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At least 703 records · Page 39
All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

Toxoplasma gondii: Biochemical and biophysical characterization of recombinant soluble dense granule proteins GRA2 and GRA6

The most prominent structural feature of the parasitophorous vacuole (PV) in which the intracellular parasite Toxoplasma gondii proliferates is a membranous nanotubular network (MNN), which interconnects the parasites and the PV membrane. The MNN function remains unclear. The GRA2 and GRA6 proteins secreted from the parasite dense granules into the PV have been implicated in the MNN biogenesis. Amphipathic alpha-helices (AAHs) predicted in GRA2 and an alpha-helical hydrophobic domain predicted in GRA6 have been proposed to be responsible for their membrane association, thereby potentially molding the MMN in its structure. Here we report an analysis of the recombinant proteins (expressed in detergent-free conditions) by circular dichroism, which showed that full length GRA2 displays an alpha-helical secondary structure while recombinant GRA6 and GRA2 truncated of its AAHs are mainly random coiled. Dynamic light scattering and transmission electron microscopy showed that recombinant GRA6 and truncated GRA2 constitute a homogenous population of small particles (6–8 nm in diameter) while recombinant GRA2 corresponds to 2 populations of particles (∼8–15 nm and up to 40 nm in diameter, respectively). The unusual properties of GRA2 due to its AAHs are discussed. - Highlights: • Toxoplasma gondii: soluble GRA2 forms 2 populations of particles. • T. gondii: the dense granule protein GRA2 folds intrinsically as an alpha-helix. • T. gondii: monomeric soluble GRA6 forms particles of 6–8 nm in diameter. • T. gondii: monomeric soluble GRA6 is random coiled. • Unusual biophysical properties of the dense granule protein GRA2 from T. gondii.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

Tuning the Electronic Structure of Anatase Through Fluorination

A highly fluorinated anatase lattice has been recently reported, providing a new class of materials whose general chemical formula is T i1-x $\square$ x X 4x O 2-4x (X - = F - or OH - ). To characterise the complex structural features of the material and the different F environments, we here apply a computational screening procedure. After deriving a polarisable force—field from DFT simulations, we screen in a step-wise fashion a large number of possible configurations differing in the positioning of the titanium vacancies ($\square$) and of the fluorine atoms. At each step only 10% of the configurations are retained. At the end of the screening procedure, a configuration is selected and simulated using DFT-based molecular dynamics. This allows us to analyse the atomic structure of the material, which is strongly disordered, leading to a strong decrease (by 0.8 eV) of the band gap compared to conventional anatase.

Science & Technology - Other Topics↗
DOE OSTI2023

Harnessing Neural Networks for Elucidating X-ray Absorption Structure–Spectrum Relationships in Amorphous Carbon

Improved understanding of structural and chemical properties through local experimental probes, such as X-ray absorption near-edge structure (XANES) spectroscopy, is crucial for the understanding and design of functional materials. In recent years, significant advancements have been made in the development of data science approaches for the automated interpretation of XANES structure–spectrum relationships. However, existing studies have primarily focused on crystalline solids and small molecules, while fewer efforts have been devoted to disordered systems. Thus, in this work, we demonstrate the development of neural network models for predicting and interpreting XANES spectra of amorphous carbon (a-C) from local structural descriptors. Comparison between different structural descriptors expectedly shows that the inclusion of both bond length and bond angle information is necessary for an accurate prediction of the spectra. Among the descriptors considered in this work, we find that the local many-body tensor representation yields the highest accuracy and greatest interpretability so that it can be leveraged to understand the importance of structural motifs in determining XANES spectra. Furthermore, we also discuss performance of neural network models for predicting both local structure features, such as bond lengths and bond angles, and global chemical composition, such as the sp:sp 2 :sp 3 ratio.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Electronic structure of boron and aluminum δ -doped layers in silicon

Recent work on atomic-precision dopant incorporation technologies has led to the creation of both boron and aluminum δ-doped layers in silicon with densities above the solid solubility limit. For this study, we use density functional theory to predict the band structure and effective mass values of such δ layers, first modeling them as ordered supercells. Structural relaxation is found to have a significant impact on the impurity band energies and effective masses of the boron layers, but not the aluminum layers. However, disorder in the δ layers is found to lead to a significant flattening of the bands in both cases. We calculate the local density of states and doping potential for these δ-doped layers, demonstrating that their influence is highly localized with spatial extents at most 4 nm. We conclude that acceptor δ-doped layers exhibit different electronic structure features dependent on both the dopant atom and spatial ordering. This suggests prospects for controlling the electronic properties of these layers if the local details of the incorporation chemistry can be fine-tuned.

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

Role of 4 f electrons in crystallographic and magnetic complexity

Here, the functionality of many magnetic materials critically depends on first manipulating and then taking advantage of highly nonlinear changes of properties that occur during phase transformations. Unique to lanthanides, property-defining 4f electrons are highly localized and, as commonly accepted, play little to no role in chemical bonding. Yet here we demonstrate that the competition between 4f-electron energy landscapes of Dy (4f 9 ) and Er (4f 11 ) is the key element of the puzzle required to explain complex interplay of magnetic and structural features observed in Er 1–x Dy x Co 2 , and likely many other mixed lanthanide systems. Unlike the parent binaries—DyCo 2 and ErCo 2 —Er 1–x Dy x Co 2 exhibits two successive magnetostructural transitions: a first order at TC, followed by a second order in the ferrimagnetically ordered state. Supported by first-principles calculations, our results offer new opportunities for targeted design of magnetic materials with multiple functionalities, and also provide a critical insight into the role of 4f electrons in controlling the magnetism and structure of lanthanide intermetallics.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
NASA NTRS2007

Electrostatic Properties of Polymers Subjected to Atmospheric Pressure Plasma Treatment; Correlation of Experimental Results with Atomistic Modeling

this study, PE, PTFE, PS and PMMA were exposed to a He+O2, APGD and pre and post treatment surface chemistries were analyzed by X-ray photoelectron spectroscopy and contact angle measurements. Semi-empirical and ab-initio calculations were performed to correlate the experimental results with sonic plausible molecular and electronic structure features of the oxidation process. For the PE and PS, significant surface oxidation showing C-O, C=O, and O-C=O bonding, and a decrease in the surface contact angles was observed. For the PTFE and PM MA, little change in the surface composition was observed. The molecular modeling calculations were performed on single and multiple oligomers and showed regardless of oxidation mechanism, e.g. -OH, =O or a combination thereof, experimentally observed levels of surface oxidation were unlikely to lead to a significant change in the electronic structure of PE and PS, and that the increased hydrophilic properties are the primary reason for the observed changes in its electrostatic behavior. Calculations for PTFE and PMMA argue strongly against significant oxidation of those materials, as confirmed by the XPS results.

Trigwell, S.↗
DOE OSTI2022

Local Atomic Configuration in Pristine and A-Site Doped Silver Niobate Perovskite Antiferroelectrics

Antiferroelectrics have attracted increasing research interests in recent years due to both their great potential in energy storage applications and intriguing structural characteristics. However, the links between the electrical properties and structural characteristics of distorted perovskite antiferroelectrics are yet to be fully deciphered. Here, we adopt local-structure methods to elucidate the nanoscale atomic structure of AgNbO3-based antiferroelectrics and their structural evolution upon La doping. The local structural features including interatomic distance distributions and atomic displacements have been analyzed using neutron small-box pair distribution function (PDF) refinement in conjunction with large-box Reverse Monte Carlo modelling. Our results highlight the correlation of cation displacements in AgNbO 3 and its disruption by the incorporation of La, apparently in corroboration with the observed anomalous dielectric properties. Spatial ordering of cation vacancies is observed in La-doped AgNbO 3 samples, which coordinates with oxygen octahedral tilting to relieve lattice strain. These results provide renewed insights into the atomic structure and antiferroelectric phase instabilities of AgNbO 3 and relevant perovskite materials, further lending versatile opportunities for enhancing their functionalities.

36 MATERIALS SCIENCE↗
NASA NTRS1973

Preliminary study of supersonic-transport configurations with low values of sonic boom

A parametric study of low-boom supersonic transport airplanes with conventional configurations was made to identify the features of specific configurations that promise relatively low sonic boom overpressures (less than 47.9 N/sq m). The range of values considered was gross weight from 28,300 to 170,000 kg; cruise Mach numbers of 2 to 3.2; and wing loadings of 1436, 2870, and 4309 N/sq m. Fuselage length was varied from 49.1 to 102.4 m and fuselage diameter from 2.75 to 3.98 m. A nominal Mach 2 configuration weighing 56,700 kg and having a wing loading of 2870 N/sq m was selected; and its gross geometric, aerodynamic, and structural features were estimated. At a cruise altitude of 18,300 m, lift-drag ratio was estimated to be 7.35, while sonic boom overpressure was 41.7 N/sq m. Takeoff thrust loading using four afterburning turbojet engines at maximum dry thrust was 0.32. Payload for a 4440-km range was 16.7 percent of gross weight, giving a direct operating cost of 0.82 cent per seat statute mile.

Dugan, J. F., Jr.↗
NASA NTRS2000

A calmodulin binding protein from Arabidopsis is induced by ethylene and contains a DNA-binding motif

Calmodulin (CaM), a key calcium sensor in all eukaryotes, regulates diverse cellular processes by interacting with other proteins. To isolate CaM binding proteins involved in ethylene signal transduction, we screened an expression library prepared from ethylene-treated Arabidopsis seedlings with 35S-labeled CaM. A cDNA clone, EICBP (Ethylene-Induced CaM Binding Protein), encoding a protein that interacts with activated CaM was isolated in this screening. The CaM binding domain in EICBP was mapped to the C-terminus of the protein. These results indicate that calcium, through CaM, could regulate the activity of EICBP. The EICBP is expressed in different tissues and its expression in seedlings is induced by ethylene. The EICBP contains, in addition to a CaM binding domain, several features that are typical of transcription factors. These include a DNA-binding domain at the N terminus, an acidic region at the C terminus, and nuclear localization signals. In database searches a partial cDNA (CG-1) encoding a DNA-binding motif from parsley and an ethylene up-regulated partial cDNA from tomato (ER66) showed significant similarity to EICBP. In addition, five hypothetical proteins in the Arabidopsis genome also showed a very high sequence similarity with EICBP, indicating that there are several EICBP-related proteins in Arabidopsis. The structural features of EICBP are conserved in all EICBP-related proteins in Arabidopsis, suggesting that they may constitute a new family of DNA binding proteins and are likely to be involved in modulating gene expression in the presence of ethylene.

Non-NASA Center↗
DOE OSTI2020

Measurement of atom resolvability in cryo-EM maps with Q-scores

Cryogenic electron microscopy (cryo-EM) maps are now at the point where resolvability of individual atoms can be achieved. However, resolvability is not necessarily uniform throughout the map. We introduce a quantitative parameter to characterize the resolvability of individual atoms in cryo-EM maps, the map Q-score. Q-scores can be calculated for atoms in proteins, nucleic acids, water, ligands and other solvent atoms, using models fitted to or derived from cryo-EM maps. Q-scores can also be averaged to represent larger features such as entire residues and nucleotides. Averaged over entire models, Q-scores correlate very well with the estimated resolution of cryo-EM maps for both protein and RNA. Here, assuming the models they are calculated from are well fitted to the map, Q-scores can be used as a measure of resolvability in cryo-EM maps at various scales, from entire macromolecules down to individual atoms. Q-score analysis of multiple cryo-EM maps of the same proteins derived from different laboratories confirms the reproducibility of structural features from side chains down to water and ion atoms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Direct comparison of elastic incoherent neutron scattering experiments with molecular dynamics simulations of DMPC phase transitions

Neutron scattering techniques have been employed to investigate 1,2-dimyristoyl-sn-glycero-3- phosphocholine (DMPC) membranes in the form of multilamellar vesicles (MLVs) and deposited, stacked multilamellar-bilayers (MLBs), covering transitions from the gel to the liquid phase. Neutron diffraction was used to characterise the samples in terms of transition temperatures, whereas elastic incoherent neutron scattering (EINS) demonstrates that the dynamics on the sub-macromolecular length-scale and pico- to nano-second time-scale are correlated with the structural transitions through a discontinuity in the observed elastic intensities and the derived mean square displacements. Molecular dynamics simulations have been performed in parallel focussing on the length-, time- and temperature-scales of the neutron experiments. They correctly reproduce the structural features of the main gel-liquid phase transition. Particular emphasis is placed on the dynamical amplitudes derived from experiment and simulations. Two methods are used to analyse the experimental data and mean square displacements. They agree within a factor of 2 irrespective of the probed time-scale, i.e. the instrument utilized. Mean square displacements computed from simulations show a comparable level of agreement with the experimental values, albeit, the best match with the two methods varies for the two instruments. Consequently, experiments and simulations together give a consistent picture of the structural and dynamical aspects of the main lipid transition and provide a basis for future, theoretical modelling of dynamics and phase behaviour in membranes. The need for more detailed analytical models is pointed out by the remaining variation of the dynamical amplitudes derived in two different ways from experiments on the one hand and simulations on the other.

Aoun, Bachir↗
DOE OSTI2020

Structural Insights into Low and High Recalcitrance Natural Poplar Variants Using Neutron and X-ray Scattering

Here, we used small-angle neutron scattering (SANS) and wide-angle X-ray scattering (WAXS) to study two Populus trichocarpa variants, GW-11012 and BESC-316, with lignin contents of 17.8 and 23.2%, respectively, to understand why the low lignin variant has increased sugar release during liquid hot water (LHW) pretreatment. SANS showed differences in cell wall polymer arrangement in the variants. In GW-11012, the cellulose microfibrils were similar in size to BESC-316 but were not equally spaced and lignin was aggregated rather than homogenously interspersed with other matrix co-polymers. However, after LHW pretreatments, the SANS profiles of the pretreated variants were almost indistinguishable, indicating that the nanoscale structural features could not adequately explain the increased sugar release observed in GW-11012. WAXS analysis revealed higher cellulose crystallinity and larger crystallite size in native and pretreated GW-11012. However, the most significant difference was that the crystallite orientation was approximately 2-fold higher in GW-11012. This suggests that higher crystallite orientation may be favorable for the action of processive cellulases leading to increased sugar release from GW-11012. Our study shows that there is a complex interplay between cell wall polymers during their deposition resulting in changes in lignin distribution and cellulose structure, highlighting the importance of investigating plant cell wall architecture across multiple length scales.

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

Statistical analysis of support thickness and particle size effects in HRTEM imaging of metal nanoparticles

High-resolution transmission electron microscopy (HRTEM) examination of nanoparticles requires their placement on some manner of support – either TEM grid membranes or part of the material itself, as in many heterogeneous catalyst systems – but a systematic quantification of the practical imaging limits of this approach has been lacking. Here, in this paper, we address this issue through a statistical evaluation of how nanoparticle size and substrate thickness affects the ability to resolve structural features of interest in HRTEM images of metallic nanoparticles on common support membranes. The visibility of lattice fringes from crystalline Au nanoparticles on amorphous carbon and silicon supports of varying thickness was investigated with both conventional and aberration-corrected TEM. Over the 1–4 nm nanoparticle size range examined, the probability of successfully resolving lattice fringes differed significantly as a function both of nanoparticle size and support thickness. Statistical analysis was used to formulate guidelines for the selection of supports and to quantify the impact a given support would have on HRTEM imaging of crystalline structure. For nanoparticles ≥1 nm, aberration-correction was found to provide limited benefit for the purpose of visualizing lattice fringes; electron dose is more predictive of lattice fringe visibility than aberration correction. These results confirm that the ability to visualize lattice fringes is ultimately dependent on the signal-to-noise ratio of the HRTEM images, rather than the point-to-point resolving power of the microscope. Lastly, this study provides a benchmark for HRTEM imaging of crystalline supported metal nanoparticles and is extensible to a wide variety of supports and nanostructures.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Interrelationships between cellulase activity and cellulose particle morphology

It is well documented that the enzymatic hydrolysis of cellulose follows a reaction pattern where an initial phase of relatively high activity is followed by a gradual slow-down over the entire course of the reaction. This phenomenon is not readily explained by conventional factors like substrate depletion, product inhibition or enzyme instability. It has been suggested that the underlying reason for the loss of enzyme activity is connected to the heterogeneous structure of cellulose, but so far attempts to establish quantitative measures of such a correlation remain speculative. Here, we have carried out an extensive microscopy study of Avicel particles during extended hydrolysis with Hypocrea jecorina cellobiohydrolase 1 (CBH1) and endoglucanase 1 and 3 (EG1 and EG3) alone and in mixtures. We have used differential interference contrast microscopy and transmission electron microscopy to observe and quantify structural features at um and nm resolution, respectively. We implemented a semi-automatic image analysis protocol, which allowed us to analyze almost 3000 individual micrographs comprising a total of more than 300,000 particles. From this analysis we estimated the temporal development of the accessible surface area throughout the reaction. We found that the number of particles and their size as well as the surface roughness contributed to surface area, and that within the investigated degree of conversion (<30 %) this measure correlated linearly with the rate of reaction. Lastly, based on this observation we argue that cellulose structure, specifically surface area and roughness, plays a major role in the ubiquitous rate loss observed for cellulases.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1981

Microstructure of Al2O3 scales formed on NiCrAl alloys

The structure of transient scales formed on pure and Y or Zr-doped Ni-15Cr-13Al alloys oxidized for 0.1 hr at 1100 C was studied by the use of transmission electron microscopy. Crystallographically oriented scales were found on all three alloys, but especially for the Zr-doped NiCrAl. The oriented scales consisted of alpha-(Al,Cr)2O3, Ni(Al,Cr)2O4 and gamma-Al2O3. They were often found in intimate contact with each other such that the close-packed planes and directions of one oxide phase were aligned with those of another. The prominent structural features of the oriented scales were approximately equal to micrometer subgrains; voids, antiphase domain boundaries and aligned precipitates were also prevalent. Randomly oriented alpha-Al2O3 was also found and was the only oxide ever observed at the immediate oxide metal interface. These approximately 0.15 micrometer grains were populated by intragranular voids which decreased in size and number towards the oxide metal interface. A sequence of oxidation was proposed in which the composition of the growing scale changed from oriented oxides rich in Ni and Cr to oriented oxides rich in Al. At the same time the structure changed from cubic spinels to hexagonal corundums with apparent precipitates of one phase in the matrix of the other. Eventually randomly oriented pure alpha-Al2O3 formed as the stable oxide with an abrupt transition: there was no gradual loss of orientation, no gradual compositional change or no gradual decrease in precipitate density.

Smialek, J. L.↗
DOE OSTI2022

Integrated Solar-Driven Device with a Front Surface Semitransparent Catalysts for Unassisted CO 2 Reduction

Monolithic integrated photovoltaic-driven electrochemical (PV-EC) artificial photosynthesis is reported for unassisted CO 2 reduction. The PV-EC structures employ triple junction photoelectrodes with a front mounted semitransparent catalyst layer as a photocathode. The catalyst layer is comprised of an array of microscale triangular metallic prisms that redirect incoming light toward open areas of the photoelectrode to reduce shadow losses. Full wave electromagnetic simulations of the prism array (PA) structure guide optimization of geometries and length scales. An integrated device is constructed with Ag catalyst prisms covering 35% of the surface area. The experimental device has close to 80% of the transmittance with a catalytic surface area equivalent 144% of the glass substrate area. Experimentally this photocathode demonstrates a direct solar-to-CO conversion efficiency of 5.9% with 50 h stability. Selective electrodeposition of Cu catalysts onto the surface of the Ag triangular prisms allows CO2 conversion to higher value products enabling demonstration of a solar-to-C 2+ product efficiency of 3.1%. This design featuring structures that have a semitransparent catalyst layer on a PV-EC cell is a general solution to light loss by shadowing for front surface mounted metal catalysts, and opens a route for the development of artificial photosynthesis based on this scalable design approach.

14 SOLAR ENERGY↗
NASA NTRS1992

A phylogenetic analysis of the myxobacteria: basis for their classification

The primary sequence and secondary structural features of the 16S rRNA were compared for 12 different myxobacteria representing all the known cultivated genera. Analysis of these data show the myxobacteria to form a monophyletic grouping consisting of three distinct families, which lies within the delta subdivision of the purple bacterial phylum. The composition of the families is consistent with differences in cell and spore morphology, cell behavior, and pigment and secondary metabolite production but is not correlated with the morphological complexity of the fruiting bodies. The Nannocystis exedens lineage has evolved at an unusually rapid pace and its rRNA shows numerous primary and secondary structural idiosyncrasies.

Non-NASA Center↗
DOE OSTI2026

Frustration-driven magnetic correlations in the spin-$\frac{5}{2}$ triangular lattice antiferromagnet RbFe⁢(HPO 3 ) 2

Here, a detailed study of the structural and magnetic properties of a spin-5/2 triangular lattice antiferromagnet RbFe⁢(HPO 3 ) 2 is presented using x-ray diffraction, magnetization, heat capacity, and 31 P nuclear magnetic resonance (NMR) experiments on a polycrystalline sample. The crystal structure features an equilateral triangular lattice of Fe 3+ ions. The thermodynamic measurements reveal the onset of a magnetic long-range order at 𝑇 N⁢1 ≃7.8K in zero field, followed by another low-temperature field-induced ordering at 𝑇 N⁢2 in higher fields. The transition at 𝑇 N⁢1 is further confirmed from the NMR spin lattice relaxation measurements. The value of the frustration ratio (𝑓≃7) implies moderate spin frustration in the compound. The 31 P NMR spectra exhibit two distinct spectral lines corresponding to two inequivalent phosphorus sites (P1 and P2), consistent with the crystal structure. The P1 site is strongly coupled with an isotropic hyperfine coupling of 𝐴$^{iso}_{hf}$ = 0.55⁢(2)⁢ T/𝜇 B while the P2 site is weakly coupled with 𝐴$^{iso}_{hf}$ = 0.25⁢(3)⁢ T/𝜇 B with the Fe 3+ ions. The magnetic susceptibility and NMR shift data are described well assuming a spin-5/2 isotropic triangular lattice antiferromagnetic model with an average exchange coupling of 𝐽/𝑘 B = 2.8⁢(2)⁢K. Below 𝑇 N⁢1 , the spectra evolve into a nearly rectangular powder pattern, indicating a commensurate antiferromagnetic type order. The 31 P spin-lattice relaxation rate well below 𝑇N⁢1 follows a 𝑇 3 temperature dependence, implying a two-magnon Raman scattering mechanism in the ordered state. Three well-defined phase regimes are clearly ascertained in the 𝐻−𝑇 phase diagram, reflecting a weak magnetic anisotropy in the compound.

Nagpal, V. [Indian Institute of Science Education ↗