPT. We find that, similar to water-like materials predicted to have the LLPT, gallium also shows different anomalous behaviors (e.g., density anomaly, diffusivity anomaly, and structural anomaly). We also find that its thermodynamic and structural response functions are continuous and show maxima in the supercritical region, the loci of which asymptotically approach to the other and merge to the Widom line. These phenomena are consistent with the supercritical phenomenon in a category of materials with a liquid-liquid critical point, which could be common features in most materials with a LLPT.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗