Measure Of Local Structure Research Articles

Charge-lattice coupling and the dynamic structure of the U–O distribution in UO2+x

The different structures and behaviors of UO2+x observed in crystallographic and local structure measurements were examined by extended X-ray absorption fine structure (EXAFS) measurements of pristine UO2.0, p+ and He2+ irradiated UO2.0, and, at multiple temperatures, bulk U4O9 and U3O7 and thin film U4O9-δ on an epitaxial substrate. The disorder caused by irradiation is mostly limited to increased widths of the existing U–O/U pair distributions, with any new neighbor shells being minor. As has been previously reported, the disorder caused by oxidative addition to U4O9 and U3O7 is much more extensive, resulting in multisite U–O distributions and greater reduction of the U–U amplitude with different distributions in bulk and thin-film U4O9. This includes the significant spectral feature near R = 1.2 Å for all U4O9 and U3O7 samples fit with a U-oxo type moiety with a U–O distance around 1.7 Å. In addition to indicating that these anomalies only occur in mixed valence materials, this work confirms the continuous rearrangement of the U–O distributions from 10 to 250 K. Although these variations of the structure are not observed in crystallography, their prominence in the EXAFS indicates that the dynamic structure underlying these effects is an essential factor of these materials.

Isotope-Edited Variable Temperature Infrared Spectroscopy for Measuring Transition Temperatures of Single A-T Watson-Crick Base Pairs in DNA Duplexes.

Experimental methods to determine transition temperatures for individual base pair melting events in DNA duplexes are lacking despite intense interest in these thermodynamic parameters. Here, we determine the dimensions of the thymine (T) C2═O stretching vibration when it is within the DNA duplex via isotopic substitutions at other atomic positions in the structure. First, we determined that this stretching state was localized enough to specific atoms in the molecule to make submolecular scale measurements of local structure and stability in high molecular weight complexes. Next, we develop a new isotope-edited variable temperature infrared method to measure melting transitions at various locations in a DNA structure. As an initial test of this "sub-molecular scale thermometer", we applied our T13C2 difference infrared signal to measure location-dependent melting temperatures (TmL) in a DNA duplex via variable temperature attenuated total reflectance Fourier transform infrared (VT-ATR-FTIR) spectroscopy. We report that the TmL of a single Watson-Crick A-T base pair near the end of an A-T rich sequence (poly T) is ∼34.9 ± 0.7°C. This is slightly lower than the TmL of a single base pair near the middle position of the poly T sequence (TmL ∼35.6±0.2°C). In addition, we also report that the TmL of a single Watson-Crick A-T base pair near the end of a 50% G-C sequence (12-mer) is ∼52.5 ± 0.3°C, which is slightly lower than the global melting Tm of the 12-mer sequence (TmL ∼54.0±0.9°C). Our results provide direct physical evidence for end fraying in DNA sequences with our novel spectroscopic methods.

Correlating structural changes in thermoresponsive hydrogels to the optical response of embedded plasmonic nanoparticles.

Stimuli-responsive microgels, composed of small beads with soft, deformable polymer networks swollen through a combination of synthetic control over the polymer and its interaction with water, form a versatile platform for development of multifunctional and biocompatible sensors. The interfacial structural variation of such materials at a nanometer length scale is essential to their function, but not yet fully comprehended. Here, we take advantage of the plasmonic response of a gold nanorod embedded in a thermoresponsive microgel (AuNR@PNIPMAm) to monitor structural changes in the hydrogel directly near the nanorod surface. By direct comparison of the plasmon response against measurements of the hydrogel structure from dynamic light scattering and nuclear magnetic resonance, we find that the microgel shell of batch-polymerized AuNR@PNIPMAm exhibits a heterogeneous volume phase transition reflected by different onset temperatures for changes in the hydrodyanmic radius (RH) and plasmon resonance, respectively. The new approach of contrasting plasmonic response (a measure of local surface hydrogel structure) with RH and relaxation times paves a new path to gain valuable insight for the design of plasmonic sensors based on stimuli-responsive hydrogels.

Aging pattern of the brainstem based on volumetric measurement and optimized surface shape analysis.

The brainstem, a small and crucial structure, is connected to the cerebrum, spinal cord, and cerebellum, playing a vital role in regulating autonomic functions, transmitting motor and sensory information, and modulating cognitive processes, emotions, and consciousness. While previous research has indicated that changes in brainstem anatomy can serve as a biomarker for aging and neurodegenerative diseases, the structural changes that occur in the brainstem during normal aging remain unclear. This study aimed to examine the age- and sex-related differences in the global and local structural measures of the brainstem in 187 healthy adults (ranging in age from 18 to 70years) using structural magnetic resonance imaging. The findings showed a significant negative age effect on the volume of the two major components of the brainstem: the medulla oblongata and midbrain. The shape analysis revealed that atrophy primarily occurs in specific structures, such as the pyramid, cerebral peduncle, superior and inferior colliculi. Surface area and shape analysis showed a trend of flattening in the aging brainstem. There were no significant differences between the sexes or sex-by-age interactions in brainstem structural measures. These findings provide a systematic description of age associations with brainstem structures in healthy adults and may provide a reference for future research on brain aging and neurodegenerative diseases.

Ptychographic measurements of varying size and shape along zeolite channels.

Sub-angstrom resolution imaging of porous materials like zeolites is important to reveal their structure-property relationships involved in ion exchange, molecule adsorption and separation, and catalysis. Using multislice electron ptychography, we successfully measured the atomic structure of zeolite at sub-angstrom lateral resolution for 100-nanometer-thick samples. Both lateral and depth deformations of the straight channels are mapped, showing the three-dimensional structural inhomogeneity and flexibility. Since most zeolites in industrial applications are usually tens to hundreds of nanometers thick, the sub-angstrom resolution imaging and accurate measurements of depth-dependent local structures with electron ptychography at low-dose condition will find wide applications in porous materials close to their industrially relevant conditions.

Enzymatic Spin-Labeling of Protein N- and C-Termini for Electron Paramagnetic Resonance Spectroscopy.

Electron paramagnetic resonance (EPR) spectroscopy is a powerful tool for investigating the structure and dynamics of proteins. The introduction of paramagnetic moieties at specific positions in a protein enables precise measurement of local structure and dynamics. This technique, termed site-directed spin-labeling, has traditionally been performed using cysteine-reactive radical-containing probes. However, large proteins are more likely to contain multiple cysteine residues and cysteine labeling at specific sites may be infeasible or impede function. To address this concern, we applied three peptide-ligating enzymes (sortase, asparaginyl endopeptidase, and inteins) for nitroxide labeling of N- and C-termini of select monomeric and dimeric proteins. Continuous wave and pulsed EPR (double electron electron resonance) experiments reveal specific attachment of nitroxide probes to ether N-termini (OaAEP1) or C-termini (sortase and intein) across three test proteins (CheY, CheA, and iLOV), thereby enabling a straightforward, highly specific, and general method for protein labeling. Importantly, the linker length (3, 5, and 9 residues for OaAEP1, intein, and sortase reactions, respectively) between the probe and the target protein has a large impact on the utility of distance measurements by pulsed EPR, with longer linkers leading to broader distributions. As these methods are only dependent on accessible N- and C-termini, we anticipate application to a wide range of protein targets for biomolecular EPR spectroscopy.

Correlating local chemical and structural order using Geographic Information Systems-based spatial statistics

Analysis of nanoscale short-range chemical and/or structural order via (scanning) transmission electron microscopy (S/TEM) imaging is fundamentally limited by projection of the three dimensional sample, which averages informational along the beam direction. Extracting statistically significant spatial correlations between the structure and chemistry determined from these two-dimensional datasets thus remains challenging. Here, we apply methods commonly used in Geographic Information Systems (GIS) to determine the spatial correlation between measures of local chemistry and structure from atomic-resolution STEM imaging of a compositionally complex relaxor, Pb(Mg1/3Nb2/3)O3 (PMN). The approach is used to determine the type of ordering present and to quantify the spatial variation of chemical order, oxygen octahedral distortions, and oxygen octahedral tilts. The extent of autocorrelation and inter-feature correlation among these short-range ordered regions are then evaluated through a spatial covariance analysis, showing correlation as a function of distance. The results demonstrate that integrating GIS tools for analyzing microscopy datasets can serve to unravel subtle relationships among chemical and structural features in complex materials that can be hidden when ignoring their spatial distributions.

Disentangling types of lattice disorder impacting superconductivity in Sr2RuO4 by quantitative local probes

The unconventional superconductivity in Sr2RuO4 is infamously susceptible to suppression by small levels of disorder such that it has been most commonly studied in extremely high-purity bulk crystals. Here, we harness local structural and spectroscopic scanning transmission electron microscopy measurements in epitaxial thin films of Sr2RuO4 to disentangle the impact of different types of crystalline disorder on superconductivity. We find that cation off-stoichiometry during growth gives rise to two distinct types of disorder: mixed-phase structural inclusions that accommodate excess ruthenium and ruthenium vacancies when the growth is ruthenium-deficient. Several superconducting films host mixed-phase intergrowths, suggesting this microstructural disorder has relatively little impact on superconductivity. In a non-superconducting film, on the other hand, we measure a high density of ruthenium-vacancies (∼14%) with no significant reduction in the crystallinity of the film. The results suggest that ruthenium vacancy disorder, which is hidden to many structural probes, plays an important role in suppressing superconductivity. We discuss the broader implications of our findings to guide the future synthesis of this and other layered systems.

Flame structure and burning velocity of ammonia/air turbulent premixed flames at high Karlovitz number conditions

This paper presents experimental studies of the structures and burning velocities of premixed ammonia/air jet flames at high Karlovitz (Ka) number conditions. Simultaneous planar laser-induced fluorescence (PLIF) imaging of imidogen (NH) and hydroxyl (OH) radicals was performed to investigate the local flame structure and Laser Doppler Anemometry (LDA) measurements were employed for extracting complement relevant turbulent quantities from the flow field. All the selected cases are located in the regime of distributed reaction zones (DRZ) in the Borghi-Peters diagram, with a maximum Karlovitz (Ka) number and turbulent intensity (u′/SL) up to 1008 and 240, respectively. The OH- and NH-PLIF data were used to determine the flame surface density, flame-surface area ratio, and turbulent burning velocity (ST). The main findings include: (a) The NH layer remains thin and continuous over the investigated range of turbulent intensity and Karlovitz number, and the thickness keeps constant statistically without any significant broadening by turbulent eddies; (b) Spatial correlations of the NH and OH radicals show that overlap of NH and OH layers always exists in a thin region where OH has a weaker signal intensity; (c) The ratio of turbulent to laminar burning velocity (ST/SL) shows a nearly linear increase with turbulent intensity, while the ratio of wrinkled flame surface area to that of ensemble-averaged flame surface area increases only slightly with turbulent intensities. The slower increase of wrinkled flame surface area with turbulent intensity can be attributed to under-resolution in the current state-of-the-art PLIF experiments, the neglection of 3D flame wrinkles in 2D experiments, and the increase in flame stretch factor at high turbulent intensities.

Recovering local structure information from high-pressure total scattering experiments.

High pressure is a powerful thermodynamic tool for exploring the structure and the phase behaviour of the crystalline state, and is now widely used in conventional crystallographic measurements. High-pressure local structure measurements using neutron diffraction have, thus far, been limited by the presence of a strongly scattering, perdeuterated, pressure-transmitting medium (PTM), the signal from which contaminates the resulting pair distribution functions (PDFs). Here, a method is reported for subtracting the pairwise correlations of the commonly used 4:1 methanol:ethanol PTM from neutron PDFs obtained under hydro-static compression. The method applies a molecular-dynamics-informed empirical correction and a non-negative matrix factorization algorithm to recover the PDF of the pure sample. Proof of principle is demonstrated, producing corrected high-pressure PDFs of simple crystalline materials, Ni and MgO, and benchmarking these against simulated data from the average structure. Finally, the first local structure determination of α-quartz under hydro-static pressure is presented, extracting compression behaviour of the real-space structure.

CheSPI: chemical shift secondary structure population inference.

NMR chemical shifts (CSs) are delicate reporters of local protein structure, and recent advances in random coil CS (RCCS) prediction and interpretation now offer the compelling prospect of inferring small populations of structure from small deviations from RCCSs. Here, we present CheSPI, a simple and efficient method that provides unbiased and sensitive aggregate measures of local structure and disorder. It is demonstrated that CheSPI can predict even very small amounts of residual structure and robustly delineate subtle differences into four structural classes for intrinsically disordered proteins. For structured regions and proteins, CheSPI provides predictions for up to eight structural classes, which coincide with the well-known DSSP classification. The program is freely available, and can either be invoked from URL www.protein-nmr.org as a web implementation, or run locally from command line as a python program. CheSPI generates comprehensive numeric and graphical output for intuitive annotation and visualization of protein structures. A number of examples are provided.

Dissimilarity measure of local structure in inorganic crystals using Wasserstein distance to search for novel phosphors

ABSTRACT To efficiently search for novel phosphors, we propose a dissimilarity measure of local structure using the Wasserstein distance. This simple and versatile method provides the quantitative dissimilarity of a local structure around a center ion. To calculate the Wasserstein distance, the local structures in crystals are numerically represented as a bag of interatomic distances. The Wasserstein distance is calculated for various ideal structures and local structures in known phosphors. The variation of the Wasserstein distance corresponds to the structural variation of the local structures, and the Wasserstein distance can quantitatively explain the dissimilarity of the local structures. The correlation between the Wasserstein distance and the full width at half maximum suggests that candidates for novel narrow-band phosphors can be identified by crystal structures that include local structures with small Wasserstein distances to local structures of known narrow-band phosphors. The quantitative dissimilarity using the Wasserstein distance is useful in the search of novel phosphors and expected to be applied in materials searches in other fields in which local structures play an important role.

Infrared nano-spectroscopy of ferroelastic domain walls in hybrid improper ferroelectric Ca3Ti2O7

Ferroic materials are well known to exhibit heterogeneity in the form of domain walls. Understanding the properties of these boundaries is crucial for controlling functionality with external stimuli and for realizing their potential for ultra-low power memory and logic devices as well as novel computing architectures. In this work, we employ synchrotron-based near-field infrared nano-spectroscopy to reveal the vibrational properties of ferroelastic (90{}^{circ } ferroelectric) domain walls in the hybrid improper ferroelectric Ca{}_{3}Ti{}_{2}O{}_{7}. By locally mapping the Ti-O stretching and Ti-O-Ti bending modes, we reveal how structural order parameters rotate across a wall. Thus, we link observed near-field amplitude changes to underlying structural modulations and test ferroelectric switching models against real space measurements of local structure. This initiative opens the door to broadband infrared nano-imaging of heterogeneity in ferroics.

Finite-temperature simulation of anharmonicity and octahedral tilting transitions in halide perovskites

Octahedral tilting transitions are observed in most inorganic halide perovskites and play an important role in determining their functional and thermodynamic properties. Despite existing near room temperature, the cubic and tetragonal forms of halide perovskites become dynamically unstable at low temperature, making it impossible to study their thermodynamic properties with commonly used quasiharmonic models. An anharmonic vibrational Hamiltonian is constructed that accurately reproduces the low-energy portion of the potential-energy surface of the halide perovskite ${\mathrm{CsPbBr}}_{3}$. The Hamiltonian is validated using a large first-principles dataset of energies calculated within density functional theory for large-amplitude deformations of the ${\mathrm{CsPbBr}}_{3}$ crystal. Monte Carlo simulations performed on the Hamiltonian reproduce the orthorhombic-tetragonal-cubic phase transitions observed in ${\mathrm{CsPbBr}}_{3}$ and many other halide perovskites, demonstrating the importance of anharmonic vibrational excitations in stabilizing the tetragonal and cubic phases in these materials. Measures of local structure and octahedral tilting in the cubic and tetragonal phases, obtained from Monte Carlo simulations, confirm the connection between large anisotropic displacement factors and octahedral tilting, as observed experimentally.

Glass formation by severe plastic deformation of crystalline Cu|Zr nano-layers

We use molecular dynamics simulation to study the formation of glasses during severe plastic deformation of crystalline Cu|Zr nano-layers in a simple shear geometry. The early stage of plasticity is governed by dislocation plasticity. Dislocation-interface interaction induces interface roughening and slow atomic-level intermixing around interfaces. A solid-state crystal-to-amorphous transition starts near the interfaces. At high strain, the interfaces are refined to merge, leading to the formation of an intermixed glassy zone that eventually spans our simulation cell. Dislocation emission is then suppressed and strain is fully accommodated by this glassy phase. We characterize the crystal-to-amorphous transition using local structural measures, such as the pair distribution function and Voronoi analysis. The onset of glass formation occurs at a critical shear strain that increases with layer thickness. Our simulations indicate that the parameter controlling this onset is the theoretical affine interface distance, i.e. the amorphization occurs at a critical value of around 3–4 nm that increases slightly with the increase of layer thickness. Our work provides insights on mechanically driven glass formation in multicomponent systems, as e.g. realized in ball-mills or high-pressure torsion experiments.

Exploring Protein Conformational Diversity.

The native state of proteins is composed of conformers in dynamical equilibrium. In this chapter, different issues related to conformational diversity are explored using a curated and experimentally based database called CoDNaS (Conformational Diversity in the Native State). This database is a collection of redundant structures for the same sequence. CoDNaS estimates the degree of conformational diversity using different global and local structural similarity measures. It allows the user to explore how structural differences among conformers change as a function of several structural features providing further biological information. This chapter explores the measurement of conformational diversity and its relationship with sequence divergence. Also, it discusses how proteins with high conformational diversity could affect homology modeling techniques.

A comparison study of local lattice distortion in Ni80Pd20 binary alloy and FeCoNiCrPd high-entropy alloy

The effect of alloying Pd on the local lattice distortion (LLD) in the Ni and FeCoNiCr host matrixes is quantified by integrating local structure characterization and theoretical calculations. The local structure measurements reveal that the mean LLD in the FeCoNiCrPd high-entropy alloy (HEA) is twice as high as the Ni80Pd20 binary alloy though the FeCoNiCr base alloy has a negligible mean LLD. Density functional theory calculations unveil that the unexpected high mean LLD in FeCoNiCrPd is related to the high fluctuation of LLD in the FeCoNiCr matrix. These observations suggest a synergetic effect of chemical complexity on HEAs' mean LLD.

Deep Defects Seen on Visual Fields Spatially Correspond Well to Loss of Retinal Nerve Fiber Layer Seen on Circumpapillary OCT Scans.

PurposeTo examine the structure–function relationship in glaucoma between deep defects on visual fields (VF) and deep losses in the circumpapillary retinal nerve fiber layer (cpRNFL) on optical coherence tomography (OCT) circle scans.MethodsThirty two glaucomatous eyes with deep VF defects, as defined by at least one test location worse than ≤ −15 dB on the 10-2 and/or 24-2 VF pattern deviation (PD) plots, were included from 87 eyes with “early” glaucoma (i.e., 24-2 mean deviation better than −6 dB). Using the location of the deep VF points and a schematic model, the location of local damage on an OCT circle scan was predicted. The thinnest location of cpRNFL (i.e., deepest loss) was also determined.ResultsIn 19 of 32 eyes, a region of complete or near complete cpRNFL loss was observed. All 19 of these had deep VF defects on the 24-2 and/or 10-2. All of the 32 eyes with deep VF defects had abnormal cpRNFL regions (red, 1%) and all but 2 had a region of cpRNFL thickness <21 μm. The midpoint of the VF defect and the location of deepest cpRNFL had a 95% limit of agreement within approximately two-thirds of a clock-hour (or 30°) sector (between −22.1° to 25.2°). Individual fovea-to-disc angle (FtoDa) adjustment improved agreement in one eye with an extreme FtoDa.ConclusionsAlthough studies relating local structural (OCT) and functional (VF) measures typically show poor to moderate correlations, there is good qualitative agreement between the location of deep cpRNFL loss and deep defects on VFs.

Picometer-scale atom position analysis in annular bright-field STEM imaging

We study the effects of specimen mistilt on the picometer-scale measurement of local structure by combing experiment and simulation in annular bright-field scanning transmission electron microscopy (ABF-STEM). A relative distance measurement method is proposed to separate the tilt effects from the scan noise and sample drift induced image distortion. We find that under a typical experimental condition a small specimen tilt (∼6 mrad) in 25 nm thick SrTiO3 along [001] causes 11.9 pm artificial displacement between O and Sr/TiO columns in ABF image, which is more than 3 times of scan noise and sample drift induced image distortion ∼3.2 pm, suggesting the tilt effect could be dominant for the quantitative analysis of ABF images. The artifact depends on the crystal mistilt angle, specimen thickness, defocus, convergence angle and uncorrected aberration. Our study provides useful insights into detecting and correcting tilt effects during both experiment operation and data analysis to extract the real structure information and avoid mis-interpretations of atomic structure as well as the properties such as oxygen octahedral distortion/shift.

RBS Analysis of Zinc Telluride Thin Films by Electron Beam Evaporation Technique

To fully characterize the structure of these alloys it is necessary to augment crystallography with local structural measurements. Here Tellurium dioxide is doped with Zinc acetate dihydrate with Glycene to synthesis the powdered particles of ZnTe by simple chemical synthesis, Zinc acetate dihydrate is taking as the ratio of 90% and Tellurium dioxide as 10% this synthesized powdered particles were pelletized to evaporate on the glass plate by using Electron beam evaporation technique. So many researchers reported this technique for the same materials but RBS scattering is the one of the different analyzing technique for this materials. It has been observed that the energy in MeV of the element is well in agreement with Zinc and Telluride which is present in the preparation.