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At least 253 records · Page 14

Effective point-charge analysis of crystal fields: Application to rare-earth pyrochlores and tripod kagome magnets 𝑅 ⁢3⁢ Mg⁢ 2 ⁢Sb⁢ 3⁢ O⁢ 14

An indispensable step to understand collective magnetic phenomena in rare-earth compounds is the determination of spatially anisotropic single-ion properties resulting from spin-orbit coupling and crystal field (CF). The CF Hamiltonian has a discrete energy spectrum—accessible to spectroscopic probes such as neutron scattering—controlled by a number of independent parameters reflecting the point symmetry of the magnetic sites. Determining these parameters in low-symmetry systems is often challenging. Here, we describe a general method to analyze CF excitation spectra using adjustable effective point-charges. We benchmark our method to existing neutron-scattering measurements on pyrochlore rare-earth oxides and obtain a universal point-charge model that describes a large family of related materials. We adapt this model to the newly discovered tripod kagome magnets (𝑅 3 ⁢Mg 2 ⁢Sb 3 ⁢O 14 , 𝑅 = Tb, Ho, Er, Yb) for which we report broadband inelastic neutron-scattering spectra. Analysis of these data using adjustable point-charges yields the CF wave functions for each compound. From this, we calculate thermomagnetic properties that accurately reflect our measurements on powder samples and predict the effective gyromagnetic tensor for pseudospin degrees of freedom—a crucial step to understand the exotic collective properties of these kagome magnets at low temperature. We present further applications of our method to other tripod kagome materials and triangular rare-earth compounds 𝑅⁢MgGaO 4 (𝑅 =Yb, Tm). Overall, this study establishes a widely applicable methodology to predict CF and single-ion properties of rare-earth compounds based on interpretable and adjustable models of effective point charges.

Crystal-field theory↗

Diverse fates of ancient horizontal gene transfers in extremophilic red algae

Abstract Horizontal genetic transfer (HGT) is a common phenomenon in eukaryotic genomes. However, the mechanisms by which HGT‐derived genes persist and integrate into other pathways remain unclear. This topic is of significant interest because, over time, the stressors that initially favoured the fixation of HGT may diminish or disappear. Despite this, the foreign genes may continue to exist if they become part of a broader stress response or other pathways. The conventional model suggests that the acquisition of HGT equates to adaptation. However, this model may evolve into more complex interactions between gene products, a concept we refer to as the ‘Integrated HGT Model’ (IHM). To explore this concept further, we studied specialized HGT‐derived genes that encode heavy metal detoxification functions. The recruitment of these genes into other pathways could provide clear examples of IHM. In our study, we exposed two anciently diverged species of polyextremophilic red algae from the Galdieria genus to arsenic and mercury stress in laboratory cultures. We then analysed the transcriptome data using differential and coexpression analysis. Our findings revealed that mercury detoxification follows a ‘one gene‐one function’ model, resulting in an indivisible response. In contrast, the ars H gene in the arsenite response pathway demonstrated a complex pattern of duplication, divergence and potential neofunctionalization, consistent with the IHM. Our research sheds light on the fate and integration of ancient HGTs, providing a novel perspective on the ecology of extremophiles.

59 BASIC BIOLOGICAL SCIENCES↗

Cosmological constraints using Minkowski functionals from the first year data of the Hyper Suprime-Cam

We use Minkowski functionals to analyse weak lensing convergence maps from the first-year data release of the Subaru Hyper Suprime-Cam (HSC-Y1) survey. Minkowski functionals provide a description of the morphological properties of a field, capturing the non-Gaussian features of the Universe matter-density distribution. Using simulated catalogues that reproduce survey conditions and encode cosmological information, we emulate Minkowski functionals predictions across a range of cosmological parameters to derive the best-fit from the data. By applying multiple scales cuts, we rigorously mitigate systematic effects, including baryonic feedback and intrinsic alignments. From the analysis, combining constraints of the angular power spectrum and Minkowski functionals, we obtain S8≡σ8Ωm/0.3=0.808−0.046+0.033 and Ωm=0.293−0.043+0.157⁠. These results represent a 40 per cent improvement on the S8 constraints compared to using power spectrum only. Minkowski functionals results are consistent with other two-point, and higher order statistics constraints using the same data, being in agreement with CMB results from the Planck S8 measurements. Our study demonstrates the power of Minkowski functionals beyond two-point statistics to constrain and break the degeneracy between Ωm and σ8⁠.

79 ASTRONOMY AND ASTROPHYSICS↗

Detection of translational noncrystallographic symmetry in Patterson functions

Detection of translational noncrystallographic symmetry (TNCS) can be critical for success in crystallographic phasing, particularly when molecular-replacement models are poor or anomalous phasing information is weak. If the correct TNCS is detected then expected intensity factors for each reflection can be refined, so that the maximum-likelihood functions underlying molecular replacement and single-wavelength anomalous dispersion use appropriate structure-factor normalization and variance terms. Here, an analysis of a curated database of protein structures from the Protein Data Bank to investigate how TNCS manifests in the Patterson function is described. These studies informed an algorithm for the detection of TNCS, which includes a method for detecting the number of vectors involved in any commensurate modulation (the TNCS order). The algorithm generates a ranked list of possible TNCS associations in the asymmetric unit for exploration during structure solution.

59 BASIC BIOLOGICAL SCIENCES↗

Sensitivity to low-mass WIMPs with an improved liquid argon ionization response model within the DarkSide program

Dark matter detection experiments using liquid argon rely on a precise characterization of the ionization response to nuclear recoils, especially in the keV energy range relevant for light dark matter interactions. In this work, we present a comprehensive analysis that combines new measurements from the ReD setup, part of the DarkSide experimental program, with calibration data from DarkSide-50, as well as results from the ARIS and SCENE experiments. These combined datasets enable improved constraints on atomic screening effects in the modeling of the ionization response of liquid argon to nuclear recoils. The analysis is performed within the Thomas-Imel recombination framework adopted in previous DarkSide studies, and is here further constrained by the inclusion of ReD data, which allow the screening function to be determined from calibration measurements. By including the updated ionization model into the DarkSide-50 analysis framework, we obtain stronger exclusion limits on low-mass weakly interacting massive particle (WIMP) interactions, setting new world-leading constraints in the 1 – 3 GeV / c 2 WIMP mass range. Finally, we recast the sensitivity projections for the upcoming DarkSide-20k detector, demonstrating a significantly enhanced discovery potential for low-mass dark matter candidates.

Acerbi, F. [Fond. Bruno Kessler, Trento]↗

Code Artifact for: Clustering Analysis of Commercial Vehicles Using Automatically Extracted Features from Time Series Data [SWR-21-96]

This repository contains data ingestion, feature extraction, and analysis code used in NREL Technical report "Clustering Analysis of Commercial Vehicles Using Automatically Extracted Features from Time Series Data." The code is written in Python. The ETL and feature extraction code must be run in a Spark context. The analysis code can be run without Spark, provided you have pre-computed features in a CSV file. Analysis code related to the NREL Technical Report NREL/TP-2C00-74212. Includes PySpark functions to perform trip segmentation and feature extraction over big time series data in Apache Spark. Includes "domain specific" features such as Aerodynamic Speed (ft/s), Characteristic Acceleration (ft/s2), Percent Below 55 (%), Percent Zero (%), Stops Per Mile, Average Speed (mph), Maximum Speed (mph), and Speed Standard Deviation (mph). Includes Pyspark UDF to compute "domain agnostic" features using the TSFresh library. This software record also includes the analysis notebooks and code to generate the results in the previously mentioned technical report.

Perr-Sauer, Jordan↗

Dark Energy Survey Year 3 results: Cosmological constraints from galaxy clustering and weak lensing

We present the first cosmology results from large-scale structure using the full 5000 deg 2 of imaging data from the Dark Energy Survey (DES) Data Release 1. We perform an analysis of large-scale structure combining three two-point correlation functions ( 3 × 2 pt ): (i) cosmic shear using 100 million source galaxies, (ii) galaxy clustering, and (iii) the cross-correlation of source galaxy shear with lens galaxy positions, galaxy–galaxy lensing. To achieve the cosmological precision enabled by these measurements has required updates to nearly every part of the analysis from DES Year 1, including the use of two independent galaxy clustering samples, modeling advances, and several novel improvements in the calibration of gravitational shear and photometric redshift inference. The analysis was performed under strict conditions to mitigate confirmation or observer bias; we describe specific changes made to the lens galaxy sample following unblinding of the results and tests of the robustness of our results to this decision. We model the data within the flat Λ CDM and w CDM cosmological models, marginalizing over 25 nuisance parameters. We find consistent cosmological results between the three two-point correlation functions; their combination yields clustering amplitude S 8 = 0.77 6 - 0.017 + 0.017 and matter density Ω m = 0.33 9 - 0.031 + 0.032 in Λ CDM , mean with 68% confidence limits; S 8 = 0.77 5 - 0.024 + 0.026 , Ω m = 0.35 2 - 0.041 + 0.035 , and dark energy equation-of-state parameter w = - 0.9 8 - 0.20 + 0.32 in w CDM . These constraints correspond to an improvement in signal-to-noise of the DES Year 3 3 × 2 pt data relative to DES Year 1 by a factor of 2.1, about 20% more than expected from the increase in observing area alone. This combination of DES data is consistent with the prediction of the model favored by the Planck 2018 cosmic microwave background (CMB) primary anisotropy data, which is quantified with a probability-to-exceed p = 0.13 –0.48. We find better agreement between DES 3 × 2 pt and Planck than in DES Y1, despite the significantly improved precision of both. When combining DES 3 × 2 pt data with available baryon acoustic oscillation, redshift-space distortion, and type Ia supernovae data, we find p = 0.34 . Combining all of these datasets with Planck CMB lensing yields joint parameter constraints of S 8 = 0.81 2 - 0.008 + 0.008 , Ω m = 0.30 6 - 0.005 + 0.004 , h = 0.68 0 - 0.003 + 0.004 , and ∑ m ν < 0.13 eV (95% C.L.) in Λ CDM ; S 8 = 0.81 2 - 0.008 + 0.008 , Ω m = 0.30 2 - 0.006 + 0.006 , h = 0.68 7 - 0.007 + 0.006 , and w = - 1.03 1 - 0.027 + 0.030 in w CDM .

79 ASTRONOMY AND ASTROPHYSICS↗

XtalCAMP: a comprehensive program for the analysis and visualization of scanning Laue X-ray micro-/nanodiffraction data

XtalCAMP is a software package based on the MATLAB platform, which is suitable for, but not limited to, the analysis and visualization of scanning Laue X-ray micro-/nanodiffraction data. The main objective of the software is to provide complementary functionalities to the Laue indexing software packages used at several synchrotron beamlines. Here, the graphical user interfaces allow the easy analysis of characteristic microstructure features, including real-time intensity mapping for a quick examination of phase, grain and defect distribution, 2D color-coded mapping of microstructural properties from the output of other Laue indexing software, crystal orientation visualization, grain boundary characterization based on orientation/misorientation calculation, principal strain/stress analysis, and strain ellipsoid representation, as well as a series of additional toolkits. As an example, XtalCAMP is applied to the microstructural investigation of a solution-heat-treated Ni-based superalloy manufactured using a laser 3D-printing technique, and a deformed natural quartzite from Val Bregaglia in the Central Alps.

36 MATERIALS SCIENCE↗

Metaanalysis of liana and tree functional traits

The objectives of this project were (i) to determine how tropical trees and lianas differed in terms of their functional traits, and (ii) to parameterize a computational model of tree-liana competition. We carried out a meta-analysis of tree and liana functional traits in order to achieve these goals. First, we downloaded functional trait data from the TRY database during November and December 2019. Traits of interest included leaf, wood, and root functional traits. We included only angiosperm tree and liana species that are found in tropical biomes. We then computed the species average for each trait. The results are included in “TRY_traits_metaanalysis.csv”. We also conducted a second meta-analysis focused on the hydraulic traits of tropical trees and lianas. We used Google Scholar and Web of Science to identify papers that contained hydraulic trait values. The papers that we found were all published between 1997-2019. As with our TRY-based meta-analysis, we included only angiosperm tree and liana species that are found in the tropics, and we computed species averages. The results are contained in the file “hydraulic_traits_metaanalysis.csv”. Both files are in csv format, so they can be read with any plain text editor, as well as programs like R or Excel.

54 ENVIRONMENTAL SCIENCES↗

Amorphous dispersions of flubendazole in hydroxypropyl methylcellulose: Formulation stability assisted by pair distribution function analysis

Here, we use X-ray pair distribution function (PDF) analysis applied to high-energy synchrotron X-ray powder diffraction data to evaluate the amorphous solid dispersions interactions and their aging stability. The obtained systems are based on hydroxypropyl methylcellulose (hypromellose) derivatives and flubendazole (FBZ) drug dispersions prepared using a spray-dryer technique. We carry out stability studies under aging parameters (40 °C/75% relative humidity) to tune the systems’ recrystallization. The results reveal that ion-base interactions between the drug-polymer matrix are responsible for reducing clustering processes yielding slower recrystallization and different ordering in the hypromellose phthalate (HPMCP/FBZ) and hypromellose acetate succinate (HPMC-AS/FBZ) systems and complete drug clustering in hypromellose (HPMC-E3/FBZ). The structural ordering was accessed using differential X-ray PDFs that revealed the region between 3.5 Å and 5.0 Å could be related to FBZ intermolecular interactions and is more ordered for the least stable system (HPMC-E3/FBZ) and less ordered for the most stable system (HPMCP/FBZ). These results show that the ion-base interactions between drug and matrix occur at these intermolecular distances.

60 APPLIED LIFE SCIENCES↗

First simultaneous global QCD analysis of kaon and pion parton distributions with lattice QCD constraints

We perform the first simultaneous global QCD analysis of pion and kaon parton distribution functions (PDFs) constrained by pion- and kaon-induced Drell-Yan (DY) and leading neutron electroproduction data together with lattice QCD data on pion and kaon PDF moments. The analysis indicates a softer valence u ¯ distribution in the K − than in the π − and a significantly more peaked valence s -quark density in K − compared with the u ¯ . The effective exponent governing the high- x behavior of the PDF is found to be larger for u ¯ in the kaon, β u ¯ K − = 1.6 ( 2 ) , than in the pion, β u ¯ π − = 1.16 ( 4 ) , in the range 0.7 ≤ x ≤ 0.95 . From the gluon momentum fractions, we find the pion’s gluon content accounts for ≈ 1 / 3 of the mass budget of the pion at μ = 2 GeV , but only ≈ 1 / 4 for the kaon.

Barry, P. C. [Argonne National Laboratory] (ORCID:↗

Illustrated formalisms for total scattering data: a guide for new practitioners

The total scattering method is the simultaneous study of both the real- and reciprocal-space representations of diffraction data. While conventional Bragg-scattering analysis (employing methods such as Rietveld refinement) provides insight into the average structure of the material, pair distribution function (PDF) analysis allows for a more focused study of the local atomic arrangement of a material. Generically speaking, a PDF is generated by Fourier transforming the total measured reciprocal-space diffraction data (Bragg and diffuse) into a real-space representation. However, the details of the transformation employed and, by consequence, the resultant appearance and weighting of the real-space representation of the system can vary between different research communities. As the worldwide total scattering community continues to grow, these subtle differences in nomenclature and data representation have led to conflicting and confusing descriptions of how the PDF is defined and calculated. This paper provides a consistent derivation of many of these different forms of the PDF and the transformations required to bridge between them. Some general considerations and advice for total scattering practitioners in selecting and defining the appropriate choice of PDF in their own research are presented. This contribution aims to benefit people starting in the field or trying to compare their results with those of other researchers.

36 MATERIALS SCIENCE↗

Python wrapper library and analysis functions for Geotab Altitude API [SWR-24-77]

This software library serves as a Python wrapper for Geotab's Altitude API. It streamlines querying of the API, converts loosely structured API outputs into a standardized tabular data format, and enables analysis of the resulting data tables. It also includes example notebooks showing how to use the library.

Bruchon, Matthew↗

Microbial sensitivity to temperature and sulfate deposition modulates greenhouse gas emissions from peat soils

Abstract Peatlands are among the largest natural sources of atmospheric methane (CH 4 ) worldwide. Microbial processes play a key role in regulating CH 4 emissions from peatland ecosystems, yet the complex interplay between soil substrates and microbial communities in controlling CH 4 emissions as a function of global change remains unclear. Herein, we performed an integrated analysis of multi‐omics data sets to provide a comprehensive understanding of the molecular processes driving changes in greenhouse gas (GHG) emissions in peatland ecosystems with increasing temperature and sulfate deposition in a laboratory incubation study. We sought to first investigate how increasing temperatures (4, 21, and 35°C) impact soil microbiome–metabolome interactions; then explore the competition between methanogens and sulfate‐reducing bacteria (SRBs) with increasing sulfate concentrations at the optimum temperature for methanogenesis. Our results revealed that peat soil organic matter degradation, mediated by biotic and potentially abiotic processes, is the main driver of the increase in CO 2 production with temperature. In contrast, the decrease in CH 4 production at 35°C was linked to the absence of syntrophic communities and the potential inhibitory effect of phenols on methanogens. Elevated temperatures further induced the microbial communities to develop high growth yield and stress tolerator trait‐based strategies leading to a shift in their composition and function. On the other hand, SRBs were able to outcompete methanogens in the presence of non‐limiting sulfate concentrations at 21°C, thereby reducing CH 4 emissions. At higher sulfate concentrations, however, the prevalence of communities capable of producing sufficient low‐molecular‐weight carbon substrates for the coexistence of SRBs and methanogens was translated into elevated CH 4 emissions. The use of omics in this study enhanced our understanding of the structure and interactions among microbes with the abiotic components of the system that can be useful for mitigating GHG emissions from peatland ecosystems in the face of global change.

AminiTabrizi, Roya↗

Uncovering DNA-PKcs ancient phylogeny, unique sequence motifs and insights for human disease

DNA-dependent protein kinase catalytic subunit (DNA-PKcs) is a key member of the phosphatidylinositol-3 kinase-like (PIKK) family of protein kinases with critical roles in DNA-double strand break repair, transcription, metastasis, mitosis, RNA processing, and innate and adaptive immunity. The absence of DNA-PKcs from many model organisms has led to the assumption that DNA-PKcs is a vertebrate-specific PIKK. Here, we find that DNA-PKcs is widely distributed in invertebrates, fungi, plants, and protists, and that threonines 2609, 2638, and 2647 of the ABCDE cluster of phosphorylation sites are highly conserved amongst most Eukaryotes. Furthermore, we identify highly conserved amino acid sequence motifs and domains that are characteristic of DNA-PKcs relative to other PIKKs. These include residues in the Forehead domain and a novel motif we have termed YRPD, located in an α helix C-terminal to the ABCDE phosphorylation site loop. Combining sequence with biochemistry plus structural data on human DNA-PKcs unveils conserved sequence and conformational features with functional insights and implications. The defined generally progressive DNA-PKcs sequence diversification uncovers conserved functionality supported by Evolutionary Trace analysis, suggesting that for many organisms both functional sites and evolutionary pressures remain identical due to fundamental cell biology. The mining of cancer genomic data and germline mutations causing human inherited disease reveal that robust DNA-PKcs activity in tumors is detrimental to patient survival, whereas germline mutations compromising function are linked to severe immunodeficiency and neuronal degeneration. We anticipate that these collective results will enable ongoing DNA-PKcs functional analyses with biological and medical implications.

59 BASIC BIOLOGICAL SCIENCES↗

Electrochemical Doping of Halide Perovskites by Noble Metal Interstitial Cations

Abstract Metal halide perovskites are an attractive class of semiconductors, but it has proven difficult to control their electronic doping by conventional strategies due to screening and compensation by mobile ions or ionic defects. Noble‐metal interstitials represent an under‐studied class of extrinsic defects that plausibly influence many perovskite‐based devices. In this work, doping of metal halide perovskites is studied by electrochemically formed Au + interstitial ions, combining experimental data on devices with a computational analysis of Au + interstitial defects based on density functional theory (DFT). Analysis suggests that Au + cations can be easily formed and migrate through the perovskite bulk via the same sites as iodine interstitials (I i + ). However, whereas I i + compensates n‐type doping by electron capture, the noble‐metal interstitials act as quasi‐stable n‐dopants. Experimentally, voltage‐dependent, dynamic doping by current density–time ( J–t ), electrochemical impedance, and photoluminescence measurements are characterized. These results provide deeper insight into the potential beneficial and detrimental impacts of metal electrode reactions on long‐term performance of perovskite photovoltaic and light‐emitting diodes, as well as offer an alternative doping explanation for the valence switching mechanism of halide‐perovskite‐based neuromorphic and memristive devices.

14 SOLAR ENERGY↗

Magnetic structure evolution of LiFe 1- x Co x PO 4 olivines upon delithiation

We present a comprehensive study of the nuclear and magnetic structures of the mixed olivine solid solution series LiFe 1-x Co x PO 4 as well as their delithiated counterparts, for metal concentrations x = 0.2 - 0.6. Through neutron powder diffraction studies, we find that the LiFe 1-x Co x PO 4 series orders in the magnetic space group Pnma', consistent with their Li(Fe/Co)PO 4 parent structures. After chemical delithiation using peracetic acid, however, the removal of over 30% of the lithium from the lattice results in a transition from an A y -type to an A x -type antiferromagnetic structure. The magnetic space group consistent with A x antiferromagnetism was found to be Pn'm'a'. Interestingly, magnetic susceptibility measurements of both series reveal that delithiation increases the magnetic transition temperature, T N , from 50 K to 115 K. We find through analysis of the diffraction data that the unit cell parameters change linearly as a function of x; consequently, the exchange pathways between the Fe/Co magnetic cations are affected by the delithiation. Here, we discuss how exchange pathways, metal oxidation states, and d-orbital occupation all contribute to the observed magnetic symmetries and trends in T N in both series.

Antiferromagnet↗

Analytic Gaussian covariance matrices for galaxy N-point correlation functions

Here, we derive analytic covariance matrices for the N-point correlation functions (NPCFs) of galaxies in the Gaussian limit. Our results are given for arbitrary N and projected onto the isotropic basis functions given by spherical harmonics and Wigner 3j symbols. A numerical implementation of the 4PCF covariance is compared to the sample covariance obtained from a set of lognormal simulations, Quijote dark matter halo catalogues, and MultiDark-Patchy galaxy mocks, with the latter including realistic survey geometry. The analytic formalism gives reasonable predictions for the covariances estimated from mock simulations with a periodic-box geometry. Furthermore, fitting for an effective volume and number density by maximizing a likelihood based on Kullback-Leibler divergence is shown to partially compensate for the effects of a nonuniform window function. Our result is recently shown to facilitate NPCF analysis on a realistic survey data.

79 ASTRONOMY AND ASTROPHYSICS↗