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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 541 records · Page 30
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Expression profile analysis of differentially expressed genes in ruptured intracranial aneurysms: In search of biomarkers

Highlights: • Bioinformatics can identify potential biomarkers of ruptured intracranial aneurysm. • BASP1, CD74, CEBPB, ECHDC2, GZMK, HLA-DRB3, KLHL3, SLC2A3 & SOCS3 affect IA rupture. • DEGs are involved in antigen processing and presentation and immune response. • Vascular brain injury affects gene expression in IA tissue. Intracranial aneurysms (IAs) result from the bulging of arterial walls secondary to several factors such as flow, vessel morphology, and genetics. Subarachnoid hemorrhage occurs when such walls rupture, leading to high disability and mortality. Despite numerous investigations pertaining to the relationship between geometric characteristics and IA rupture, only a few have obtained consistent results. This study aimed to further identify the potential genes associated with the pathogenesis of IAs, which may provide novel molecular biomarkers. We downloaded and reanalyzed six datasets, which were divided into four groups. IA walls and blood samples were screened for differentially expressed genes (DEGs); then, functional and pathway enrichment analyses were conducted. In total, 158 common DEGs were identified from Groups 1–3 and 396 genes (187 upregulated and 209 downregulated genes) were differentially expressed in Group 4. The functional analysis revealed that the DEGs were mainly associated with the major histocompatibility complex class II protein complex and antigen processing and presentation. Finally, we identified nine key genes, both in aneurysm tissue samples and blood samples, of which three were mostly associated with the progression and rupture of IAs. Bioinformatics was used to analyze the datasets of the ruptured IAs and identify potential biomarkers, which may provide information for the early detection and treatment of IAs.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

A Class of Sparse Johnson–Lindenstrauss Transforms and Analysis of their Extreme Singular Values

The Johnson–Lindenstrauss (JL) lemma is a powerful tool for dimensionality reduction in modern algorithm design. The lemma states that any set of high-dimensional points in a Euclidean space can be projected into lower dimensions while approximately preserving pairwise Euclidean distances. Random matrices satisfying this lemma are called JL transforms (JLTs). Inspired by existing $s$-hashing JLTs with exactly $s$ nonzero elements on each column, the present work introduces an ensemble of sparse matrices encompassing so-called $s$-hashing-like matrices whose expected number of nonzero elements on each column is $s$. The independence of the sub-Gaussian entries of these matrices and the knowledge of their exact distribution play an important role in their analyses. Using properties of independent sub-Gaussian random variables, these matrices are demonstrated to be JLTs, and their smallest nontrivial singular values and largest singular values are estimated nonasymptotically using a technique from geometric functional analysis. As the dimensions of the matrix grow to infinity, these singular values are proved to converge almost surely to fixed quantities (by using the universal Bai–Yin law) and in distribution to the Gaussian orthogonal ensemble Tracy–Widom law after proper rescalings. Understanding the behaviors of extreme singular values is important in general because they are often used to define a measure of stability of matrix algorithms. For example, JLTs were recently used in derivative-free optimization algorithmic frameworks to select random subspaces in which are constructed random models or poll directions to achieve scalability, and hence estimating their smallest singular value in particular helps determine the dimension of these subspaces.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2018

Shear-Assisted Formation of Cation-Disordered Rocksalt NaMO 2 (M = Fe or Mn)

Herein we report the synthesis of cation-disordered rocksalt NaMO 2 (M = 3d transition metal), i.e., NaFeO 2–δ (δ ~ 0.18), for the first time via a martensitic-like phase transformation from β-NaFeO 2 . This disordered rocksalt NaFeO 2–δ does not exhibit long-range cation ordering, as evidenced by synchrotron X-ray diffraction, neutron diffraction, and transmission electron microscopy analyses. Pair distribution function analysis revealed that although the cation sublattice mostly preserved the rocksalt symmetry, O atoms were significantly displaced to accommodate the different Na + –O, Fe 2+ –O, and Fe 3+ –O bond lengths (~2.4, 2.1, and 2 Å, respectively). In addition, we confirmed the presence of O vacancies and partial Fe reduction from 3+ to 2+ in NaFeO 2–δ based on 57 Fe Mössbauer and X-ray absorption spectroscopy analyses. Controlled experiments revealed that three factors are essential for the successful synthesis of the rocksalt structure: (1) an appropriate precursor structure, (2) the application of a large stress by high-energy milling, and (3) the creation of O vacancies via carbon reduction. Density functional theory calculations demonstrated that these factors substantially affect the energetics of the minimum-energy reaction path of the phase transformation, making the highly metastable disordered rocksalt phase accessible. Our work suggests the effectiveness of mechanical milling to access metastable phases that are structurally related to the precursors via a shearing transformation. Utilizing this mechanism, we were able to predict and synthesize another cation-disordered rocksalt structure, NaMnO 2 , and explain the syntheses of several other related materials.

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

Local Structural Investigation of SmFeAsO1−xFx High Temperature Superconductors

A strong revitalization of the field of high temperature superconductivity (HTSC) has been induced recently by the discovery of T{sub C} around 26 K in F-doped LaFeAsO iron pnictides. Starting from this discovery, a huge amount of experimental data have been accumulated. This important corpus of results will allow the development of suitable theoretical models aimed at describing the basic electronic structure properties and nature of superconducting states in these fascinating new systems. A close correlation between structural features and physical properties of the normal and superconducting states has already been demonstrated in the current literature. Advanced theoretical models are also based on the close correlation with structural properties and in particular with the Fe-As tetrahedral array. As for other complex materials, a deeper understanding of their structure-properties correlation requires a full knowledge of the atomic arrangement within the structure. Here we report an investigation of the local structure in the SmFeAsO{sub 1-x}F{sub x} system carried out by means of x-ray total scattering measurements and pair distribution function analysis. The results presented indicate that the local structure of these HTSC significantly differs from the average structure determined by means of traditional diffraction techniques, in particular the distribution of Fe-As bond lengths. In addition, a model for describing the observed discrepancies is presented.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2026

Multi-scale structural analysis of swift heavy ion-irradiated ZrO 2 and HfO 2

The radiation-induced monoclinic-to-tetragonal phase transition in ZrO 2 and HfO 2 has been the subject of many investigations, but the transformation pathways and underlying structural mechanisms are still not well understood. In this study, microcrystalline powder samples of ZrO 2 and HfO 2 were irradiated with 946 MeV and 1470 MeV Au ions to a wide fluence range up to 3 × 10 13 ions/cm 2 . To characterize beam-induced structural modifications across all spatial length scales, complementary experimental techniques such as synchrotron X-ray diffraction and spallation neutron total scattering were used. The phase evolution of the tetragonal polymorph with increasing ion fluence is accurately described by a heterogeneous track-overlap model that incorporates both direct- and double-impact processes. These damage accumulation processes are an expression of a core-shell ion track morphology that depends on irradiation conditions and target material. Neutron pair distribution function analysis revealed that ion-beam-induced tetragonal ZrO 2 is merely a configurational average of short-range orthorhombic (Pbcn) domains stabilized by a dense network of domain walls. Furthermore, this knowledge is critical for a better understanding of how crystalline-to-crystalline phase transformations proceed at the atomic scale under extreme conditions.

Monoclinic-to-tetragonal phase transformation↗
DOE OSTI2012

Pair distribution function-derived mechanism of a single-crystal to disordered to single-crystal transformation in a hemilabile metal-organic framework

Flexible metal-organic frameworks (MOFs) are materials of great current interest. A small class of MOFs show flexibility driven by reversible bonding rearrangements that lead directly to unusual properties. Cu-SIP-3 is a MOF based on the 5-sulfoisophthalate ligand, where the strong copper-carboxylate bonds ensure that the three-dimensional integrity of the structure is retained while allowing bonding changes to occur at the more weakly bonding sulfonate group leading to unusual properties such as the ultra-selective adsorption of only certain gases. While the integrity of the framework remains intact during bonding changes, crystalline order is not retained at all times during the transformations. X-Ray diffraction reveals that highly crystalline single crystals lose order during the transformation before regaining crystallinity once it is complete. Here we show how X-ray pair distribution function analysis can be used to reveal the mechanism of the transformations in Cu-SIP-3, identifying the sequence of atomic displacements that occur in the disordered phase. A similar approach reveals the underlying mechanism of Cu-SIP-3's ultra-selective gas adsorption.

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

The evolution of contact prediction: Evidence that contact selection in statistical contact prediction is changing

Over the last few years, the field of protein structure prediction has been transformed by increasingly-accurate contact prediction software. These methods are based on the detection of coevolutionary relationships between residues from multiple sequence alignments. However, despite speculation, there is little evidence of a link between contact prediction and the physico-chemical interactions which drive amino-acid coevolution. Furthermore, existing protocols predict only a fraction of all protein contacts and it is not clear why some contacts are favoured over others. Using a dataset of 863 protein domains, we assessed the physico-chemical interactions of contacts predicted by CCMpred, MetaPSICOV, and DNCON2, as examples of direct coupling analysis, meta-prediction, and deep learning. We considered correctly-predicted contacts and compared their properties against the protein contacts that were not predicted. Predicted contacts tend to form more bonds than non-predicted contacts, which suggests these contacts may be more important than contacts that were not predicted. Comparing the contacts predicted by each method, we found that metaPSICOV and DNCON2 favour accuracy whereas CCMPred detects contacts with more bonds. This suggests that the push for higher accuracy may lead to a loss of physico-chemically important contacts. These results underscore the connection between protein physico-chemistry and the coevolutionary couplings that can be derived from multiple sequence alignments. This relationship is likely to be relevant to protein structure prediction and functional analysis of protein structure and may be key to understanding their utility for different problems in structural biology. We use publicly-available databases. Our code is available for download at http://opig.stats.ox.ac.uk/.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Inhibition of PD1:PD-L1 interaction by an E. coli-derived optimized PD1 variant

Highlights: • Cancer cells interact with immune checkpoints to shut down T cell response. • An optimization system for the selection of modified immune checkpoint proteins. • Using the described system improved PD1 variants were identified. • The improved variants are active in a cellular assay that mimics T cell:cancer interaction. Immune-checkpoint receptors are a set of signal transduction proteins that can stimulate or inhibit specific anti-tumor responses. It is well established that cancer cells interact with different immune checkpoints to shut down T-cell response, thereby enabling cancer proliferation. Given the importance of immune checkpoint receptors, a structure-function analysis of these systems is imperative. However, recombinant expression and purification of these membrane originated proteins is still a challenge. Therefore, many attempts are being made to improve their expression and solubility while preserving their biological relevance. For this purpose, we designed an E. coli-based optimization system that enables the acquisition of mutations that increases protein solubility and affinity towards its native ligand, while maintaining biological activity. Here we focused on the well-characterized extracellular domain of the 'programmed cell death protein 1' (PD1), an immune checkpoint receptor known to inhibit T-cell proliferation by interacting with its ligands PD-L1 and PD-L2. The simple ELISA-based screening system shown here enabled the identification of high-affinity, highly soluble, functional variants derived from the extracellular domain of human PD1. The system was based on the expression of a GST-tagged variants library in E. coli, which enabled the selection of improved PD1 variants after a single optimization round. Within only two screening rounds, the most active variant showed a 5-fold higher affinity and 2.4-fold enhanced cellular activity as compared to the wild type protein. This scheme can be translated toward other types of challenging receptors toward development of research tools or alternative therapeutics.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Survey of Surveys: I. The largest compilation of radial velocities for the Galaxy

In the present-day panorama of large spectroscopic surveys, the amount, diversity, and complexity of the available data continuously increase. The overarching goal of studying the formation and evolution of our Galaxy is hampered by the heterogeneity of instruments, selection functions, analysis methods, and measured quantities. Here, we present a comprehensive catalogue, the Survey of Surveys (SoS), built by homogeneously merging the radial velocity (RV) determinations of the largest ground-based spectroscopic surveys to date, such as APOGEE, GALAH, Gaia-ESO, RAVE, and LAMOST, using Gaia as a reference. This pilot study serves to prove the concept and to test the methodology that we plan to apply in the future to the stellar parameters and abundance ratios as well. We have devised a multi-staged procedure that includes: (i) the cross match between Gaia and the spectroscopic surveys using the official Gaia cross-match algorithm, (ii) the normalisation of uncertainties using repeated measurements or the three-cornered hat method, (iii) the cross calibration of the RVs as a function of the main parameters on which depend (magnitude, effective temperature, surface gravity, metallicity, and signal-to-noise ratio) to remove trends and zero point offsets, and (iv) the comparison with external high-resolution samples, such as the Gaia RV standards and the Geneva-Copenhagen survey, to validate the homogenisation procedure and to calibrate the RV zero-point of the SoS catalogue. We provide the largest homogenised RV catalogue to date, containing almost 11 million stars, of which about half come exclusively from Gaia and half in combination with the ground-based surveys. We estimate the accuracy of the RV zero-point to be about 0.16–0.31 km s –1 and the RV precision to be in the range 0.05–1.50 km s –1 depending on the type of star and on its survey provenance. We validate the SoS RVs with open clusters from a high resolution homogeneous samples and provide the systemic velocity of 55 individual open clusters. Additionally, we provide median RVs for 532 clusters recently discovered by Gaia data. The SoS is publicly available and ready to be applied to various research projects, such as the study of star clusters, Galactic archaeology, stellar streams, or the characterisation of planet-hosting stars, to name a few. We also plan to include survey updates and more data sources in future versions of the SoS.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

A quantitative model for a nanoscale switch accurately predicts thermal actuation behavior

Manipulation of temperature can be used to actuate DNA origami nano-hinges containing gold nanoparticles. We develop a physical model of this system that uses partition function analysis of the interaction between the nano-hinge and nanoparticle to predict the probability that the nano-hinge is open at a given temperature. The model agrees well with experimental data and predicts experimental conditions that allow the actuation temperature of the nano-hinge to be tuned over a range of temperatures from 30 °C to 45 °C. Additionally, the model identifies microscopic interactions that are important to the macroscopic behavior of the system, revealing surprising features of the system. This combination of physical insight and predictive potential is likely to inform future designs that integrate nanoparticles into dynamic DNA origami structures or use strand binding interactions to control dynamic DNA origami behavior. Furthermore, our modeling approach could be expanded to consider the incorporation, stability, and actuation of other types of functional elements or actuation mechanisms integrated into nucleic acid devices.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Local Sn Dipolar-Character Displacements behind the Low Thermal Conductivity in SnSe Thermoelectric

The local atomic structure of SnSe was characterized across its orthorhmbic-to-orthorhombic structural phase transition using x-ray pair distribution function analysis. Substantial Sn displacements with a dipolar character persist in the high symmetry high temperature phase, albeit with a symmetry different from that of the ordered displacements below the transition. The analysis implies that the transition is neither order-disorder nor displacive, but rather a complex crossover. Robust ferro-coupled SnSe intra-layer distortions suggest a ferroelectric-like instability as the driving force. Furthermore, these local symmetry-lowering Sn displacements are likely integral to the ultra-low lattice thermal conductivity mechanism in SnSe.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Model-free reconstruction of magnetic correlations in frustrated magnets

Frustrated magnetic systems exhibit extraordinary physical properties, but quantification of their magnetic correlations poses a serious challenge to experiment and theory. Current insight into frustrated magnetic correlations relies on modelling techniques such as reverse Monte-Carlo methods, which require knowledge about the exact ordered atomic structure. Here, we present a method for direct reconstruction of magnetic correlations in frustrated magnets by three-dimensional difference pair distribution function analysis of neutron total scattering data. The methodology is applied to the disordered frustrated magnet bixbyite, (Mn 1– x Fe x ) 2 O 3 , which reveals nearest-neighbor antiferromagnetic correlations for the metal sites up to a range of approximately 15 Å. Pertinently, this technique allows for magnetic correlations to be determined directly from the experimental data without any assumption about the atomic structure.

36 MATERIALS SCIENCE↗
DOE OSTI2011

Elucidating the structure of surface acid sites on {gamma}-Al{sub 2}O{sub 3}.

Differential pair distribution function analysis was applied to resolve, with crystallographic detail, the structure of catalytic sites on the surface of nanoscale {gamma}-Al{sup 2}O{sub 3}. The structure was determined for a basic probe molecule, monomethylamine (MMA), bound at the minority Lewis acid sites. These active sites were found to be five-coordinate, forming distorted octahedra upon MMA binding. This approach could be applied to study the interaction of molecules at surfaces in dye-sensitized solar cells, nanoparticles, sensors, materials for waste remediation, and catalysts.

14 SOLAR ENERGY↗
DOE OSTI2024

Suppressed Lone Pair Electrons Explain Unconventional Rise of Lattice Thermal Conductivity in Defective Crystalline Solids

Manipulating thermal properties of materials can be interpreted as the control of how vibrations of atoms (known as phonons) scatter in a crystal lattice. Compared to a perfect crystal, crystalline solids with defects are expected to have shorter phonon mean free paths caused by point defect scattering, leading to lower lattice thermal conductivities than those without defects. While this is true in many cases, alloying can increase the phonon mean free path in the Cd-doped AgSnSbSe 3 system to increase the lattice thermal conductivity from 0.65 to 1.05 W m –1 K –1 by replacing 18% of the Sb sites with Cd. It is found that the presence of lone pair electrons leads to the off-centering of cations from the centrosymmetric position of a cubic lattice. X-ray pair distribution function analysis reveals that this structural distortion is relieved when the electronic configuration of the dopant element cannot produce lone pair electrons. Furthermore, a decrease in the Grüneisen parameter with doping is experimentally confirmed, establishing a relationship between the stereochemical activity of lone pair electrons and the lattice anharmonicity. The observed “harmonic” behavior with doping suggests that lone pair electrons must be preserved to effectively suppress phonon transport in these systems.

36 MATERIALS SCIENCE↗
DOE OSTI2015

SU-E-T-760: Tolerance Design for Site-Specific Range in Proton Patient QA Process Using the Six Sigma Model

Purpose: To show how tolerance design and tolerancing approaches can be used to predict and improve the site-specific range in patient QA process in implementing the Six Sigma. Methods: In this study, patient QA plans were selected according to 6 site-treatment groups: head &neck (94 cases), spine (76 cases), lung (89 cases), liver (53 cases), pancreas (55 cases), and prostate (121 cases), treated between 2007 and 2013. We evaluated a model of the Six Sigma that determines allowable deviations in design parameters and process variables in patient-specific QA, where possible, tolerance may be loosened, then customized if it necessary to meet the functional requirements. A Six Sigma problem-solving methodology is known as DMAIC phases, which are used stand for: Define a problem or improvement opportunity, Measure process performance, Analyze the process to determine the root causes of poor performance, Improve the process by fixing root causes, Control the improved process to hold the gains. Results: The process capability for patient-specific range QA is 0.65 with only ±1 mm of tolerance criteria. Our results suggested the tolerance level of ±2–3 mm for prostate and liver cases and ±5 mm for lung cases. We found that customized tolerance between calculated and measured range reduce that patient QA plan failure and almost all sites had failure rates less than 1%. The average QA time also improved from 2 hr to less than 1 hr for all including planning and converting process, depth-dose measurement and evaluation. Conclusion: The objective of tolerance design is to achieve optimization beyond that obtained through QA process improvement and statistical analysis function detailing to implement a Six Sigma capable design.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2014

MicroRNA-490-3p inhibits proliferation of A549 lung cancer cells by targeting CCND1

Highlights: • We examined the level of miR-490-3p in A549 lung cancer cells compared with normal bronchial epithelial cell line. • We are the first to show the function of miR-490-3p in A549 lung cancer cells. • We demonstrate CCND1 may be one of the targets of miR-490-3p. - Abstract: MicroRNAs (miRNAs) are small non-coding RNAs that negatively regulate the translation of messenger RNAs by binding their 3′-untranslated region (3′UTR). In this study, we found that miR-490-3p is significantly down-regulated in A549 lung cancer cells compared with the normal bronchial epithelial cell line. To better characterize the role of miR-490-3p in A549 cells, we performed a gain-of-function analysis by transfecting the A549 cells with chemically synthesized miR-490-3P mimics. Overexpression of miR-490-3P evidently inhibits cell proliferation via G1-phase arrest. We also found that forced expression of miR-490-3P decreased both mRNA and protein levels of CCND1, which plays a key role in G1/S phase transition. In addition, the dual-luciferase reporter assays indicated that miR-490-3P directly targets CCND1 through binding its 3′UTR. These findings indicated miR-490-3P could be a potential suppressor of cellular proliferation.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2014

Local atomic structure of K{sub x}Na{sub (1−x)}NbO{sub 3} by total x-ray diffraction

Local atomic structure of K{sub x}Na{sub (1−x)}NbO{sub 3} with 0.0 ≤ x ≤ 1.0 was studied using atomic Pair Distribution Function analysis based on x-ray diffraction. Powdered crystals were found to exhibit a re-entrant behavior by being orthorhombic (Amm2) for x < 0.42, monoclinic (Pm) for 0.42 ≤ x ≤ 0.63 and again orthorhombic (Amm2) for x > 0.63. Non-centrosymmetric structure of NaNbO{sub 3} (Amm2) was also evident in the piezoresponse force microscopy analysis revealing the presence of the ferroelectric domains and switching behavior. Lowering of the crystallographic symmetry for 0.42 ≤ x ≤ 0.63 is discussed in terms of differences in the sizes of Na{sup +} and K{sup +} ions and Na–O and K–O bond lengths. Besides being a bridging phase, as suggested by the previous studies on lead-based compositions, present study suggests that lower symmetry monoclinic phase of compositionally disordered perovskite solid solutions could also be a manifestation of the difference in the sizes of constituent ions and bond lengths.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗