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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 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Transferable Hirshfeld atom model for rapid evaluation of aspherical atomic form factors

Form factors based on aspherical models of atomic electron density have brought great improvement in the accuracies of hydrogen atom parameters derived from X-ray crystal structure refinement. Today, two main groups of such models are available, the banks of transferable atomic densities parametrized using the Hansen–Coppens multipole model which allows for rapid evaluation of atomic form factors and Hirshfeld atom refinement (HAR)-related methods which are usually more accurate but also slower. In this work, a model that combines the ideas utilized in the two approaches is tested. It uses atomic electron densities based on Hirshfeld partitions of electron densities, which are precalculated and stored in a databank. This model was also applied during the refinement of the structures of five small molecules. A comparison of the resulting hydrogen atom parameters with those derived from neutron diffraction data indicates that they are more accurate than those obtained with the Hansen–Coppens based databank, and only slightly less accurate than those obtained with a version of HAR that neglects the crystal environment. The advantage of using HAR becomes more noticeable when the effects of the environment are included. To speed up calculations, atomic densities were represented by multipole expansion with spherical harmonics up to l = 7, which used numerical radial functions (a different approach to that applied in the Hansen–Coppens model). Calculations of atomic form factors for the small protein crambin (at 0.73 Å resolution) took only 68 s using 12 CPU cores.

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

Average Atom models

This report discusses average atom models, relatively cheap EOS models based on DFT that can access any temperature or density point for any element.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2018

New tools for the analysis and validation of cryo-EM maps and atomic models

Recent advances in the field of electron cryomicroscopy (cryo-EM) have resulted in a rapidly increasing number of atomic models of biomacromolecules that have been solved using this technique and deposited in the Protein Data Bank and the Electron Microscopy Data Bank. Similar to macromolecular crystallography, validation tools for these models and maps are required. While some of these validation tools may be borrowed from crystallography, new methods specifically designed for cryo-EM validation are required. Here, new computational methods and tools implemented in PHENIX are discussed, including d 99 to estimate resolution, phenix.auto_sharpen to improve maps and phenix.mtriage to analyze cryo-EM maps. It is suggested that cryo-EM half-maps and masks should be deposited to facilitate the evaluation and validation of cryo-EM-derived atomic models and maps. The application of these tools to deposited cryo-EM atomic models and maps is also presented.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Free-free opacity in dense plasmas with an average atom model

A model for the free-free opacity of dense plasmas is presented. The model uses a previously developed average atom model, together with the Kubo-Greenwood model for optical conductivity. This, in turn, is used to calculate the opacity with the Kramers-Kronig dispersion relations. Furthermore, comparisons to other methods for dense deuterium results in excellent agreement with DFT-MD simulations, and reasonable agreement with a simple Yukawa screening model corrected to satisfy the conductivity sum rule.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2023

A physics-driven Σ-Y atomization model for heavy-duty engine simulations

The atomization of a liquid jet is a multi-scale and multi-physics problem of interest for many engineering applications. Particularly, it drives the fuel-oxidizer mixing and dictates the efficiency of combustion engines. High-fidelity multi-phase simulations remain challenging due to the excessive computational cost required to capture all the atomization scales. Thus, atomization models are necessary to represent sub-grid liquid structures. Here, in this work, a modified Σ-Y model in the context of Eulerian-Lagrangian Spray Atomization (ELSA) is used to transport the surface area density of the spray. The model's predictive performance is assessed under various operating conditions relevant to heavy-duty engines using the Engine Combustion Network (ECN) Spray C and Spray D research-grade injectors. The classic droplet collision formulation of the Σ-Y model alone does not replicate the response of the measured spray surface area to changes in injector, ambient pressure, and injection pressure, requiring individual tuning of the model's parameters. Instead, a transition between dense and dilute spray breakup mechanisms is proposed in terms of the average droplet spacing. The collision breakup mechanism represents the dilute spray, whereas the droplet size in the dense spray is driven by a competition between the integral scale of turbulence and the balance between the turbulent kinetic energy and the surface energy of the droplets. Such an approach minimizes the requirements for model tuning. Moreover, the role of the constants of a compressible standard k-ε RANS model is assessed in the injector's internal flow and external spray simulation framework, and an updated set is proposed. The results are validated against x-ray radiography and Ultra-Small Angle X-ray Scattering (USAXS) data and highlight the predictive capabilities of the proposed physics-driven Σ-Y model, which is compatible with engine simulation turnaround times.

42 ENGINEERING↗
DOE OSTI2023

Average-atom model with Siegert states

In plasmas, electronic states can be well-localized bound states or itinerant free states, or something in between. In self-consistent treatments of plasma electronic structure such as the average-atom model, all states must be accurately resolved in order to achieve a converged numerical solution. Furthermore, this is a challenging numerical and algorithmic problem in large part due to the continuum of free states which is relatively expensive and difficult to resolve accurately. Siegert states are an appealing alternative. They form a complete eigenbasis with a purely discrete spectrum while still being equivalent to a representation in terms of the usual bound states and free states. However, many of their properties are unintuitive, and it is not obvious that they are suitable for self-consistent plasma electronic structure calculations. Here it is demonstrated that Siegert states can be used to accurately solve an average-atom model and offer advantages over the traditional finite-difference approach, including a concrete physical picture of pressure ionization and continuum resonances.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2016

From deep TLS validation to ensembles of atomic models built from elemental motions. Addenda and corrigendum

Researcher feedback has indicated that in Urzhumtsev et al. [(2015) Acta Cryst. D 71 , 1668–1683] clarification of key parts of the algorithm for interpretation of TLS matrices in terms of elemental atomic motions and corresponding ensembles of atomic models is required. Also, it has been brought to the attention of the authors that the incorrect PDB code was reported for one of test models. Lastly, these issues are addressed in this article.

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

Atomic modeling of photoionization fronts in nitrogen gas

Photoionization fronts play a dominant role in many astrophysical environments but remain difficult to achieve in a laboratory experiment. Recent papers have suggested that experiments using a nitrogen medium held at ten atmospheres of pressure which is irradiated by a source with a radiation temperature of T R ~ 100 eV can produce viable photoionization fronts. We present a suite of one-dimensional numerical simulations using the Helios multimaterial radiation hydrodynamics code that models these conditions and the formation of a photoionization front. We study the effects of varying the atomic kinetics and radiative transfer model on the hydrodynamics and ionization state of the nitrogen gas, finding that more sophisticated physics, in particular, a multi-angle long characteristic radiative transfer model and a collisional-radiative atomics model, dramatically changes the atomic kinetic evolution of the gas. A photoionization front is identified by computing the ratios between the photoionization rate, the electron impact ionization rate, and the total recombination rate. We find that due to the increased electron temperatures found using more advanced physics that photoionization fronts are likely to form in our nominal model. We report the results of several parameter studies. In one of these, the nitrogen pressure is fixed at ten atmospheres and the source radiation temperature is varied, while in another, the temperature is fixed at 100 eV and the nitrogen pressure is varied. In conclusion, lower nitrogen pressures increase the likelihood of generating a photoionization front while varying the peak source temperature has little effect.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2023

Self-consistent and detailed opacities from a non-equilibrium average-atom model

Modern density functional theory (DFT) is a powerful tool for accurately predicting self-consistent material properties such as equations of state, transport coefficients and opacities in high energy density plasmas, but it is generally restricted to conditions of local thermodynamic equilibrium (LTE) and produces only averaged electronic states instead of detailed configurations. We propose a simple modification to the bound-state occupation factor of a DFT-based average-atom model that captures essential non-LTE effects in plasmas—including autoionization and dielectronic recombination—thus extending DFT-based models to new regimes. Finally, we then expand the self-consistent electronic orbitals of the non-LTE DFT-AA model to generate multi-configuration electronic structure and detailed opacity spectra. This article is part of the theme issue ‘Dynamic and transient processes in warm dense matter’.

36 MATERIALS SCIENCE↗
DOE OSTI2018

From deep TLS validation to ensembles of atomic models built from elemental motions. II. Analysis of TLS refinement results by explicit interpretation

TLS modelling was developed by Schomaker and Trueblood to describe atomic displacement parameters through concerted (rigid-body) harmonic motions of an atomic group [Schomaker & Trueblood (1968), Acta Cryst. B24, 63–76]. The results of a TLS refinement are T, L and S matrices that provide individual anisotropic atomic displacement parameters (ADPs) for all atoms belonging to the group. These ADPs can be calculated analytically using a formula that relates the elements of the TLS matrices to atomic parameters. Alternatively, ADPs can be obtained numerically from the parameters of concerted atomic motions corresponding to the TLS matrices. Both procedures are expected to produce the same ADP values and therefore can be used to assess the results of TLS refinement. Here, the implementation of this approach in PHENIX is described and several illustrations, including the use of all models from the PDB that have been subjected to TLS refinement, are provided.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Reproducibility of protein x-ray diffuse scattering and potential utility for modeling atomic displacement parameters

Protein structure and dynamics can be probed using x-ray crystallography. Whereas the Bragg peaks are only sensitive to the average unit-cell electron density, the signal between the Bragg peaks—diffuse scattering—is sensitive to spatial correlations in electron-density variations. Although diffuse scattering contains valuable information about protein dynamics, the diffuse signal is more difficult to isolate from the background compared to the Bragg signal, and the reproducibility of diffuse signal is not yet well understood. We present a systematic study of the reproducibility of diffuse scattering from isocyanide hydratase in three different protein forms. Both replicate diffuse datasets and datasets obtained from different mutants were similar in pairwise comparisons (Pearson correlation coefficient ≥0.8). The data were processed in a manner inspired by previously published methods using custom software with modular design, enabling us to perform an analysis of various data processing choices to determine how to obtain the highest quality data as assessed using unbiased measures of symmetry and reproducibility. The diffuse data were then used to characterize atomic mobility using a liquid-like motions (LLM) model. This characterization was able to discriminate between distinct anisotropic atomic displacement parameter (ADP) models arising from different anisotropic scaling choices that agreed comparably with the Bragg data. Our results emphasize the importance of data reproducibility as a model-free measure of diffuse data quality, illustrate the ability of LLM analysis of diffuse scattering to select among alternative ADP models, and offer insights into the design of successful diffuse scattering experiments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Development of a Turbulent Liquid Spray Atomization Model for Diesel Engine Simulations (Final Technical Report)

This project addresses the systematic lack of predictive capabilities by spray models within engine CFD codes. We develop a new modeling approach to predict the breakup of diesel sprays based on recent literature showing that liquid turbulence plays a fundamental role in spray atomization. A new body of quantitative validation data is also developed as a critical element of the project, leveraging the joint capabilities of Georgia Tech’s high-pressure continuous-flow spray chamber and Argonne National Lab’s near-nozzle x-ray diagnostics at the Advanced Photon Source. This project contributes spatially-resolved measurements of drop size distribution within well-characterized diesel injectors, Spray A and D, from the Engine Combustion Network (ECN) to the engine combustion community for the first time. Utilizing this new body of measurements, we validate and demonstrate a new spray model for diesel sprays, termed the KH-Faeth model, that predicts global and local spray characteristic more accurately than the widely adopted and employed KH model. Predicted drop size distributions are seen to predict measured drops sizes both quantitatively and predictively, with accurate response in droplet size distributions over a wide range of ambient density, injection pressure, and injector nozzle size (Spray A and D) without model tuning. The KH-Faeth model can reduce error in the predicted centerline droplet size profile by up to 80% for ECN Spray D simulations when compared to use of the widely employed KH model.

33 ADVANCED PROPULSION SYSTEMS↗
DOE OSTI2017

An interface capturing scheme for modeling atomization in compressible flows

The study of atomization in supersonic flow is critical to ensuring reliable ignition of scramjet combustors under startup conditions. Numerical methods incorporating surface tension effects have largely focused on the incompressible regime as most atomization applications occur at low Mach numbers. Simulating surface tension effects in compressible flow requires robust numerical methods that can handle discontinuities caused by both shocks and material interfaces with high density ratios. In this work, a shock and interface capturing scheme is developed that uses the Harten–Lax–van Leer–Contact (HLLC) Riemann solver while a Tangent of Hyperbola for INterface Capturing (THINC) interface reconstruction scheme retains the fluid immiscibility condition in the volume fraction and phasic densities in the context of the five equation model. The approach includes the effects of compressibility, surface tension, and molecular viscosity. One and two-dimensional benchmark problems demonstrate the desirable interface sharpening and conservation properties of the approach. Simulations of secondary atomization of a cylindrical water column after its interaction with a shockwave show good qualitative agreement with experimentally observed behavior. Three-dimensional examples of primary atomization of a liquid jet in a Mach 2 crossflow demonstrate the robustness of the method.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Modeling atomically mixed graded density impactors

Graded density impactors (GDIs) are multi-material composite impactors used in gas gun experiments to tailor the drive conditions imparted to a sample test material. Previous graded density impactors generally rely on thin, but discrete, layers of different materials. The thinner and the greater number of layers will result in smoother compression. Taken to the limit of very thin layers would be pure material 1 at one surface, such as the front surface of an impactor, smoothly transitioning at the atomic scale to pure material 2 on the back surface. Such an impactor can initially shock, then smoothly compresses a material during a dynamic experiment. This type of experiment can serve to explore a larger region of thermodynamic space than a single or even multi-shock experiments. An overview of how graded density impactors are made is reviewed and sample results are given. Additionally, a strategy for modeling these kinds of impactors is presented. The length scales of constituent mixing are given from the experimental build through electrochemical-deposition. Equation of state models for pure constituents and their subsequent mixtures are presented. It is demonstrated that the time scales for pressure and temperature equilibration, for atomically mixed GDIs, are short enough to be a justifiable closure for the resulting multiphase flow. Furthermore, we present simulation results of dynamic shock followed by a ramp compression, utilizing a silver/gold graded density impactor, onto a tantalum sample.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2019

Atomic modeling for the initial stage of chromium passivation

The well-known anti-corrosive property of stainless steels is largely attributed to the addition of Cr, which can assist in forming an inert film on the corroding surface. To maximize the corrosion-resistant ability of Cr, a thorough study dealing with the passivation behaviors of this metal, including the structure and composition of the passive film as well as related reaction mechanisms, is required. In this work, continuous electrochemical adsorptions of OH-groups of water molecules onto Cr terraces in acid solutions are investigated using DFT methods. Different models with various surface conditions are applied. Passivation is found to begin in the active region, and a fully coated surface mainly with oxide is likely to be the starting point of the passive region. The measured limiting potentials are in reasonable agreement with passivation potentials observed via experiment.

58 GEOSCIENCES↗
DOE OSTI2017

Detailed assessment of diesel spray atomization models using visible and X-ray extinction measurements

The physical mechanisms characterizing the breakup of a diesel spray into droplets are still unknown. This gap in knowledge has largely been due to the challenges of directly imaging this process or quantitatively measuring the outcomes of spray breakup, such as droplet size. Recent x-ray measurements by Argonne National Laboratory, utilized in this work, provide needed information about the spatial evolution of droplet sizes in selected regions of the spray under a range of injection pressures (50–150 MPa) and ambient densities (7.6–22.8 kg/m3) relevant for diesel operating conditions. Ultra-small angle x-ray scattering (USAXS) measurements performed at the Advanced Photon Source are presented, which quantify Sauter mean diameters (SMD) within optically thick regions of the spray that are inaccessible by conventional droplet sizing measurement techniques, namely in the near-nozzle region, along the spray centerline, and within the core of the spray. To quantify droplet sizes along the periphery of the spray, a complementary technique is proposed and introduced, which leverages the ratio of path-integrated x-ray and visible laser extinction (SAMR) measurements to quantify SMD. The SAMR and USAXS measurements are then utilized to evaluate current spray models used for engine computational fluid dynamic (CFD) simulations. We explore the ability of a carefully calibrated spray model, premised on aerodynamic wave growth theory, to capture the experimentally observed trends of SMD throughout the spray. The spray structure is best predicted with an aerodynamic primary and secondary breakup process that is represented with a slower time constant and larger formed droplet size than conventionally recommended for diesel spray models. Additionally, spray model predictions suggest that droplet collisions may not influence the resultant droplet size distribution along the spray centerline in downstream regions of the spray.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗