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At least 271 records · Page 15

pyDiSCaMB : enabling the use of multipolar scattering factors in Phenix

Multipolar scattering models, such as the transferable aspherical atom model, account for atomic chemical interactions and provide a more accurate representation of experimental data. However, the simpler independent atom model (IAM), which assumes non-interacting atoms, is the only model available in the most widely used macromolecular refinement programs. This is primarily because IAM offers a hard-to-beat combination of computational efficiency and modelling power at typical macromolecular resolutions. By contrast, more accurate multipolar modelling has historically been limited due to its computational cost and the absence of an interface between software capable of calculating structure factors and gradients based on multipolar models and software designed for macromolecular refinement. This work introduces pyDiSCaMB , a Python software package designed to integrate between the computational crystallography toolbox ( cctbx ) and the quantum crystallography library DiSCaMB ( Densities in Structural Chemistry and Molecular Biology ), thus enabling multipolar scattering models in Phenix 's toolkit. The implementation, features and capabilities of pyDiSCaMB are presented, the runtimes for the calculation of structure factor and target gradients with respect to atomic parameters are explored, and Fourier images of electrostatic potential, electron density and deformation maps are computed as illustrative examples. The pyDiSCaMB library will make multipolar modelling widely available to the structural biology community, potentially transforming refinement and model-building for both crystallography and cryogenic electron microscopy (cryoEM).

MATTS data bank↗

Estimating tropical cyclone outer surface winds from satellite microwave data

Warm temperature anomalies over tropical cyclones are sensed by the 55.45 GHz channel of the Nimbus 6 Scanning Microwave Spectrometer. Radial brightness temperature gradients are related to radial surface pressure gradients through the hydrostatic and radiative transfer equations. Surface wind speeds outside of the radius of maximum wind are calculated from the pressure gradients and compared with observations.

Kidder, S. Q.↗

Null Space Monte Carlo Evaluation of the Plateau to River Model

The Plateau to River Groundwater Model (P2R Model) is a groundwater flow and contaminant fate and transport (F&T) simulation model used to support remedial activities conducted by CH2M HILL Plateau Remediation Company at the Hanford Site in Washington State. Figure 1-1 illustrates the P2R Model extents, discretization, and boundary conditions. The P2R Model provides a computational framework to simulate the F&T of contaminants in groundwater associated with the 200-PO-1, 200-UP-1, 200-BP-5, and 200-ZP-1 Groundwater Operable Units (OUs) in the Hanford Site Central Plateau. In addition, the model includes adjacent areas and facilities (e.g., the State Approved Land Disposal Site). Intended and anticipated uses of the model include calculating water levels, hydraulic gradients, and groundwater flows throughout the model domain (encompassing the 200 West and 200 East Areas) for use in subsequent F&T calculations for contaminants of concern and developing scale-appropriate, telescopic-mesh refinement models for detailed evaluation of areas within the model domain where required. The overall objective of the modeling effort is to provide a basis for making informed remedial action decisions based on descriptions of current and expected future contaminant concentrations in groundwater at decision points within the OU boundaries. The objective for the model development phase is to create a common modeling platform that can be used for investigations of the Central Plateau groundwater OUs and areas downgradient toward the Columbia River. The P2R Model calibration to historical data observed at the Hanford Site is documented in CP-57037, Model Package Report for the Plateau to River Model Version 8.3. The purpose of this environmental calculation is to describe a null space Monte Carlo (NSMC) evaluation was conducted with the historic calibration of the P2R model. Use of numerical groundwater models is always accompanied with uncertainty in the results produced by a model because models are approximations of reality. Thus, by definition, lack the detail to fully represent observed behavior. Use of numerical techniques, such as a NSMC analysis, can help in identifying and quantifying the potential uncertainties associated with a numerical model such as the P2R Model. Use of the NSMC approach results in 100 groundwater flow models that are variants of the calibrated P2R Model. These variant models can be used to evaluate uncertainty in model predictions made by the calibrated P2R Model for other analyses. A secondary purpose of the environmental calculation is to establish these variant models for use with other applications.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

MOOSE-Based Fast Reactor Core Bowing Capabilities: Coupled Structural Mechanics – Thermal Fluids Demonstration and Related Verification Efforts

Under the U.S. Department of Energy Office of Nuclear Energy’s Advanced Modeling and Simulation (NEAMS) Program, an integrated multiphysics approach is being developed to model the core bowing phenomena important to liquid metal-cooled fast reactors. Core bowing is an important passive safety mechanism in liquid metal-cooled fast reactors and involves multiphysics effects including radiation transport, fluid flow, heat transfer, and mechanical response to temperature and flux gradients. Verification and assessment efforts continued on the Multiphysics Object Oriented Simulation Environment (MOOSE) capabilities relevant for modeling thermo-mechanical core bowing behavior. IAEA Verification Problem 4, which was started in FY23, was further examined with MOOSE capabilities to rectify discrepancies observed in previous years when compared to IAEA benchmark participant data. Meshing and postprocessing capabilities in MOOSE were also advanced by other teams and utilized this year. A thermal fluids-structural mechanical coupling demonstration has performed on 7-assemblyand 19-assembly fast reactor assembly configurations using MOOSE. Subchannel capabilities are used to calculate coolant temperature, and heat conduction capabilities calculate duct wall temperature as well as heat transfer through the inter-assembly gap. Structural mechanical capabilities then deform the mesh, accounting for contact between assemblies, according to the temperature gradients calculated by the thermal solvers. Power distributions are imposed rather than calculated to demonstrate different deformations.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

The structural and electronic properties of cubic AgMO{sub 3} (M=Nb, Ta) by first principles calculations

We report the electronic structure of the AgMO{sub 3}(M=Nb, Ta) within the frame work of density functional theory and calculations are performed within the generalized gradient approximation (GGA) by using ultrasoft pseudopotentials. The calculated equilibrium lattice parameters and volumes are extracted from fitting of Birch third order equation of state and which are reasonable agreement with the available experimental results. The density of states,band structure of Ag(Nb,Ta)O{sub 3} reveals that the valance bands mostly occupied with O-2p and O-2s states and whereas conduction band occupied with Nb (Ta) 4d(5d) states including less contribution from Ag 5s states.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Recovering the real density field of galaxies from redshift space

This paper proposes a number of methods for recovering the true, real-space large-scale density distributions from redshift data sets. On the largest scales, the effects of peculiar velocities is to compress the galaxy clustering along the line of sight and consequently the density gradient in the radial direction is enhanced in comparison with the density gradient perpendicular to the line of sight. We calculate the relation between the density gradients in real and redshift space in the linear regime and show that it is a simple function of the density parameter, Omega. By considering the anisotropy of density gradients in redshift space it is possible, in principle, to obtain information about the value of Omega. Using N-body simulations we examine different methods for correcting the effects of large-scale velocities to obtain the true density distributions. We derive the peculiar velocity field from the redshift data and iterate to place each galaxy at a distance consistent with its measured redshift and its derived velocity. Linear theory, as well as second-order solutions for the peculiar velocity field are tested. The density distributions in low-density regions predicted by both linear theory and second-order theory are similar, and in good agreement with the true density field in the simulation. The use of the second-order corrections improves the prediction of the density field in high-density regions.

Gramann, Mirt↗

ISEE-3/IMP-8 observations of simultaneous upstream proton events

Upstream 50-200 keV proton events were observed simultaneously by the low energy proton detectors on ISEE-3 and IMP-8, and the gradient from the spin averaged fluxes at the two spacecraft was calculated. The dependence of that gradient upon the angular distributions at IMP-8 was investigated as well as the distance from IMP-8 to the bow shock. The pitch angle distributions are narrow at ISEE-3 and wide and often pancake-shaped at IMP-8 with a peak near 90 degrees. This implies the existence of a weak scattering region about 5-15 earth radii upstream of the earth's bow shock.

Sanderson, T. R.↗

Force Balance at the Magnetopause Determined with MMS: Application to Flux Transfer Events

The Magnetospheric Multiscale mission (MMS) consists of four identical spacecraft forming a closely separated (less than or equal to 10 km) and nearly regular tetrahedron. This configuration enables the decoupling of spatial and temporal variations and allows the calculation of the spatial gradients of plasma and electromagnetic field quantities. We make full use of the well cross-calibrated MMS magnetometers and fast plasma instruments measurements to calculate both the magnetic and plasma forces in flux transfer events (FTEs) and evaluate the relative contributions of different forces to the magnetopause momentum variation. This analysis demonstrates that some but not all FTEs, consistent with previous studies, are indeed force-free structures in which the magnetic pressure force balances the magnetic curvature force. Furthermore, we contrast these events with FTE events that have non-force-free signatures.

MMS↗

Characterizing Peatland Microtopography Using Gradient and Microform-Based Approaches

Abstract Peatlands represent an important component of the global carbon cycle, storing 180–621 Gt of carbon (C). Small-scale spatial variations in elevation, frequently referred to as microtopography, influence ecological processes associated with the peatland C cycle, including Sphagnum photosynthesis and methane flux. Microtopography can be characterized with measures of topographic variability and by using conceptual classes (microforms) linked to function: most commonly hummocks and hollows. However, the criteria used to define these conceptual classes are often poorly described, if at all, and vary between studies. Such inconsistencies compel development of explicit quantitative methods to classify microforms. Furthermore, gradient-based characterizations that describe spatial variability without the use of microforms are lacking in the literature. Therefore, the objectives of this study were to (1) calculate peatland microtopographical elevation gradients and measures of spatial variability, (2) develop three microform classification methods intended for specific purposes, and (3) evaluate and contrast classification methods. Our results suggest that at spatial scales much larger than microforms, elevation distributions are unimodal and are well approximated with parametric probability density functions. Results from classifications were variable between methods and years and exhibited significant differences in mean hollow areal coverages of a raised ombrotrophic bog. Our results suggest that the conceptualization and classification of microforms can significantly influence microtopographic structural metrics. The three explicit methods for microform classification described here may be used and built upon for future applications.

54 ENVIRONMENTAL SCIENCES↗

A comparison of methods for computing the sigma-coordinate pressure gradient force for flow over sloped terrain in a hybrid theta-sigma model

In connection with the employment of the sigma coordinates introduced by Phillips (1957), problems can arise regarding an accurate finite-difference computation of the pressure gradient force. Over steeply sloped terrain, the calculation of the sigma-coordinate pressure gradient force involves computing the difference between two large terms of opposite sign which results in large truncation error. To reduce the truncation error, several finite-difference methods have been designed and implemented. The present investigation has the objective to provide another method of computing the sigma-coordinate pressure gradient force. Phillips' method is applied for the elimination of a hydrostatic component to a flux formulation. The new technique is compared with four other methods for computing the pressure gradient force. The work is motivated by the desire to use an isentropic and sigma-coordinate hybrid model for experiments designed to study flow near mountainous terrain.

Johnson, D. R.↗

Electronic and magnetic properties of Mo doped graphene; full potential approach

The electronic and magnetic properties of Pristine and Mo doped Graphene have been calculated using WIEN2k implementation of full potential linearized augmented plane wave (FPLAPW) method based on Density Functional Theory (DFT). The exchange and correlation (XC) effects were taken into account by generalized gradient approximation (GGA). The calculated results show that Mo doping creates magnetism in Graphene by shifting the energy levels at E{sub F} and opens up a channel for Graphene to be used in real nanoscale device applications. The unpaired d-electrons of Mo atom are responsible for induced magnetism in Graphene. Magnetic ordering created in Graphene in this way makes it suitable for recording media, magnetic sensors, magnetic inks and spintronic devices.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Electronic and magnetic properties of Cr doped graphene; Full potential approach

The electronic and magnetic properties of pristine and Cr doped graphene have been calculated using WIEN2k implementation of full potential linearized augmented plane wave (FPLAPW) method based on Density Functional Theory (DFT). The exchange and correlation (XC) effects were taken into account by generalized gradient approximation (GGA). The calculated results show that Cr doping introduces appropriate magnetic moment on graphene. The p-d interaction between 3d states of Cr atom and p-states of C atom are responsible for half metallicity in graphene. The calculated Half-metallic behavior of Cr-doped graphene makes it an ideal candidate for spintronic applications.

36 MATERIALS SCIENCE↗

First determination of ground state electromagnetic moments of Fe 53

Here, the hyperfine coupling constants of neutron deficient 53 Fe were deduced from the atomic hyperfine spectrum measured using the bunched-beam collinear laser spectroscopy technique. The low-energy 53 Fe beam was produced by projectile-fragmentation reactions followed by gas stopping, and used for the first time for laser spectroscopy. Ground state magnetic-dipole and electric-quadrupole moments were determined as μ= –0.65(1)μ N and Q=+35(15)e 2 fm 2 , respectively. The multiconfiguration Dirac-Fock method was used to calculate the electric field gradient to deduce Q from the quadrupole hyperfine coupling constant, since the quadrupole coupling constant has not been determined for any Fe isotopes. Both experimental values agree well with nuclear shell model calculations using the GXPF1A effective interaction performed in a full fp shell model space, which support the soft nature of the 56 Ni nucleus.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

First-principles investigation of uranium mononitride (UN): Effect of magnetic ordering, spin-orbit interactions and exchange correlation functional

Uranium mononitride (UN) is a promising nuclear fuel that combines the advantageous properties of readily used UO 2 and uranium alloys. Various properties of UN have been previously studied using different density functional theory (DFT) methodologies; however, there are still inconsistencies when it comes to the dynamical stability and defect properties of UN. We address these inconsistencies by studying the UN phonons and defect properties using DFT calculations employing two generalized gradient approximation (GGA) exchange-correlation functionals: PBE and AM05, with and without an added on-site Coulomb repulsion term (+U). Furthermore, we investigate the importance of spin-orbit coupling (SOC) when calculating the properties of UN. We use the different methodologies to determine the preference of UN to have antiferromagnetic (AFM) ordering, as seen in experiments, or ferromagnetic (FM) ordering of the uranium spins. We compare the crystallographic properties, density of states, the DFT X-ray photoelectron spectra and phonon dispersions calculated using the different methodologies. We demonstrate that GGA + U reproduces the AFM ordering in UN, but the crystal structure is dynamically unstable. We also show that magnetic ordering is important in finding the lowest energy defective structure, and that SOC has a distinct influence on the energy of the different uranium interstitial defects. Lastly, we discuss the point defect formation energies under U-rich and N-rich conditions, and the stoichiometric formation energies calculated with the different methodologies, providing insight into the observed tendency for forming hypostoichiometric UN.

36 MATERIALS SCIENCE↗

Study aids accuracy of turbopump axial thrust analysis

Test program to verify theory used in calculating axial thrust uses turbopump instrumented with /a/ proximity transducers for measuring shaft position, /b/ a strain gage thrust bearing carrier to measure axial thrust, and /c/ internal pressure taps to define component pressure gradients used in thrust calculations.

Nielson, C. E.↗

Competing adsorption mechanisms of pyridine on Cu, Ag, Au, and Pt(110) surfaces

We explore the adsorption of pyridine on Cu, Ag, Au, and Pt(110) surfaces using density functional theory. To account for the van der Waals interaction, we use the optB86b-vdW, optB88-vdW, optPBE-vdW, revPBE-vdW, and rPW86-vdW2 functionals. For comparison, we also run calculations using the generalized gradient approximation-PBE (Perdew–Burke–Ernzerhof) functional. We find the most stable adsorption site to depend on both metal and functional, with two energetically favorable adsorption sites, namely, a vertically oriented site and a flat pyridine site. We calculate that every functional predicts pyridine to lie in the vertical configuration on the coinage metals at a low coverage. On Pt(110), by contrast, we calculate all the functionals—except rPW86-vdW2—to predict pyridine to lie flat at a low coverage. By analyzing these differences for these adsorption configurations, along with various geometric and electronic properties of the adsorbate/substrate system, we access in detail the performance of the 6 functionals we use. We also characterize the nature of the bonding of pyridine on the coinage metals from weak to strong physisorption, depending on the functional used. On Pt(110), we characterize the nature of the bonding of pyridine as ranging from strong physisorption to strong chemisorption depending again on the functional used, illustrating both the importance of the van der Waals interaction to this system and that this system can make a stringent test for computational methods.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Hybrid functional band gap calculation of SnO{sub 6} containing perovskites and their derived structures

We have studied the properties of SnO{sub 6} octahedra-containing perovskites and their derived structures using ab initio calculations with different density functionals. In order to predict the correct band gap of the materials, we have used B3LYP hybrid density functional, and the results of B3LYP were compared with those obtained using the local density approximation and generalized gradient approximation data. The calculations have been conducted for the orthorhombic ground state of the SnO{sub 6} containing perovskites. We also have expended the hybrid density functional calculation to the ASnO{sub 3}/A'SnO{sub 3} system with different cation orderings. We propose an empirical relationship between the tolerance factor and the band gap of SnO{sub 6} containing oxide materials based on first principles calculation. - Graphical abstract: (a) Structure of ASnO{sub 3} for orthorhombic ground state. The green ball is A (Ba, Sr, Ca) cation and the small (red) ball on edge is oxygen. SnO{sub 6} octahedrons are plotted as polyhedron. (b) Band gap of ASnO{sub 3} as a function of the tolerance factor for different density functionals. The experimental values of the band gap are marked as green pentagons. (c) ASnO{sub 3}/A'SnO{sub 3} superlattices with two types cation arrangement: [001] layered structure and [111] rocksalt structure, respectively. (d) B3LYP hybrid functional band gaps of ASnO{sub 3}, [001] ordered superlattices, and [111] ordered superlattices of ASnO{sub 3}/A'SnO{sub 3} as a function of the effective tolerance factor. Note the empirical linear relationship between the band gap and effective tolerance factor. - Highlights: • We report the hybrid functional band gap calculation of ASnO{sub 3} and ASnO{sub 3}/A'SnO{sub 3}. • The band gap of ASnO{sub 3} using B3LYP functional reproduces the experimental value. • We propose the linear relationship between the tolerance factor and the band gap.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗