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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 991 records · Page 55
All sourcesNASA NTRSDOE OSTI
NASA NTRS1991

Solution and shock-induced exsolution of argon in vitreous carbon

To add to the knowledge of noble gas solution and exsolution in carbonaceus material, experiments were performed on vitreous carbon. Ar-rich vitreous carbon samples were prepared under vapor-saturated conditions using argon as the pressurizing medium. Solubility data were obtained for temperatures of 773 to 973 K and pressures of 250 to 1500 bars. Up to 7 wt pct Ar was dissolved in the carbon. The solubility data were compared to a thermodynamic model of argon atoms dissolving into a fixed population of 'holes' in the carbon. Two variations of the model yielded estimates of the enthalpy of solution of Ar in vitreous carbon equal to about -4700 cal/mole. Preliminary shock experiments showed that 28 percent of the total argon was released by driving 4 GPa shocks into the argon-rich carbon. It was demonstrated that shock-induced argon loss is not simply caused by the impact-induced diminution of grain size. The present value of shock pressure required for partial impact devolatilization of Ar from carbon is below the range (5-30 GPa) at which H2O is released from phyllosilicates.

Gazis, Carey↗
NASA NTRS2012

Auto Code Generation for Simulink-Based Attitude Determination Control System

This paper details the work done to auto generate C code from a Simulink-Based Attitude Determination Control System (ADCS) to be used in target platforms. NASA Marshall Engineers have developed an ADCS Simulink simulation to be used as a component for the flight software of a satellite. This generated code can be used for carrying out Hardware in the loop testing of components for a satellite in a convenient manner with easily tunable parameters. Due to the nature of the embedded hardware components such as microcontrollers, this simulation code cannot be used directly, as it is, on the target platform and must first be converted into C code; this process is known as auto code generation. In order to generate C code from this simulation; it must be modified to follow specific standards set in place by the auto code generation process. Some of these modifications include changing certain simulation models into their atomic representations which can bring new complications into the simulation. The execution order of these models can change based on these modifications. Great care must be taken in order to maintain a working simulation that can also be used for auto code generation. After modifying the ADCS simulation for the auto code generation process, it is shown that the difference between the output data of the former and that of the latter is between acceptable bounds. Thus, it can be said that the process is a success since all the output requirements are met. Based on these results, it can be argued that this generated C code can be effectively used by any desired platform as long as it follows the specific memory requirements established in the Simulink Model.

MolinaFraticelli, Jose Carlos↗
NASA NTRS1987

Theoretical approach to oxygen atom degradation of silver

Based on available Rutherford backscattering spectrometry (RBS), proton induced X-ray emission (PIXE) and ellipsometry data obtained on silver specimens subjected to atomic oxygen attack in low Earth orbit STS flight 41-G, a theory was developed to model the oxygen atom degradation of silver. The diffusion of atomic oxygen in a microscopically nonuniform medium is an essential constituent of the theory. The driving force for diffusion is the macroscopic electrochemical potential gradient developed between the specimen surface exposed to the ambient and the bulk of the silver specimen. The longitudinal electric effect developed parallel to the gradient is modified by space charge of the diffusing charged species. Lateral electric fields and concentration differences also exist due to the nonuniform nature of the medium. The lateral concentration differences are found to be more important than the lateral electric fields in modifying the diffusion rate. The model was evaluated numerically. Qualitative agreement exists between the kinetics predicted by the theory and kinetic data taken in ground-based experiments utilizing a plasma asher.

Fromhold, Albert T., Jr.↗
DOE OSTI2014

Iterative derivation of effective potentials to sample the conformational space of proteins at atomistic scale

The current capacity of computers makes it possible to perform simulations of small systems with portable, explicit-solvent potentials achieving high degree of accuracy. However, simplified models must be employed to exploit the behavior of large systems or to perform systematic scans of smaller systems. While powerful algorithms are available to facilitate the sampling of the conformational space, successful applications of such models are hindered by the availability of simple enough potentials able to satisfactorily reproduce known properties of the system. We develop an interatomic potential to account for a number of properties of proteins in a computationally economic way. The potential is defined within an all-atom, implicit solvent model by contact functions between the different atom types. The associated numerical values can be optimized by an iterative Monte Carlo scheme on any available experimental data, provided that they are expressible as thermal averages of some conformational properties. We test this model on three different proteins, for which we also perform a scan of all possible point mutations with explicit conformational sampling. The resulting models, optimized solely on a subset of native distances, not only reproduce the native conformations within a few Angstroms from the experimental ones, but show the cooperative transition between native and denatured state and correctly predict the measured free-energy changes associated with point mutations. Moreover, differently from other structure-based models, our method leaves a residual degree of frustration, which is known to be present in protein molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Modeling protein structures from predicted contacts with modern molecular dynamics potentials: accuracy, sensitivity, and refinement

Protein structure prediction has become increasingly popular and successful in recent years. An essential step for fragment-free, template-free methods is the generation of a final three-dimensional protein model from a set of predicted amino acid contacts that are often described by interresidue pairwise atomic distances. Here we explore the use of modern, open-source molecular dynamics (MD) engines, which have been continually developed over the last three decades with all-atom Hamiltonians to model biomolecular structure and dynamics, to generate accurate protein structures starting from a set of inferred pairwise distances. Additionally, the ability of MD empirical physical potentials to correct inaccuracies in the predicted geometries is tested. We rigorously characterize the effect of modeling parameters on results, the effect of different amounts of error in the predicted distances on the final structures, and test the ability of post-processing analysis to sort the best models out of a set of statistical replicas. We find that with exact distances and with noisy distances, the method can produce excellent structural models, and that the molecular dynamics force field seems to help correct errors in distance predictions, resisting the effects of applied noise.

Davidson, Russ↗
DOE OSTI2024

Dielectronic satellite emission from a solid-density Mg plasma: Relationship to models of ionization potential depression

Here, we report on experiments where solid-density Mg plasmas are created by heating with the focused output of the Linac Coherent Light Source x-ray free-electron laser. We study the K-shell emission from the helium- and lithium-like ions using Bragg crystal spectroscopy. Observation of the dielectronic satellites in lithium-like ions confirms that the M-shell electrons appear bound for these high charge states. An analysis of the intensity of these satellites indicates that when modeled with an atomic-kinetics code, the ionization potential depression model employed needs to produce depressions for these ions which lie between those predicted by the well known Stewart-Pyatt and Ecker-Kroll models. These results are largely consistent with recent density functional theory calculations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

Phase evolution in two-phase alloys during severe plastic deformation

Herein, phase evolution in FCC metals with strongly interacting alloy components during severe plastic deformation is investigated using molecular dynamics simulations. Specifically, we study the alloy microstructure in steady state, nucleation and growth of precipitates in supersaturated alloys, and the decomposition of precipitates in undersaturated alloys. The results are compared to a modified effective temperature model, providing a physical understanding for the atomic processes underlying the model and a perspective on its strengths and weaknesses. Key observations in this work are nucleation and growth of precipitates during SPD at a temperature of 100 K; Gibbs-Thomson-like behavior relating solubility to precipitate size under steady-state shearing; a direct relationship between the effective temperature and the shear modulus; and the importance of cluster agglomeration during precipitate growth. The study also reveals that the mechanisms of forced chemical mixing depends on precipitate size, adding complications for effective temperature models describing inhomogeneous systems. The simulations are shown to provide good semiquantitative agreement with experimental findings reported in the literature.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Structural determination of a full-length plant cellulose synthase informed by experimental and in silico methods

Three-dimensional structure determination and prediction of proteins with intrinsically disordered regions, unstructured regions, conformational flexibility, and lacking homologous structures are challenging. We previously predicted and refined an in silico structure of a plant cellulose synthase from cotton (GhCESA1), and more recently, cryo-electron microscopy (cryo-EM) has resolved a majority of the lengths of two CESA structures from poplar (PttCESA8) and cotton (GhCESA7). However, 26–30% of these cryo-EM structures remain unresolved, including the N-terminal domain, half of the class-specific region, the gating loop region, and the C-terminal domain. Here, we describe the generation and evaluation of a full-length hybrid GhCESA1 model based on this cryo-EM PttCESA8 structure, with unresolved regions completed using this in silico refined GhCESA1 model. All-atom molecular dynamics simulations and subsequent energy minimizations were performed for the in silico and hybrid GhCESA1 models in a lipid bilayer-water-ion environment, and structural stability, dynamics, energetics, contacts, and quality were evaluated. The unresolved regions were found to be the most dynamic, in agreement with their poor electron density with cryo-EM. The hybrid model exhibited a higher total secondary structure content, more favorable intra-protein and protein-lipid interaction energies, and improved quality metrics. Moreover, hydrogen bonding was revealed to be a primary mechanism for intra-protein and protein-lipid contacts. These results demonstrate that in silico structure prediction and refinement may be useful to augment experimental structure determination, especially for disordered and unstructured regions. Furthermore, this hybrid model can serve as a steppingstone to derive full-length homology models of other CESAs found in more experimentally tractable organisms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Identification of O-rich structures on platinum(111)-supported ultrathin iron oxide films

Using high-resolution scanning tunneling microscopy (STM) we have studied the oxidation of ultrathin FeO films grown on Pt(111). At the initial stage of the FeO film oxidation by atomic oxygen exposure, we identified three distinct types of line defects, all of which form boundaries between FeO domains of opposite orientation. Two types of line defects appearing bright ( type-i ) and dark ( type-ii ) in the STM images at typical scanning parameters are “metallic”, whereas the third line defect exhibits nonmetallic behavior ( type-iii ). Atomic-scale structure models of these line defects are proposed, with type-i defects exhibiting 4-fold coordinated Fe atoms, type-ii exhibiting 2-fold coordinated O atoms, and type-iii exhibiting tetrahedrally-coordinated Fe atoms. In addition, FeO 2 trilayer islands are formed upon oxidation, which appear at FCC-type domains of the moiré structure. At high scanning bias, distinct protrusions on the trilayer islands are observed over surface O ions, which are assigned to H adatoms. The experimental data are supported by density functional theory (DFT) calculations, in which bare and hydroxylated FeO 2 trilayer islands are compared. Finally, we compare the formation of O-rich features on continuous FeO films using atomic oxygen with the oxidation of Pt(111)-supported FeO islands accomplished by O 2 exposure.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Substitutional impurity in single-layer graphene: The Koster–Slater and Anderson models

The Koster–Slater and Anderson models are used to consider substitutional impurities in free-standing single-layer graphene. The density of states of graphene is described using a model (the M model). For the nitrogen and boron impurities, the occupation numbers and the parameter η which defines the fraction of delocalized electrons of the impurity are determined. In this case, experimental data are used for both determination of the model parameters and comparison with the results of theoretical estimations. The general features of the Koster–Slater and Anderson models and the differences between the two models are discussed. Specifically, it is shown that the band contributions to the occupation numbers of a nitrogen atom in both models are comparable, whereas the local contributions are substantially different: the local contributions are decisive in the Koster–Slater model and negligible in the Anderson model. The asymptotic behavior of the wave functions of a defect is considered in the Koster–Slater model, and the electron states of impurity dimers are considered in the Anderson model.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Benchmark of few-level quantum theory vs ab initio numerical solutions for the strong-field Autler–Townes effect in photoionization of hydrogen

Abstract The temporal and spectral consequences of an intermediate resonance en route to photoionization are investigated theoretically in two ways: by solving few-level model equations and by ab initio numerical solution of the time-dependent Schrödinger equation, in both cases for hydrogen in three dimensions. The model consists of atomic states resonantly field-dressed in a three-level reduction of the hydrogen atom that consists of the 2 p –3 d (Balmer) transition and one energetically-distant continuum state. The model’s level occupation probabilities are derived from three Schrödinger amplitude equations and are benchmarked against an ab initio numerical solution for the hydrogen electron’s wavefunction under the same field. We examine contrasts between the results of the two approaches with a particular focus on Autler–Townes doublets that appear in the photoelectron spectrum.

74 ATOMIC AND MOLECULAR PHYSICS↗
NASA NTRS1986

Multistep modeling of protein structure: application to bungarotoxin

Modelling of bungarotoxin in atomic details is presented in this article. The model-building procedure utilizes the low-resolution crystal coordinates of the c-alpha atoms of bungarotoxin, sequence homology within the neurotoxin family, as well as high-resolution x-ray diffraction data of cobratoxin and erabutoxin. Our model-building procedure involves: (a) principles of comparative modelling, (b) embedding procedures of distance geometry, and (c) use of molecular mechanics for optimizing packing. The model is not only consistent with the c-alpha coordinates of crystal structure, but also agrees with solution conformational features of the triple-stranded beta sheet as observed by NOE measurements.

NASA Discipline Exobiology↗
DOE OSTI2016

Ab initio Modeling of the Electronic Structures and Physical Properties of a‐Si 1− x Ge x O 2 Glass ( x = 0 to 1)

The amorphous silica (a‐SiO 2 ) and germania (a‐GeO 2 ) have a wide range of applications in glass industry. Based on a previously constructed near‐perfect continuous random network model with 1296 atoms and periodic boundary conditions, we extend our study to amorphous Si 1− x G e x O 2 models of homogeneous random substitution of Si by Ge with x ranging from 0 to 1. We have calculated the structural, electronic, mechanical, and optical properties for the series by using the first‐principles density functional theory methods. The x ‐dependence of the variations in the properties is analyzed and critically compared with available experimental data. The mass density, volume, total bond order density, bulk mechanical properties, and refractive index are found to vary linearly as a function of x . For x = 0.5, we have also constructed six different kinds of particle immersion models to test the effect of inclusion of spherical particles of one glass of different sizes in the medium of the other glass on their physical properties. It is shown that particle sizes do affect the properties of particle immersion. Our calculations provide deep insight on the properties of mixture and nanocomposites of a‐SiO 2 and a‐GeO 2 glasses.

Baral, Khagendra↗
DOE OSTI2015

Model-free estimation of the effective correlation time for C–H bond reorientation in amphiphilic bilayers: {sup 1}H–{sup 13}C solid-state NMR and MD simulations

Molecular dynamics (MD) simulations give atomically detailed information on structure and dynamics in amphiphilic bilayer systems on timescales up to about 1 μs. The reorientational dynamics of the C–H bonds is conventionally verified by measurements of {sup 13}C or {sup 2}H nuclear magnetic resonance (NMR) longitudinal relaxation rates R{sub 1}, which are more sensitive to motional processes with correlation times close to the inverse Larmor frequency, typically around 1-10 ns on standard NMR instrumentation, and are thus less sensitive to the 10-1000 ns timescale motion that can be observed in the MD simulations. We propose an experimental procedure for atomically resolved model-free estimation of the C–H bond effective reorientational correlation time τ{sub e}, which includes contributions from the entire range of all-atom MD timescales and that can be calculated directly from the MD trajectories. The approach is based on measurements of {sup 13}C R{sub 1} and R{sub 1ρ} relaxation rates, as well as {sup 1}H−{sup 13}C dipolar couplings, and is applicable to anisotropic liquid crystalline lipid or surfactant systems using a conventional solid-state NMR spectrometer and samples with natural isotopic composition. The procedure is demonstrated on a fully hydrated lamellar phase of 1-palmitoyl-2-oleoyl-phosphatidylcholine, yielding values of τ{sub e} from 0.1 ns for the methyl groups in the choline moiety and at the end of the acyl chains to 3 ns for the g{sub 1} methylene group of the glycerol backbone. MD simulations performed with a widely used united-atom force-field reproduce the τ{sub e}-profile of the major part of the acyl chains but underestimate the dynamics of the glycerol backbone and adjacent molecular segments. The measurement of experimental τ{sub e}-profiles can be used to study subtle effects on C–H bond reorientational motions in anisotropic liquid crystals, as well as to validate the C–H bond reorientation dynamics predicted in MD simulations of amphiphilic bilayers such as lipid membranes.

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

Laboratory measurements of resistivity in warm dense plasmas relevant to the microphysics of brown dwarfs

Since the observation of the first brown dwarf in 1995, numerous studies have led to a better understanding of the structures of these objects. Here we present a method for studying material resistivity in warm dense plasmas in the laboratory, which we relate to the microphysics of brown dwarfs through viscosity and electron collisions. Here we use X-ray polarimetry to determine the resistivity of a sulphur-doped plastic target heated to Brown Dwarf conditions by an ultra-intense laser. The resistivity is determined by matching the plasma physics model to the atomic physics calculations of the measured large, positive, polarization. Furthermore, the inferred resistivity is larger than predicted using standard resistivity models, suggesting that these commonly used models will not adequately describe the resistivity of warm dense plasma related to the viscosity of brown dwarfs.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗