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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 1,009 records · Page 56
All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

Impact of chain microstructure on solution and thin film self-assembly of PCHD-based semi-flexible/flexible diblock copolymers

We examine self-assembly of semi-flexible/flexible block copolymers in a selective solvent iusing a set of diblock copolymers where the chain microstructure of the semi-flexible block is manipulated in order to tune chain stiffness. The reduced conformational space of the semi-flexible block is anticipated to alter the way the chains pack, potentially changing the structure of self-assembled aggregates in comparison to flexible diblock copolymer analogs. Semi-flexible/flexible diblock copolymers comprised of poly(styrene)-block-poly(1,3-cyclohexadiene) (PS-b-PCHD) having systematic changes in chain microstructure, as captured by the ratio of 1,4/1,2-linkages between cyclohexenyl repeat units, and molecular weight of the PCHD blocks were synthesized using anionic polymerization. Moreover, these diblocks were dissolved in tetrahydrofuran (THF), which is a preferential solvent for PS, and the structures formed were examined using laser light scattering and complementary imaging techniques. Results show that PS-b-PCHD copolymers with a chain microstructure of 90% 1,4/10% 1,2 linkages between cyclohexenyl repeat units (referred to simply as 90/10) are able to micellize, forming spherical structures, while diblocks of 70/30 and 50/50 1,4-to-1,2 ratios remain as single chains and ill-defined aggregates, respectively, when dissolved in THF. With inferences drawn from simple structural models, we speculate that this self-assembly behavior arises due to the change in the chain configuration with increasing content of 1,2-links in the backbone. Finally, this renders the chain with higher 1,2 content incapable of swelling in response to solvent and unable to pack into well-defined self-assembled structures.

36 MATERIALS SCIENCE↗
DOE OSTI2014

Correlation between medium-range order structure and glass-forming ability for Al-based metallic glasses

To clarify the correlation of medium-range order (MRO) structure with glass forming ability (GFA) of Al-based metallic glasses, Al{sub 86}Ni{sub 14-a}Y{sub a} (a = 2∼9 at. %) metallic glasses were analyzed by x-ray diffraction in detail and further verified by synchrotron high-energy x-ray diffraction. The prepeak that reflects the MRO structural evolution was found to be much sensitive to alloy composition. We have proposed an icosahedral supercluster MRO structure model in Al-TM (transition metal)-RE (rare earth metal) system, which consists of 12 RE(TM)-centered clusters on the vertex of icosahedral supercluster, one RE(TM)-centered clusters in the center, and TM(RE) atoms located at RE(TM)-centered cluster tetrahedral interstices in the icosahedral supercluster. It was indicated that the MRO structural stability mainly depends on the interaction of efficient dense packing and electrochemical potential equalization principle. The Al{sub 86}Ni{sub 9}Y(La){sub 5} alloys present good GFA due to the combination of the two structural factors.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2019

A quick guide for student-driven community genome annotation

High quality gene models are necessary to expand the molecular and genetic tools available for a target organism, but these are available for only a handful of model organisms that have undergone extensive curation and experimental validation over the course of many years. The majority of gene models present in biological databases today have been identified in draft genome assemblies using automated annotation pipelines that are frequently based on orthologs from distantly related model organisms and usually have minor or major errors. Manual curation is time consuming and often requires substantial expertise, but is instrumental in improving gene model structure and identification. Manual annotation may seem to be a daunting and cost-prohibitive task for small research communities but involving undergraduates in community genome annotation consortiums can be mutually beneficial for both education and improved genomic resources. We outline a workflow for efficient manual annotation driven by a team of primarily undergraduate annotators. This model can be scaled to large teams and includes quality control processes through incremental evaluation. Moreover, it gives students an opportunity to increase their understanding of genome biology and to participate in scientific research in collaboration with peers and senior researchers at multiple institutions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Linear two-pool models are insufficient to infer soil organic matter decomposition temperature sensitivity from incubations

Abstract Terrestrial carbon (C)-climate feedbacks depend strongly on how soil organic matter (SOM) decomposition responds to temperature. This dependency is often represented in land models by the parameter Q 10 , which quantifies the relative increase of microbial soil respiration per 10 °C temperature increase. Many studies have conducted paired laboratory soil incubations and inferred “active” and “slow” pool Q 10 values by fitting linear two-pool models to measured respiration time series. Using a recently published incubation study (Qin et al. in Sci Adv 5(7):eaau1218, 2019) as an example, here we first show that the very high parametric equifinality of the linear two-pool models may render such incubation-based Q 10 estimates unreliable. In particular, we show that, accompanied by the uncertain initial active pool size, the slow pool Q 10 can span a very wide range, including values as high as 100, although all parameter combinations are producing almost equally good model fit with respect to the observations. This result is robust whether or not interactions between the active and slow pools are considered (typically these interactions are not considered when interpreting incubation data, but are part of the predictive soil carbon models). This very large parametric equifinality in the context of interpreting incubation data is consistent with the poor temporal extrapolation capability of linear multi-pool models identified in recent studies. Next, using a microbe-explicit SOM model (RESOM), we show that the inferred two pools and their associated parameters (e.g., Q 10 ) could be artificial constructs and are therefore unreliable concepts for integration into predictive models. We finally discuss uncertainties in applying linear two-pool (or more generally multiple-pool) models to estimate SOM decomposition parameters such as temperature sensitivities from laboratory incubations. We also propose new observations and model structures that could enable better process understanding and more robust predictive capabilities of soil carbon dynamics.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2016

Identification of O-rich structures on platinum(111)-supported ultrathin iron oxide films

Using high-resolution scanning tunneling microscopy (STM) we have studied the oxidation of ultrathin FeO films grown on Pt(111). At the initial stage of the FeO film oxidation by atomic oxygen exposure, we identified three distinct types of line defects, all of which form boundaries between FeO domains of opposite orientation. Two types of line defects appearing bright ( type-i ) and dark ( type-ii ) in the STM images at typical scanning parameters are “metallic”, whereas the third line defect exhibits nonmetallic behavior ( type-iii ). Atomic-scale structure models of these line defects are proposed, with type-i defects exhibiting 4-fold coordinated Fe atoms, type-ii exhibiting 2-fold coordinated O atoms, and type-iii exhibiting tetrahedrally-coordinated Fe atoms. In addition, FeO 2 trilayer islands are formed upon oxidation, which appear at FCC-type domains of the moiré structure. At high scanning bias, distinct protrusions on the trilayer islands are observed over surface O ions, which are assigned to H adatoms. The experimental data are supported by density functional theory (DFT) calculations, in which bare and hydroxylated FeO 2 trilayer islands are compared. Finally, we compare the formation of O-rich features on continuous FeO films using atomic oxygen with the oxidation of Pt(111)-supported FeO islands accomplished by O 2 exposure.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Structures of the ApoL1 and ApoL2 N-terminal domains reveal a non-classical four-helix bundle motif

Apolipoprotein L1 (ApoL1) is a circulating innate immunity protein protecting against trypanosome infection. However, two ApoL1 coding variants are associated with a highly increased risk of chronic kidney disease. Here we present X-ray and NMR structures of the N-terminal domain (NTD) of ApoL1 and of its closest relative ApoL2. In both proteins, four of the five NTD helices form a four-helix core structure which is different from the classical four-helix bundle and from the pore-forming domain of colicin A. The reactivity with a conformation-specific antibody and structural models predict that this four-helix motif is also present in the NTDs of ApoL3 and ApoL4, suggesting related functions within the small ApoL family. The long helix 5 of ApoL1 is conformationally flexible and contains the BH3-like region. This BH3-like α-helix resembles true BH3 domains only in sequence and structure but not in function, since it does not bind to the pro-survival members of the Bcl-2 family, suggesting a Bcl-2-independent role in cytotoxicity. These findings should expedite a more comprehensive structural and functional understanding of the ApoL immune protein family.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Cesium vacancy ordering in phase-separated C s x F e 2 - y S e 2

By simultaneously displaying magnetism and superconductivity in a single phase, the iron-based superconductors provide a model system for the study of magnetism's role in superconductivity. The class of intercalated iron selenide superconductors is unique among these in having the additional property of phase separation and coexistence of two distinct phases—one majority phase with iron vacancy ordering and strong antiferromagnetism, and the other a poorly understood minority microscopic phase with a contested structure. Adding to the intrigue, the majority phase has never been found to show superconductivity on its own while the minority phase has never been successfully synthesized separate from the majority phase. In order to better understand this minority phase, a series of high-quality Cs x Fe 2–y Se 2 single crystals with (0.8 ≤ x ≤ 1;0 ≤ y ≤ 0.3) were grown and studied. Neutron and x-ray powder diffraction performed on ground crystals show that the average I4/mmm structure of the minority phase is distinctly different from the high-temperature I4/mmm parent structure. Moreover, single-crystal diffraction reveals the presence of discrete superlattice reflections that remove the degeneracy of the Cs sites in both the majority and minority phases and reduce their structural symmetries from body centered to primitive. Group theoretical analysis in conjunction with structural modeling shows that the observed superlattice reflections originate from three-dimensional Cs vacancy ordering. This model predicts a 25% vacancy of the Cs site in the minority phase which is consistent with the site's refined occupancy. Magnetization measurements performed in tandem with neutron single-crystal diffraction provide evidence that the minority phase is the host of superconductivity. Lastly, our results also reveal a superconducting dome in which the superconducting transition temperature varies as a function of the nominal valence of iron.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Benchmarking and parameter sensitivity of physiological and vegetation dynamics using the Functionally Assembled Terrestrial Ecosystem Simulator (FATES) at Barro Colorado Island, Panama

Plant functional traits determine vegetation responses to environmental variation, but variation in trait values is large, even within a single site. Likewise, uncertainty in how these traits map to Earth system feedbacks is large. We use a vegetation demographic model (VDM), the Functionally Assembled Terrestrial Ecosystem Simulator (FATES), to explore parameter sensitivity of model predictions, and comparison to observations, at a tropical forest site: Barro Colorado Island in Panama. We define a single 12-dimensional distribution of plant trait variation, derived primarily from observations in Panama, and define plant functional types (PFTs) as random draws from this distribution. We compare several model ensembles, where individual ensemble members vary only in the plant traits that define PFTs, and separate ensembles differ from each other based on either model structural assumptions or non-trait, ecosystem-level parameters, which include (a) the number of competing PFTs present in any simulation and (b) parameters that govern disturbance and height-based light competition. While single-PFT simulations are roughly consistent with observations of productivity at Barro Colorado Island, increasing the number of competing PFTs strongly shifts model predictions towards higher productivity and biomass forests. Different ecosystem variables show greater sensitivity than others to the number of competing PFTs, with the predictions that are most dominated by large trees, such as biomass, being the most sensitive. Changing disturbance and height-sorting parameters, i.e., the rules of competitive trait filtering, shifts regimes of dominance or coexistence between early- and late-successional PFTs in the model. Increases to the extent or severity of disturbance, or to the degree of determinism in height-based light competition, all act to shift the community towards early-successional PFTs. In turn, these shifts in competitive outcomes alter predictions of ecosystem states and fluxes, with more early-successional-dominated forests having lower biomass. It is thus crucial to differentiate between plant traits, which are under competitive pressure in VDMs, from those model parameters that are not and to better understand the relationships between these two types of model parameters to quantify sources of uncertainty in VDMs.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2017

The introspective may achieve more: Enhancing existing Geoscientific models with native-language emulated structural reflection

Geoscientific models manage myriad and increasingly complex data structures as trans -disciplinary models are integrated. They often incur significant redundancy with cross-cutting tasks. Reflection, the ability of a program to inspect and modify its structure and behavior at runtime, is known as a powerful tool to improve code reusability, abstraction, and separation of concerns. Reflection is rarely adopted in high-performance Geoscientific models, especially with Fortran, where it was previously deemed implausible. Practical constraints of language and legacy often limit us to feather-weight, native-language solutions. We demonstrate the usefulness of a structural-reflection-emulating, dynamically-linked metaObjects, gd . We show real-world examples including data structure self-assembly, effortless save/restart and upgrade to parallel I/O, recursive actions and batch operations. We share gd and a derived module that reproduces MATLAB-like structure in Fortran and C++. We suggest that both a gd representation and a Fortran-native representation are maintained to access the data, each for separate purposes. In conclusion, embracing emulated reflection allows generically-written codes that are highly re-usable across projects.

58 GEOSCIENCES↗
DOE OSTI2020

X-ray atomic mapping of quantum dots

We report a model-independent atomic-mapping technique for quantum dots (QDs) by combining Bragg reflection x-ray standing wave (XSW) and grazing incidence diffraction (GID) measurements. In this study, we choose GaAs capped InGaAs QDs/GaAs(001) as a model system to show the locations and arrangements of indium atoms within the QDs along various [hkl] directions. This technique directly reveals the actual amount of positional anisotropy and ordering fraction of indium atoms within the QDs by probing the (1¯11), (111), (311), (1¯31), (113), and (1¯13) crystallographic planes. We find that indium atoms are outwardly shifted along the [001] direction by small fractions of the lattice constant, 0.04a GaAs and 0.06a GaAs from Ga sites for 50- and 150-Å GaAs capped InGaAs QDs, respectively. We observe that an improved coherency factor of the indium atoms within the QDs by 45–60% along the [001] and [011] directions reduces the photoluminescence linewidth by 22%, thus making the QDs efficient for QD-laser and optoelectronic device applications. Here, we also find that the position and ordering of In atoms along the (113) and (1¯13) planes are most sensitive to the thickness of the GaAs cap layer. Our XSW-based results are supported by numerical calculations using a QD-macroscopic structural model based on our GID study. We thus show that this atomic-mapping technique will be useful for studying various quantum structures and tuning their properties.

36 MATERIALS SCIENCE↗
DOE OSTI2015

Crystal and Electronic Structures of Complex Bismuth Iodides A 3 Bi 2 I 9 ( A = K, Rb, Cs) Related to Perovskite: Aiding the Rational Design of Photovoltaics

Ternary bismuth halides form an interesting functional materials class in the context of the closely related Pb halide perovskite photovoltaics, especially given the significantly reduced toxicity of Bi when compared with Pb. The compounds A 3 Bi 2 I 9 (A = K, Rb, Cs) examined here crystallize in two different structure types: the layered defect-perovskite K 3 Bi 2 I 9 type, and the Cs 3 Cr 2 Cl 9 type. The latter structure type features isolated Bi 2 I 9 3– anions. Here, the crystal structures of the ternary iodides are redetermined and a corrected structural model for Rb 3 Bi 2 I 9 , as established by single crystal X-ray diffraction and solid state 87Rb NMR spectroscopy and supported by density functional theory (DFT) calculations is presented. A variety of facile preparation techniques for single crystals, bulk materials, as well as solution-processed thin films are described. The optical properties and electronic structures are investigated experimentally by optical absorption and ultraviolet photoemission spectroscopy and computationally by DFT calculations. Absolute band positions of the valence and conduction bands of these semiconductors, with excellent agreement of experimental and calculated values, are reported, constituting a useful input for the rational interface design of efficient electronic and optoelectronic devices. The different structural connectivity in the two different structure types, somewhat surprisingly, appears to not impact band positions or band gaps in a significant manner. Computed dielectric properties, including the finding of anomalously large Born effective charge tensors on Bi 3+ , suggest proximal structural instabilities arising from the Bi 3+ 6s 2 lone pair. These anomalous Born effective charges are promising for defect screening and effective charge carrier transport. The structural, electronic, and optical properties of the complex bismuth iodides are to some extent similar to the related lead iodide perovskites. In conclusion, the deeper valence band positions in the complex bismuth iodides point to the need for different choices of hole transport materials for Bi-iodide based solar cell architectures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2013

Study of multilayered SiGe semiconductor structures by X-ray diffractometry, grazing-incidence X-ray reflectometry, and secondary-ion mass spectrometry

In this publication, we report the results of studying a multilayerd nonperiodic SiGe/Si structure by the methods of X-ray diffractometry, grazing-angle X-ray reflectometry, and secondary-ion mass spectrometry (SIMS). Special attention is paid to the processing of the component distribution profile using the SIMS method and to consideration of the most significant experimental distortions introduced by this method. A method for processing the measured composition distribution profile with subsequent consideration of the influence of matrix effects, variation in the etching rate, and remnants of ion sputtering is suggested. The results of such processing are compared with a structure model obtained upon combined analysis of X-ray diffractometry and grazing-angle reflectometry data. Good agreement between the results is established. It is shown that the combined use of independent techniques makes it possible to improve the methods of secondary-ion mass spectrometry and grazing-incidence reflectometry as applied to an analysis of multilayered heteroepitaxial structures (to increase the accuracy and informativity of these methods)

36 MATERIALS SCIENCE↗
DOE OSTI2024

Structured information extraction from scientific text with large language models

Extracting structured knowledge from scientific text remains a challenging task for machine learning models. Here, we present a simple approach to joint named entity recognition and relation extraction and demonstrate how pretrained large language models (GPT-3, Llama-2) can be fine-tuned to extract useful records of complex scientific knowledge. We test three representative tasks in materials chemistry: linking dopants and host materials, cataloging metal-organic frameworks, and general composition/phase/morphology/application information extraction. Records are extracted from single sentences or entire paragraphs, and the output can be returned as simple English sentences or a more structured format such as a list of JSON objects. This approach represents a simple, accessible, and highly flexible route to obtaining large databases of structured specialized scientific knowledge extracted from research papers.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2022

A Review of Bayesian Networks for Spatial Data

We report Bayesian networks are a popular class of multivariate probabilistic models as they allow for the translation of prior beliefs about conditional dependencies between variables to be easily encoded into their model structure. Due to their widespread usage, they are often applied to spatial data for inferring properties of the systems under study and also generating predictions for how these systems may behave in the future. We review published research on methodologies for representing spatial data with Bayesian networks and also summarize the application areas for which Bayesian networks are employed in the modeling of spatial data. We find that a wide variety of perspectives are taken, including a GIS-centric focus on efficiently generating geospatial predictions, a statistical focus on rigorously constructing graphical models controlling for spatial correlation, as well as a range of problem-specific heuristics for mitigating the effects of spatial correlation and dependency arising in spatial data analysis. Special attention is also paid to potential future directions for integration of Bayesian networks with spatial processes.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2015

Decoupling of epitaxial graphene via gold intercalation probed by dispersive Raman spectroscopy

Signatures of a superlattice structure composed of a quasi periodic arrangement of atomic gold clusters below an epitaxied graphene (EG) layer are examined using dispersive Raman spectroscopy. The gold-graphene system exhibits a laser excitation energy dependant red shift of the 2D mode as compared to pristine epitaxial graphene. The phonon dispersions in both the systems are mapped using the experimentally observed Raman signatures and a third-nearest neighbour tight binding electronic band structure model. Our results reveal that the observed excitation dependent Raman red shift in gold EG primarily arise from the modifications of the phonon dispersion in gold-graphene and shows that the extent of decoupling of graphene from the underlying SiC substrate can be monitored from the dispersive nature of the Raman 2D modes. The intercalated gold atoms restore the phonon band structure of epitaxial graphene towards free standing graphene.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2013

Quantifying stoichiometry-induced variations in structure and energy of a SrTiO 3 symmetric Σ13 {510}/<100> grain boundary

Grain boundaries (GBs) in complex oxides such as perovskites have been shown to readily accommodate nonstoichiometry changing the electrostatic potential at the boundary plane and effectively controlling material properties such as capacitance, magnetoresistance and superconductivity. Understanding and quantifying exactly how variations in atomic scale nonstoichiometry at the boundary plane extend to the practical mesoscale operating length of the system is therefore critical for improving the overall properties. Bicrystals of SrTiO 3 were fabricated to provide the model GB model structures that are analysed in this paper. We show that statistical analysis of aberration-corrected scanning transmission electron microscope images acquired from a large area of GB is an effective routine to understanding the variation in boundary structure that occurs to accommodate nonstoichiometry. In the case of the SrTiO 3 22.6° Σ13 (510)/[100] GB analysed here, the symmetric atomic structures observed from a micron-long GB can be categorized as two different competing structural arrangements, with and without a rigid-body translation along the boundary plane. How this quantified experimental approach can provide direct insights into the GB energetics is further confirmed from the first principles density functional theory, and the effect of nonstoichiometry in determining the GB energies is quantified.

atomic structure↗
DOE OSTI2019

Computational Evidence for Kinetically Controlled Radical Coupling during Lignification

Lignin is an alkyl-aromatic biopolymer that, despite its abundance, is underutilized as a renewable feedstock because of its highly complex structure. A method to overcome this challenge that has gained prominence in recent years leverages the plasticity and malleability of lignin biosynthesis to tune lignin structure in planta through genetic approaches. An improved understanding of lignin biosynthesis can thus provide fundamental insights critical for the development of effective tailoring and valorization strategies. Although it is widely accepted that lignin monomers and growing chains are oxidized enzymatically into radicals that then undergo kinetically controlled coupling in planta, direct experimental evidence has been scarce because of the difficulty of exactly replicating in planta lignification conditions. Here, we computationally investigate a set of radical reactions representative of lignin biosynthesis. We demonstrate that, contrary to the notion that radical coupling reactions are usually barrierless and dynamically controlled, the computed activation energies can be qualitatively consistent with key structural observations made empirically for native lignin in a variety of biomass types. We also rationalize the origins of regioselectivity in coupling reactions through structural and activation strain analyses. Our findings lay the groundwork for first-principles lignin structural models and more detailed multiscale simulations of the lignification process.

09 BIOMASS FUELS↗
DOE OSTI2023

Involvement of the Streptococcus mutans PgfE and GalE 4-epimerases in protein glycosylation, carbon metabolism, and cell division

Streptococcus mutans is a key pathogen associated with dental caries and is often implicated in infective endocarditis. This organism forms robust biofilms on tooth surfaces and can use collagen-binding proteins (CBPs) to efficiently colonize collagenous substrates, including dentin and heart valves. One of the best characterized CBPs of S. mutans is Cnm, which contributes to adhesion and invasion of oral epithelial and heart endothelial cells. These virulence properties were subsequently linked to post-translational modification (PTM) of the Cnm threonine-rich repeat region by the Pgf glycosylation machinery, which consists of 4 enzymes: PgfS, PgfM1, PgfE, and PgfM2. Inactivation of the S. mutans pgf genes leads to decreased collagen binding, reduced invasion of human coronary artery endothelial cells, and attenuated virulence in the Galleria mellonella invertebrate model. The present study aimed to better understand Cnm glycosylation and characterize the predicted 4-epimerase, PgfE. Using a truncated Cnm variant containing only 2 threonine-rich repeats, mass spectrometric analysis revealed extensive glycosylation with HexNAc2. Compositional analysis, complemented with lectin blotting, identified the HexNAc2 moieties as GlcNAc and GalNAc. Comparison of PgfE with the other S. mutans 4-epimerase GalE through structural modeling, nuclear magnetic resonance, and capillary electrophoresis demonstrated that GalE is a UDP-Glc-4-epimerase, while PgfE is a GlcNAc-4-epimerase. While PgfE exclusively participates in protein O-glycosylation, we found that GalE affects galactose metabolism and cell division. Furthermore, this study further emphasizes the importance of O-linked protein glycosylation and carbohydrate metabolism in S. mutans and identifies the PTM modifications of the key CBP, Cnm.

4-epimerases↗