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At least 109 records · Page 6

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↗

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↗

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↗

New Insights into the Structure of Nanoporous Carbons from NMR, Raman, and Pair Distribution Function Analysis

The structural characterization of nanoporous carbons is a challenging task as they generally lack long-range order and can exhibit diverse local structures. Such characterization represents an important step toward understanding and improving the properties and functionality of porous carbons, yet few experimental techniques have been developed for this purpose. In this paper, we demonstrate the application of nuclear magnetic resonance (NMR) spectroscopy and pair distribution function (PDF) analysis as new tools to probe the local structures of porous carbons, alongside more conventional Raman spectroscopy. Together, the PDFs and the Raman spectra allow the local chemical bonding to be probed, with the bonding becoming more ordered for carbide-derived carbons (CDCs) synthesized at higher temperatures. The ring currents induced in the NMR experiment (and thus the observed NMR chemical shifts for adsorbed species) are strongly dependent on the size of the aromatic carbon domains. We exploit this property and use computer simulations to show that the carbon domain size increases with the temperature used in the carbon synthesis. The techniques developed here are applicable to a wide range of porous carbons and offer new insights into the structures of CDCs (conventional and vacuum-annealed) and coconut shell-derived activated carbons.

36 MATERIALS SCIENCE↗

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)↗

Mechanisms for carbon adsorption on Au(110)-(2 × 1): A work function analysis

In this paper, the variation of the work function upon carbon adsorption on the reconstructed Au(110) surface is measured experimentally and compared to density functional calculations. The adsorption dynamics is simulated with ab-initio molecular dynamics techniques. Finally, the contribution of various energetically available adsorption sites on the deposition process is analyzed, and the work function behavior with carbon coverage is explained by the resultant electron charge density distributions.

74 ATOMIC AND MOLECULAR PHYSICS↗

Total-scattering pair-distribution function analysis of zinc from high-energy synchrotron data

The crystal structure of zinc metal deviates from the ideal hexagonal close packing structure by a significantly increased axial ratio (c/a). The local atomic structure of zinc metal is investigated using the total scattering atomic pair distribution function (PDF) analysis based on X-ray powder diffraction data collected at ambient conditions. The X-ray total scattering PDF analysis confirms that the crystal structure of zinc can be described in terms of wurtzite structure, but with an anomalously atomic displacement parameters U 33 , indicating a significant displacement disorder along the c-axis. For the long r-range PDF refinements, the thermal motion of zinc shows a notable anisotropy as expressed by the ratio U 33 /U 11 of 2.5 at ambient conditions. This average distortion level along the c-axis, was not reflected locally for the features below 5.0 Å as it fits the high r region. Based on PDF refinements over different r-ranges, we measure an interesting increase of the U 33 value with decreasing the r-range of the refinement. Finally, this suggests that the local structure features in zinc metal differ from the average structure ones.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Structural Study of Biotic and Abiotic Poorly-crystalline Manganese Oxides Using Atomic Pair Distribution Function Analysis

Manganese (Mn) oxides are among the most reactive natural minerals and play an important role in elemental cycling in oceanic and terrestrial environments. A large portion of naturally-occurring Mn oxides tend to be poorly-crystalline and/or nanocrystalline, with not fully resolved crystal structures. In this study, the crystal structures of their synthetic analogs including acid birnessite (AcidBir), {delta}-MnO{sub 2}, polymeric MnO{sub 2} (PolyMnO{sub 2}) and a bacteriogenic Mn oxide (BioMnO{sub x}), have been revealed using atomic pair distribution function (PDF) analysis. Results unambiguously verify that these Mn oxides are layered materials. The best models that accurately allow simulation of pair distribution functions (PDFs) belong to the monoclinic C12/m1 space group with a disk-like shape. The single MnO{sub 6} layers in the average structures deviate significantly from hexagonal symmetry, in contrast to the results of previous studies based on X-ray diffraction analysis in reciprocal space. Manganese occupancies in MnO{sub 6} layers are estimated to be 0.936, 0.847, 0.930 and 0.935, for AcidBir, BioMnO{sub x}, {delta}-MnO{sub 2} and PolyMnO{sub 2}, respectively; however, occupancies of interlayer cations and water molecules cannot be accurately determined using the models in this study. The coherent scattering domains (CSDs) of PolyMnO{sub 2}, {delta}-MnO{sub 2} and BioMnO{sub x} are at the nanometer scale, comprising one to three MnO{sub 6} layers stacked with a high disorder in the crystallographic c-axis direction. Overall, the results of this study advance our understanding of the mineralogy of Mn oxide minerals in the environment.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Structural and Functional Analysis of the Spermatogenic Epithelium in Rats Exposed to Titanium Dioxide Nanoparticles

We studied immunohistochemical and morphometric characteristics of the spermatogenic epithelium in rats against the background of peroral administration of nanoparticles containing titanium dioxide. Substantial degenerative changes in the spermatogenic epithelium were revealed: thinning, disorganization of layers, and detachment of sperm cells from the basement membrane. Immunohistochemical analysis revealed reduced proliferative activity and differentiation potential of epithelial cells, which was confirmed by changes in the expression of Ki-67 and c-kit markers. Our data attest to unfavorable effects of titanium dioxide nanoparticles on the structural and functional characteristics of the reproductive system in male rats leading to spermatogenesis disturbances.

60 APPLIED LIFE SCIENCES↗

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↗

Local structure of ion pair interaction in lapatinib amorphous dispersions characterized by synchrotron x-ray diffraction and pair distribution function analysis

For many years, the idea of analyzing atom-atom contacts in amorphous drug-polymer systems has been of major interest, because this method has always had the potential to differentiate between amorphous systems with domains and amorphous systems which are molecular mixtures. In this study, local structure of ionic and noninonic interactions were studied by High-Energy X-ray Diffraction and Pair Distribution Function (PDF) analysis in amorphous solid dispersions of lapatinib in hypromellose phthalate (HPMCP) and hypromellose (HPMC-E3). The strategy of extracting lapatinib intermolecular drug interactions from the total PDF x-ray pattern was successfully applied allowing the detection of distinct nearest neighbor contacts for the HPMC-E3 rich preparations showing that lapatinib molecules do not cluster in the same way as observed in HPMC-P, where ionic interactions are present. Orientational correlations up to nearest neighbor molecules at about 4.3 Å were observed for polymer rich samples; both observations showed strong correlation to the stability of the systems. Lasty, the superior physical stability of 1:3 LP:HPMCP was consistent with the absence of significant intermolecular interactions in (ΔD inter LP (r)) in the range of 3.0 to 6.0 Å, which are attributed to C-C, C-N and C-O nearest neighbor contacts present in drug-drug interactions.

36 MATERIALS SCIENCE↗

Domain Structures of Ni and NiFe (Oxy)Hydroxide Oxygen-Evolution Catalysts from X-ray Pair Distribution Function Analysis

Ni-Fe (oxy)hydroxides, Ni( i-z )Fe z O x H y , are among the fastest-known water oxidation catalysts in alkaline media on a per-cation basis. At current densities relevant for electrolysis (e.g., >0.5 A/cm( -2 )), mass and electron transport through catalyst films with high mass loading are critical and depend substantially on the extended and intermediate catalyst architecture. We use X-ray pair distribution function (PDF) analysis to determine the intermediate nanostructures of electrodeposited Ni( i-z )Fe z O x H y films. We report the effects of electrodeposition technique (pulsed versus continuous), electrochemical cycling, and Fe content on the structure of the catalyst film. The PDF patterns for Ni( i-z )Fe z O x H y films are best simulated by model structures consisting of brucite-like β-Ni(OH) 2 fragments 1 to 3 layers in thickness. Only the oxidation state of the film significantly affects the intralayer scattering behavior (i.e., metal-oxygen bond distance). The interlayer interactions, however, are affected by Fe content and deposition conditions. The domain size of many of the systems are similar, extending to similar to ~5 nm, which are best modeled by sheets containing upward of similar to ~250 metal cations. Smaller domains were found for films deposited through a larger number of electrochemical cathodic current pulses. Films can be cycled between as-deposited, oxidized, and reduced states, with minimal loss of intrasheet coherence, indicating a degree of structural stability. We estimate heterogeneity in the domain structures by modeling the PDF data to linear combinations of oxyhydroxide fragments with different sizes and numbers of layers.

36 MATERIALS SCIENCE↗

Phylogenetic and Functional Analysis of Metagenome Sequence from High-Temperature Archaeal Habitats Demonstrate Linkages between Metabolic Potential and Geochemistry

Geothermal habitats in Yellowstone National Park (YNP) provide an unparalleled opportunity to understand the environmental factors that control the distribution of archaea in thermal habitats. Here we describe, analyze, and synthesize metagenomic and geochemical data collected from seven high-temperature sites that contain microbial communities dominated by archaea relative to bacteria. The specific objectives of the study were to use metagenome sequencing to determine the structure and functional capacity of thermophilic archaeal-dominated microbial communities across a pH range from 2.5 to 6.4 and to discuss specific examples where the metabolic potential correlated with measured environmental parameters and geochemical processes occurring in situ. Random shotgun metagenome sequence (~40–45 Mb Sanger sequencing per site) was obtained from environmental DNA extracted from high-temperature sediments and/or microbial mats and subjected to numerous phylogenetic and functional analyses. Analysis of individual sequences (e.g., MEGAN and G + C content) and assemblies from each habitat type revealed the presence of dominant archaeal populations in all environments, 10 of whose genomes were largely reconstructed from the sequence data. Analysis of protein family occurrence, particularly of those involved in energy conservation, electron transport, and autotrophic metabolism, revealed significant differences in metabolic strategies across sites consistent with differences in major geochemical attributes (e.g., sulfide, oxygen, pH). These observations provide an ecological basis for understanding the distribution of indigenous archaeal lineages across high-temperature systems of YNP.

54 ENVIRONMENTAL SCIENCES↗

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↗

Local Structure of Zr(OH) 4 and the Effect of Calcination Temperature from X-ray Pair Distribution Function Analysis

Analysis of X-ray pair distribution function data has provided a detailed picture of the local structure of amorphous Zr(OH) 4 and its thermal decomposition into ZrO 2 . In the untreated phase, the Zr atoms tend to be coordinated by six or seven oxygen atoms. The Zr centered polyhedra connect to each other primarily by sharing edges, but also with a significant amount of corner sharing, to form two-dimensional sheets in which the Zr are connected to an average of about five other Zr. This local structure is related to the structure of monoclinic ZrO 2 and can be derived from it by removing certain Zr neighbors to form sheets and reduce the corner to edge sharing ratio. The maximum correlation length in Zr(OH) 4 is about 12 Å. Heating up to 125 °C results in significant water loss but does not alter the network of Zr and bridging O atoms. Additional water loss caused by heating to 250 °C triggers a reorganization into a new type of amorphous phase with a three-dimensional network and a greater number of Zr–Zr neighbors. Further heating to 330 °C causes crystallization into a mixture of tetragonal and monoclinic ZrO 2 , with the minor tetragonal phase having a smaller average domain size. Here, the tetragonal component vanishes by 900 °C.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

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↗