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At least 1,459 records · Page 81

Applications of NMR and computational methodologies to study protein dynamics

The overwhelming evidence now illustrates the defining role of atomic-scale protein flexibility in biological events such as allostery, cell signaling, and enzyme catalysis. Over the years, spin relaxation nuclear magnetic resonance (NMR) has provided significant insights on the structural motions occurring on multiple time frames over the course of a protein life span. The present review article aims to illustrate to the broader community how this technique continues to shape many areas of protein science and engineering, in addition to being an indispensable tool for studying atomic-scale motions and functional characterization. Continuing developments in underlying NMR technology alongside software and hardware developments for complementary computational approaches now enable methodologies to routinely provide spatial directionality and structural representations traditionally harder to achieve solely using NMR spectroscopy. In addition to its well-established role in structural elucidation, we present recent examples that illustrate the combined power of selective isotope labeling, relaxation dispersion experiments, chemical shift analyses, and computational approaches for the characterization of conformational sub-states in proteins and enzymes.

59 BASIC BIOLOGICAL SCIENCES↗

Detailed characterization of the LLNL imaging proton spectrometer

Ultra-intense short pulse lasers incident on solid targets (e.g., thin Au foils) produce well collimated, broad-spectrum proton beams. These proton beams can be used to characterize magnetic fields, electric fields, and density gradients in high energy-density systems. The LLNL-Imaging Proton Spectrometer (L-IPS) was designed and built [H. Chen et al., Rev. Sci. Instrum. 81, 10D314 (2010)] for use with such laser produced proton beams. The L-IPS has an energy range of 50 keV-40 MeV with a resolving power (E/dE) of about 275 at 1 MeV and 21 at 20 MeV, as well as a single spatial imaging axis. In order to better characterize the dispersion and imaging capability of this diagnostic, a 3D finite element analysis solver is used to calculate the magnetic field of the L-IPS. Particle trajectories are then obtained via numerical integration to determine the dispersion relation of the L-IPS in both energy and angular space.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Spatial quantification of maps or images - Cell size or pixel size implications

The paper discusses spatial quantification of maps or images. Spatial accuracies evaluated by mapping and inventory measures were observed with a range of cell sizes for a 10.36 sq km soil survey segment. The distribution of interboundary distances in a map was evaluated as unique, characterizing information; experimentally observed relationships between accuracy and cell size and interboundary distance distribution parameters and cell size led to a model of the process of spatial quantization. Grid positioning effects were evaluated and were significant only at the level of individual mapping units; two generations of 'universal' process models were derived, implemented, and evaluated.

Wehde, M. E.↗

Development and characterization of monolithic multilayer Laue lens nanofocusing optics

We have developed an experimental approach to bond two independent linear Multilayer Laue Lenses (MLLs) together. A monolithic MLL structure was characterized using ptychography at 12 keV photon energy, and we demonstrated 12 nm and 24 nm focusing in horizontal and vertical directions, respectively. Fabrication of 2D MLL optics allows installation of these focusing elements in more conventional microscopes suitable for x-ray imaging using zone plates, and opens easier access to 2D imaging with high spatial resolution in the hard x-ray regime.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Quantitative Imaging of Cobalt Phthalocyanine Distribution on Carbon Nanotubes: A Deep Learning Approach to Catalyst Characterization

Electrochemical reduction of carbon dioxide (CO 2 ) offers a pathway to valuable products, with catalysts playing a crucial role. This study investigates the distribution of cobalt tetraaminophthalocyanine (CoPc-NH 2 ) immobilized on carbon nanotubes (CNTs), utilizing high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM) to characterize CoPc-NH 2 distribution. A challenge in the quantitative HAADF-STEM analysis is the introduction of bias from manual Co atom identification. To address this, we developed and trained a convolutional neural network (CNN) using a data set generated from images of CoPc-NH 2 /CNT samples with varying Co loadings. The CNN, implemented in TensorFlow and Keras, facilitated Co atom detections. Analysis of the CNN-generated data confirmed a correlation between Co loading and surface density, consistent with findings from UV–vis spectroscopy. Furthermore, the application of Ripley’s L(d) function highlighted the presence of slight Co atom clustering. Furthermore, this work demonstrates the utility of the combined HAADF-STEM and CNN approach for providing spatially resolved information about catalyst distribution on nonplanar supports, revealing structural details that are typically lost through other characterization methods.

HAADF-STEM↗

Aerothermodynamic Measurements in Hypersonic Non-Equilibrium Flows

High enthalpy arc-jets are unique facilities particularly suited for simulating complex flows in the aerospace field, such as the aerothermodynamics of a re-entry vehicle. Arc-jets are often used to evaluate important design factors such as heat shield materials and vehicle design. Characterization of these facilities is important, as studies often match specific in-flight environments during experiments. Due to the complex environment produced by an arc-jet, with effects such as thermodynamic and chemical non-equilibrium occurring in the flow, characterization experiments are significantly more difficult than in traditional blow-down wind tunnels. The current work aims to characterize an arc-jet facility in terms of flow temperature, velocity and unsteadiness, in a spatially-resolved analysis. To achieve this goal, a non-intrusive imaging technique called “planar laser-induced fluorescence” was performed in the NASA Langley Hypersonic Materials Environ-mental Test System arc-jet facility. The experimental data was analyzed to produce the quantitative measurements in multiple regions of the flow around a blunt body sample. A quasi-1D low fidelity solver was created to numerically simulate the flow to investigate non-equilibrium effects occur-ring outside the imaging region in the arc-jet nozzle. Unsteadiness in the test section was minimized by analyzing a subset of data assessing the gas injection location. Radial velocity, rotational temperature and translational temperature measurements are provided that can be used to validate future high-fidelity computational studies. The temperature measurements revealed rotational non-equilibrium potentially occurring in the flow. This work provides a methodology for characterizing arc-jet facilities, identifying and correcting sources of systematic error, and estimating the uncertainty associated with the quantitative measurements.

laser induced fluorescence↗

Transport of High-energy Charged Particles through Spatially Intermittent Turbulent Magnetic Fields

Identifying the sources of the highest energy cosmic rays requires understanding how they are deflected by the stochastic, spatially intermittent intergalactic magnetic field. Here we report measurements of energetic charged-particle propagation through a laser-produced magnetized plasma with these properties. We characterize the diffusive transport of the particles experimentally. The results show that the transport is diffusive and that, for the regime of interest for the highest-energy cosmic rays, the diffusion coefficient is unaffected by the spatial intermittency of the magnetic field.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Transport coefficient approach for characterizing nonequilibrium dynamics in soft matter

Nonequilibrium states in soft condensed matter require a systematic approach to characterize and model materials, enhancing predictability and applications. Among the tools, X-ray photon correlation spectroscopy (XPCS) provides exceptional temporal and spatial resolution to extract dynamic insight into the properties of the material. However, existing models might overlook intricate details. We introduce an approach for extracting the transport coefficient, denoted as $J(t)$, from the XPCS studies. This coefficient is a fundamental parameter in nonequilibrium statistical mechanics and is crucial for characterizing transport processes within a system. Our method unifies the Green–Kubo formulas associated with various transport coefficients, including gradient flows, particle–particle interactions, friction matrices, and continuous noise. We achieve this by integrating the collective influence of random and systematic forces acting on the particles within the framework of a Markov chain. We initially validated this method using molecular dynamics simulations of a system subjected to changes in temperatures over time. Subsequently, we conducted further verification using experimental systems reported in the literature and known for their complex nonequilibrium characteristics. The results, including the derived $J(t)$ and other relevant physical parameters, align with the previous observations and reveal detailed dynamical information in nonequilibrium states. This approach represents an advancement in XPCS analysis, addressing the growing demand to extract intricate nonequilibrium dynamics. Further, the methods presented are agnostic to the nature of the material system and can be potentially expanded to hard condensed matter systems.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

THE ISLANDS PROJECT. I. ANDROMEDA XVI, AN EXTREMELY LOW MASS GALAXY NOT QUENCHED BY REIONIZATION

Based on data aquired in 13 orbits of Hubble Space Telescope time, we present a detailed evolutionary history of the M31 dSph satellite Andromeda XVI, including its lifetime star formation history (SFH), the spatial distribution of its stellar populations, and the properties of its variable stars. And XVI is characterized by prolonged star formation activity from the oldest epochs until star formation was quenched ∼6 Gyr ago, and, notably, only half of the mass in stars of And XVI was in place 10 Gyr ago. And XVI appears to be a low-mass galaxy for which the early quenching by either reionization or starburst feedback seems highly unlikely, and thus it is most likely due to an environmental effect (e.g., an interaction), possibly connected to a late infall in the densest regions of the Local Group. Studying the SFH as a function of galactocentric radius, we detect a mild gradient in the SFH: the star formation activity between 6 and 8 Gyr ago is significantly stronger in the central regions than in the external regions, although the quenching age appears to be the same, within 1 Gyr. We also report the discovery of nine RR Lyrae (RRL) stars, eight of which belong to And XVI. The RRL stars allow a new estimate of the distance, (m − M){sub 0} = 23.72 ± 0.09 mag, which is marginally larger than previous estimates based on the tip of the red giant branch.

79 ASTRONOMY AND ASTROPHYSICS↗

Scanning Transmission Electron Microscopy–Atom Probe Tomography Correlative Analysis for the Characterization of Solute-defect Interactions

Atom probe tomography (APT) and (scanning) transmission electron microscopy ((S)TEM) are complementary techniques that provide spatially resolved chemical and structural information at the atomic scale. Here, in this study, we employ two different STEM/APT correlative analysis methods to investigate Cr segregation at dislocation loops in ultra-high purity Fe–Cr alloys. APT needles for the correlative analysis were extracted either from bulk material or from thinned TEM lamellae. STEM analysis was used to determine the Burgers vectors of ion-irradiation-induced dislocation loops, while APT reconstruction of the same region revealed the Cr segregation to these loops. We extended the g•b = 0 invisibility criterion of dislocation loops from TEM mode in a lamella to STEM mode in a needle-shaped specimen. STEM and APT analysis on the same needle provide straightforward correlative analysis, although it is limited by a small observation volume. In contrast, iterative STEM analysis of TEM lamellae, followed by the selective extraction of specific regions of interest for APT analysis, expands the observation area by up to 100 times but requires additional time-consuming steps for APT needle extraction from the lamellae.

47 OTHER INSTRUMENTATION↗

Characterization of the yeast copper-inducible promoter system in Arabidopsis thaliana

Inducible promoters or gene-switches are used to both spatially and temporally regulate gene expression. Such regulation can provide information concerning the function of a gene in a developmental context as well as avoid potential harmful effects due to overexpression. A gfp construct under the control of a copper-inducible promoter was introduced into Arabidopsis thaliana (L.) Heynh. and the regulatory parameters of this inducible promoter were determined. Here, we describe the time-course of up- and down-regulation of GFP expression in response to copper level, the optimal regulatory levels of copper, and the tissue specificity of expression in three transgenic lines. We conclude that the copper-inducible promoter system may be useful in regulating the time and location of gene expression in A. thaliana.

Non-NASA Center↗

High-Spatial-Resolution Quantitative Chemomechanical Mapping of Organic Composite Cathodes for Sulfide-Based Solid-State Batteries

Understanding the chemo-mechanical behaviors of electrodes, particularly at the electrode/electrolyte interfaces, is critical for improving the performance of all-solid-state batteries. However, due to the instability of electrolyte materials under ambient conditions, such characterizations are challenging, particularly for sulfide-based all-solid-state batteries. Herein, by combining time-of-flight secondary-ion mass spectroscopy (ToF-SIMS) and in-SEM nanoindentation measurements, a systematic quantitative investigation of the chemo-mechanical behaviors of pyrene-4,5,9,10-tetraone (PTO) /Li 6 PS 5 Cl composite cathodes is carried out. Chemical and quantitative mechanical information of the composite cathode were collected with high spatial resolution after developing and implementing an air-free characterization protocol. By directly connecting the Young’s modulus and hardness with the Li distribution in the composite cathode, a comprehensive chemo-mechanical mapping of the PTO/ Li 6 PS 5 Cl composite cathode has been established. Furthermore, this work improves our knowledge of the critical chemo-mechanical phenomena that occur at the cathode/electrolyte interfaces in all-solid-state batteries.

25 ENERGY STORAGE↗

String-based model with Hagedorn temperature of 𝑇 𝐻 ∼ 300 MeV describes the spectrum of mesons and glueballs

We consider the thermodynamics of a color-confined phase of quantum chromodynamics (QCD) and pure gauge theory within a string-inspired corresponding to a physical spatial dimension, 𝑑 = 3. We show that the physical mass spectrum of massive mesons—in both the strange and nonstrange sectors separately—is reasonably well described and extended by the exponential mass spectrum of open strings, 𝜌⁡(𝑚), characterized by a unique Hagedorn temperature 𝑇 𝐻 = $\sqrt3⁢𝜎/2⁢𝜋$, expressed by the string tension 𝜎. This 𝑇 𝐻 is the value appropriate for 𝑑 = 3 spatial dimensions and is of the order of 𝑇 𝐻 ∼ 300 MeV for typical values of the string tension. It is much larger than the values of 𝑇 𝐻 which have been phenomenologically extracted so far to describe the meson spectrum. Glueball states in pure gauge theory, modeled by closed strings, exhibit a similarly large Hagedorn temperature, highlighting a universal feature of the exponential spectrum. We further analyze the thermodynamic properties of the equation of state at finite temperature and demonstrate that, in the confined phase, the string models agree with lattice QCD results. This lends further support to the recent interpretation of the QCD phase diagram that incorporates strings as relevant degrees of freedom.

Phase transitions↗

The dilation aided single–line–of–sight x–ray camera for the National Ignition Facility: Characterization and fielding

Crystal x–ray imaging is commonly used in inertial confinement fusion and laser-plasma interaction applications as it has advantages compared to pinhole imaging, such as higher signal throughput, better achievable spatial resolution, and chromatic selection. Yet, currently used x–ray detectors are only able to obtain a single time resolved image per crystal. The dilation aided single–line–of–sight x–ray camera described here was designed for the National Ignition Facility (NIF) and combines two recent diagnostic developments, the pulse dilation principle used in the dilation x-ray imager and a ns–scale multi-frame camera that uses a hold and readout circuit for each pixel. This enables multiple images to be taken from a single–line–of–sight with high spatial and temporal resolution. Presently, the instrument can record two single–line–of–sight images with spatial and temporal resolution of 35 μm and down to 35 ps, respectively, with a planned upgrade doubling the number of images to four. Here we present the dilation aided single–line–of–sight camera for the NIF, including the x–ray characterization measurements obtained at the COMET laser, as well as the results from the initial timing shot on the NIF.

47 OTHER INSTRUMENTATION↗

Correlative X-ray micro-nanotomography with scanning electron microscopy at the Advanced Light Source

Geological samples are inherently multi-scale. Understanding their bulk physical and chemical properties requires characterization down to the nano-scale. A powerful technique to study the three-dimensional microstructure is X-ray tomography, but it lacks information about the chemistry of samples. To develop a methodology for measuring the multi-scale 3D microstructure of geological samples, correlative X-ray micro- and nanotomography were performed on two rocks followed by scanning electron microscopy with energy-dispersive spectroscopy (SEM-EDS) analysis. The study was performed in five steps: (i) micro X-ray tomography was performed on rock sample cores, (ii) samples for nanotomography were prepared using laser milling, (iii) nanotomography was performed on the milled sub-samples, (iv) samples were mounted and polished for SEM analysis and (v) SEM imaging and compositional mapping was performed on micro and nanotomography samples for complimentary information. Correlative study performed on samples of serpentine and basalt revealed multiscale 3D structures involving both solid mineral phases and pore networks. Significant differences in the volume fraction of pores and mineral phases were also observed dependent on the imaging spatial resolution employed. This highlights the necessity for the application of such a multiscale approach for the characterization of complex aggregates such as rocks. Information acquired from the chemical mapping of different phases was also helpful in segmentation of phases that did not exhibit significant contrast in X-ray imaging. Adoption of the protocol used in this study can be broadly applied to 3D imaging studies being performed at the Advanced Light Source and other user facilities.

58 GEOSCIENCES↗

Three-dimensional characterization of hardened paste of hydrated tricalcium silicate by serial block-face scanning electron microscopy

With the application of a three-dimensional (3D) characterization technique, serial block-face scanning electron microscopy (SBFSEM), the 3D microstructure of a hydrated cement monomineral, tricalcium silicate (C 3 S), was measured with nanoscale resolution. The 3D morphologies of anhydrous particles, hydrated products, and capillary pores were visualized. Closed and open pores were discovered inside an anhydrous particle. The size and distribution of both the anhydrous C 3 S particles and their capillary pores were analyzed quantitatively and the porosity was determined to be 9%. The distribution of pores was found to be in a good agreement with the inner and outer product model of Hu et. al., with an inner shell distance of 860 nm. Here, considering the spatial resolution of the instrument and the volume of sample measured, most pores in this experiment could be characterized as capillary pores.

3D microstructure↗

Detection of surface water temperature variations of Mongolian lakes benefiting from the spatially and temporally gap-filled MODIS data

Lakes provide critical water resources for human activities and ecosystems, particularly in the Mongolian Plateau (MP), which is characterized by a dry climate and a harsh environment. As a region that is sensitive to anthropogenic warming, tracking lake surface water temperature (LSWT) changes in Mongolian lakes is crucial for understanding the consequences of a warming climate on lake ecosystems. However, the long-term monitoring of LSWT is restricted by the spatiotemporal gaps in the raw imagery of remote sensing-based land surface temperature (LST), e.g., the commonly used Moderate Resolution Imaging Spectroradiometer (MODIS) LST products. This study applied an improved gap-filling method by utilizing the discrete cosine transform-based penalized least squares (DCT-PLS) strategy in the spatial domain combined with the linear interpolation (LI) algorithm in the temporal domain. The method was applied to fill gaps in the LSWT imagery of 12 representative lakes across MP. The randomly sampled high-quality MODIS LSWT values in the spatial and temporal domains were excavated as false data gaps and considered “virtual true” validation datasets. The spatial validation results showed that the estimated LSWT for all the lake cases were comparable with the “virtual true” LSWT values, with the average values of the coefficient of determination, mean absolute error, mean square error, and root mean square error being 0.98, 0.38 °C, 0.45 °C, and 0.59 °C, respectively. Meanwhile, the error of nighttime LSWT results was relatively lower than that of daytime LSWT. For temporal interpolation validation, the LI algorithm exhibited relatively better performance and could more objectively indicate the variation in LSWT. Benefiting from the spatially and temporally well-constrained data, we analyzed the interannual and intra-annual change characteristics of the LSWTs of the 12 lakes. The long-term variations of annual and seasonal mean LSWTs in the 12 selected lakes exhibited no evident trends in 2000–2020, while presented apparent interannual fluctuations. The slight changes in the average LSWTs of the 12 selected lakes were in excellent synchronization with the surrounding LST derived from the reanalysis datasets, confirming the widely reported phenomenon of “global warming hiatus” that occurred in the early 21st century. This study improves the understanding of the LSWT variations in Mongolian lakes in response to global climate change. It has the potential to provide an effective approach for monitoring LSWT changes in other large-scale studies.

54 ENVIRONMENTAL SCIENCES↗

Solutions of the Taylor-Green Vortex Problem Using High-Resolution Explicit Finite Difference Methods

A computational fluid dynamics code that solves the compressible Navier-Stokes equations was applied to the Taylor-Green vortex problem to examine the code s ability to accurately simulate the vortex decay and subsequent turbulence. The code, WRLES (Wave Resolving Large-Eddy Simulation), uses explicit central-differencing to compute the spatial derivatives and explicit Low Dispersion Runge-Kutta methods for the temporal discretization. The flow was first studied and characterized using Bogey & Bailley s 13-point dispersion relation preserving (DRP) scheme. The kinetic energy dissipation rate, computed both directly and from the enstrophy field, vorticity contours, and the energy spectra are examined. Results are in excellent agreement with a reference solution obtained using a spectral method and provide insight into computations of turbulent flows. In addition the following studies were performed: a comparison of 4th-, 8th-, 12th- and DRP spatial differencing schemes, the effect of the solution filtering on the results, the effect of large-eddy simulation sub-grid scale models, and the effect of high-order discretization of the viscous terms.

DeBonis, James R.↗