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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 199 records · Page 11
All sourcesNASA NTRSDOE OSTI
DOE OSTI2014

Free kick instead of cross-validation in maximum-likelihood refinement of macromolecular crystal structures

The maximum-likelihood free-kick target, which calculates model error estimates from the work set and a randomly displaced model, proved superior in the accuracy and consistency of refinement of crystal structures compared with the maximum-likelihood cross-validation target, which calculates error estimates from the test set and the unperturbed model. The refinement of a molecular model is a computational procedure by which the atomic model is fitted to the diffraction data. The commonly used target in the refinement of macromolecular structures is the maximum-likelihood (ML) function, which relies on the assessment of model errors. The current ML functions rely on cross-validation. They utilize phase-error estimates that are calculated from a small fraction of diffraction data, called the test set, that are not used to fit the model. An approach has been developed that uses the work set to calculate the phase-error estimates in the ML refinement from simulating the model errors via the random displacement of atomic coordinates. It is called ML free-kick refinement as it uses the ML formulation of the target function and is based on the idea of freeing the model from the model bias imposed by the chemical energy restraints used in refinement. This approach for the calculation of error estimates is superior to the cross-validation approach: it reduces the phase error and increases the accuracy of molecular models, is more robust, provides clearer maps and may use a smaller portion of data for the test set for the calculation of R{sub free} or may leave it out completely.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2015

Programming new geometry restraints: Parallelity of atomic groups

Improvements in structural biology methods, in particular crystallography and cryo-electron microscopy, have created an increased demand for the refinement of atomic models against low-resolution experimental data. One way to compensate for the lack of high-resolution experimental data is to use a priori information about model geometry that can be utilized in refinement in the form of stereochemical restraints or constraints. Here, the definition and calculation of the restraints that can be imposed on planar atomic groups, in particular the angle between such groups, are described. Detailed derivations of the restraint targets and their gradients are provided so that they can be readily implemented in other contexts. Practical implementations of the restraints, and of associated data structures, in the Computational Crystallography Toolbox ( cctbx ) are presented.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Spectroscopy of Very Hot Plasma in Non-flaring Parts of a Solar Limb Active Region: Spatial and Temporal Properties

In this work we investigate the thermal structure of an off-limb active region (AR) in various non-flaring areas, as it provides key information on the way these structures are heated. In particular, we concentrate on the very hot component (>3 MK) as it is a crucial element to distinguish between different heating mechanisms. We present an analysis using Fe and Ca emission lines from both the Solar Ultraviolet Measurement of Emitted Radiation (SUMER) on board the Solar and Heliospheric Observatory (SOHO) and the EUV Imaging Spectrometer (EIS) on board Hinode. A data set covering all ionization stages from Fe x to Fe xix has been used for the thermal analysis (both differential emission measure and emission measure, EM). Ca xiv is used for the SUMER-EIS radiometric cross calibration. We show that the very hot plasma is present and persistent almost everywhere in the core of the limb AR. The off-limb AR is clearly structured in Fe xviii. Almost everywhere, the EM analysis reveals plasma at 10 MK (visible in Fe xix emission), which is down to 0.1% of EM of the main 3 MK plasma. We estimate the power-law index of the hot tail of the EM to be between −8.5 and −4.4. However, the question about the possible existence of a small minor peak at around 10 MK remains open. The absence in some part of the AR of the Fe xix and Fe xxiii lines (which fall into our spectral range) enables us to determine an upper limit on the EM at these temperatures. Our results include a new Ca xiv 943.59 Å atomic model.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2015

Dynamic force matching: A method for constructing dynamical coarse-grained models with realistic time dependence

Coarse-grained (CG) models of molecular systems, with fewer mechanical degrees of freedom than an all-atom model, are used extensively in chemical physics. It is generally accepted that a coarse-grained model that accurately describes equilibrium structural properties (as a result of having a well constructed CG potential energy function) does not necessarily exhibit appropriate dynamical behavior when simulated using conservative Hamiltonian dynamics for the CG degrees of freedom on the CG potential energy surface. Attempts to develop accurate CG dynamic models usually focus on replacing Hamiltonian motion by stochastic but Markovian dynamics on that surface, such as Langevin or Brownian dynamics. However, depending on the nature of the system and the extent of the coarse-graining, a Markovian dynamics for the CG degrees of freedom may not be appropriate. In this paper, we consider the problem of constructing dynamic CG models within the context of the Multi-Scale Coarse-graining (MS-CG) method of Voth and coworkers. We propose a method of converting a MS-CG model into a dynamic CG model by adding degrees of freedom to it in the form of a small number of fictitious particles that interact with the CG degrees of freedom in simple ways and that are subject to Langevin forces. The dynamic models are members of a class of nonlinear systems interacting with special heat baths that were studied by Zwanzig [J. Stat. Phys. 9, 215 (1973)]. The properties of the fictitious particles can be inferred from analysis of the dynamics of all-atom simulations of the system of interest. This is analogous to the fact that the MS-CG method generates the CG potential from analysis of equilibrium structures observed in all-atom simulation data. The dynamic models generate a non-Markovian dynamics for the CG degrees of freedom, but they can be easily simulated using standard molecular dynamics programs. We present tests of this method on a series of simple examples that demonstrate that the method provides realistic dynamical CG models that have non-Markovian or close to Markovian behavior that is consistent with the actual dynamical behavior of the all-atom system used to construct the CG model. Both the construction and the simulation of such a dynamic CG model have computational requirements that are similar to those of the corresponding MS-CG model and are good candidates for CG modeling of very large systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Atom-in-jellium equations of state in the high-energy-density regime

Recent path-integral Monte Carlo and quantum molecular dynamics simulations have shown that computationally efficient average-atom models can predict thermodynamic states in warm dense matter to within a few percent. One such atom-in-jellium model has typically been used to predict the electron-thermal behavior only, although it was previously developed to predict the entire equation of state (EOS). In this work, we report completely atom-in-jellium EOS calculations for Be, Al, Si, Fe, and Mo, as elements representative of a range of atomic number and low-pressure electronic structure. Comparing the more recent method of pseudoatom molecular dynamics, atom-in-jellium results were similar: sometimes less accurate, sometimes more. All these techniques exhibited pronounced effects of electronic shell structure in the shock Hugoniot which are not captured by Thomas-Fermi based EOS. These results demonstrate the value of a hierarchical approach to EOS construction, using average-atom techniques with shell structure to populate a wide-range EOS surface efficiently, complemented by more rigorous three-dimensional multiatom calculations to validate and adjust the EOS.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Improving Predictive Capability in REHEDS Simulations with Fast, Accurate, and Consistent Non-Equilibrium Material Properties

Predictive design of REHEDS experiments with radiation-hydrodynamic simulations requires knowledge of material properties (e.g. equations of state (EOS), transport coefficients, and radiation physics). Interpreting experimental results requires accurate models of diagnostic observables (e.g. detailed emission, absorption, and scattering spectra). In conditions of Local Thermodynamic Equilibrium (LTE), these material properties and observables can be pre-computed with relatively high accuracy and subsequently tabulated on simple temperature-density grids for fast look-up by simulations. When radiation and electron temperatures fall out of equilibrium, however, non-LTE effects can profoundly change material properties and diagnostic signatures. Accurately and efficiently incorporating these non-LTE effects has been a longstanding challenge for simulations. At present, most simulations include non-LTE effects by invoking highly simplified inline models. These inline non-LTE models are both much slower than table look-up and significantly less accurate than the detailed models used to populate LTE tables and diagnose experimental data through post-processing or inversion. Because inline non-LTE models are slow, designers avoid them whenever possible, which leads to known inaccuracies from using tabular LTE. Because inline models are simple, they are inconsistent with tabular data from detailed models, leading to ill-known inaccuracies, and they cannot generate detailed synthetic diagnostics suitable for direct comparisons with experimental data. This project addresses the challenge of generating and utilizing efficient, accurate, and consistent non-equilibrium material data along three complementary but relatively independent research lines. First, we have developed a relatively fast and accurate non-LTE average-atom model based on density functional theory (DFT) that provides a complete set of EOS, transport, and radiative data, and have rigorously tested it against more sophisticated first-principles multi-atom DFT models, including time-dependent DFT. Next, we have developed a tabular scheme and interpolation methods that compactly capture non-LTE effects for use in simulations and have implemented these tables in the GORGON magneto-hydrodynamic (MHD) code. Finally, we have developed post-processing tools that use detailed tabulated non-LTE data to directly predict experimental observables from simulation output.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Cartesian message passing neural networks for directional properties: Fast and transferable atomic multipoles

The message passing neural network (MPNN) framework is a promising tool for modeling atomic properties but is, until recently, incompatible with directional properties, such as Cartesian tensors. We propose a modified Cartesian MPNN (CMPNN) suitable for predicting atom-centered multipoles, an essential component of ab initio force fields. The efficacy of this model is demonstrated on a newly developed dataset consisting of 46 623 chemical structures and corresponding high-quality atomic multipoles, which was deposited into the publicly available Molecular Sciences Software Institute QCArchive server. We show that the CMPNN accurately predicts atom-centered charges, dipoles, and quadrupoles and that errors in the predicted atomic multipoles have a negligible effect on multipole–multipole electrostatic energies. The CMPNN is accurate enough to model conformational dependencies of a molecule’s electronic structure. This opens up the possibility of recomputing atomic multipoles on the fly throughout a simulation in which they might exhibit strong conformational dependence.

Glick, Zachary L. (ORCID:0000000309002849)↗
DOE OSTI2024

Identifying point defects and ordering in the high-entropy layered oxide Li 1.5 MO 3-δ (M=Mn, Al, Fe, Co, Ni) for energy storage applications

High-entropy layered oxides (HELOs) represent a very promising class of next-generation battery cathodes, combining the well-studied properties of layered cathode materials such as LiCoO 2 with the chemical tunability and stability of high-entropy materials. HELO materials often form particles with complex defects and domain structures, complicating accurate characterization of structure and cation mixing. Understanding disorder and order in HELO materials is necessary for understanding their performance and utility as cathodes. Here we demonstrate the characterization of the HELO Li 1.5 MO 3-δ (M = Mn, Al, Fe, Co, Ni), wherein X-ray powder diffraction, transmission electron microscopy imaging, and electron diffraction patterns are analyzed to reveal the presence of ordering in the HELO, with imaging and diffraction simulation employed to compare experimental results to atomic modeling. Finally, without rigorous characterization at the atomic scale, important features such as defect ordering can be easily overlooked and therefore remain unconsidered when interpreting experimental results.

36 MATERIALS SCIENCE↗
NASA NTRS2012

LSPRAY-IV: A Lagrangian Spray Module

LSPRAY-IV is a Lagrangian spray solver developed for application with parallel computing and unstructured grids. It is designed to be massively parallel and could easily be coupled with any existing gas-phase flow and/or Monte Carlo Probability Density Function (PDF) solvers. The solver accommodates the use of an unstructured mesh with mixed elements of either triangular, quadrilateral, and/or tetrahedral type for the gas flow grid representation. It is mainly designed to predict the flow, thermal and transport properties of a rapidly vaporizing spray. Some important research areas covered as a part of the code development are: (1) the extension of combined CFD/scalar-Monte- Carlo-PDF method to spray modeling, (2) the multi-component liquid spray modeling, and (3) the assessment of various atomization models used in spray calculations. The current version contains the extension to the modeling of superheated sprays. The manual provides the user with an understanding of various models involved in the spray formulation, its code structure and solution algorithm, and various other issues related to parallelization and its coupling with other solvers.

Raju, M. S.↗
DOE OSTI2018

Understanding Chemical Bonding in Alloys and the Representation in Atomistic Simulations

Alloys are widely used in catalysts and structural materials. The nature of chemical bonding and the origin of alloy formation energies, defect energies, and interfacial properties have not been well understood to date but are critical to material performance. In this contribution, we explain the polar nature of chemical bonding and an implementation in classical and reactive atomistic simulations to understand such properties more quantitatively. Electronegativity differences between metal atoms lead to polar bonding, and exothermic alloy formation energies are related to charge transfer between the different elements. These differences can be quantified by atomic charges using pairwise charge increments, determined by matching the computed alloy formation energy to experimentally measured alloy formation energies using pair potentials for the pure metals. The polar character of alloys is comparable to organic molecules and partially ionic minerals, for example, AlNi and AlNi3 alloys assume significant atomic charges of ±0.40e and +0.60e/–0.20e, respectively. The subsequent analysis of defect sites and defect energies using force-field-based calculations shows excellent agreement with calculations using density functional theory and embedded atom models (EAM). The formation of vacancy and antisite defects is characterized by a redistribution of charge in the first shell of neighbor atoms in the classical models whereby electroneutrality is maintained and charge increments correlate with differences in electronegativity. The proposed atomic charges represent internal dipole and multipole moments, consistent with existing definitions for organic and inorganic compounds and with the extended Born model (Heinz, H.; Suter, U. W. J. Phys. Chem. B2004,108 (47), 18341–18352). The method can be applied to any alloy and has a reproducibility of ±10%. In contrast, quantum mechanical charge schemes remain associated with deviations exceeding ±100%. The atomic charges for alloys provide a simple initial measure for the internal electronic structure, surface adsorption of molecules, and reactivity in catalysis and corrosion. The models are compatible with the Interface force field (IFF), CHARMM, AMBER, OPLS-AA, PCFF, CVFF, and GROMOS for reliable atomistic simulations of alloys and their interfaces with minerals and electrolytes from the nanometer scale to the micrometer scale.

Chemistry↗
DOE OSTI2016

Electron-ion collision-frequency for x-ray Thomson scattering in dense plasmas

Two methods are presented to calculate the electron-ion collision-frequency in dense plasmas using an average-atom model. The first one is based on the Kubo-Greenwood approach. The second one uses the Born and Lenard-Balescu approximations. The two methods are used to calculate x-ray Thomson scattering spectra. Illustrations are shown for dense beryllium and aluminum plasmas. Comparisons with experiment are presented in the case of an x-ray Thomson scattering spectrum.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2016

Synthesis of reduced carbon nitride at the reduction by hydroquinone of water-soluble carbon nitride oxide (g-C{sub 3}N{sub 4})O

For the first time at the reduction by hydroquinone of water-soluble carbon nitride oxide (g-C{sub 3}N{sub 4})O reduced carbon nitride (or reduced multi-layer azagraphene) is obtained. It is differed from usually synthesized carbon nitride by a significantly large (on 0.09 nm) interplanar distance is. At the same time, the chemical bonds between atoms in a heteroatomic plane of reduced carbon nitride correspond to the bonds in a synthesized g-C{sub 3}N{sub 4}. The samples of water-soluble carbon nitride oxide were synthesized under the special reactionary conditions of a pyrolysis of melamine and urea. We believe that reduced carbon nitride consists of weakly connected carbon-nitrogen monosheets (azagraphene sheets) as well as reduced (from graphene oxide) graphene contains weakly connected graphene sheets. - Graphical abstract: XRD pattern and schematic atomic model of one layer of reduced carbon nitride, carbon nitride oxide and synthesized carbon nitride. For the first time at the reduction by hydroquinone of the water-soluble carbon nitride oxide (g-C{sub 3}N{sub 4})O is obtained the reduced carbon nitride (or reduced multi-layer azagraphene). Display Omitted - Highlights: • First the reduced carbon nitride (RCN) at the reduction of the carbon nitride oxide was obtained. • Water-soluble carbon nitride oxide was reduced by hydroquinone. • The chemical bonds in a heteroatomic plane of RCN correspond to the bonds in a synthesized g-C{sub 3}N{sub 4}. • Reduced carbon nitride consists of poorly connected heteroatomic azagraphene layers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Equations of state and transport properties of mixtures in the warm dense regime

We have performed average-atom molecular dynamics to simulate the CH and LiH mixtures in the warm dense regime, and obtained equations of state and the ionic transport properties. The electronic structures are calculated by using the modified average-atom model, which have included the broadening of energy levels, and the ion-ion pair potentials of mixtures are constructed based on the temperature-dependent density functional theory. The ionic transport properties, such as ionic diffusion and shear viscosity, are obtained through the ionic velocity correlation functions. The equations of state and transport properties for carbon, hydrogen and lithium, hydrogen mixtures in a wide region of density and temperature are calculated. Through our computing the average ionization degree, average ion-sphere diameter and transition properties in the mixture, it is shown that transport properties depend not only on the ionic mass but also on the average ionization degree.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Structural and magnetic properties of La2Ni1−xCoxMnO6 compounds

Highlights: • Monoclinic La2Ni1−xCoxMnO6 samples have been prepared using Sol-gel technique. • Rietveld analysis shows an octahedrally distorted double perovskite structure. • The nature of FM interaction and TC depend on the B-site ions. • The short range FM ordering above TC is induced by antisite disorders. • The existence of any spin glass like phase in such system is discarded. - Abstract: Single phase monoclinic La{sub 2}Ni{sub 1−x}Co{sub x}MnO{sub 6} (x = 0.2, 0.4, 0.8) compounds, henceforth, referred as LNC{sub x}MO (x = 0.2, 0.4, 0.8) have been prepared by Sol–gel technique. The structural study and redox titration suggest that the samples are both La and O deficient. The generated atomic models using Rietveld refined structural parameters show octahedral distortion in the double perovskite structure. X-ray photoelectron spectroscopy (XPS) study has been used to determine the predominant valence states of Ni, Mn and Co ions. LNC{sub x}MO (x = 0.2, 0.4) are found to be Heisenberg ferromagnets whereas LNC{sub 0.8}MO is a phase segregated system. In LNC{sub 0.4}MO and LNC{sub 0.8}MO, at temperatures above T{sub C}, χ{sup −1}(T) curve shows the characteristics of Griffiths phase. The study of ac susceptibility and isothermal remanent magnetization (IRM) discard the possibility of any glassy state at low temperatures. The antiphase boundaries (APBs), antisite disorders (ASDs) and oxygen vacancies play important roles in this system.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2013

Bulkiness or aromatic nature of tyrosine-143 of actin is important for the weak binding between F-actin and myosin-ADP-phosphate

Highlights: •The effect of mutation of Tyr143 that becomes more exposed on assembly was examined. •Mutation of tyrosine-143 of Dictyostelium actin changed actin polymerizability. •The bulkiness or aromatic nature of Tyr143 is important for the weak binding. •The weak interaction between myosin and actin strengthened by Tyr143Trp mutation. -- Abstract: Actin filaments (F-actin) interact with myosin and activate its ATPase to support force generation. By comparing crystal structures of G-actin and the quasi-atomic model of F-actin based on high-resolution cryo-electron microscopy, the tyrosine-143 was found to be exposed more than 60 Å{sup 2} to the solvent in F-actin. Because tyrosine-143 flanks the hydrophobic cleft near the hydrophobic helix that binds to myosin, the mutant actins, of which the tyrosine-143 was replaced with tryptophan, phenylalanine, or isoleucine, were generated using the Dictyostelium expression system. It polymerized significantly poorly when induced by NaCl, but almost normally by KCl. In the presence of phalloidin and KCl, the extents of the polymerization of all the mutant actins were comparable to that of the wild-type actin so that the actin-activated myosin ATPase activity could be reliably compared. The affinity of skeletal heavy meromyosin to F-actin and the maximum ATPase activity (V{sub max}) were estimated by a double reciprocal plot. The Tyr143Trp-actin showed the higher affinity (smaller K{sub app}) than that of the wild-type actin, with the V{sub max} being almost unchanged. The K{sub app} and V{sub max} of the Tyr143Phe-actin were similar to those of the wild-type actin. However, the activation by Tyr143Ile-actin was much smaller than the wild-type actin and the accurate determination of K{sub app} was difficult. Comparison of the myosin ATPase activated by the various mutant actins at the same concentration of F-actin showed that the extent of activation correlates well with the solvent-accessible surface areas (ASA) of the replaced amino acid molecule. Because 1/K{sub app} reflects the affinity of F-actin for the myosin–ADP-phosphate intermediate (M.ADP.Pi) through the weak binding, these data suggest that the bulkiness or the aromatic nature of the tyrosin-143 is important for the initial binding of the M.ADP.Pi intermediate with F-actin but not for later processes such as the phosphate release.

60 APPLIED LIFE SCIENCES↗
NASA NTRS1978

Solution of the comoving-frame equation of transfer in spherically symmetric flows. V - Multilevel atoms

The coupled radiative transfer and statistical equilibrium equations for multilevel ionic structures in the atmospheres of early-type stars are solved. Both lines and continua are treated consistently; the treatment is applicable throughout a transonic wind, and allows for the presence of background continuum sources and sinks in the transfer. An equivalent-two-level-atoms approach provides the solution for the equations. Calculations for simplified He (+)-like model atoms in parameterized isothermal wind models indicate that subordinate line profiles are sensitive to the assumed mass-loss rate, and to the assumed structure of the velocity law in the atmospheres.

Mihalas, D.↗
DOE OSTI2014

Precipitates of Cr at Σ3 <110> {112} GB in α-Fe

Precipitates of Cr at Σ3 <110> {112} GB in α-Fe have been studied using molecular dynamics with a two-band embedded atomic model potential. The accumulation and segregation of Cr atoms and the evolution of the GB depend on local Cr concentration and temperature. At the early stage, with the existence of vacancies, the strong attraction of Cr with the GB core provides a pathway for Cr atoms to quickly accumulate within the GB core. With the increase of Cr concentration, the size of Cr dilute precipitates increases dramatically. And the strong segregation of Cr at the GB is observed, when Cr concentration reach 20%. Also, the size of Cr precipitates increases with increasing the temperatures from 300 K to 1000 K. The accumulation and segregation of Cr atoms at the GB lead to significant deformation of the GB structure and the formation of GB steps, causing the displacement and broadening of the GB.

Grain boundary↗