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At least 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

From deep TLS validation to ensembles of atomic models built from elemental motions

Procedures are described for extracting the vibration and libration parameters corresponding to a given set of TLS matrices and their simultaneous validation. Knowledge of these parameters allows the generation of structural ensembles corresponding to these matrices. The translation–libration–screw model first introduced by Cruickshank, Schomaker and Trueblood describes the concerted motions of atomic groups. Using TLS models can improve the agreement between calculated and experimental diffraction data. Because the T, L and S matrices describe a combination of atomic vibrations and librations, TLS models can also potentially shed light on molecular mechanisms involving correlated motions. However, this use of TLS models in mechanistic studies is hampered by the difficulties in translating the results of refinement into molecular movement or a structural ensemble. To convert the matrices into a constituent molecular movement, the matrix elements must satisfy several conditions. Refining the T, L and S matrix elements as independent parameters without taking these conditions into account may result in matrices that do not represent concerted molecular movements. Here, a mathematical framework and the computational tools to analyze TLS matrices, resulting in either explicit decomposition into descriptions of the underlying motions or a report of broken conditions, are described. The description of valid underlying motions can then be output as a structural ensemble. All methods are implemented as part of the PHENIX project.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2016

Quantifying element incorporation in multispecies biofilms using nanoscale secondary ion mass spectrometry image analysis

Elucidating nutrient exchange in microbial communities is an important step in understanding the relationships between microbial systems and global biogeochemical cycles, but these communities are complex and the interspecies interactions that occur within them are not well understood. Phototrophic consortia are useful and relevant experimental systems to investigate such interactions as they are not only prevalent in the environment, but some are cultivable in vitro and amenable to controlled scientific experimentation. Nanoscale secondary ion mass spectrometry (NanoSIMS) is a powerful, high spatial resolution tool capable of visualizing the metabolic activities of single cells within a biofilm, but quantitative analysis of the resulting data has typically been a manual process, resulting in a task that is both laborious and susceptible to human error. In this work, the authors describe the creation and application of a semiautomated image-processing pipeline that can analyze NanoSIMS-generated data, applied to phototrophic biofilms as an example. The tool employs an image analysis process, which includes both elemental and morphological segmentation, producing a final segmented image that allows for discrimination between autotrophic and heterotrophic biomass, the detection of individual cyanobacterial filaments and heterotrophic cells, the quantification of isotopic incorporation of individual heterotrophic cells, and calculation of relevant population statistics. The authors demonstrate the functionality of the tool by using it to analyze the uptake of 15 N provided as either nitrate or ammonium through the unicyanobacterial consortium UCC-O and imaged via NanoSIMS. The authors found that the degree of 15N incorporation by individual cells was highly variable when labeled with 15 NH 4 + , but much more even when biofilms were labeled with 15 NO 3 – . In the 15 NH 4 + -amended biofilms, the heterotrophic distribution of 15 N incorporation was highly skewed, with a large population showing moderate 15 N incorporation and a small number of organisms displaying very high 15 N uptake. The results showed that analysis of NanoSIMS data can be performed in a way that allows for quantitation of the elemental uptake of individual cells, a technique necessary for advancing research into the metabolic networks that exist within biofilms with statistical analyses that are supported by automated, user-friendly processes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

High-Order Curvilinear Finite Element Methods for Lagrangian Hydrodynamics [High Order Curvilinear Finite Elements for Lagrangian Hydrodynamics]

The numerical approximation of the Euler equations of gas dynamics in a movingLagrangian frame is at the heart of many multiphysics simulation algorithms. Here, we present a general framework for high-order Lagrangian discretization of these compressible shock hydrodynamics equations using curvilinear finite elements. This method is an extension of the approach outlined in [Dobrev et al., Internat. J. Numer. Methods Fluids, 65 (2010), pp. 1295--1310] and can be formulated for any finite dimensional approximation of the kinematic and thermodynamic fields, including generic finite elements on two- and three-dimensional meshes with triangular, quadrilateral, tetrahedral, or hexahedral zones. We discretize the kinematic variables of position and velocity using a continuous high-order basis function expansion of arbitrary polynomial degree which is obtained via a corresponding high-order parametric mapping from a standard reference element. This enables the use of curvilinear zone geometry, higher-order approximations for fields within a zone, and a pointwise definition of mass conservation which we refer to as strong mass conservation. Moreover, we discretize the internal energy using a piecewise discontinuous high-order basis function expansion which is also of arbitrary polynomial degree. This facilitates multimaterial hydrodynamics by treating material properties, such as equations of state and constitutive models, as piecewise discontinuous functions which vary within a zone. To satisfy the Rankine--Hugoniot jump conditions at a shock boundary and generate the appropriate entropy, we introduce a general tensor artificial viscosity which takes advantage of the high-order kinematic and thermodynamic information available in each zone. Finally, we apply a generic high-order time discretization process to the semidiscrete equations to develop the fully discrete numerical algorithm. Our method can be viewed as the high-order generalization of the so-called staggered-grid hydrodynamics (SGH) approach and we show that under specific low-order assumptions, we exactly recover the classical SGH method. We also present numerical results from an extensive series of verification tests that demonstrate several important practical advantages of using high-order finite elements in this context.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2016

Overcoming element quality dependence of finite elements with adaptive extended stencil FEM (AES‐FEM)

Summary The finite element methods (FEMs) are important techniques in engineering for solving partial differential equations, but they depend heavily on element shape quality for stability and good performance. In this paper, we introduce the Adaptive Extended Stencil Finite Element Method (AES‐FEM) as a means for overcoming this dependence on element shape quality. Our method replaces the traditional basis functions with a set of generalized Lagrange polynomial basis functions , which we construct using local weighted least‐squares approximations. The method preserves the theoretical framework of FEM and allows imposing essential boundary conditions and integrating the stiffness matrix in the same way as the classical FEM. In addition, AES‐FEM can use higher‐degree polynomial basis functions than the classical FEM, while virtually preserving the sparsity pattern of the stiffness matrix. We describe the formulation and implementation of AES‐FEM and analyze its consistency and stability. We present numerical experiments in both 2D and 3D for the Poisson equation and a time‐independent convection–diffusion equation. The numerical results demonstrate that AES‐FEM is more accurate than linear FEM, is also more efficient than linear FEM in terms of error versus runtime, and enables much better stability and faster convergence of iterative solvers than linear FEM over poor‐quality meshes. Copyright © 2016 John Wiley & Sons, Ltd.

Conley, Rebecca↗
DOE OSTI2011

Structural Basis for Promoter ;#8722;10 Element Recognition by the Bacterial RNA Polymerase [sigma] Subunit

The key step in bacterial promoter opening is recognition of the -10 promoter element (T-{sub 12}A-{sub 11}T-{sub 10}A-{sub 9}A-{sub 8}T{sub -7} consensus sequence) by the RNA polymerase {alpha} subunit. We determined crystal structures of {alpha} domain 2 bound to single-stranded DNA bearing -10 element sequences. Extensive interactions occur between the protein and the DNA backbone of every -10 element nucleotide. Base-specific interactions occur primarily with A{sub -11} and T{sub -7}, which are flipped out of the single-stranded DNA base stack and buried deep in protein pockets. The structures, along with biochemical data, support a model where the recognition of the -10 element sequence drives initial promoter opening as the bases of the nontemplate strand are extruded from the DNA double-helix and captured by {alpha}. These results provide a detailed structural basis for the critical roles of A{sub -11} and T{sub -7} in promoter melting and reveal important insights into the initiation of transcription bubble formation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

Origin of sulfide replacement textures in lunar breccias. Implications for vapor element transport in the lunar crust

Lunar samples 67016,294, 67915,150, and 67016,297 represent clasts of Mg-suite and ferroan anorthosite lithologies that have interacted with a S-rich vapor. Numerous studies have speculated on the composition and source of these 'fluids', their capability for the transport of vapor-mobilized elements, and the scale and environment under which these types of process occurred. These models all assumed a Moon with a very 'dry' mantle, crust, and surface. The olivine in these lithologies is partially to totally replaced by troilite and low-Ca pyroxene. The troilite makes up 30-54 vol% of the troilite + low-Ca pyroxene pseudomorphs after olivine. Other silicates and oxides in the assemblages have experienced post-magmatic reequilibration (pyroxene exsolution, recrystallization, 'exsolution' of ilmenite in spinel). The troilite also occurs in veins cross cutting individual phases and metamorphic textures. The sulfide veining and replacement features are restricted to individual clasts and do not cut across the matrix surrounding the clasts, and thus predate the breccia-forming event. The proportion of troilite to low-Ca pyroxene and silicate chemistries indicate that simple reactions (such as olivine + S{sub 2} {leftrightarrow} low-Ca pyroxene + troilite + O{sub 2}) do not adequately represent the replacement process. The sulfides have compositions that are similar to those found in mare basalts. In particular, the sulfides generally are enriched in Co relative to Ni. Exsolution of Ni-Co-Cu in the sulfides is distinctly different between the breccias and mare basalts and suggests a different cooling or crystallization (melt versus vapor) history. The sulfur isotopic composition of the vein and replacement troilite ranges from approximately {delta}{sup 34}S = -1.0{per_thousand} to -3.3{per_thousand}. Based on our observations, it appears that the model suggested by Norman et al. (1995) is the most appropriate for the origin of the troilite veining and troilite-pyroxene pseudomorphs after olivine. Our data add significant definition to this model. This process occurs in the relatively shallow lunar crust on a scale that involves vapor interaction with multiple plutonic lithologies of various ages and compositions. These reactions occur at distinct conditions of f{sub S{sub 2}}, f{sub O{sub 2}}, and temperature. The reacting vapor is S-rich, and perhaps low in H. The reduction of the oxides in the clasts was not a product of H-streaming as has been suggested for similar textures in lunar rocks, but more likely related to 'S-streaming'. These vapors had the capability to transport chalcophile-siderophile elements. However, a proportion of the minor elements making up the troilite (Fe, Ni, Co) did come directly from the olivine being replaced. Further, there is evidence to suggest minor mobility of Mg from the olivine pseudomorphs into the adjacent pyroxene. One of the heat sources driving the transport of elements is closely tied to the emplacement of magmas into the shallow lunar crust. These intrusions were either the source for the S or provided heat to remobilized troilite already in the lunar crust. The process that drove the derivation of the S-rich volatiles was instrumental in fractionating the isotopic composition of S. The enrichment of S{sup 32} in the vapor phase may be attributed to either the stable S species during degassing (COS, S{sub 2} and CS{sub 2}) or the high-temperature partial breakdown of troilite in the shallow crust.

58 GEOSCIENCES↗
DOE OSTI2020

The role of ternary alloying elements in eutectoid transformation of U-10Mo alloy part II. In and Ex-situ Neutron diffraction-based assessment of eutectoid phase transformation kinetics in U-9.8Mo-0.2X alloy (X = Cr, Ni or Co)

HExploring the effects of minor ternary alloying additions, typically impurity elements, on the phase stability of U-10Mo is important for preventing undesirable phase decomposition during processing or during service. This work examines the influence small ternary additions of Cr, Ni, and Co. Both in-situ and ex-situ neutron diffraction measurements made during and after high temperature (450 – 525°C) exposures were used to better define the influence of these elements on the time-temperature-transformation (TTT) behavior of U-10Mo, providing information which is complementary to electron microscopy investigations of the same alloy systems performed in the first part of this work. Minor additions of Ni and Co decrease the ?-phase stability at all temperatures investigated. Signatures of U6X (X = Ni or Co) compounds were shown to be present in amounts of up to 6 wt% in the heat treated alloys, suggesting that the initial precipitation of this phase may catalyze further ?-phase decomposition. On the other hand, the Cr containing alloys were observed to have nearly the same, and in some cases slower, phase transformation kinetics when compared to the binary U-10Mo control samples. The results of the study have enabled preliminary estimates of the TTT curves for the ternary alloys.

phase transformation, kinetics, discontinuous prec↗
DOE OSTI2015

The Bionanoprobe: Synchrotron-Based Hard X-ray Fluorescence Microscopy for 2D/3D Trace Element Mapping

Trace elements, particularly metals, play an important role in a large variety of cellular processes in a biological system. In the context of biological organisms and tissues, the term trace element means that over the entire organisms an element is present at only trace levels, 100ppm or lower. Trace element distribution and content can be analyzed using several techniques, for example, visible light optical fluorescence imaging, energy-dispersive X-ray spectroscopy on an election microscope, synchrotron-based X-ray fluorescence (XRF) imagine,

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

A Low-Power, Radiation-Resistant, Silicon-Drift-Detector Array for Extraterrestrial Element Mapping

We are developing a modular Silicon Drift Detector (SDD) X-Ray Spectrometer (XRS) for measuring the abundances of light surface elements (C to Fe) fluoresced by ambient radiation on remote airless bodies. The value of fluorescence spectrometry for surface element mapping is demonstrated by its inclusion on three recent lunar missions and by exciting new data that have recently been announced from the Messenger Mission to Mercury. The SDD-XRS instrument that we have been developing offers excellent energy resolution and an order of magnitude lower power requirement than conventional CCDs, making much higher sensitivities possible with modest spacecraft resources. In addition, it is significantly more radiation resistant than x-ray CCDs and therefore will not be subject to the degradation that befell recent lunar instruments. In fact, the intrinsic radiation resistance of the SDD makes it applicable even to the harsh environment of the Jovian system where it can be used to map the light surface elements of Europa. In this paper, we first discuss our element-mapping science-measurement goals. We then derive the necessary instrument requirements to meet these goals and discuss our current instrument development status with respect to these requirements.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2020

Computationally aided, entropy-driven synthesis of highly efficient and durable multi-elemental alloy catalysts

Multi-elemental alloy nanoparticles (MEA-NPs) hold great promise for catalyst discovery in a virtually unlimited compositional space. However, rational and controllable synthesize of these intrinsically complex structures remains a challenge. Here, we report the computationally aided, entropy-driven design and synthesis of highly efficient and durable catalyst MEA-NPs. The computational strategy includes prescreening of millions of compositions, prediction of alloy formation by density functional theory calculations, and examination of structural stability by a hybrid Monte Carlo and molecular dynamics method. Selected compositions can be efficiently and rapidly synthesized at high temperature (e.g., 1500 K, 0.5 s) with excellent thermal stability. We applied these MEA-NPs for catalytic NH 3 decomposition and observed outstanding performance due to the synergistic effect of multi-elemental mixing, their small size, and the alloy phase. We anticipate that the computationally aided rational design and rapid synthesis of MEA-NPs are broadly applicable for various catalytic reactions and will accelerate material discovery.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Rare earth elements: Mendeleev’s bane, modern marvels

The rare earths (REs) are a family of 17 elements that exhibit pronounced chemical similarities as a group, while individually expressing distinctive and varied electronic properties. These atomistic electronic properties are extraordinarily useful and motivate the application of REs in many technologies and devices. From their discovery to the present day, a major challenge faced by chemists has been the separation of RE elements, which has evolved from tedious crystallization to highly engineered solvent extraction schemes. The increasing incorporation and dependence of REs in technology have raised concerns about their sustainability and motivated recent studies for improved separations to achieve a circular RE economy.

charge transport↗
DOE OSTI2016

Review of even element super-heavy nuclei and search for element 120

The reaction 54Cr$ + $248Cm was investigated at the velocity filter SHIP at GSI, Darmstadt, with the intention to study production and decay properties of isotopes of element 120. Three correlated signals were measured, which occurred within a period of 279ms. The heights of the signals correspond with the expectations for a decay sequence starting with an isotope of element 120. However, a complete decay chain cannot be established, since a signal from the implantation of the evaporation residue cannot be identified unambiguously. Measured properties of the event chain are discussed in detail. The result is compared with theoretical predictions. Previously measured decay properties of even element super-heavy nuclei were compiled in order to find arguments for an assignment from the systematics of experimental data. In the course of this review, a few tentatively assigned data could be corrected. New interpretations are given for results which could not be assigned definitely in previous studies. The discussion revealed that the cross-section for production of element 120 could be high enough so that a successful experiment seems possible with presently available techniques. However, a continuation of the experiment at SHIP for a necessary confirmation of the results obtained in a relatively short irradiation of five weeks is not possible at GSI presently. Furthermore, we decided to publish the results of the measurement and of the review as they exist now. In the summary and outlook section we also present concepts for the continuation of research in the field of super-heavy nuclei.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2017

Metallic Fuels Handbook, Part 1: Alloys Based on U-Zr, Pu-Zr, U-Pu, or U-Pu-Zr, Including Those with Minor Actinides (Np, Am, Cm), Rare-earth Elements (La, Ce, Pr, Nd, Gd), and Y; and Part 2: Elements and Alloys not Based on U-Zr, Pu-Zr, U-Pu, or U-Pu-Zr

The Metallic Fuels Handbook summarizes currently available information about phases and phase diagrams, heat capacity, thermal expansion, and thermal conductivity of elements and alloys in the U-Pu-Zr-Np-Am-La-Ce-Pr-Nd system. Although many sections are reviews and updates of material in previous versions of the Handbook, this revision is the first to include alloys with four or more elements. In addition to presenting information about materials properties, the handbook attempts to provide information about how well each property is known and how much variation exists between measurements. Although it includes some results from models, its primary focus is experimental data. Because of its size, the Handbook has been split into two parts, which are presented as separate documents. This (the first) part contains introductory material and information about the U-Pu-Zr system (U-Zr, Pu-Zr, U-Pu, and U-Pu-Zr alloys, including those with minor actinides, rare-earth elements, and Y). The second part contains information about elements and the remaining alloys in the U-Np-Pu-Am-La-Ce-Pr-Nd-Zr system.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2021

Analysis of Element Size and Element Type on SS304L Material Model Performance

Finite element solutions are only valid if the information inputted into the models is a valid assumption. This is why it is important to determine if the model behaves as expected especially in the material response. Material models that consider deformation in the elastic and plastic regions are desirable. As a material deforms plastically, hardening will occur until the ultimate strength is reached due to the reduction of the cross sectional area in a uniaxial tensile test environment. A phenomenological approximation of this behavior which is known as power law hardening (plh) can be expressed as σ = σ y + K $ϵ^{n}_{p}$ where K and n are empirically determined constants, and σ y is the proportional limit of the material. The first objective of this study is to verify the behavior for a calibrated plh material model for selective deviatoric hexahedral elements when applied to a different material stock. The Sierra SM input for this calibrated model can be found in the appendix. The second objective of this study is to determine the differences in failure characteristics for considerably large shell elements versus that of fine hexahedral elements.

36 MATERIALS SCIENCE↗