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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 OSTI2024

RNA language models predict mutations that improve RNA function

Structured RNA lies at the heart of many central biological processes, from gene expression to catalysis. RNA structure prediction is not yet possible due to a lack of high-quality reference data associated with organismal phenotypes that could inform RNA function. We present GARNET (Gtdb Acquired RNa with Environmental Temperatures), a new database for RNA structural and functional analysis anchored to the Genome Taxonomy Database (GTDB). GARNET links RNA sequences to experimental and predicted optimal growth temperatures of GTDB reference organisms. Using GARNET, we develop sequence- and structure-aware RNA generative models, with overlapping triplet tokenization providing optimal encoding for a GPT-like model. Leveraging hyperthermophilic RNAs in GARNET and these RNA generative models, we identify mutations in ribosomal RNA that confer increased thermostability to the Escherichia coli ribosome. The GTDB-derived data and deep learning models presented here provide a foundation for understanding the connections between RNA sequence, structure, and function.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

The AMPIX electrochemical cell: a versatile apparatus for in situ X-ray scattering and spectroscopic measurements

This article presents a versatile easy-to-use electrochemical cell suitable for in operando , in situ measurements of battery materials during electrochemical cycling using a variety of X-ray techniques. Argonne's multi-purpose in situ X-ray (AMPIX) cell provides reliable electrochemical cycling over extended periods owing to the uniform stack pressure applied by rigid X-ray windows and the formation of a high-fidelity hermetic seal. The suitability of the AMPIX cell for a broad range of synchrotron-based X-ray scattering and spectroscopic measurements has been demonstrated with studies at eight Advanced Photon Source beamlines to date. Compatible techniques include pair distribution function analysis, high-resolution powder diffraction, small-angle scattering and X-ray absorption spectroscopy. These techniques probe a broad range of electronic, structural and morphological features relevant to battery materials. The AMPIX cell enables experiments providing greater insight into the complex processes that occur in operating batteries by allowing the electrochemical reactions to be probed at fine reaction intervals with greater consistency (within the charge–discharge cycle and between different methodologies) with potential for new time-dependent kinetic studies or studies of transient species. Representative X-ray and electrochemical data to demonstrate the functionality of the AMPIX cell are presented.

energy storage (including batteries and capacitors↗
DOE OSTI2011

Effect of Temperature on the Local Structure of Kaolinite Intercalated with Potassium Acetate

Kaolinite intercalated with potassium acetate is of great interest in the areas of environmental remediation and industrial application; however, its exact atomic structure and the changes which occur when heated have remained largely elusive. Here, neutron pair distribution function analysis is used to investigate the local structural characteristics of this complex material, revealing that hydrated potassium acetate exists as a single layer in the interlamellar spacing of kaolinite. Furthermore, the potassium ions within the intercalated complex are most likely associated with the resonance structure of the acetate molecules, and upon heating (and decomposition of the carbon containing molecules), these ions become strongly associated with the negative charge located on the oxygen atoms in the alumina layers of dehydroxylated kaolinite. Several possible orientations of hydrated potassium acetate within the interlamellar spacing of kaolinite have been proposed and investigated using density functional modeling, revealing the complex nature of this material. Nevertheless, this investigation has shown that the dehydroxylated form of the intercalated compound contains highly strained alumina and available alkali (potassium), making it a viable alternative to traditional aluminosilicates.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2012

Orbital-selective magnetism in the spin-ladder iron selenides Ba[subscript 1;#8722;x]K[subscript x]Fe[subscript 2]Se[subscript 3]

Here we show that the 2.80(8){mu}{sub B} Fe{sup -1} block antiferromagnetic order of BaFe{sub 2}Se{sub 3} transforms into stripe antiferromagnetic order in KFe{sub 2}Se{sub 3} with a decrease in moment to 2.1(1){mu}{sub B} Fe{sup -1}. This reduction is larger than expected from the change in electron count from Ba{sup 2+} to K{sup +}, and occurs with the loss of the displacements of Fe atoms from ideal positions in the ladders, as found by neutron pair distribution function analysis. Intermediate compositions remain insulating, and magnetic susceptibility measurements show a suppression of magnetic order and probable formation of a spin glass. Together, these results imply an orbital-dependent selection of magnetic versus bonded behavior, driven by relative bandwidths and fillings.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2026

Numerical Analysis of Offshore Wind-Farm-Induced Drag Effects on Coastal Upwelling Dynamics

Wind farms extract momentum from the atmospheric flow, generating wind-speed deficits both within the plant, and extending downstream. When located offshore, these deficits modulate air-sea coupling, potentially impacting coastal upwelling in sensitive regions. We investigate impacts of wind farms on coastal upwelling using kilometre-scale, three-way-coupled simulations with the coupled ocean-atmosphere-wave-sediment transport system for the US West Coast. Wind-farm effects are represented by a generalised turbine drag formulation, an idealised, height-dependent body force whose magnitude is systematically varied. This approach isolates the leading-order fluid-dynamical response in a realistic coastal configuration. The atmospheric adjustment exhibits an approximately linear relation between drag force and wind-speed deficit, with wakes that expand downstream and increase in magnitude as drag increases. An empirical orthogonal function analysis of sea-surface-temperature anomalies reveals the emergence of a canonical dipole pattern under strong drag forcing. Subsurface diagnostics show consistent shoaling of the mixed layer and suppressed upward velocities in areas near wind-farm region, accompanied by compensating enhancements of shoaling closer to the coast. These results identify turbine drag as a control parameter in assessing interactions between wind-farm wake and coastal upwelling and provide scaling relationships for understanding offshore wind-farm effects on the coastal circulation dynamics.

16 TIDAL AND WAVE POWER↗
DOE OSTI2025

Structure-function studies of Vibrio cholerae quorum-sensing receptor CqsR signal recognition

Ethanolamine signaling through the transmembrane quorum-sensing receptor CqsR influencesVibrio choleraeniche recognition and host colonization. In this study, we present a comprehensive structure-function analysis of CqsR. Specifically, we have determined X-ray crystal structures of the CqsR periplasmic domain bound to the signaling agonist ethanolamine and its analogs, serinol and L-alaninol, as well as the ligand-free (apo) form of CqsR. The periplasmic ligand-binding domain of CqsR is a Cache domain, the most prevalent extracellular sensory module in prokaryotes. Our findings provide a rare structural comparison of ligand-bound and unbound states of a Cache domain receptor. Coupled with thermodynamic binding assays and genetic analyses, these structures elucidate the molecular basis of CqsR ligand specificity. This study not only advances the understanding of Cache domain function but also informs the identification of ligands for orphan Cache receptors and the rational design of signaling agonists and antagonists. Lastly, we discuss ligand-induced conformational changes in the CqsR Cache domains and explore the potential for the existence of additional regulatory ligands.

Microbiology↗
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↗