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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 235 records · Page 13
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

A proteomic meta-analysis refinement of plasma extracellular vesicles

Extracellular vesicles play major roles in cell-to-cell communication and are excellent biomarker candidates. However, studying plasma extracellular vesicles is challenging due to contaminants. Here, we performed a proteomics meta-analysis of public data to refine the plasma EV composition by separating EV proteins and contaminants into different clusters. We obtained two clusters with a total of 1717 proteins that were depleted of known contaminants and enriched in EV markers with independently validated 71% true-positive. These clusters had 133 clusters of differentiation (CD) antigens and were enriched with proteins from cell-to-cell communication and signaling. We compared our data with the proteins deposited in PeptideAtlas, making our refined EV protein list a resource for mechanistic and biomarker studies. As a use case example for this resource, we validated the type 1 diabetes biomarker proplatelet basic protein in EVs and showed that it regulates apoptosis of β cells and macrophages, two key players in the disease development. Our approach provides a refinement of the EV composition and a resource for the scientific community.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

Refined algebraic quantisation in a system with nonconstant gauge invariant structure functions

In a previous work [J. Louko and E. Martínez-Pascual, “Constraint rescaling in refined algebraic quantisation: Momentum constraint,” J. Math. Phys. 52, 123504 (2011)], refined algebraic quantisation (RAQ) within a family of classically equivalent constrained Hamiltonian systems that are related to each other by rescaling one momentum-type constraint was investigated. In the present work, the first steps to generalise this analysis to cases where more constraints occur are developed. The system under consideration contains two momentum-type constraints, originally abelian, where rescalings of these constraints by a non-vanishing function of the coordinates are allowed. These rescalings induce structure functions at the level of the gauge algebra. Providing a specific parametrised family of real-valued scaling functions, the implementation of the corresponding rescaled quantum momentum-type constraints is performed using RAQ when the gauge algebra: (i) remains abelian and (ii) undergoes into an algebra of a nonunimodular group with nonconstant gauge invariant structure functions. Case (ii) becomes the first example known to the author where an open algebra is handled in refined algebraic quantisation. Challenging issues that arise in the presence of non-gauge invariant structure functions are also addressed.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2015

Monitoring the refinement of crystal structures with {sup 15}N solid-state NMR shift tensor data

The {sup 15}N chemical shift tensor is shown to be extremely sensitive to lattice structure and a powerful metric for monitoring density functional theory refinements of crystal structures. These refinements include lattice effects and are applied here to five crystal structures. All structures improve based on a better agreement between experimental and calculated {sup 15}N tensors, with an average improvement of 47.0 ppm. Structural improvement is further indicated by a decrease in forces on the atoms by 2–3 orders of magnitude and a greater similarity in atom positions to neutron diffraction structures. These refinements change bond lengths by more than the diffraction errors including adjustments to X–Y and X–H bonds (X, Y = C, N, and O) of 0.028 ± 0.002 Å and 0.144 ± 0.036 Å, respectively. The acquisition of {sup 15}N tensors at natural abundance is challenging and this limitation is overcome by improved {sup 1}H decoupling in the FIREMAT method. This decoupling dramatically narrows linewidths, improves signal-to-noise by up to 317%, and significantly improves the accuracy of measured tensors. A total of 39 tensors are measured with shifts distributed over a range of more than 400 ppm. Overall, experimental {sup 15}N tensors are at least 5 times more sensitive to crystal structure than {sup 13}C tensors due to nitrogen’s greater polarizability and larger range of chemical shifts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Rietveld refined structural and room temperature vibrational properties of BaTiO{sub 3} doped La{sub 0.67}Ba{sub 0.33}MnO{sub 3} composites

The composites of (1-x) La{sub 0.67}Ba{sub 0.33}MnO{sub 3} (LBMO) + xBaTiO{sub 3} (BTO) (x = 0, 0.25 and 1.0) were synthesized by conventional solid-state reaction method. Rietveld refinement was employed to characterize the structural information of the prepared ceramics. The result of the Rietveld refinement of X-ray powder diffraction of La{sub 0.67}Ba{sub 0.33}MnO{sub 3} and BaTiO{sub 3} shows that these compounds crystallize in rhombohedral (R3c) and tetragonal (P4mm), respectively. The structural parameters and the reliability factors for the LBMO-BTO composite ceramics were successfully determined by the Rietveld refinement. At room temperature, Raman active phonon modes predicted by the group theory were observed only in BaTiO{sub 3} and composite sample. Pure LBMO does not show any Raman active Phonon mode at room temperature.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Data-guided Multi-Map variables for ensemble refinement of molecular movies

Driving molecular dynamics simulations with data-guided collective variables offer a promising strategy to recover thermodynamic information from structure-centric experiments. In this study, the three-dimensional electron density of a protein, as it would be determined by cryo-EM or x-ray crystallography, is used to achieve simultaneously free-energy costs of conformational transitions and refined atomic structures. Unlike previous density-driven molecular dynamics methodologies that determine only the best map-model fits, our work employs the recently developed Multi-Map methodology to monitor concerted movements within equilibrium, non-equilibrium, and enhanced sampling simulations. Construction of all-atom ensembles along the chosen values of the Multi-Map variable enables simultaneous estimation of average properties, as well as real-space refinement of the structures contributing to such averages. Using three proteins of increasing size, we demonstrate that biased simulation along the reaction coordinates derived from electron densities can capture conformational transitions between known intermediates. The simulated pathways appear reversible with minimal hysteresis and require only low-resolution density information to guide the transition. The induced transitions also produce estimates for free energy differences that can be directly compared to experimental observables and population distributions. The refined model quality is superior compared to those found in the Protein Data Bank. We find that the best quantitative agreement with experimental free-energy differences is obtained using medium resolution density information coupled to comparatively large structural transitions. Practical considerations for probing the transitions between multiple intermediate density states are also discussed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

The matryoshka run: A Eulerian refinement strategy to study the statistics of turbulence in virialized cosmic structures

We study the statistical properties of turbulence driven by structure formation in a massive merging galaxy cluster at redshift z = 0. The development of turbulence is ensured as the largest eddy turnover time is much shorter than the Hubble time independent of mass and redshift. We achieve a large dynamic range of spatial scales through a novel Eulerian refinement strategy where the cluster volume is refined with progressively finer uniform nested grids during gravitational collapse. This provides an unprecedented resolution of 7.3 h {sup –1} kpc across the virial volume. The probability density functions of various velocity-derived quantities exhibit the features characteristic of fully developed compressible turbulence observed in dedicated periodic-box simulations. Shocks generate only 60% of the total vorticity within the R {sub vir}/3 region and 40% beyond that. We compute second- and third-order longitudinal and transverse structure functions for both solenoidal and compressional components in the cluster core, virial region, and beyond. The structure functions exhibit a well-defined inertial range of turbulent cascade. The injection scale is comparable to the virial radius but increases toward the outskirts. Within R {sub vir}/3, the spectral slope of the solenoidal component is close to Kolmogorov's, but for the compressional component is substantially steeper and close to Burgers's; the flow is mostly solenoidal and statistically rigorously, which is consistent with fully developed homogeneous and isotropic turbulence. Small-scale anisotropy appears due to numerical artifact. Toward the virial region, the flow becomes increasingly compressional, the structure functions become flatter, and modest genuine anisotropy appear particularly close to the injection scale. In comparison, mesh adaptivity based on Lagrangian refinement and the same finest resolution leads to a lack of turbulent power on a small scales, an excess thereof on large scales, and unreliable density-weighted structure functions.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Spinteract: a program to refine magnetic interactions to diffuse scattering data

Magnetic diffuse scattering—the broad magnetic scattering features observed in neutron-diffraction data above a material's magnetic ordering temperature—provides a rich source of information about the material's magnetic Hamiltonian. However, this information has often remained under-utilised due to a lack of available computer software that can fit values of magnetic interaction parameters to such data. Here, an open-source computer program, Spinteract, is presented, which enables straightforward refinement of magnetic interaction parameters to powder and single-crystal magnetic diffuse scattering data. Here, the theory and implementation of this approach are summarised. Examples are presented of refinements to published experimental diffuse-scattering data sets for the canonical antiferromagnet MnO and the highly-frustrated classical spin liquid Gd 3 Ga 5 O 12 . Guidelines for data collection and refinement are outlined, and possible developments of the approach are discussed.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2015

Refined BCF-type boundary conditions for mesoscale surface step dynamics

Deposition on a vicinal surface with alternating rough and smooth steps is described by a solid-on-solid model with anisotropic interactions. Kinetic Monte Carlo (KMC) simulations of the model reveal step pairing in the absence of any additional step attachment barriers. We explore the description of this behavior within an analytic Burton-Cabrera-Frank (BCF)-type step dynamics treatment. Without attachment barriers, conventional kinetic coefficients for the rough and smooth steps are identical, as are the predicted step velocities for a vicinal surface with equal terrace widths. However, we determine refined kinetic coefficients from a two-dimensional discrete deposition-diffusion equation formalism which accounts for step structure. These coefficients are generally higher for rough steps than for smooth steps, reflecting a higher propensity for capture of diffusing terrace adatoms due to a higher kink density. Such refined coefficients also depend on the local environment of the step and can even become negative (corresponding to net detachment despite an excess adatom density) for a smooth step in close proximity to a rough step. Incorporation of these refined kinetic coefficients into a BCF-type step dynamics treatment recovers quantitatively the mesoscale step-pairing behavior observed in the KMC simulations.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2012

Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution

Traditional methods for macromolecular refinement often have limited success at low resolution (3.0–3.5 Å or worse), producing models that score poorly on crystallographic and geometric validation criteria. To improve low-resolution refinement, knowledge from macromolecular chemistry and homology was used to add three new coordinate-restraint functions to the refinement program phenix.refine . Firstly, a `reference-model' method uses an identical or homologous higher resolution model to add restraints on torsion angles to the geometric target function. Secondly, automatic restraints for common secondary-structure elements in proteins and nucleic acids were implemented that can help to preserve the secondary-structure geometry, which is often distorted at low resolution. Lastly, we have implemented Ramachandran-based restraints on the backbone torsion angles. In this method, a φ,ψ term is added to the geometric target function to minimize a modified Ramachandran landscape that smoothly combines favorable peaks identified from nonredundant high-quality data with unfavorable peaks calculated using a clash-based pseudo-energy function. All three methods show improved MolProbity validation statistics, typically complemented by a lowered R free and a decreased gap between R work and R free .

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Ensemble refinement shows conformational flexibility in crystal structures of human complement factor D

Ensemble-refinement analysis of native and mutant factor D (FD) crystal structures indicates a dynamical transition in FD from a self-inhibited inactive conformation to a substrate-bound active conformation that is reminiscent of the allostery in thrombin. Comparison with previously observed dynamics in thrombin using NMR data supports the crystallographic ensembles. Human factor D (FD) is a self-inhibited thrombin-like serine proteinase that is critical for amplification of the complement immune response. FD is activated by its substrate through interactions outside the active site. The substrate-binding, or ‘exosite’, region displays a well defined and rigid conformation in FD. In contrast, remarkable flexibility is observed in thrombin and related proteinases, in which Na{sup +} and ligand binding is implied in allosteric regulation of enzymatic activity through protein dynamics. Here, ensemble refinement (ER) of FD and thrombin crystal structures is used to evaluate structure and dynamics simultaneously. A comparison with previously published NMR data for thrombin supports the ER analysis. The R202A FD variant has enhanced activity towards artificial peptides and simultaneously displays active and inactive conformations of the active site. ER revealed pronounced disorder in the exosite loops for this FD variant, reminiscent of thrombin in the absence of the stabilizing Na{sup +} ion. These data indicate that FD exhibits conformational dynamics like thrombin, but unlike in thrombin a mechanism has evolved in FD that locks the unbound native state into an ordered inactive conformation via the self-inhibitory loop. Thus, ensemble refinement of X-ray crystal structures may represent an approach alternative to spectroscopy to explore protein dynamics in atomic detail.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2014

Flexible torsion-angle noncrystallographic symmetry restraints for improved macromolecular structure refinement

One of the great challenges in refining macromolecular crystal structures is a low data-to-parameter ratio. Historically, knowledge from chemistry has been used to help to improve this ratio. When a macromolecule crystallizes with more than one copy in the asymmetric unit, the noncrystallographic symmetry relationships can be exploited to provide additional restraints when refining the working model. However, although globally similar, NCS-related chains often have local differences. To allow for local differences between NCS-related molecules, flexible torsion-based NCS restraints have been introduced, coupled with intelligent rotamer handling for protein chains, and are available in phenix.refine for refinement of models at all resolutions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

A numerical method for deriving shape functions of nanoparticles for pair distribution function refinements

We report that in the structural refinement of nanoparticles, discrete atomistic modeling can be used for small nanocrystals (< 15 nm), but becomes computationally unfeasible at larger sizes, where instead unit-cell-based small-box modeling is usually employed. However, the effect of the nanocrystal's shape is often ignored or accounted for with a spherical model regardless of the actual shape due to the complexities of solving and implementing accurate shape effects. Recent advancements have provided a way to determine the shape function directly from a pair distribution function calculated from a discrete atomistic model of any given shape, including both regular polyhedra (e.g. cubes, spheres, octahedra) and anisotropic shapes (e.g. rods, discs, ellipsoids) [Olds et al. (2015). J. Appl. Cryst. 48, 1651–1659], although this approach is still limited to small size regimes due to computational demands. In order to accurately account for the effects of nanoparticle size and shape in small-box refinements, a numerical or analytical description is needed. This article presents a methodology to derive numerical approximations of nanoparticle shape functions by fitting to a training set of known shape functions; the numerical approximations can then be employed on larger sizes yielding a more accurate and physically meaningful refined nanoparticle size. Lastly, the method is demonstrated on a series of simulated and real data sets, and a table of pre-calculated shape function expressions for a selection of common shapes is provided.

36 MATERIALS SCIENCE↗
DOE OSTI2015

Resident Block-Structured Adaptive Mesh Refinement on Thousands of Graphics Processing Units, In: 2015 44th International Conference on Parallel Processing

Block-structured adaptive mesh refinement (AMR) is a technique that can be used when solving partial differential equations to reduce the number of cells necessary to achieve the required accuracy in areas of interest. These areas (shock fronts, material interfaces, etc.) are recursively covered with finer mesh patches that are grouped into a hierarchy of refinement levels. Despite the potential for large savings in computational requirements and memory usage without a corresponding reduction in accuracy, AMR adds overhead in managing the mesh hierarchy, adding complex communication and data movement requirements to a simulation. In this paper, we describe the design and implementation of a resident GPU-based AMR library, including: the classes used to manage data on a mesh patch, the routines used for transferring data between GPUs on different nodes, and the data-parallel operators developed to coarsen and refine mesh data. We validate the performance and accuracy of our implementation using three test problems and two architectures: an 8 node cluster, and 4,196 nodes of Oak Ridge National Laboratory's Titan supercomputer. Our GPU-based AMR hydrodynamics code performs up to 4.87× faster than the CPU-based implementation, and is scalable on 4,196 K20x GPUs using a combination of MPI and CUDA.

Computer Science↗
DOE OSTI2026

Cryogenic-Refined MOSFET Modeling for Oscillator, Frequency Divider, and Amplifier Designs Below 4 K

Capturing device characteristic changes at cryogenic temperatures is crucial for cryo-CMOS circuit designs. In this work, we present an isothermal cryogenic-refined modeling approach for CMOS transistors that is simple, low overhead, and easy to implement while offering the required accuracy for predicting circuit performance at the designated temperatures. Guided by die-level measurement data and circuit design principles, the model introduces corrections to only five critical parameters: threshold voltage, carrier mobility, elevated low-frequency flicker noise, dominant high-frequency shot noise, and subthreshold swing (SS). These refinements are implemented around the foundry-provided SPICE model, which is typically validated only down to about 200 K. With these adjustments, the proposed cryogenic-refined model achieves less than 5% error in both large-signal metrics (I–V characteristics) and small-signal parameters (e.g., transconductance) when compared with device measurements at deep-cryogenic temperatures. The methodology is validated in two advanced technologies: TSMC 40-nm CMOS and GlobalFoundries (GF) 45-nm RF-SOI. We further demonstrate its applicability in three representative RF circuits: a 30-GHz LC oscillator, a high-speed current-mode-logic (CML) frequency divider (FD), and a subthreshold Gb/s amplifier, all showing close agreement between simulated predictions and measurements performed at 4 and 2.5 K. Finally, we believe that the proposed approach is implementation-friendly and can significantly accelerate the development of cryo-CMOS integrated circuits.

circuit modeling↗
DOE OSTI2016

Analyzing the Adaptive Mesh Refinement (AMR) Characteristics of a High-Order 2D Cubed-Sphere Shallow-Water Model

Adaptive mesh refinement (AMR) is a technique that has been featured only sporadically in atmospheric science literature. This study aims to demonstrate the utility of AMR for simulating atmospheric flows. Several test cases are implemented in a 2D shallow-water model on the sphere using the Chombo-AMR dynamical core. This high-order finite-volume model implements adaptive refinement in both space and time on a cubed-sphere grid using a mapped-multiblock mesh technique. The tests consist of the passive advection of a tracer around moving vortices, a steady-state geostrophic flow, an unsteady solid-body rotation, a gravity wave impinging on a mountain, and the interaction of binary vortices. Both static and dynamic refinements are analyzed to determine the strengths and weaknesses of AMR in both complex flows with small-scale features and large-scale smooth flows. The different test cases required different AMR criteria, such as vorticity or height-gradient based thresholds, in order to achieve the best accuracy for cost. The simulations show that the model can accurately resolve key local features without requiring global high-resolution grids. The adaptive grids are able to track features of interest reliably without inducing noise or visible distortions at the coarse–fine interfaces. Finally and furthermore, the AMR grids keep any degradations of the large-scale smooth flows to a minimum.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

End-to-end GPU acceleration of low-order-refined preconditioning for high-order finite element discretizations

In this article, we present algorithms and implementations for the end-to-end GPU acceleration of matrix-free low-order-refined preconditioning of high-order finite element problems. The methods described here allow for the construction of effective preconditioners for high-order problems with optimal memory usage and computational complexity. The preconditioners are based on the construction of a spectrally equivalent low-order discretization on a refined mesh, which is then amenable to, for example, algebraic multigrid preconditioning. The constants of equivalence are independent of mesh size and polynomial degree. For vector finite element problems in H(curl) and H(div) (e.g., for electromagnetic or radiation diffusion problems), a specially constructed interpolation–histopolation basis is used to ensure fast convergence. Detailed performance studies are carried out to analyze the efficiency of the GPU algorithms. The kernel throughput of each of the main algorithmic components is measured, and the strong and weak parallel scalability of the methods is demonstrated. The different relative weighting and significance of the algorithmic components on GPUs and CPUs is discussed. Results on problems involving adaptively refined nonconforming meshes are shown, and the use of the preconditioners on a large-scale magnetic diffusion problem using all spaces of the finite element de Rham complex is illustrated.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

A refined assessment of nuclear data target accuracy requirements for ALFRED

The interest in target accuracy assessment has been recently renewed within the OECD/NEA Working Party on International Nuclear Data Evaluation Cooperation with an update exercise, thanks to the invaluable initiative of Massimo Salvatores. This work, moving from evaluations on the main core integral parameters of the Advanced Lead-cooled Fast Reactor European Demonstrator (ALFRED), and the identification of the associated target accuracies needed for improving its design, approaches the retrieval of target accuracy requirements for nuclear data, as the inverse problem of uncertainty quantification. The preliminary results obtained in a previous work are here refined by explicitly taking into account the total contribution due to correlations among variables in the optimization constraint, while its various components are evaluated individually. Moreover, three different sets of cost parameters are considered to introduce a bias in the solution in order to take in due account the relative difficulties in the execution of new differential experiments as needed for achieving the proposed target accuracies. By this, the obtained results are deemed usefully informative, and proposed for the update of a High Priority List which identifies the isotopes-reaction couples of most interest for future refinement experiments, especially when integrated with further analogous information collected on other advanced nuclear systems. Among the cross-sections whose refinement contributes the most to the reduction of the multiplication factor, the fission of Pu{sup 239} was found, which needs to be fixed below 1% in the range of interest for ALFRED (2 keV-4 MeV). Another contribution for the amelioration of the multiplication factor calculation accuracy, is due to the capture channel of Pu{sup 239}, for which the initial high uncertainty (around 15%) can be significantly reduced resorting to easily practicable experiments. The same occurs for the inelastic of Pb{sup 207}, for which the initial uncertainty value of around 50% can be drastically reduced up to target values between 4% and 7%.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2013

Energy-Saving Melting and Revert Reduction Technology (E-SMARRT), Task 5.3: Casting Porosity-Free Grain Refined Magnesium Alloys

The objective of this project was to identify the root causes for micro-porosity in magnesium alloy castings and recommend remedies that can be implemented in production. Three casting magnesium alloys were used to determine the causes of porosity that is a common problem in the magnesium casting industry. These alloys were AM50A, AM60A, and AZ91D, and all were grain refined with C 2 Cl 6 . Gas porosity was found to have little effect if proper degassing methods and foundry practices were used. It was found that sound gating practice, directional solidification towards the riser and generous risering should always dominate in order to produce sound castings. In sand cast magnesium, thermal gradients were found to be an important indicator of heat transfer in the mold. A minimum thermal gradient was found for each alloy that would produce sound castings. There were 2.02°C/cm for AM50A, 1.99°C/cm for AM60A, and 1.97°C/cm for AZ91D. If these gradients are met or exceeded when an area of the casting reaches 50°C below the liquidus for the alloy, the casting will be free of shrinkage porosity in that area. The cooling rates measured during casting magnesium alloys in a pre-heated step permanent mold ranged from 12°F/min in the three inches thick step to 200o F/min in the one inch step. The effect of the cooling rate on the grain size and the mechanical properties was noticeable but not substantial. Grain refining with C 2 Cl 6 had a marked effect on the grain size of the permanent mold step casting. It reduced it by 10-15% in AM50A and by a factor of six in AZ91E from 300 µm to around 55 µm. The mechanical properties of both permanent mold cast AZ91E and AM50A were improved by grain refinement. The most prominent increase was in the elongation of AM50A that more than doubled from 8% to 17%. Computer simulation of porosity was conducted for a well gated commercial wheel casting. The simulation did not predict significant porosity in the wheel. The mechanical testing of tensile specimens excised from the wheel indeed confirmed good properties, in line with the specifications for this alloy. Evidence of minimal micro-porosity was detected in sections cut from the wheel and investigated under optical microscopy. This finding confirms the key role played by utilizing optimal gating and risering practices in minimizing porosity in magnesium castings.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗