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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 289 records · Page 16
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

The early-stage growth and reversibility of Li electrodeposition in Br-rich electrolytes

Significance Spatial variations in chemical composition and transport properties of the material phases (interphases) formed on reactive metals in liquid electrolytes are thought to be responsible for the propensity of metal battery electrodes to electrodeposit in irregular, nonplanar morphologies. Equilibrium theoretical calculations using joint density functional analysis in vacuum and generic liquid media indicate that in-plane transport at such interphases is enhanced substantially if LiX (X = Br > Cl > F) species predominate. This study employs optical visualization experiments and nucleation theory to experimentally investigate nucleation and early-stage growth dynamics of metallic lithium in electrolytes enriched with LiBr. It is shown that the Li-Br–rich interphases formed profoundly alter the morphology of Li electrodeposits by enhancing Li-ion surface diffusion.

25 ENERGY STORAGE↗
DOE OSTI2022

Molecular determinants of pH sensing in the proton-activated chloride channel

In response to acidic pH, the widely expressed proton-activated chloride (PAC) channel opens and conducts anions across cellular membranes. By doing so, PAC plays an important role in both cellular physiology (endosome acidification) and diseases associated with tissue acidosis (acid-induced cell death). Despite the available structural information, how proton binding in the extracellular domain (ECD) leads to PAC channel opening remains largely unknown. Here, through comprehensive mutagenesis and electrophysiological studies, we identified several critical titratable residues, including two histidine residues (H130 and H131) and an aspartic acid residue (D269) at the distal end of the ECD, together with the previously characterized H98 at the transmembrane domain–ECD interface, as potential pH sensors for human PAC. Mutations of these residues resulted in significant changes in pH sensitivity. Some combined mutants also exhibited large basal PAC channel activities at neutral pH. By combining molecular dynamics simulations with structural and functional analysis, we further found that the β12 strand at the intersubunit interface and the associated “joint region” connecting the upper and lower ECDs allosterically regulate the proton-dependent PAC activation. Our studies suggest a distinct pH-sensing and gating mechanism of this new family of ion channels sensitive to acidic environment.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

The DESI DR1 peculiar velocity survey: growth rate measurements from the maximum likelihood fields method

We present the constraint on the growth rate of structure from the combination of DESI DR1 BGS sample, Fundamental Plane, and Tully-Fisher peculiar velocity catalogues using the maximum likelihood fields method. The combined catalogue contains 415,523 galaxy redshifts and 76,616 peculiar velocity measurements. To handle the large amount of data in the DESI DR1 peculiar velocity catalogue, we significantly improve the computational efficiency by rewriting the algorithm with JAX. After removing outliers and Tully-Fisher galaxies that are affected by systematics, we find fσ 8 = 0.483 -0.043 +0.080 (stat) ± 0.018(sys), consistent within 1σ with the power spectrum and correlation function analysis using the same dataset. Combining all three measurements with appropriate correlations, the consensus measurement is fσ 8 (z eff = 0.07) = 0.450±0.055, consistent with Planck +ΛCDM cosmology (fσ 8 = 0.449±0.008). Combining with the high redshift growth rate of structure measurements from DESI ShapeFit, the constraint on the growth index is γ = 0.58±0.11, consistent with GR.

cosmic flows↗
DOE OSTI2023

A gated graph transformer for protein complex structure quality assessment and its performance in CASP15

Abstract Motivation Proteins interact to form complexes to carry out essential biological functions. Computational methods such as AlphaFold-multimer have been developed to predict the quaternary structures of protein complexes. An important yet largely unsolved challenge in protein complex structure prediction is to accurately estimate the quality of predicted protein complex structures without any knowledge of the corresponding native structures. Such estimations can then be used to select high-quality predicted complex structures to facilitate biomedical research such as protein function analysis and drug discovery. Results In this work, we introduce a new gated neighborhood-modulating graph transformer to predict the quality of 3D protein complex structures. It incorporates node and edge gates within a graph transformer framework to control information flow during graph message passing. We trained, evaluated and tested the method (called DProQA) on newly-curated protein complex datasets before the 15th Critical Assessment of Techniques for Protein Structure Prediction (CASP15) and then blindly tested it in the 2022 CASP15 experiment. The method was ranked 3rd among the single-model quality assessment methods in CASP15 in terms of the ranking loss of TM-score on 36 complex targets. The rigorous internal and external experiments demonstrate that DProQA is effective in ranking protein complex structures. Availability and implementation The source code, data, and pre-trained models are available at https://github.com/jianlin-cheng/DProQA.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

GWAS identifies candidate genes controlling adventitious rooting in Populus trichocarpa

Adventitious rooting (AR) is critical to the propagation, breeding, and genetic engineering of trees. The capacity for plants to undergo this process is highly heritable and of a polygenic nature; however, the basis of its genetic variation is largely uncharacterized. To identify genetic regulators of AR, we performed a genome-wide association study (GWAS) using 1148 genotypes of Populus trichocarpa. GWASs are often limited by the abilities of researchers to collect precise phenotype data on a high-throughput scale; to help overcome this limitation, we developed a computer vision system to measure an array of traits related to adventitious root development in poplar, including temporal measures of lateral and basal root length and area. GWAS was performed using multiple methods and significance thresholds to handle non-normal phenotype statistics and to gain statistical power. These analyses yielded a total of 277 unique associations, suggesting that genes that control rooting include regulators of hormone signaling, cell division and structure, reactive oxygen species signaling, and other processes with known roles in root development. Numerous genes with uncharacterized functions and/or cryptic roles were also identified. These candidates provide targets for functional analysis, including physiological and epistatic analyses, to better characterize the complex polygenic regulation of AR.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Dark Energy Survey year 3 results: covariance modelling and its impact on parameter estimation and quality of fit

ABSTRACT We describe and test the fiducial covariance matrix model for the combined two-point function analysis of the Dark Energy Survey Year 3 (DES-Y3) data set. Using a variety of new ansatzes for covariance modelling and testing, we validate the assumptions and approximations of this model. These include the assumption of Gaussian likelihood, the trispectrum contribution to the covariance, the impact of evaluating the model at a wrong set of parameters, the impact of masking and survey geometry, deviations from Poissonian shot noise, galaxy weighting schemes, and other sub-dominant effects. We find that our covariance model is robust and that its approximations have little impact on goodness of fit and parameter estimation. The largest impact on best-fitting figure-of-merit arises from the so-called fsky approximation for dealing with finite survey area, which on average increases the χ2 between maximum posterior model and measurement by $3.7{{\ \rm per\ cent}}$ (Δχ2 ≈ 18.9). Standard methods to go beyond this approximation fail for DES-Y3, but we derive an approximate scheme to deal with these features. For parameter estimation, our ignorance of the exact parameters at which to evaluate our covariance model causes the dominant effect. We find that it increases the scatter of maximum posterior values for Ωm and σ8 by about $3{{\ \rm per\ cent}}$ and for the dark energy equation-of-state parameter by about $5{{\ \rm per\ cent}}$.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

A near magnetic-to-kinetic energy equipartition flare from the relativistic jet in AO 0235 + 164 during 2013–2019

ABSTRACT We present the multiwavelength flaring activity of the blazar AO 0235 + 164 during its recent active period from 2013 to 2019. From a discrete correlation function analysis, we find a significant ($\gt 95~{{\ \rm per\ cent}}$) correlation between radio and gamma-ray light curves with flares at longer wavelengths following flares at shorter wavelengths. We identify a new jet component in 43 GHz Very Long Baseline Array data that was ejected from the radio core on MJD $57246^{+26}_{-30}$ (2015 August 12), during the peak of the 2015 radio flare. From the analysis of the jet component, we derived a Doppler factor of δvar = 28.5 ± 8.4, a bulk Lorentz factor of $\Gamma =16.8^{+3.6}_{-3.1}$, and an intrinsic viewing angle of $\theta _{\rm v}=1.42^{+1.07}_{-0.52}\textrm {~degrees}$. Investigation of the quasi-simultaneous radio data revealed a partially absorbed spectrum with the turnover frequency varying in the range of 10−70 GHz and the peak flux density varying in the range of 0.7−4 Jy. We find the synchrotron self-absorption magnetic field strength to be $B_{\rm SSA}=15.3^{+12.6}_{-14.0}\textrm {~mG}$ at the peak of the 2015 radio flare, which is comparable to the equipartition magnetic field strength of $B_{\rm EQ}=43.6^{+10.6}_{-10.4}\textrm {~mG}$ calculated for the same epoch. Additional analysis of the radio emission region in the relativistic jet of AO 0235 + 164 suggests that it did not significantly deviate from equipartition during its recent flaring activity.

Astronomy & Astrophysics↗
DOE OSTI2026

Predictive models of the genetic bases underlying budding yeast fitness in multiple environments

Abstract The ability of organisms to adapt and survive depends on the effects of genes and the environment on fitness. However, the multigenic nature of fitness and genotype-by-environment interactions hinder our understanding of the genetic basis of fitness. Here, we established fitness prediction models for 35 environments using machine learning and existing fitness data and different genetic variant types for a Saccharomyces cerevisiae population. Models revealed that the predictive ability of genetic variants varied across environments, with copy number variants explaining the majority of fitness variation in most cases. Model interpretation showed that different variant types identified distinct gene sets associated with predictive variants. These gene sets were significantly enriched in experimentally validated genes affecting fitness in only a subset of environments, indicating that many genes influencing fitness remain unexplored. Notably, non-experimentally validated genes were more important than validated ones for fitness predictions. Gene contributions to predictions were both isolate- and environment-dependent, pointing to gene-by-gene and gene-by-environment interactions. Furthermore, models uncovered experimentally validated and novel candidate genetic interactions for a well-characterized stress, the fungicide benomyl. These findings highlight the feasibility of identifying the genetic basis of fitness by using different genetic variant types and offer novel targets for future functional analysis.

DNA copy number variations↗
DOE OSTI2020

Nanoscale degeneracy lifting in a geometrically frustrated antiferromagnet

The local atomic and magnetic structures of the compounds A MnO 2 (A = Na, Cu), which realize a geometrically frustrated, spatially anisotropic triangular lattice of Mn spins, have been investigated by atomic and magnetic pair distribution function analysis of neutron total scattering data. Relief of frustration in CuMnO 2 is accompanied by a conventional cooperative symmetry-lowering lattice distortion driven by Néel order. In NaMnO 2 , however, the distortion has a short-range nature. A cooperative interaction between the locally broken symmetry and short-range magnetic correlations lifts the magnetic degeneracy on a nanometer length scale, enabling long-range magnetic order in the Na derivative. The degree of frustration, mediated by residual disorder, contributes to the rather differing pathways to a single, stable magnetic ground state in these two related compounds. This study demonstrates how nanoscale structural distortions that cause local-scale perturbations can lift the ground-state degeneracy and trigger macroscopic magnetic order.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Lattice symmetry breaking transition and critical size limit for ferroic orders in nanophase BiFeO3

Finite size effects on the ferroic orders in BiFeO 3 are studied by atomic pair distribution function analysis and magnetic measurements. While bulk rhombohedral BiFeO 3 exhibits ferroelectricity and antiferromagnetism with a cycloidal magnetic moment arrangement leading to zero magnetization and weak magnetoelectric coupling, BiFeO 3 nanoparticles with a size smaller than the spin cycloid period of 62 nm preserve their polar rhombohedral structure and develop ferromagnetism, thus exhibiting coexisting polarization and nonzero magnetization that enhances the magnetoelectric coupling. When the nanoparticles become smaller than 17 nm, however, their crystal lattice expands and becomes nonpolar cubic. They also become superparamagnetic and thus simultaneously cease exhibiting both ferroelectricity and ferromagnetism. Our findings shed light on the interaction between the lattice structure and ferroic orders in nanophase perovskites and also provide a rare example of a lattice symmetry breaking phase transition that determines their critical size.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Two-step charge density wave transition and hidden transient phase in 1 T – TiSe 2

Using variable temperature atomic pair distribution function analysis, we study the emergence of charge density wave (CDW) order in 1T-TiSe 2 and find that it takes place via a two-step transition. First, upon decreasing temperature to about 235(3) K, CDW related lattice distortions emerge in the individual TiSe 2 layers alone. Then, upon further decreasing the temperature, the two-dimensional distortions in the layers couple and the widely recognized three-dimensional 2a o x 2a o x 2c o superstructure emerges at about 205(3) K. Because two different band gaps are known to emerge at the same temperatures, the finding indicates the presence of strong electron-phonon coupling. The transient phase between the two steps lacks inversion symmetry and may serve as a precursor of the debated chiral 1T-TiSe 2 phase. Finally, our findings are important for the understanding of the enigmatic CDW transition in 1T-TiSe 2 and CDW instabilities in van der Waals materials in general.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Local spin structure in the layered van der Waals materials MnPS 𝑥 ⁢Se 3−𝑥

Two-dimensional (2D) layered materials, whether in bulk form or reduced to just a single layer, have potential applications in spintronics and capacity for advanced quantum phenomena. A prerequisite for harnessing these opportunities lies in gaining a comprehensive understanding of the spin behavior in 2D materials. The low dimensionality motivates an understanding of the spin correlations over a wide length scale, from local to long-range order. In this context, we focus on the magnetism in bulk MnPSe 3 and MnPS 3 , 2D layered van der Waals antiferromagnetic semiconductors. These materials have similar honeycomb Mn layers and magnetic ordering temperatures, but distinct spin orientations and exchange interactions. Here, we utilize neutron scattering to gain deeper insights into the local magnetic structures and spin correlations in the paramagnetic and ordered phases by systematically investigating a MnPS 𝑥 ⁢Se 3−𝑥 (𝑥 = 0, 1, 1.5, 2, 3) series of powder samples using total neutron scattering measurements. By employing magnetic pair distribution function analysis, we unraveled the short-range magnetic correlations in these materials and explored how the nonmagnetic anion S/Se mixing impacts the magnetic correlations. The results reveal that the magnetism can be gradually tuned through alteration of the nonmagnetic S/Se content, which tunes the atomic structure. The change in magnetic structure is also accompanied by a control of the magnetic correlation length within the 2D honeycomb layers. Complimentary inelastic neutron scattering measurements allowed a quantification of the change in the magnetic exchange interactions for the series and further highlighted the gradual evolution of spin interactions in the series MnPS 𝑥 ⁢Se 3−𝑥 .

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Nanoscale structural correlations in a model cuprate superconductor

Understanding the extent and role of inhomogeneity is a pivotal challenge in the physics of cuprate superconductors. While it is known that structural and electronic inhomogeneity is prevalent in the cuprates, it has proven difficult to disentangle compound-specific features from universally relevant effects. Here, in this study, we combine advanced neutron and x-ray diffuse scattering with numerical modeling to obtain insight into bulk structural correlations in HgBa 2 ⁢ CuO 4+δ . This cuprate exhibits a high optimal transition temperature of nearly 100 K, pristine charge-transport behavior, and a simple average crystal structure without long-range structural instabilities, and is therefore uniquely suited for investigations of intrinsic inhomogeneity. We uncover diffuse reciprocal-space patterns that correspond to prominent nanoscale correlations of atomic displacements perpendicular to the CuO 2 planes. The real-space nature of the correlations is revealed through three-dimensional pair distribution function analysis and complementary numerical refinement. We find that relative displacements of ionic and CuO 2 layers play a crucial role, and that the structural inhomogeneity is not directly caused by the presence of conventional point defects. The observed correlations are therefore intrinsic to HgBa 2 ⁢ CuO 4+δ , and thus likely important for the physics of cuprates more broadly. It is possible that the structural correlations are closely related to the unusual superconducting fluctuations and Mott-localization in these complex oxides. As advances in scattering techniques yield increasingly comprehensive data, the experimental and analysis tools developed here for large volumes of diffuse scattering data can be expected to aid future investigations of a wide range of materials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Evaluating the effects of structural disorder on the magnetic properties of Nd 2 Zr 2 O 7

Motivated by the variation in reported lattice parameters of floating-zone-grown Nd 2 Zr 2 O 7 crystals, we have performed a detailed study of the relationship between synthesis environment, structural disorder, and magnetic properties. Using a combination of polycrystalline standards, electron-probe microanalysis, and scattering techniques, we show that crystals grown under atmospheric conditions have a reduced lattice parameter relative to pristine polycrystalline powders due to occupation of the Nd site by excess Zr (i.e., negative stuffing). In contrast, crystals grown under high-pressure Ar are nearly stoichiometric with an average lattice parameter approaching the polycrystalline value. While minimal disorder of the oxygen sublattices is observed on the scale of the average structure, neutron pair-distribution function analysis indicates a highly local disorder of the oxygen coordination, which is only weakly dependent on growth environment. Most importantly, our magnetization, heat capacity, and single-crystal neutron scattering data show that the magnetic properties of crystals grown under high-pressure Ar match closely with those of stoichiometric powders. Neutron scattering measurements reveal that the signature of magnetic moment fragmentation—the coexistence of all-in-all-out (AIAO) magnetic Bragg peaks and diffuse pinch-point scattering due to spin-ice correlations–persists in these nearly stoichiometric crystals. However, in addition to an increased AIAO transition temperature, the diffuse signal is seemingly stabilized and remains nearly unchanged upon warming to 800 mK. This behavior indicates that both the AIAO magnetic order and spin-ice correlations are sensitive to deviations of the Nd stoichiometry.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Chemical compression and ferroic orders in La substituted BiFe O 3

Chemical compression effects on the ferroic orders in La substituted BiFeO 3 are studied by atomic pair distribution function analysis and structure modeling. While rhombohedral BiFeO 3 exhibits ferroelectricity and antiferromagnetism (AF) with a cycloidal Fe spin arrangement leading to zero magnetization, La substituted BiFeO 3 exhibits a reduced lattice polarization, strengthened AF order, and an apparently suppressed spin cycloid leading to nonzero magnetization. Furthermore, the observed changes in the ferroic orders arise from the chemical compression induced changes in the octahedral rotation and ferroelectric displacement of Bi atoms, which appear as lattice degrees of freedom entangling the electronic and magnetic orders in BiFeO 3 .

36 MATERIALS SCIENCE↗
DOE OSTI2020

Distributed Many-to-Many Protein Sequence Alignment using Sparse Matrices

Identifying similar protein sequences is a core step in many computational biology pipelines such as detection of homologous protein sequences, generation of similarity protein graphs for downstream analysis, functional annotation, and gene location. Performance and scalability of protein similarity search have proven to be a bottleneck in many bioinformatics pipelines due to increase in cheap and abundant sequencing data. This work presents a new distributed-memory software PASTIS. PASTIS relies on sparse matrix computations for efficient identification of possibly similar proteins. We use distributed sparse matrices for scalability and show that the sparse matrix infrastructure is a great fit for protein similarity search when coupled with a fully-distributed dictionary of sequences that allow remote sequence requests to be fulfilled. Our algorithm incorporates the unique bias in amino acid sequence substitution in search without altering basic sparse matrix model, and in turn, achieves ideal scaling up to millions of protein sequences.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Use of virus‐induced gene silencing to characterize genes involved in modulating hypersensitive cell death in maize

Abstract Plant disease resistance proteins (R‐proteins) detect specific pathogen‐derived molecules, triggering a defence response often including a rapid localized cell death at the point of pathogen penetration called the hypersensitive response (HR). The maize Rp1‐D21 gene encodes a protein that triggers a spontaneous HR causing spots on leaves in the absence of any pathogen. Previously, we used fine mapping and functional analysis in a Nicotiana benthamiana transient expression system to identify and characterize a number of genes associated with variation in Rp1‐D21 ‐induced HR. Here we describe a system for characterizing genes mediating HR, using virus‐induced gene silencing (VIGS) in a maize line carrying Rp1‐D21 . We assess the roles of 12 candidate genes. Three of these genes, SGT1 , RAR1 , and HSP90 , are required for HR induced by a number of R‐proteins across several plant–pathogen systems. We confirmed that maize HSP90 was required for full Rp1‐D21 ‐induced HR. However, suppression of SGT1 expression unexpectedly increased the severity of Rp1‐D21 ‐induced HR while suppression of RAR1 expression had no measurable effect. We confirmed the effects on HR of two genes we had previously validated in the N. benthamiana system, hydroxycinnamoyltransferase and caffeoyl CoA O‐methyltransferase . We further showed the suppression the expression of two previously uncharacterized, candidate genes, IQ calmodulin binding protein ( IQM3 ) and vacuolar protein sorting protein 37 , suppressed Rp1‐D21 ‐induced HR. This approach is an efficient way to characterize the roles of genes modulating the hypersensitive defence response and other dominant lesion phenotypes in maize.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Nannochloropsis oceanica IMET1 and its bacterial symbionts for carbon capture, utilization, and storage: biomass and calcium carbonate production under high pH and high alkalinity

ABSTRACT To combat the increasing levels of carbon dioxide (CO 2 ) released from the combustion of fossil fuels, microalgae have emerged as a promising strategy for biological carbon capture, utilization, and storage. This study used a marine microalgal strain, Nannochloropsis oceanica IMET1, which thrives in high CO 2 concentrations. A high-pH, high-alkalinity culture was designed for CO 2 capture through algal biomass production as well as permanent sequestration through calcium carbonate (CaCO 3 ) precipitation. This was accomplished by timed pH elevation and the addition of sodium bicarbonate to cultures of N. oceanica grown at lab scale (1 L) and pilot scale (500 L) with 10% and 5% CO 2 , respectively. Our data showed that 0.02 M NaHCO 3 promoted algal growth and that sparging cultures with ambient air after 12 days raised pH and created favorable CaCO 3 formation conditions. At the 1 L scale, we reached 1.52 g L −1 biomass after 12 days and an extra 9.3% CO 2 was captured in the form of CaCO 3 precipitates. At the 500 L pilot scale, an extra 60% CO 2 was captured (Day 40) with a maximum CO 2 capture rate of 63.2 g m −2 day −1 (Day 35). Bacterial communities associated with the microalgae were dominated by two novel Patescibacteria. Functional analysis revealed that genes for several plant growth-promotion traits (PGPTs) were enriched within this group. The microalgal-bacterial coculture system offers advantages for enhanced carbon mitigation through biomass production and simultaneous precipitation of recalcitrant CaCO 3 for long-term CO 2 storage. IMPORTANCE Capturing carbon dioxide (CO 2 ) released from fossil fuel combustion is of the utmost importance as the impacts of climate change continue to worsen. Microalgae can remove CO 2 through their natural photosynthetic pathways and are additionally able to convert CO 2 into a stable, recalcitrant form as calcium carbonate (CaCO 3 ). We demonstrate that microalgae-based carbon capture systems can be greatly improved with high pH and high alkalinity by providing optimal conditions for carbonate precipitation. Our results with the microalga, Nannochloropsis oceanica strain IMET1, show an extra 9.3% CO 2 captured as CaCO 3 at the 1 L scale and an extra 60% CO 2 captured at the 500 L (pilot) scale. Our optimized system provides a novel approach to capture CO 2 through two mechanisms: (i) as organic carbon within microalgal biomass and (ii) as inorganic carbon stored permanently in the form of CaCO 3.

20 FOSSIL-FUELED POWER PLANTS↗