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At least 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Cosmic shear cosmology beyond two-point statistics: a combined peak count and correlation function analysis of DES-Y1

ABSTRACT We constrain cosmological parameters from a joint cosmic shear analysis of peak-counts and the two-point shear correlation functions, as measured from the Dark Energy Survey (DES-Y1). We find the structure growth parameter $S_8\equiv \sigma _8\sqrt{\Omega _{\rm m}/0.3} = 0.766^{+0.033}_{-0.038}$ which, at 4.8 per cent precision, provides one of the tightest constraints on S8 from the DES-Y1 weak lensing data. In our simulation-based method we determine the expected DES-Y1 peak-count signal for a range of cosmologies sampled in four w cold dark matter parameters (Ωm, σ8, h, w0). We also determine the joint covariance matrix with over 1000 realizations at our fiducial cosmology. With mock DES-Y1 data we calibrate the impact of photometric redshift and shear calibration uncertainty on the peak-count, marginalizing over these uncertainties in our cosmological analysis. Using dedicated training samples we show that our measurements are unaffected by mass resolution limits in the simulation, and that our constraints are robust against uncertainty in the effect of baryon feedback. Accurate modelling for the impact of intrinsic alignments on the tomographic peak-count remains a challenge, currently limiting our exploitation of cross-correlated peak counts between high and low redshift bins. We demonstrate that once calibrated, a fully tomographic joint peak-count and correlation functions analysis has the potential to reach a 3 per cent precision on S8 for DES-Y1. Our methodology can be adopted to model any statistic that is sensitive to the non-Gaussian information encoded in the shear field. In order to accelerate the development of these beyond-two-point cosmic shear studies, our simulations are made available to the community upon request.

Harnois-Déraps, Joachim↗
DOE OSTI2022

Collaboration 51 Correlation Function Analysis Suite (c51_corr_analysis) v0.1.0

This is a data analysis package designed for analyzing correlation functions generated with lattice QCD calculations. The purpose is to make a centralized software suite for use by all members of my collaboration, so that various members can spend less time developing their own analysis codes, and more time extracting the interesting physics from our calculations. There are also 3 independent collaborations that have expressed interest in using this code, so there is some expectation it will be used in the broader international lattice QCD community.

Walker-Loud, Andre↗
DOE OSTI2025

Describing Function Analysis of Transformer Magnetizing Inductance for Direct Power Control of Back-to-Back Modular Multilevel Converters with Advanced Grid Support

This paper provides a detailed investigation into the application of describing function-based analysis for assessing transformer magnetizing inductance and its impact on system performance. The focus is on a back-to-back modular multilevel converter architecture, designed to interconnect systems operating at different frequencies. The study explores the implementation of a Direct Power Control strategy, examining its effects on transformer magnetizing inductance saturation and offering effective mitigation techniques. Furthermore, the integration of advanced grid support functionalities is highlighted, demonstrating how these enhancements bolster the converter's ability to improve grid stability and power quality, positioning it as a robust solution for modern power systems. The proposed approach is validated through extensive computer simulations based MAT LAB/Simulink domain, supported by significant case study results, confirming its practical effectiveness.

back-to-back modular multilevel converters (B2B- M↗
DOE OSTI2020

SAS PDF: pair distribution function analysis of nanoparticle assemblies from small-angle scattering data

SASPDF, a method for characterizing the structure of nanoparticle assemblies (NPAs), is presented. The method is an extension of the atomic pair distribution function (PDF) analysis to the small-angle scattering (SAS) regime. The PDFgetS3 software package for computing the PDF from SAS data is also presented. An application of the SASPDF method to characterize structures of representative NPA samples with different levels of structural order is then demonstrated. The SASPDF method quantitatively yields information such as structure, disorder and crystallite sizes of ordered NPA samples. The method was also used to successfully model the data from a disordered NPA sample. The SASPDF method offers the possibility of more quantitative characterizations of NPA structures for a wide class of samples.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2025

Local orthorhombic phase in zirconium oxide nanocrystals: insights from X-ray pair distribution function analysis

Zirconium dioxide (ZrO 2 ) and hafnium dioxide (HfO 2 ) have emerged as promising alternatives to conventional ferroelectric materials. Understanding the crystal phases of these oxides under different conditions is crucial for optimizing their properties. There are several theories for the (anti)ferroelectric properties; however, comprehensive analysis, particularly at the local structure level, is lacking. In this study, we investigate the local structure of ZrO 2 nanocrystals using X-ray pair distribution function (PDF) analysis, revealing an unexpected local orthorhombic distortion irrespective of crystallite size. This finding suggests the potential existence of an intermediate orthorhombic phase during the microscopic switching pathway observed in previous studies. Additionally, we explore the influence of crystallite size and surface effects on the PDF. These results contribute to a deeper understanding of the structural dynamics in ZrO 2 and offer insights for the design of next-generation ferroelectric materials.

Pokratath, Rohan (ORCID:0000000268383939)↗
DOE OSTI2021

JGI QC impact on assembly, binning, phylogenomics, and functional analysis

Background Investigators using metagenomic sequencing to study their microbiomes are often provided data that has been trimmed and decontaminated or do it themselves without knowing the effect these procedures can have on their downstream analyses. Here we evaluated the impact that JGI trimming and decontamination procedures had on assembly and binning metrics, placement of metagenome assembled genomes into species trees, and functional profiles of metagenome-assembled genomes (MAGs) extracted from twenty three complex rhizosphere metagenomes. We also investigated how more aggressive trimming impacts these binning metrics. Results We found that JGI trimmed and decontamination of input reads had some significant impacts in assembly and binning metrics compared to raw reads, and that differences in placement of MAGs in species trees increased with decreasing completeness and contamination thresholds. More aggressive trimming beyond those used by JGI were found to reduce MAG counts. Conclusions Mild trimming and decontamination of metagenomics reads prior to assembly can change an investigator’s answer to the questions, “Who is there and what are they doing? However, mild trimming and decontamination of metagenomic reads with high quality scores is recommended for those who elect to do so.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Structure refinement and anisotropic atomic displacement parameters of 1M Illite: Rietveld and pair distribution function analysis using synchrotron X-ray radiation

Illite, a widespread clay mineral, plays a pivotal role in geological processes, notably as an indicator in diagenetic and hydrothermal alteration environments, and possesses significant industrial relevance in applications including ceramics, construction and catalysis. However, challenges including its nanoscale crystallinity, structural disorder and frequent interstratification with other clay minerals have hindered detailed structural characterization using conventional X-ray diffraction (XRD) techniques. This study employs integrated synchrotron XRD and pair distribution function (PDF) analysis to elucidate the crystal structure of the 1M illite polytype, yielding the first determination of its anisotropic atomic displacement parameters (U aniso ). TheseU aniso parameters provide critical insights into atomic dynamics and static disorder within the structure, enabling a more refined understanding of structure–property relationships. This integrated approach, combining synchrotron XRD, Rietveld refinement and PDF analysis, yields a comprehensive structural characterization, capturing both average crystallographic and local atomic arrangements. Considering illite's widespread geological occurrence and industrial importance, this high-precision structural dataset, especially the determinedU aniso values, provides a crucial benchmark for future modeling and simulation efforts targeting accurate prediction of its physicochemical behavior.

Chemistry↗
DOE OSTI2020

In situ synchrotron pair distribution function analysis to monitor synthetic pathways under electromagnetic excitation

Electromagnetic (EM) fields, specifically microwave radiation (MWR), can significantly influence the synthesis of ceramic oxide materials and promote rapid, low-temperature growth. However, the mechanisms by which EM fields affect the phase formation process are not well understood. A major limitation to increasing this understanding has been the lack of information regarding dynamic changes in local atomic structure during MWR exposure compared to conventional hydrothermal synthesis routes. Here, we utilize in situ synchrotron X-ray pair distribution function (PDF) analysis to monitor MWR-assisted SnO 2 nanoparticle synthesis. A clear impact of the EM field is demonstrated, with MWR inducing changes in nearest neighbor distances and peaks in oxygen atomic displacement that do not occur during synthesis without MWR exposure. The observed local structural disorder serves as a precursor to rapid rutile SnO 2 nanoparticle crystallization, suggesting that EM field-assisted growth is mediated by changes to the oxygen sublattice. These findings further our understanding of the mechanisms underlying MWR-assisted synthesis and represent a step towards utilizing EM fields to engineer tailored atomic structures for a broad range of applications.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Stacking disorder in α – RuCl 3 investigated via x-ray three-dimensional difference pair distribution function analysis

The van der Waals layered magnet α-RuCl 3 offers tantalizing prospects for the realization of Majorana quasiparticles. Efforts to understand this are, however, hampered by inconsistent magnetic and thermal transport properties likely coming from the formation of structural disorder during crystal growth, postgrowth processing, or upon cooling through the first order structural transition. Here, we investigate structural disorder in α-RuCl 3 using x-ray diffuse scattering and three-dimensional difference pair distribution function (3D-ΔPDF) analysis. We develop a quantitative model that describes disorder in α-RuCl 3 in terms of rotational twinning and intermixing of the high and low-temperature structural layer stacking. As a result, this disorder may be important to consider when investigating the detailed magnetic and electronic properties of this widely studied material.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Surfactant-free syntheses and pair distribution function analysis of osmium nanoparticles

A surfactant-free synthesis of precious metal nanoparticles (NPs) performed in alkaline low-boiling-point solvents has been recently reported. Monoalcohols are here investigated as solvents and reducing agents to obtain colloidal Os nanoparticles by using low-temperature (<100 °C) surfactant-free syntheses. The effect of the precursor (OsCl 3 or H 2 OsCl 6 ), precursor concentration (up to 100 mM), solvent (methanol or ethanol), presence or absence of a base (NaOH), and addition of water (0 to 100 vol %) on the resulting nanomaterials is discussed. It is found that no base is required to obtain Os nanoparticles as opposed to the case of Pt or Ir NPs. The robustness of the synthesis for a precursor concentration up to 100 mM allows for the performance of X-ray total scattering with pair distribution function (PDF) analysis, which shows that 1–2 nm hexagonal close packed (hcp) NPs are formed from chain-like [OsO x Cl y ] complexes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Large-scale tearing-mode hazard function analysis with standard matched equilibrium reconstructions

The association between features from standard tokamak equilibrium reconstructions and the onset of n = 1 tearing modes (TMs) is analyzed at scale. The TM onset rate is directly modeled with a ‘hazard’ function which gives the expected number of onsets (per unit time spent) in a given equilibrium parameter region. In particular the different statistical modeling performance achieved for magnetics-only reconstructions and motional Stark effect (MSE) enhanced reconstructions is studied. It is observed that a better hazard model for the TM onset rate can be built with the MSE-enhanced equilibria compared to the matched magnetics-only situation. This advantage disappears if internal profile details are withheld from the matched analysis. Plausibility of the hazard function is further demonstrated with visualizations of global trends in the operational space, and time-traces from specific tokamak discharges. As a result, TMs typically degrade tokamak plasma performance and may lead to plasma termination, motivating this statistical study.

equilibrium↗
DOE OSTI2022

Bibliometric review and recent advances in total scattering pair distribution function analysis: 21 years in retrospect

Global research activities have been driven by the quest to develop and characterize novel materials for technological advancements. The total scattering pair distribution function (TSPDF) is a powerful and versatile characterization technique for examining the structural details of diverse complex materials including liquid, amorphous, disordered crystalline, and nanostructured materials. Thus, it is critical to keep track of research progress, identify research gaps, and future research directions of the application of the TSPDF technique in materials development and discovery. In this work, a bibliometric analysis of literature regarding the TSPDF technique between 2000 and 2021 was conducted using datasets retrieved from the Web of Science database. The research trends based on publication outputs, research subject distribution, co-authorships among institutions, countries/regions, co-citation of referenced sources, and keyword co-occurrence are evaluated and discussed herein. The impact of the TSPDF technique is projected to increase due to its importance in probing emerging functional materials, and the advances in specialized facilities and instrumentation among the scientific communities engaged with it. Finally, current and emerging research hotspots related to TSPDF technique such as catalysis, computer modeling and simulation, pharmaceutics, machine learning, hydrogen storage, battery materials, and layered structured materials are also identified and discussed.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Functional analysis of Pogostemon cablin farnesyl pyrophosphate synthase gene and its binding transcription factor PcWRKY44 in regulating biosynthesis of patchouli alcohol

Farnesyl pyrophosphate synthase (FPPS) plays an important role in the synthesis of plant secondary metabolites, but its function and molecular regulation mechanism remain unclear in Pogostemon cablin . In this study, the full-length cDNA of the FPP synthase gene from P. cablin ( PcFPPS ) was cloned and characterized. The expressions of PcFPPS are different among different tissues (highly in P. cablin flowers). Subcellular localization analysis in protoplasts indicated that PcFPPS was located in the cytoplasm. PcFPPS functionally complemented the lethal FPPS deletion mutation in yeast CC25. Transient overexpression of PcFPPS in P. cablin leaves accelerated terpene biosynthesis, with an ~47% increase in patchouli alcohol. Heterologous overexpression of PcFPPS in tobacco plants was achieved, and it was found that the FPP enzyme activity was significantly up-regulated in transgenic tobacco by ELISA analysis. In addition, more terpenoid metabolites, including stigmasterol, phytol, and neophytadiene were detected compared with control by GC-MS analysis. Furthermore, with dual-LUC assay and yeast one-hybrid screening, we found 220 bp promoter of PcFPPS can be bound by the nuclear-localized transcription factor PcWRKY44. Overexpression of PcWRKY44 in P. cablin upregulated the expression levels of PcFPPS and patchoulol synthase gene ( PcPTS ), and then promote the biosynthesis of patchouli alcohol. Taken together, these results strongly suggest the PcFPPS and its binding transcription factor PcWRKY44 play an essential role in regulating the biosynthesis of patchouli alcohol.

Wang, Xiaobing↗
DOE OSTI2020

Wave function analysis with a maximum flow algorithm

An efficient algorithm for computing the maximum-flow path in a network is applied to the identification of the dominant configuration state functions (CSFs) in a graphically contracted function (GCF), configuration interaction, wave function. The flow network is a space of spin-adapted CSFs represented by a Shavitt graph, wherein the nodes correspond to orbital occupations and spin quantum numbers. The graph nodes are connected by arcs, and an arc density is defined as sums of the associated squared CSF coefficients. A max-min approach determines an upper bound to the maximum possible incoming flow for each graph node. A backtracking step generates a candidate walk and is followed by a limited search of alternative branching paths for the dominant CSF. The arc density contributions are removed from the graph, and the algorithm is reapplied to the updated graph. This list of generated walks can be partitioned in order to guarantee that the dominant CSFs have been identified. All of the steps in this algorithm are computationally efficient and do not depend on the potentially large dimension of the underlying linear CSF expansion space. An analysis of low-lying valence states of C-2 illustrates the method.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2022

Structural and functional analysis of the human cone‐rod homeobox transcription factor

Abstract The cone‐rod homeobox (CRX) protein is a critical K50 homeodomain transcription factor responsible for the differentiation and maintenance of photoreceptor neurons in the vertebrate retina. Mutant alleles in the human gene encoding CRX result in a variety of distinct blinding retinopathies, including retinitis pigmentosa, cone‐rod dystrophy, and Leber congenital amaurosis. Despite the success of using in vitro biochemistry, animal models, and genomics approaches to study this clinically relevant transcription factor over the past 25 years since its initial characterization, there are no high‐resolution structures in the published literature for the CRX protein. In this study, we use bioinformatic approaches and small‐angle X‐ray scattering (SAXS) structural analysis to further understand the biochemical complexity of the human CRX homeodomain (CRX‐HD). We find that the CRX‐HD is a compact, globular monomer in solution that can specifically bind functional cis‐regulatory elements encoded upstream of retina‐specific genes. This study presents the first structural analysis of CRX, paving the way for a new approach to studying the biochemistry of this protein and its disease‐causing mutant protein variants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Structure-function analysis of the FCRL5–IgG1 Fc complex reveals an unappreciated pathway for B cell modulation by Fc-attenuated IgG

The Fc region of therapeutic IgG antibodies is often engineered to remove or “silence” Fc effector functions, but it remains unclear whether these mutations eliminate all Fc-mediated effector activity. Human Fc receptor-like 5 (FCRL5/FcRH5) is a low-affinity IgG Fc receptor expressed on B cells and is an actively pursued antibody target in multiple myeloma. Here, we show that common Fc function-silencing mutations do not impair FCRL5-mediated activity and therefore attenuate, rather than eliminate, Fc effector function. The crystal structure of the FCRL5-IgG1 Fc complex, solved at 3.4 Å resolution, revealed that FCRL5 binds IgG1 Fc in a 1:1 complex through a binding mode distinct from that of classical Fcγ receptors, explaining why mutations that attenuate Fc effector function spare FCRL5 binding. Fc-engineered antibodies that selectively engage FCRL5 inhibited B cell receptor-induced Ca 2+ flux in FCRL5-expressing B cells. These findings demonstrate that Fc-attenuated therapeutic IgG retains the ability to engage FCRL5, identifying an unappreciated pathway for B cell modulation.

Herpers, Bart M. [Department of Biomedical Enginee↗
DOE OSTI2020

Structure-function analysis of microRNA 3'-end trimming by Nibbler

Nibbler (Nbr) is a 3'-to-5' exoribonuclease whose catalytic 3'-end trimming activity impacts microRNA (miRNA) and PIWI-interacting RNA (piRNA) biogenesis. Here, we report on structural and functional studies to decipher the contributions of Nbr’s N-terminal domain (NTD) and exonucleolytic domain (EXO) in miRNA 3'-end trimming. We have solved the crystal structures of the NTD core and EXO domains of Nbr, both in the apo-state. The NTD-core domain of Aedes aegypti Nbr adopts a HEAT-like repeat scaffold with basic patches constituting an RNA-binding surface exhibiting a preference for binding double-strand RNA (dsRNA) over single-strand RNA (ssRNA). Structure-guided functional assays in Drosophila S2 cells confirmed a principal role of the NTD in exonucleolytic miRNA trimming, which depends on basic surface patches. Gain-of-function experiments revealed a potential role of the NTD in recruiting Nbr to Argonaute-bound small RNA substrates. The EXO domain of A. aegypti and Drosophila melanogaster Nbr adopt a mixed α/β-scaffold with a deep pocket lined by a DEDDy catalytic cleavage motif. We demonstrate that Nbr’s EXO domain exhibits Mn2+-dependent ssRNA-specific 3'-to-5' exoribonuclease activity. Modeling of a 3' terminal Uridine into the catalytic pocket of Nbr EXO indicates that 2'-O-methylation of the 3'-U would result in a steric clash with a tryptophan side chain, suggesting that 2'-O-methylation protects small RNAs from Nbr-mediated trimming. Overall, our data establish that Nbr requires its NTD as a substrate recruitment platform to execute exonucleolytic miRNA maturation, catalyzed by the ribonuclease EXO domain.

59 BASIC BIOLOGICAL SCIENCES↗