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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 361 records · Page 20
All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

EMMA: an adaptive mesh refinement cosmological simulation code with radiative transfer

EMMA is a cosmological simulation code aimed at investigating the reionization epoch. It handles simultaneously collisionless and gas dynamics, as well as radiative transfer physics using a moment-based description with the M1 approximation. Field quantities are stored and computed on an adaptive three-dimensional mesh and the spatial resolution can be dynamically modified based on physically motivated criteria. Physical processes can be coupled at all spatial and temporal scales. We also introduce a new and optional approximation to handle radiation: the light is transported at the resolution of the non-refined grid and only once the dynamics has been fully updated, whereas thermo-chemical processes are still tracked on the refined elements. Such an approximation reduces the overheads induced by the treatment of radiation physics. A suite of standard tests are presented and passed by EMMA, providing a validation for its future use in studies of the reionization epoch. The code is parallel and is able to use graphics processing units (GPUs) to accelerate hydrodynamics and radiative transfer calculations. Depending on the optimizations and the compilers used to generate the CPU reference, global GPU acceleration factors between ×3.9 and ×16.9 can be obtained. As a result, vectorization and transfer operations currently prevent better GPU performance and we expect that future optimizations and hardware evolution will lead to greater accelerations.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Bayesian refinement of covariant energy density functionals

The last five years have seen remarkable progress in our quest to determine the equation of state of neutron rich matter. Here, recent advances across the theoretical, experimental, and observational landscape have been incorporated in a Bayesian framework to refine existing covariant energy density functionals previously calibrated by the properties of finite nuclei. In particular, constraints on the maximum neutron star mass from pulsar timing, on stellar radii from the NICER mission, on tidal deformabilities from the LIGO-Virgo collaboration, and on the dynamics of pure neutron matter as predicted from chiral effective field theories have resulted in significant refinements to the models, particularly to those predicting a stiff symmetry energy. Still, even after these improvements, we find it challenging to reproduce simultaneously the neutron skin thickness of both 208 Pb and 48 Ca recently reported by the PREX/CREX collaboration.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2012

Low-resolution refinement tools in REFMAC5

Low-resolution refinement tools implemented in REFMAC5 are described, including the use of external structural restraints, helical restraints and regularized anisotropic map sharpening. Two aspects of low-resolution macromolecular crystal structure analysis are considered: (i) the use of reference structures and structural units for provision of structural prior information and (ii) map sharpening in the presence of noise and the effects of Fourier series termination. The generation of interatomic distance restraints by ProSMART and their subsequent application in REFMAC5 is described. It is shown that the use of such external structural information can enhance the reliability of derived atomic models and stabilize refinement. The problem of map sharpening is considered as an inverse deblurring problem and is solved using Tikhonov regularizers. It is demonstrated that this type of map sharpening can automatically produce a map with more structural features whilst maintaining connectivity. Tests show that both of these directions are promising, although more work needs to be performed in order to further exploit structural information and to address the problem of reliable electron-density calculation.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2014

High-resolution structure of the M14-type cytosolic carboxypeptidase from Burkholderia cenocepacia refined exploiting PDB-REDO strategies

The structure of a bacterial M14-family carboxypeptidase determined exploiting microfocus synchrotron radiation and highly automated refinement protocols reveals its potential to act as a polyglutamylase. A potential cytosolic metallocarboxypeptidase from Burkholderia cenocepacia has been crystallized and a synchrotron-radiation microfocus beamline allowed the acquisition of diffraction data to 1.9 Å resolution. The asymmetric unit comprises a tetramer containing over 1500 amino acids, and the high-throughput automated protocols embedded in PDB-REDO were coupled with model–map inspections in refinement. This approach has highlighted the value of such protocols for efficient analyses. The subunit is constructed from two domains. The N-terminal domain has previously only been observed in cytosolic carboxypeptidase (CCP) proteins. The C-terminal domain, which carries the Zn{sup 2+}-containing active site, serves to classify this protein as a member of the M14D subfamily of carboxypeptidases. Although eukaryotic CCPs possess deglutamylase activity and are implicated in processing modified tubulin, the function and substrates of the bacterial family members remain unknown. The B. cenocepacia protein did not display deglutamylase activity towards a furylacryloyl glutamate derivative, a potential substrate. Residues previously shown to coordinate the divalent cation and that contribute to peptide-bond cleavage in related enzymes such as bovine carboxypeptidase are conserved. The location of a conserved basic patch in the active site adjacent to the catalytic Zn{sup 2+}, where an acetate ion is identified, suggests recognition of the carboxy-terminus in a similar fashion to other carboxypeptidases. However, there are significant differences that indicate the recognition of substrates with different properties. Of note is the presence of a lysine in the S1′ recognition subsite that suggests specificity towards an acidic substrate.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Multidimensional Rietveld refinement of high-pressure neutron diffraction data of PbNCN

High-pressure neutron powder diffraction data from PbNCN were collected on the high-pressure diffraction beamline SNAP located at the Spallation Neutron Source (SNS) of Oak Ridge National Laboratory (Tennessee, USA). The diffraction data were analyzed using the novel method of multidimensional (two dimensions for now, potentially more in the future) Rietveld refinement and, for comparison, employing the conventional Rietveld method. To achieve two-dimensional analysis, a detailed description of the SNAP instrument characteristics was created, serving as an instrument parameter file, and then yielding both cell and spatial parameters as refined under pressure for the first time for solid-state cyanamides/carbodiimides. The bulk modulus B 0 = 25.1 (15) GPa and its derivative B ′ 0 = 11.1 (8) were extracted for PbNCN following the Vinet equation of state. Surprisingly, an internal transition was observed beyond 2.0 (2) GPa, resulting from switching the bond multiplicities (and bending direction) of the NCN 2− complex anion. The results were corroborated using electronic structure calculation from first principles, highlighting both local structural and chemical bonding details.

Meinerzhagen, Yannick↗
DOE OSTI2025

Structure refinement and anisotropic atomic displacement parameters of 1M Illite: Rietveld and pair distribution function analysis using synchrotron X-ray radiation

Illite, a widespread clay mineral, plays a pivotal role in geological processes, notably as an indicator in diagenetic and hydrothermal alteration environments, and possesses significant industrial relevance in applications including ceramics, construction and catalysis. However, challenges including its nanoscale crystallinity, structural disorder and frequent interstratification with other clay minerals have hindered detailed structural characterization using conventional X-ray diffraction (XRD) techniques. This study employs integrated synchrotron XRD and pair distribution function (PDF) analysis to elucidate the crystal structure of the 1M illite polytype, yielding the first determination of its anisotropic atomic displacement parameters (U aniso ). TheseU aniso parameters provide critical insights into atomic dynamics and static disorder within the structure, enabling a more refined understanding of structure–property relationships. This integrated approach, combining synchrotron XRD, Rietveld refinement and PDF analysis, yields a comprehensive structural characterization, capturing both average crystallographic and local atomic arrangements. Considering illite's widespread geological occurrence and industrial importance, this high-precision structural dataset, especially the determinedU aniso values, provides a crucial benchmark for future modeling and simulation efforts targeting accurate prediction of its physicochemical behavior.

Chemistry↗
DOE OSTI2020

Refinement for single-nanoparticle structure determination from low-quality single-shot coherent diffraction data

With the emergence of X-ray free-electron lasers, it is possible to investigate the structure of nanoscale samples by employing coherent diffractive imaging in the X-ray spectral regime. In this work, we developed a refinement method for structure reconstruction applicable to low-quality coherent diffraction data. The method is based on the gradient search method and considers the missing region of a diffraction pattern and the small number of detected photons. We introduced an initial estimate of the structure in the method to improve the convergence. The present method is applied to an experimental diffraction pattern of an Xe cluster obtained in an X-ray scattering experiment at the SPring-8 Angstrom Compact free-electron LAser (SACLA) facility. It is found that the electron density is successfully reconstructed from the diffraction pattern with a large missing region, with a good initial estimate of the structure. The diffraction pattern calculated from the reconstructed electron density reproduced the observed diffraction pattern well, including the characteristic intensity modulation in each ring. Our refinement method enables structure reconstruction from diffraction patterns under difficulties such as missing areas and low diffraction intensity, and it is potentially applicable to the structure determination of samples that have low scattering power.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2013

Refinement of the crystal structure of calcioancylite-(Ce) by the Rietveld method

The crystal structure of calcioancylite-(Ce) of the (Ca{sub 0.30}Sr{sub 0.22}){sub {Sigma}0.52}(Ce{sub 0.78}La{sub 0.47}Nd{sub 0.16}Pr{sub 0.05}Sm{sub 0.02}){sub {Sigma}1.48}(CO{sub 3}){sub 2} ((OH){sub 1.20}F{sub 0.28}){sub {Sigma}1.48} {center_dot} 1.97H{sub 2}O composition from alkali hydrothermalites of Mont Saint-Hilaire, Canada, has been refined by the Rietveld method. The refinement details are as follows: ADP-2 diffractometer, {lambda}CuK{sub {alpha}} radiation, Ni filter, 10.50 Degree-Sign < 2{theta} < 140.00 Degree-Sign , and the number of reflections ({alpha}{sub 1} + {alpha}{sub 2}) 652. All calculations have been performed within the sp. gr. Pmcn (a = 5.0095(1) A, b = 8.5006(1) A, c = 7.2670(1) A, V = 309.46(1) A{sup 3}, R{sub wp} = 3.45) in the anisotropic approximation of thermal vibrations for cations.

36 MATERIALS SCIENCE↗
DOE OSTI2013

Crystal-structure refinement of zirconium-rich eudialyte and its place among calcium-poor eudialyte-group minerals

The repeated refinement of the crystal structure of zirconium-rich eudialyte based on the X-ray diffraction data set collected earlier revealed new structural features. The trigonal unit-cell parameters are a = 14.222(3) A, c = 30.165(5) A, V = 5283.9 A{sup 3}. The refinement resulted in the reduction of the R factor from 0.045 (2347F > 4{sigma}(F)) to 0.035 (3124F > 3{sigma}(F)). It was found that the ordering of Ca and Fe in six-membered rings leads to the lowering of the symmetry to R3. An excess amount of zirconium (more than three atoms per symmetrically independent unit) is located in the M2 microregion in square and five-vertex polyhedral positions. However, this amount is insufficient to be dominant, and the deficiency of zirconium is compensated for by sodium atoms. Based on the new data, zirconium-rich eudialyte can be assigned to the oneillite subtype, being a zirconium-rich and aluminum variety of raslakite.

36 MATERIALS SCIENCE↗
DOE OSTI2013

Yttrium barium heptaoxocobaltate YBaCo{sub 4}O{sub 7+{delta}}: Refinement of the structure and determination of the composition

Parameters of the crystal structure of compound YBaCo{sub 4}O{sub 7} are refined. The experimental data [3917 reflections measured, 469 unique I{sub hkl}, and 420 observed reflections with I > 2{sigma}(I)] are obtained on a Bruker X8APEX automated diffractometer equipped with a CCD detector [MoK{sub {alpha}}, graphite monochromator, {theta}{sub max} = 33.09 Degree-Sign , space group P6{sub 3}mc, a = 6.3058(4) A, c = 10.2442(7) A, V = 352.77 A{sup 3}, Z = 2, d{sub calcd} = 5.404 g/cm{sup 3}, R{sub 1} = 0.0183 for 420 observed reflections and 0.0216 for all unique reflections]. The refinement shows that the occupancy factors of all sites of the space group correspond within three standard deviations to the standard values, that is, to the Y: Ba: Co: O = 1: 1: 4: 7 whole-number ratio of elements in the formula of the compound and to the absence of an aluminum impurity in the crystal.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Refined dynamic structure factor of a lipid bilayer on scales comparable to its thickness

The structural inhomogeneity of a lipid bilayer is an obstacle to applying the classical Canham–Helfrich model to describe its dynamics on nanometer length scales. In this paper, a refined expression for the free energy of a single-component lipid bilayer is used to describe the dynamics of lipid density fluctuations. In particular, the expression with a term involving the gradient of the area per lipid [8] is used for the free energy per lipid. A refined expression has been derived for the dynamic structure factor of a free lipid bilayer in the hydrodynamic region. It leads to differences in the interpretation and values of the bilayer parameters in comparison with the standard model.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Efficient Low-Order Refined Preconditioners for High-Order Matrix-Free Continuous and Discontinuous Galerkin Methods

In this paper, we design preconditioners for the matrix-free solution of high-order continuous and discontinuous Galerkin discretizations of elliptic problems based on finite element method--spectral element method (FEM-SEM) equivalence and additive Schwarz methods. The high-order operators are applied without forming the system matrix, making use of sum factorization for efficient evaluation. The system is preconditioned using a spectrally equivalent low-order (p = 1) finite element operator discretization on a refined mesh. The low-order refined mesh is anisotropic and not shape regular in the polynomial degree of the high-order operator, requiring specialized solvers to treat the anisotropy. We make use of an element-structured, geometric multigrid V-cycle with ordered ILU(0) smoothing. The preconditioner is parallelized through an overlapping additive Schwarz method that is robust in h and p. The method is extended to interior penalty and Bassi and Rebay (BR2) discontinuous Galerkin discretizations, for which it is also robust in the size of the penalty parameter. Finally, numerical results are presented on a variety of examples, verifying the uniformity of the preconditioner.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2017

Machine and Application Aware Partitioning for Adaptive Mesh Refinement Applications. In: HPDC '17 Proceedings of the 26th International Symposium on High-Performance Parallel and Distributed Computing

Load balancing and partitioning are critical when it comes to parallel computations. Popular partitioning strategies based on space filling curves focus on equally dividing work. The partitions produced are independent of the architecture or the application. Given the ever-increasing relative cost of data movement and increasing heterogeneity of our architectures, it is no longer sufficient to only consider an equal partitioning of work. Minimizing communication costs are equally if not more important. Our hypothesis is that an unequal partitioning that minimizes communication costs significantly can scale and perform better than conventional equal-work partitioning schemes. This tradeoff is dependent on the architecture as well as the application. We validate our hypothesis in the context of a finite-element computation utilizing adaptive mesh-refinement. Our central contribution is a new partitioning scheme that minimizes the overall runtime of subsequent computations by performing architecture and application-aware non-uniform work assignment in order to decrease time to solution, primarily by minimizing data-movement. We evaluate our algorithm by comparing it against standard space-filling curve based partitioning algorithms and observing time-to-solution as well as energy-to-solution for solving Finite Element computations on adaptively refined meshes. We demonstrate excellent scalability of our new partition algorithm up to $262,144$ cores on ORNL's Titan and demonstrate that the proposed partitioning scheme reduces overall energy as well as time-to-solution for application codes by up to 22.0%.

Fernando, Milinda↗
DOE OSTI2023

MARBLES (Multi-scale Adaptively Refined Boltzmann LatticE Solver) [SWR-23-37]

MARBLES (Multi-scale Adaptively Refined Boltzmann LatticE Solver) is an open-source computational fluid dynamics package powered by the lattice Boltzmann equations and built on AMReX. In the lattice Boltzmann method, local collisions between meso-scale fictitious particles drive the governing equations which enables MARBLES to easily simulate flow around complex and/or moving geometry without the generation of a body-conforming mesh. Using AMReX data structures and operations ensures a high level of computational performance and parallel scaling on heterogenous architectures while also naturally supporting locally enhanced grid resolution and fidelity through automatic mesh refinement. New domains and problem definitions are easily specified through an input file with examples and guidance on all options and variables provided in the MARBLES documentation.

Henry de Frahan, Marc↗
DOE OSTI2012

Comparative Omics-Driven Genome Annotation Refinement: Application across Yersiniae

Genome sequencing continues to be a rapidly evolving technology, yet most downstream aspects of genome annotation pipelines remain relatively stable or are even being abandoned. To date, the perceived value of manual curation for genome annotations is not offset by the real cost and time associated with the process. In order to balance the large number of sequences generated, the annotation process is now performed almost exclusively in an automated fashion for most genome sequencing projects. One possible way to reduce errors inherent to automated computational annotations is to apply data from 'omics' measurements (i.e. transcriptional and proteomic) to the un-annotated genome with a proteogenomic-based approach. This approach does require additional experimental and bioinformatics methods to include omics technologies; however, the approach is readily automatable and can benefit from rapid developments occurring in those research domains as well. The annotation process can be improved by experimental validation of transcription and translation and aid in the discovery of annotation errors. Here the concept of annotation refinement has been extended to include a comparative assessment of genomes across closely related species, as is becoming common in sequencing efforts. Transcriptomic and proteomic data derived from three highly similar pathogenic Yersiniae (Y. pestis CO92, Y. pestis pestoides F, and Y. pseudotuberculosis PB1/+) was used to demonstrate a comprehensive comparative omic-based annotation methodology. Peptide and oligo measurements experimentally validated the expression of nearly 40% of each strain's predicted proteome and revealed the identification of 28 novel and 68 previously incorrect protein-coding sequences (e.g., observed frameshifts, extended start sites, and translated pseudogenes) within the three current Yersinia genome annotations. Gene loss is presumed to play a major role in Y. pestis acquiring its niche as a virulent pathogen, thus the discovery of many translated pseudogenes underscores a need for functional analyses to investigate hypotheses related to divergence. Refinements included the discovery of a seemingly essential ribosomal protein, several virulence-associated factors, and a transcriptional regulator, among other proteins, most of which are annotated as hypothetical, that were missed during annotation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

Zone Refining for Low Loss Plutonium Purification

In an effort to enhance plutonium purification capabilities at Los Alamos National Laboratory, further develop of the currently existing zone refining capabilities is needed to create a functional low loss processing option in support of programmatic and materials science research activities. Currently, the most effective process for converting impure plutonium dioxide (~96% pure) to high-purity plutonium metal (>99.9%), consists of the following steps: (1) reducing the dioxide to an impure Plutonium metal with calcium metal in molten calcium chloride, (2) casting the impure metal into an anode and (3) electrorefining the impure metal to produce high-purity plutonium metal. The final step in this method is only 83% efficient as compared to the >95% efficiency of the other processing steps. Other more efficient processing methods are desirable to enhance current purification activities, thereby, reducing waste generation and conserving precious materials in need of purification. Although zone refining has been used extensively to purify many lanthanides and actinides, its usefulness in purifying plutonium has yet to be fully realized.

36 MATERIALS SCIENCE↗
DOE OSTI2013

Geochemistry, extent, signatures, and chronology of basaltic and young silicic pyroclastic eruptions: Refining existing data to support a future volcanic hazards assessment of LANL

Volcanic activities represent a primary natural phenomena hazards element within DOE regulatory drivers. Los Alamos National Laboratory lies within the Jemez Mountains volcanic field, which has erupted both small and large volumes of volcanic materials during the Quaternary (the last 2.6 million years, including as recently as ~40,000 years ago), and is bounded on the east by the Cerros del Rio volcanic field, which has also erupted during the Quaternary. Current and future Los Alamos National Laboratory facility performance goals may be affected by future volcanic eruptions of the same type observed during the Quaternary. This report addresses key questions to more completely define the extent, magnitude, composition, and timing of recent silicic and basaltic eruptions, and their associated tephras, sourced from volcanic centers within 20 km of Los Alamos National Laboratory. The stratigraphic and chronologic record of basaltic and dacitic lavas that underlie the Pajarito Plateau are summarized herein. Additionally, the field, laboratory, and spatial analyses undertaken to further refine the age and extent of the El Cajete Pyroclastic Beds are described. The data presented will support and refine future efforts towards development of a LANL probabilistic volcanic hazards assessment.

58 GEOSCIENCES↗
DOE OSTI2015

Use Case Realization Report: UCR-02.08 System Refines Event Location

This architecturally significant use case describes how the System refines event hypothesis location solutions. The System locates events by finding the event location minimizing the difference between signal detection feature measurements and signal detection feature predictions (see 'System Measures Signal Features' UC). The System references both empirical knowledge from past events and geophysical models to form the signal detection feature predictions. The System also computes an uncertainty bound for each event hypothesis location solution describing a region bounding the event hypothesis' hypocenter and origin time at a particular confidence level. The System creates a variety of location solutions for each event hypothesis. These location solutions vary from one another in either the input parameters the System uses or in the location solution components the System restrains to fixed values (e.g. depth) during event location calculations. The System computes location solutions using input parameters configured by the System Maintainer (see ‘Configures Processing Components’ UC). The Analyst has the option to override input parameters originally configured by the System Maintainer (see 'Refines Event Location' UC). This use case is architecturally significant due to the processing and memory resource consumption of 3D earth model calculations.

97 MATHEMATICS AND COMPUTING↗