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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 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Quantifying resolution in cosmological N- body simulations using self-similarity

ABSTRACT We demonstrate that testing for self-similarity in scale-free simulations provides an excellent tool to quantify the resolution at small scales of cosmological N-body simulations. Analysing two-point correlation functions measured in simulations using abacus , we show how observed deviations from self-similarity reveal the range of time and distance scales in which convergence is obtained. While the well-converged scales show accuracy below 1 per cent, our results show that, with a small force softening length, the spatial resolution is essentially determined by the mass resolution. At later times, the lower cut-off scale on convergence evolves in comoving units as a−1/2 (a being the scale factor), consistent with a hypothesis that it is set by two-body collisionality. A corollary of our results is that N-body simulations, particularly at high red-shift, contain a significant spatial range in which clustering appears converged with respect to the time-stepping and force softening but has not actually converged to the physical continuum result. The method developed can be applied to determine the resolution of any clustering statistic and extended to infer resolution limits for non-scale-free simulations.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Testing dark matter halo properties using self-similarity

ABSTRACT We use self-similarity in N-body simulations of scale-free models to test for resolution dependence in the mass function and two-point correlation functions of dark matter haloes. We use 10243 particle simulations performed with abacus , and compare results obtained with two halo finders: friends-of-friends (fof ), and rockstar . The fof mass functions show a systematic deviation from self-similarity which is explained by resolution dependence of the fof mass assignment previously reported in the literature. Weak evidence for convergence is observed only starting from haloes of several thousand particles, and mass functions are overestimated by at least as much as $20-25{{\ \rm per\ cent}}$ for haloes of 50 particles. The mass function of the default rockstar halo catalogue (with bound virial spherical overdensity mass), on the other hand, shows good convergence of the order of 50 to 100 particles per halo, with no detectable evidence at the few percent level of any systematic dependence for larger particle number. Tests show that the mass unbinding procedure in rockstar is the key factor in obtaining this much improved resolution. Applying the same analysis to the halo–halo two point correlation function, we find again strong evidence for convergence only for rockstar haloes, at separations sufficiently large so that haloes do not overlap. At these separations, we can exclude dependence on resolution at the $5-10{{\ \rm per\ cent}}$ level once haloes have of the order of 50 to 100 particles. At smaller separations results are not converged even at significantly larger particle number, and bigger simulations would be required to establish the resolution required for convergence.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Similarities behind the high- and low- α disc: small intrinsic abundance scatter and migrating stars

The detailed age-chemical abundance relations of stars measure time-dependent chemical evolution. These trends offer strong empirical constraints on nucleosynthetic processes, as well as the homogeneity of star-forming gas. Characterizing chemical abundances of stars across the Milky Way over time has been made possible very recently, thanks to surveys like Gaia , APOGEE, and Kepler . Studies of the low- α disc have shown that individual elements have unique age–abundance trends and the intrinsic dispersion around these relations is small. In this study, we examine and compare the age distribution of stars across both the high and low- α disc and quantify the intrinsic dispersion of 16 elements around their age–abundance relations at [Fe/H] = 0 using APOGEE DR16. Here, we examine the age–metallicity relation and visualize the temporal and spatial distribution of disc stars in small chemical cells. We find: (1) the high- α disc has shallower age–abundance relations compared to the low- α disc, but similar median intrinsic dispersions of ~0.03 dex; (2) turnover points in the age-[Fe/H] relations across radius for both the high- and low- α disc. The former constrains the mechanisms that set similar intrinsic dispersions, regardless of differences in the enrichment history, for stars in both disc, and the latter indicates the presence of radial migration in both disc. Our study is accompanied by an age catalogue for 64 317 stars in APOGEE derived using THE CANNON with a median uncertainty of 1.5 Gyr (26 per cent; APO-CAN stars), and a red clump catalogue of 22 031 stars with a contamination rate of 2.7 per cent.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Two self-similar Reynolds-stress transport models with anisotropic eddy viscosity

Two Reynolds-averaged Navier-Stokes models with full Reynolds-stress transport (RST) and tensor eddy viscosity are presented. These new models represent RST extensions of the $k−2L−a−\mathscr{C}$ and $k−ϕ−L−a−\mathscr{C}$ models by Morgan. Self-similarity analysis is used to derive constraints on model coefficients required to reproduce expected growth parameters for a variety of canonical flows, including Rayleigh-Taylor (RT) and Kelvin-Helmholtz (KH) mixing layers. Both models are then applied in one-dimensional simulation of RT and KH mixing layers, and the expected self-similar growth rates and anisotropy are obtained. Next, models are applied in two-dimensional simulation of the so-called “tilted rocket rig” inclined RT experiment and in simulation of a shock-accelerated localized patch of turbulence. Here it is found that RST is required to capture the qualitative growth of the shock-accelerated patch, and an anisotropic eddy viscosity provides substantial improvement over a Boussinesq treatment for the tilted rocket rig problem.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2026

Spectral Similarity Masks Structural Diversity at Hydrophobic Water Interfaces

The air-water and graphene-water interfaces represent quintessential examples of the liquid-gas and liquid-solid boundaries, respectively. While the sum-frequency generation (SFG) spectra of these interfaces show similarities, a consensus on their signals and interpretations has yet to be reached. Leveraging deep learning, we computed first-principles SFG spectra for both systems, addressing experimental discrepancies. Here, our findings reveal that similarities in SFG signals do not translate into comparable interfacial microscopic properties. Instead, graphene-water and air-water interfaces exhibit fundamental differences in SFG-active thicknesses, hydrogen-bonding networks, and surface dynamics. These distinctions underscore roughness suppression and electronic interactions present at the solid-liquid interface but absent at the gas-liquid interface.

Wang, Yong [Princeton Univ., NJ (United States)] (↗
DOE OSTI2024

Efficient graph representation framework for chemical molecule similarity tasks

Graph data has emerged in numerous scientific domains and machine learning techniques have been widely used for analysis and learning of diverse data for prediction and decision. Machine learning techniques can readily address complex problems by leveraging their structural information. But graphs cannot be directly used for existing machine learning algorithms unless encoded as vectors. The problem of efficient representation of graphs is a substantial challenge in graph machine learning. In this paper, we propose a novel two-stage framework for the representation of chemical molecule graphs based on the strengths of Graph Isomorphism Networks (GINs) and Siamese autoencoders. In the first stage, the GIN model is constructed and trained using the structural information of chemical molecule graphs. Node attributes, edge attributes, and edge indices are used as input data, while graph attributes are used as labels. The GIN model effectively captures the structural characteristics of graphs and can accurately predict graph attributes, i.e., molecular properties. It also generates Graph Embeddings, represented as vectors that encode the structural information of graphs. In the second stage, Graph Embedding vectors are further optimized for downstream similarity tasks while preserving the graph structural information. The Siamese autoencoder is constructed and trained, which reduces the dimensionality of the Graph Embedding vectors, while maximizing the preservation of structural information in the original high-dimensional vectors. The resulting low-dimensional Graph Embeddings can be effectively utilized for tasks such as approximate nearest neighbor search. The experimental results demonstrate the effectiveness of our proposed framework in accurately predicting graph similarity.

Ma, Jiaji↗
DOE OSTI2024

Improving Property Graph Layouts by Leveraging Attribute Similarity for Structurally Equivalent Nodes

Many real-world networks contain structurally-equivalent nodes. These are defined as vertices that share the same set of neighboring nodes, making them interchangeable with a traditional graph layout approach. However, many real-world graphs also have properties associated with nodes, adding additional meaning to them. We present an approach for swapping locations of structurally-equivalent nodes in graph layout so that those with more similar properties have closer proximity to each other. This improves the usefulness of the visualization from an attribute perspective without negatively impacting the visualization from a structural perspective. We include an algorithm for finding these sets of nodes in linear time, as well as methodologies for ordering nodes based on their attribute similarity, which works for scalar, ordinal, multidimensional, and categorical data.

graph drawing, network visualization, property gra↗
DOE OSTI2023

Precursor recommendation for inorganic synthesis by machine learning materials similarity from scientific literature

Synthesis prediction is a key accelerator for the rapid design of advanced materials. However, determining synthesis variables such as the choice of precursor materials is challenging for inorganic materials because the sequence of reactions during heating is not well understood. In this work, we use a knowledge base of 29,900 solid-state synthesis recipes, text-mined from the scientific literature, to automatically learn which precursors to recommend for the synthesis of a novel target material. The data-driven approach learns chemical similarity of materials and refers the synthesis of a new target to precedent synthesis procedures of similar materials, mimicking human synthesis design. When proposing five precursor sets for each of 2654 unseen test target materials, the recommendation strategy achieves a success rate of at least 82%. Our approach captures decades of heuristic synthesis data in a mathematical form, making it accessible for use in recommendation engines and autonomous laboratories.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Bovine adapted transmissible mink encephalopathy is similar to L-BSE after passage through sheep with the VRQ/VRQ genotype but not VRQ/ARQ

Background: Transmissible mink encephalopathy (TME) is a fatal neurologic disease of farmed mink. Evidence indicates that TME and L-BSE are similar and may be linked in some outbreaks of TME. We previously transmitted bovine adapted TME (bTME) to sheep. The present study compared ovine passaged bTME (o-bTME) to C-BSE and L-BSE in transgenic mice expressing wild type bovine prion protein (TgBovXV). To directly compare the transmission efficiency of all prion strains in this study, we considered the attack rates and mean incubation periods. Additional methods for strain comparison were utilized including lesion profiles, fibril stability, and western blotting. Results: Sheep donor genotype elicited variable disease phenotypes in bovinized mice. Inoculum derived from a sheep with the VRQ/VRQ genotype (o-bTME VV ) resulted in an attack rate, incubation period, western blot profile, and neuropathology most similar to bTME and L-BSE. Conversely, donor material from a sheep with the VRQ/ARQ genotype (o-bTME AV ) elicited a phenotype distinct from o-bTME VV , bTME and L-BSE. The TSE with the highest transmission efficiency in bovinized mice was L-BSE. The tendency to efficiently transmit to TgBovXV mice decreased in the order bTME, C-BSE, o-bTME VV , and o-bTME AV . The transmission efficiency of L-BSE was approximately 1.3 times higher than o-bTMEVV and 3.2 times higher than o-bTME AV . Conclusions: Our findings provide insight on how sheep host genotype modulates strain genesis and influences interspecies transmission characteristics. Given that the transmission efficiencies of L-BSE and bTME are higher than C-BSE, coupled with previous reports of L-BSE transmission to mice expressing the human prion protein, continued monitoring for atypical BSE is advisable in order to prevent occurrences of interspecies transmission that may affect humans or other species.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Data from: "Lab and Field Warming Similarly Advance Germination Date and Limit Germination Rate for High and Low Elevation Provenances of Two Widespread Subalpine Conifers"

This archive contains data used to draw conclusions in “Lab and Field Warming Similarly Advance Germination Date and Limit Germination Rate for High and Low Elevation Provenances of Two Widespread Subalpine Conifers”, by Kueppers et al. 2017. Cone collection and field experiments were conducted on Niwot Ridge, Colorado, with the latter completed within the Alpine Treeline Warming Experiment (ATWE). Laboratory germination experiments were conducted at the University of California Merced. Geospatial files are also provided for additional geographical context.There are four data file formats in this package: comma-separated values (.csv), Microsoft Excel (.xlsx), keyhole markup language (.kml), and ESRI shapefile (.shp). The latter two are geospatial file formats. .csv files can be opened using any simple text editor program such as TextEdit (Mac) and Notepad (Windows), and .xlsx files can be opened using Microsoft Excel or Google Sheets. The .kml file contains coordinate data, and is compatible with Google Earth and Google Maps. ESRI shapefiles (.shp) are compatible with any geospatial software able to read the file type, such as QGIS and ESRI’s ArcGIS Suite. This data user’s guide is available in as a .pdf, and can be opened using software such as Adobe Acrobat Reader.-----------------------------------------------------------------------------------------------------------------------------------Accurately predicting upslope shifts in subalpine tree ranges with warming requires understanding how future forest populations will be affected by climate change, as these are the seed sources for new tree line and alpine populations. Early life history stages are particularly sensitive to climate and are also influenced by genetic variation among populations. We tested the climate sensitivity of germination and initial development for two widely distributed subalpine conifers, using controlled-environment growth chambers with one temperature regime from subalpine forest in the Colorado Rocky Mountains and one 5 °C warmer, and two soil moisture levels. We tracked germination rate and timing, rate of seedling development, and seedling morphology for two seed provenances separated by ~300 m elevation. Warming advanced germination timing and initial seedling development by a total of ~2 weeks, advances comparable to mean differences between provenances. Advances were similar for both provenances and species; however, warming reduced the overall germination rate, as did low soil moisture, only for Picea engelmannii. A three-year field warming and watering experiment planted with the same species and provenances yielded responses qualitatively consistent with the lab trials. Together these experiments indicate that in a warmer, drier climate, P. engelmannii germination, and thus regeneration, could decline, which could lead to declining subalpine forest populations, while Pinus flexilis forest populations could remain robust as a seed source for upslope range shifts.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Impact of Thermal Scattering Law on Similarity Assessment in Light-Water or Polyethylene-Moderated Systems [Slides]

This presentation found validation efforts revealed noticeable differences in c k for light-water and polyethylene moderated systems when compared to PST-002-001. Additionally, although 1 H-H 2 O and 1 H-poly use the same cross section and covariance data, the treatment of TSLs in SCALE lead to no contribution to ck between polyethylene application and benchmark experiment. When H 2 O contribution were removed the difference in c k appears to come from 239 Pu chi. Sensitivity profiles and data-induced uncertainty confirmed that the polyethylene application was more closely resembling the benchmark experiment. Specific differences between similar systems can be accounted for and examined to help understand differences in similarity (c k ) between systems was a conclusion reached by this presentation.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

Investigating Similarity Differences for Light-Water-Moderated and Polyethylene-Moderated Systems [Slides]

Validation efforts revealed noticeable differences in c k for light-water and polyethylene moderated systems when compared to experimental systems. Although 1 H-H 2 O and 1 H-poly use some of the same cross section and identical covariance data, the treatment of TSLs in SCALE lead to no contribution to c k between polyethylene application and benchmark experiment. When H 2 O contribution is removed the difference in c k appears to come from 239 Pu chi. Sensitivity profiles and data-induced uncertainty confirm that the polyethylene application more closely resembles the benchmark experiment. Interrogation techniques were used to observe how TSLs and nuclide IDs affect c k . Specific differences between similar systems can be accounted for and examined to help understand differences in similarity (c k ) between systems

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Intestinal single-cell atlas reveals novel lymphocytes in pigs with similarities to human cells

Lymphocytes can heavily influence intestinal health, but resolving intestinal lymphocyte function is challenging as the intestine contains a vastly heterogeneous mixture of cells. Pigs are an advantageous biomedical model, but deeper understanding of intestinal lymphocytes is warranted to improve model utility. Twenty-six cell types were identified in the porcine ileum by single-cell RNA sequencing and further compared with cells in human and murine ileum. Though general consensus of cell subsets across species was revealed, some porcine-specific lymphocyte subsets were identified. Differential tissue dissection and in situ analyses conferred spatial context, revealing similar locations of lymphocyte subsets in Peyer’s patches and epithelium in pig-to-human comparisons. Like humans, activated and effector lymphocytes were abundant in the ileum but not periphery of pigs, suggesting tissue-specific and/or activation-associated gene expression. Gene signatures for peripheral and ileal innate lymphoid cells newly discovered in pigs were defined and highlighted similarities to human innate lymphoid cells. Overall, we reveal novel lymphocyte subsets in pigs and highlight utility of pigs for intestinal research applications.

Life Sciences & Biomedicine - Other Topics↗
DOE OSTI2026

Beyond sequence similarity: toward function-based screening of nucleic acid synthesis

Synthetic nucleic acids are a key input to modern biotechnology, yet they represent dual-use materials that require robust screening to mitigate biosecurity risks. The prevailing screening paradigm, which identifies sequences of concern (SoCs) through sequence similarity to controlled pathogens and toxins, may not fully capture risks posed by AI tools that can decouple biomolecular function from reliance on known sequences. Rapidly advancing biodesign capabilities enable the generation of genes and proteins that might evade sequence-based detection. We highlight the critical need for function-based screening approaches that can detect sequences capable of hazardous biological functions, regardless of similarity to known SoCs. We examine the feasibility of function-based screening with an initial focus on proteins, arguing that, while protein sequence space is vast, biologically functional proteins are significantly constrained by biophysical and biochemical requirements that can be learned and modeled. We propose a concrete implementation framework organized along a continuum of complexity, starting with toxins as the most tractable targets before expanding to more complex pathogenic functions. We then discuss open challenges and describe a research and development strategy to address them.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Similarities and Differences in the Effects of Toxic Concentrations of Cadmium and Chromium on the Structure and Functions of Thylakoid Membranes in Chlorella variabilis

Trace metal contaminations in natural waters, wetlands, and wastewaters pose serious threats to aquatic ecosystems—mainly via targeting microalgae. In this work, we investigated the effects of toxic amounts of chromium and cadmium ions on the structure and function of the photosynthetic machinery of Chlorella variabilis cells. To halt the propagation of cells, we used high concentrations of Cd and Cr, 50–50 mg L –1 , in the forms of CdCl 2 x 2.5 H 2 O and K 2 Cr 2 O 7 , respectively. Both treatments led to similar, about 50% gradual diminishment of the chlorophyll contents of the cells in 48 h, which was, however, accompanied by a small (~10%) but statistically significant enrichment (Cd) and loss (Cr) of ß-carotene. Both Cd and Cr inhibited the activity of photosystem II (PSII)—but with more severe inhibitions with Cr. On the contrary, the PsbA (D1) protein of PSII and the PsbO protein of the oxygen-evolving complex were retained more in Cr-treated cells than in the presence of Cd. These data and the higher susceptibility of P700 redox transients in Cr-treated cells suggest that, unlike with Cd, PSII is not the main target in the photochemical apparatus. These differences at the level of photochemistry also brought about dissimilarities at higher levels of the structural complexity of the photosynthetic apparatus. Circular dichroism (CD) spectroscopy measurements revealed moderate perturbations in the macro-organization of the protein complexes—with more pronounced decline in Cd-treated cells than in the cells with Cr. Also, as reflected by transmission electron microscopy and small-angle neutron scattering, the thylakoid membranes suffered shrinking and were largely fragmented in Cd-treated cells, whereas no changes could be discerned with Cr. The preservation of integrity of membranes in Cr-treated cells was most probably aided by high proportion of the de-epoxidized xanthophylls, which were absent with Cd. It can thus be concluded that beside strong similarities of the toxic effects of Cr and Cd, the response of the photosynthetic machinery of C. variabilis to these two trace metal ions substantially differ from each other—strongly suggesting different inhibitory and protective mechanisms following the primary toxic events.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

HLA Class I Supertype Classification Based on Structural Similarity

HLA class I proteins, a critical component in adaptive immunity, bind and present intracellular Ags to CD8+ T cells. The extreme polymorphism of HLA genes and associated peptide binding specificities leads to challenges in various endeavors, including neoantigen vaccine development, disease association studies, and HLA typing. Supertype classification, defined by clustering functionally similar HLA alleles, has proven helpful in reducing the complexity of distinguishing alleles. However, determining supertypes via experiments is impractical, and current in silico classification methods exhibit limitations in stability and functional relevance. In this study, by incorporating three-dimensional structures we present a method for classifying HLA class I molecules with improved breadth, accuracy, stability, and flexibility. Critical for these advances is our finding that structural similarity highly correlates with peptide binding specificity. The new classification should be broadly useful in peptide-based vaccine development and HLA–disease association studies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

On the similarity of hillslope hydrologic function: a clustering approach based on groundwater changes

Abstract. Hillslope similarity is an active topic in hydrology because of its importance in improving our understanding of hydrologic processes and enabling comparisons and paired studies. In this study, we propose a holistic bottom-up hillslope clustering based on a region's integrative hydrodynamic response quantified by the seasonal changes in groundwater levels ΔP. The main advantage of the ΔP clustering is its ability to capture recharge and discharge processes. We test the performance of the ΔP clustering by comparing it to seven other common hillslope clustering approaches. These include clustering approaches based on the aridity index, topographic wetness index, elevation, land cover, and machine-learning that jointly integrate multiple data. We assess the ability of these clustering approaches to identify and categorize hillslopes with similar static characteristics, hydroclimate, land surface processes, and subsurface dynamics in a mountainous watershed – the East River – located in the headwaters of the Upper Colorado River Basin. The ΔP clustering performs very well in identifying hillslopes with six out of the nine characteristics studied. The variability among clusters as quantified by the coefficient of variation (0.2) is less in the ΔP and the machine learning approaches than in the others (> 0.3 for TWI, elevation, and land cover). We further demonstrate the robustness of the ΔP clustering by testing its ability to predict hillslope responses to wet and dry hydrologic conditions, of which it performs well when based on average conditions.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Detecting CAN Masquerade Attacks with Signal Clustering Similarity

Vehicular Controller Area Networks (CANs) are susceptible to cyber attacks of different levels of sophistication. Fabrication attacks are the easiest to administer—an adversary simply sends (extra) frames on a CAN—but also the easiest to detect because they disrupt frame frequency. To overcome time-based detection methods, adversaries must administer masquerade attacks by sending frames in lieu of (and therefore at the expected time of) benign frames but with malicious payloads. Research efforts have proven that CAN attacks, and masquerade attacks in particular, can affect vehicle functionality. Examples include causing unintended acceleration, deactivation of vehicle’s brakes, as well as steering the vehicle. We hypothesize that masquerade attacks modify the nuanced correlations of CAN signal time series and how they cluster together. Therefore, changes in cluster assignments should indicate anomalous behavior. We confirm this hypothesis by leveraging our previously developed capability for reverse engineering CAN signals (i.e., CAN-D [Controller Area Network Decoder]) and focus on advancing the state of the art for detecting masquerade attacks by analyzing time series extracted from raw CAN frames. Specifically, we demonstrate that masquerade attacks can be detected by computing time series clustering similarity using hierarchical clustering on the vehicle’s CAN signals (time series) and comparing the clustering similarity across CAN captures with and without attacks. We test our approach in a previously collected CAN dataset with masquerade attacks (i.e., the ROAD dataset) and develop a forensic tool as a proof of concept to demonstrate the potential of the proposed approach for detecting CAN masquerade attacks.

Moriano Salazar, Pablo↗