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At least 1,369 records · Page 76

Tracing the transient reaction kinetics of adsorbed species by in situ/operando infrared spectroscopy

The dynamic reaction behavior (i.e., transient responses) of IR-observable adsorbed species and gaseous products obtained from transient kinetic studies provide valuable kinetic and mechanistic information, namely: the abundance of active intermediates and their reactivity distribution, the chemical structure of IR-observable active and spectator species, the sequence of their formation, and the kinetically significant and rate-determining step under reaction conditions of practical catalysis. We discuss the use of transient response data to elucidate the reaction mechanisms of several gas-solid reactions: CO/H 2 , CO/H 2 /C 2 H 4 , photocatalytic oxidation of ethanol, and the CO 2 -amine reaction. The IR coupled with transient kinetic techniques is especially useful for investigating the mechanisms of photocatalytic reactions because both photogenerated electrons and many adsorbed species are IR-active (exhibiting measurable IR bands), and their evolution occurs on a time scale of seconds at ambient temperature. We highlight the key features and limitations of in situ IR with transient kinetics, as well as their significance in catalyst design.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Local Order in Liquid Gallium–Indium Alloys

Liquid metals such as eutectic Ga–In alloys have low melting points and low toxicity and are used in catalysis and micro-robotics. This study investigates the local atomic structure of liquid gallium-indium alloys by a combination of density measurements, diffraction data, and Monte-Carlo simulation via the empirical potential structure refinement approach. A high-Q shoulder observed in liquid Ga is related to structural rearrangements in the second coordination shell. Structure analysis found coordination environments close to a random distribution for eutectic Ga–In alloy, while electronic effects appear to dominate the mixing enthalpy.

36 MATERIALS SCIENCE↗

Atomically Precise Single-Site Catalysts via Exsolution in a Polyoxometalate–Metal–Organic-Framework Architecture

Single-site catalysts (SSCs) achieve a high catalytic performance through atomically dispersed active sites. A challenge facing the development of SSCs is aggregation of active catalytic species. Reducing the loading of these sites to very low levels is a common strategy to mitigate aggregation and sintering; however, this limits the tools that can be used to characterize the SSCs. Here we report a sintering-resistant SSC with high loading that is achieved by incorporating Anderson–Evans polyoxometalate clusters (POMs, MMo 6 O 24 , M = Rh/Pt) within NU-1000, a Zr-based metal–organic framework (MOF). The dual confinement provided by isolating the active site within the POM, then isolating the POMs within the MOF, facilitates the formation of isolated noble metal sites with low coordination numbers via exsolution from the POM during activation. The high loading (up to 3.2 wt %) that can be achieved without sintering allowed the local structure transformation in the POM cluster and the surrounding MOF to be evaluated using in situ X-ray scattering with pair distribution function (PDF) analysis. Notably, the Rh/Pt···Mo distance in the active catalyst is shorter than the M···M bond lengths in the respective bulk metals. Furthermore, models of the active cluster structure were identified based on the PDF data with complementary computation and X-ray absorption spectroscopy analysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Comparison of short-range order in irradiated dysprosium titanates

Abstract The structural response of Dy 2 TiO 5 oxide under swift heavy ion irradiation (2.2 GeV Au ions) was studied over a range of structural length scales utilizing neutron total scattering experiments. Refinement of diffraction data confirms that the long-range orthorhombic structure is susceptible to ion beam-induced amorphization with limited crystalline fraction remaining after irradiation to 8 × 10 12 ions/cm 2 . In contrast, the local atomic arrangement, examined through pair distribution function analysis, shows only subtle changes after irradiation and is still described best by the original orthorhombic structural model. A comparison to Dy 2 Ti 2 O 7 pyrochlore oxide under the same irradiation conditions reveals a different behavior: while the dysprosium titanate pyrochlore is more radiation resistant over the long-range with smaller degree of amorphization as compared to Dy 2 TiO 5 , the former involves more local atomic rearrangements, best described by a pyrochlore-to-weberite-type transformation. These results highlight the importance of short-range and medium-range order analysis for a comprehensive description of radiation behavior.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Powder diffraction

Powder diffraction is a non-destructive technique, which is experimentally simple in principle. Because the physics behind diffraction is well understood, an exceptionally large amount of information can be obtained from a single measurement. The positions and relative intensities of the peaks yield a fingerprint that can be used for qualitative phase analysis. Quantitative phase analysis can be obtained by detailed analysis of the intensities. Unit cells can be derived from the peak positions. Crystal structures can be solved using powder diffraction data and refined by the Rietveld method. The peak profiles contain information about crystallite size, strain and nanostructure. Non-idealities in the intensities give information on texture. Abandoning the crystallographic model provides information about local structure, by pair distribution function analysis. For powder diffraction, everything is a sample; the technique is commonly applied to characterize minerals, ceramics, metals and alloys, catalysts, polymers, pharmaceuticals, organic compounds, environmental and forensic samples, among others. The major features of contemporary laboratory powder diffractometers are described. Methods for obtaining suitable powder specimens are summarized. Major applications of qualitative and quantitative phase analysis, structure solution, size/strain/nanostructure analysis using peak profiles, texture analysis and pair distribution function analysis are introduced.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

New methodology for measuring electron density perturbations caused by plasma coherent modes using profile reflectometry: Magnitudes and radial profiles in DIII-D

New capabilities of fast-sweep frequency-modulated profile reflectometry are explored to measure electron density ne perturbation magnitudes and radial profiles due to plasma coherent modes in DIII-D. The first approach is based on the frequency analysis of phase perturbations associated with high frequency (~MHz) Alfvén eigenmodes (AEs). The measurement of ~5.5 MHz fast-ion-driven global Alfvén eigenmodes (GAEs) is demonstrated in a neutral beam-heated DIII-D plasma. The GAE induced a broad radial distribution of phase perturbations in the profile reflectometer data. Analysis of these data determined the effective cutoff location displacement and the estimated ne fluctuation profile. In the second approach, high resolution ne profiles are used directly to determine the radial structure of ne perturbations due to a neo-classical tearing mode. These new measurements broaden the application of profile reflectometry and advance the development of AE spectroscopy as a tool for non-invasive diagnosis of fast-ion-driven modes in DIII-D and burning plasmas such as ITER.

47 OTHER INSTRUMENTATION↗

DeepNeo: a webserver for predicting immunogenic neoantigens

Abstract Non-self epitopes, whether originated from foreign substances or somatic mutations, trigger immune responses when presented by major histocompatibility complex (MHC) molecules and recognized by T cells. Identification of immunogenically active neoepitopes has significant implications in cancer and virus medicine. However, current methods are mostly limited to predicting physical binding of mutant peptides and MHCs. We previously developed a deep-learning based model, DeepNeo, to identify immunogenic neoepitopes by capturing the structural properties of peptide-MHC pairs with T cell reactivity. Here, we upgraded our DeepNeo model with up-to-date training data. The upgraded model (DeepNeo-v2) was improved in evaluation metrics and showed prediction score distribution that better fits known neoantigen behavior. The immunogenic neoantigen prediction can be conducted at https://deepneo.net.

Kim, Jeong Yeon↗

Hadronic structure in high-energy collisions

Here, Parton distribution functions (PDFs) describe the structure of hadrons as composed of quarks and gluons. They are needed to make predictions for short-distance processes in high-energy collisions and are determined by fitting to cross-section data. Definitions of the PDFs and their relations to high-energy cross sections are reviewed. The focus is on the PDFs in protons, but PDFs in nuclei are also discussed. The standard statistical treatment needed to fit the PDFs to data using the Hessian method is reviewed in some detail. Tests are discussed that critically examine whether the needed assumptions are indeed valid. Also presented are some ideas of what one can do in case tests indicate that the assumptions fail.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

RadSim: Math, Utility & RTK

This package includes three parts, (1) gov.llnl.math, (2)gov.llnl.utility and (3)gov.llnl.rtk, which are utilized in the development of Radiation Detector Simulator (RadSim) project. RadSim is being developed to provide the capability to: (1) simulate radiation source emissions, (2) interpolate results from radiation transport tools into a common format to prepare incident flux, and (3) model radiation detector response to rapidly produce synthetic radiation measurement templates. RadSim is targeted for open-source release, which will enable researchers and industry partners to model gamma-ray detectors response to simulated flux from the transport tool of their choice. The techniques and implementation will be entirely transparent, which will allow for improvements and boutique modifications by future researchers beyond the lifespan of this specific project. The first tool of the package, gov.llnl.math, includes classes and functions to define and perform basic math operations. Some of the example features available in the package include defining statistical distributions and performing algebra and matrix operations, all of which are already accessible on publicly available software packages such as MATLAB and ROOT. The second package gov.llnl.utility includes tools commonly used to enable optimization and readability of various data structures such as Java lists and external xml files. Lastly, the gov.llnl.rtk package includes classes and functions to implement methods commonly used in radiation physics, such as data structures to represent and characterize photon spectra and tools to apply well-defined and published methods to calibrate a given spectra.

Cheung, Hoi Sing↗

Kinetic characterization of 3D magnetic reconnection: A transformative step (Final Report)

We investigated magnetic reconnection in the Earth’s magnetopause, magnetotail, and the bow shock, by means of fully kinetic simulations and analysis of space data obtained by NASA’s Magnetospheric Multiscale mission. We elucidated signatures of particle energization in particle distribution functions in the vicinity of reconnection X-line, properties of reconnection in shock-driven turbulence, and wave excitations and nonlinear structures. We advanced the understanding of magnetic reconnection from the viewpoint of particle kinetics in the diffusion region.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Cadmium alters whole animal ionome and promotes the re-distribution of iron in intestinal cells of Caenorhabditis elegans

The chronic exposure of humans to the toxic metal cadmium (Cd), either occupational or from food and air, causes various diseases, including neurodegenerative conditions, dysfunction of vital organs, and cancer. While the toxicology of Cd and its effect on the homeostasis of biologically relevant elements is increasingly recognized, the spatial distribution of Cd and other elements in Cd toxicity-caused diseases is still poorly understood. Here, we use Caenorhabditis elegans as a non-mammalian multicellular model system to determine the distribution of Cd at the tissue and cellular resolution and its effect on the internal levels and the distribution of biologically relevant elements. Using inductively coupled plasma-mass spectrophotometry (ICP-MS), we show that exposure of worms to Cd not only led to its internal accumulation but also significantly altered the C. elegans ionome. Specifically, Cd treatment was associated with increased levels of toxic elements such as arsenic (As) and rubidium (Rb) and a decreased accumulation of essential elements such as zinc (Zn), copper (Cu), manganese (Mn), calcium (Ca), cobalt (Co) and, depending on the Cd-concentration used in the assay, iron (Fe). We regarded these changes as an ionomic signature of Cd toxicity in C. elegans. We also show that supplementing nematode growth medium with Zn but not Cu, rescues Cd toxicity and that mutant worms lacking Zn transporters CDF-1 or SUR-7, or both are more sensitive to Cd toxicity. Finally, using synchrotron X-Ray fluorescence Microscopy (XRF), we showed that Cd significantly alters the spatial distribution of mineral elements. The effect of Cd on the distribution of Fe was particularly striking: while Fe was evenly distributed in intestinal cells of worms grown without Cd, in the presence of Cd, Fe, and Cd co-localized in punctum-like structures in the intestinal cells. Together, this study advances our understanding of the effect of Cd on the accumulation and distribution of biologically relevant elements. Considering that C. elegans possesses the principal tissues and cell types as humans, our data may have important implications for future therapeutic developments aiming to alleviate Cd-related pathologies in humans.

59 BASIC BIOLOGICAL SCIENCES↗

The Structural Characterisation and DFT-Aided Interpretation of Vibrational Spectra for Cyclo(l-Cys-d-Cys) Cyclic Dipeptide in a Solid State

Cyclic dipeptides with two intramolecular peptide bonds forming a six-membered 2,5-diketopiperazine ring are gaining significant attention due to their biological and chemical properties. Small changes in the local geometry of such molecules (from cis to trans) can lead to significant structural differences. This work presents the results of a study of cyclo(l-Cys-d-Cys), a dipeptide comprising two cysteine molecules in opposite chiral configurations, with the functional groups situated at both sides of the diketopiperazine ring. X-ray diffraction (XRD) experiment revealed that the molecule crystallises in the $P$-1 space group, which includes the centre of inversion. The IR and Raman vibrational spectra of the molecule were acquired and interpreted in terms of the potential energy distribution (PED) according to the results of density functional theory (DFT) calculations. The DFT-assisted analysis of energy frameworks for the hydrogen bond network within molecular crystals was performed to support the interpretation of X-ray structural data. The optimisation of the computational model based on three-molecule geometry sections from the crystallographic structure, selected to appropriately reflect the intermolecular interactions responsible for the formation of 1D molecular tapes in cyclo(l-Cys-d-Cys) crystal, allowed for better correspondence between theoretical and experimental vibrational spectra. This work can be considered the first complete structural characterisation of cyclo(l-Cys-d-Cys), complemented via vibrational spectroscopy results with full band assignment aided with the use of the DFT method.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Noble gas incorporation into silicate glasses: implications for planetary volatile storage

Incorporation of small molecules in silicate melts may provide an important mechanism for storing noble gases in the deep Earth, yet the means by which chemically inert noble gases enter and are retained in silica-based materials is not understood. High pressure, room temperature sound velocity measurements on silica and natural basalt glasses in different pressure-transmitting media reveal that neon enters the structure of silicate glasses and enhances their elastic strengths, whereas an ethanol-methanol mixture does not. Combined with literature data, we found the incorporation of small molecules into silica and basalt glasses is controlled by the void size distribution of the glass and size of the molecules. Pressure primarily reduces the size of noble gases, thereby increasing their solubilities in silicate melts and glasses.

58 GEOSCIENCES↗

Optimum structural design based on reliability and proof-load testing

Proof-load test eliminates structures with strength less than the proof load and improves the reliability value in analysis. It truncates the distribution function of strength at the proof load, thereby alleviating verification of a fitted distribution function at the lower tail portion where data are usually nonexistent.

Shinozuka, M.↗

Planetary astronomy program

A program was developed in which asteroids and two planets, namely, Saturn and Uranus, were investigated. This included: (1) asteroid spectrophotometry; (2) the nature of the Trojan asteroids; (3) an investigation to determine asteroid masses; (4) the photometry, structure, and dynamics of the rings surrounding the planet Saturn; and (5) aerosol distribution in the atmosphere of Uranus. Plans were finalized to obtain observations of the nucleus of the dying comet P/Arend-Rigaux. Further work was accomplished in asteroid data reduction. Data were entered into the TRIAD data file and a program generated classifications for over 560 different asteroids. A photoelectric area scanner was used to obtain UBV scans of the disk of the planet Saturn on several winter and spring nights in 1977. Intensity profiles show pronounced limb brightening in U, moderate limb brightening in B, and limb darkening in V. Narrow band photoelectric area-scanning photometry of the Uranus disk is also reported. Results are given.

Source record↗

The NASTRAN user's manual (level 17.0)

NASTRAN embodies a lumped element approach, wherein the distributed physical properties of a structure are represented by a model consisting of a finite number of idealized substructures or elements that are interconnected at a finite of grid points, to which loads are applied. All input and output data pertain to the idealized structural model. The general procedures for defining structural models are described and instructions are given for each of the bulk data cards and case control cards. Additional information on the case control cards and use of parameters is included for each rigid format.

Source record↗

Generic functional requirements for a NASA general-purpose data base management system

Generic functional requirements for a general-purpose, multi-mission data base management system (DBMS) for application to remotely sensed scientific data bases are detailed. The motivation for utilizing DBMS technology in this environment is explained. The major requirements include: (1) a DBMS for scientific observational data; (2) a multi-mission capability; (3) user-friendly; (4) extensive and integrated information about data; (5) robust languages for defining data structures and formats; (6) scientific data types and structures; (7) flexible physical access mechanisms; (8) ways of representing spatial relationships; (9) a high level nonprocedural interactive query and data manipulation language; (10) data base maintenance utilities; (11) high rate input/output and large data volume storage; and adaptability to a distributed data base and/or data base machine configuration. Detailed functions are specified in a top-down hierarchic fashion. Implementation, performance, and support requirements are also given.

Lohman, G. M.↗

The asteroid ring

From a statistical analysis of asteroid orbital period data, it is shown that the present distribution of asteroids is strongly correlated with the present orbital period of Jupiter (to 1 part in 5000). By analyzing the distribution of orbital eccentricities and inclinations it is shown that the resonant structure of the belt was formed after the asteroids dispersed from the near-coplanar disk in which they accreted.

Dermott, S. F.↗