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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 307 records · Page 17
All sourcesNASA NTRSDOE OSTI
NASA NTRS2014

NASA Numerical and Experimental Evaluation of UTRC Low Emissions Injector

Computational and experimental analyses of a PICS-Pilot-In-Can-Swirler technology injector, developed by United Technologies Research Center (UTRC) are presented. NASA has defined technology targets for near term (called "N+1", circa 2015), midterm ("N+2", circa 2020) and far term ("N+3", circa 2030) that specify realistic emissions and fuel efficiency goals for commercial aircraft. This injector has potential for application in an engine to meet the Pratt & Whitney N+3 supersonic cycle goals, or the subsonic N+2 engine cycle goals. Experimental methods were employed to investigate supersonic cruise points as well as select points of the subsonic cycle engine; cruise, approach, and idle with a slightly elevated inlet pressure. Experiments at NASA employed gas analysis and a suite of laser-based measurement techniques to characterize the combustor flow downstream from the PICS dump plane. Optical diagnostics employed for this work included Planar Laser-Induced Fluorescence of fuel for injector spray pattern and Spontaneous Raman Spectroscopy for relative species concentration of fuel and CO2. The work reported here used unheated (liquid) Jet-A fuel for all fuel circuits and cycle conditions. The initial tests performed by UTRC used vaporized Jet-A to simulate the expected supersonic cruise condition, which anticipated using fuel as a heat sink. Using the National Combustion Code a PICS-based combustor was modeled with liquid fuel at the supersonic cruise condition. All CFD models used a cubic non-linear k-epsilon turbulence wall functions model, and a semi-detailed Jet-A kinetic mechanism based on a surrogate fuel mixture. Two initial spray droplet size distribution and spray cone conditions were used: 1) an initial condition (Lefebvre) with an assumed Rosin-Rammler distribution, and 7 degree Solid Spray Cone; and 2) the Boundary Layer Stripping (BLS) primary atomization model giving the spray size distribution and directional properties. Contour and line plots are shown in comparison with experimental data (where this data is available) for flow velocities, fuel, and temperature distribution. The CFD results are consistent with experimental observations for fuel distribution and vaporization. Analysis of gas sample results, using a previously-developed NASA NOx correlation, indicates that for sea-level takeoff, the PICS configuration is predicted to deliver an EINOx value of about 3 for the targeted supersonic aircraft. Emissions results at supersonic cruise conditions show potential for meeting the NASA goals with liquid fuel.

Hicks, Yolanda R.↗
DOE OSTI2018

Real-space refinement in PHENIX for cryo-EM and crystallography

This article describes the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite. The use of a simplified refinement target function enables very fast calculation, which in turn makes it possible to identify optimal data-restraint weights as part of routine refinements with little runtime cost. Refinement of atomic models against low-resolution data benefits from the inclusion of as much additional information as is available. In addition to standard restraints on covalent geometry, phenix.real_space_refine makes use of extra information such as secondary-structure and rotamer-specific restraints, as well as restraints or constraints on internal molecular symmetry. The re-refinement of 385 cryo-EM-derived models available in the Protein Data Bank at resolutions of 6 Å or better shows significant improvement of the models and of the fit of these models to the target maps.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

AlCl 3 -Dosed Si(100)-2 × 1: Adsorbates, Chlorinated Al Chains, and Incorporated Al

The adsorption of AlCl 3 on Si(100) and the effect of annealing the AlCl 3 -dosed substrate were studied to reveal key surface processes for the development of atomic-precision, acceptor-doping techniques. This investigation was performed via scanning tunneling microscopy (STM), X-ray photoelectron spectroscopy (XPS), and density functional theory (DFT) calculations. At room temperature, AlCl 3 readily adsorbed to the Si substrate dimers and dissociated to form a variety of species. Annealing the AlCl 3 -dosed substrate at temperatures below 450 °C produced unique chlorinated aluminum chains (CACs) elongated along the Si(100) dimer row direction. An atomic model for the chains is proposed with supporting DFT calculations. Al was incorporated into the Si substrate upon annealing at 450 °C and above, and Cl desorption was observed for temperatures beyond 450 °C. Al-incorporated samples were encapsulated in Si and characterized by secondary ion mass spectrometry (SIMS) depth profiling to quantify the Al atom concentration, which was found to be in excess of 10 20 cm –3 across a ~2.7 nm-thick δ-doped region. Here, the Al concentration achieved here and the processing parameters utilized promote AlCl 3 as a viable gaseous precursor for novel acceptor-doped Si materials and devices for quantum computing.

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

Systematic Parameterization of Lignin for the CHARMM Force Field

Lignin is an abundant aromatic biopolymer within plant cell walls formed through radical coupling chemistry, whose composition and topology can vary greatly depending on the biomass source. Computational modeling provides a complementary approach to traditional experimental techniques to probe lignin interactions, lignin structure, and lignin material properties. However, current modeling approaches are limited based on the subset of lignin chemistries covered by existing lignin force fields. To fill the gap, we developed a comprehensive lignin force field that accounts for more lignin-lignin and lignin-carbohydrate interlinkages than existing lignin force fields, and also greatly expands the lignin monomer chemistries that can be modeled beyond simple alcohols and into the rich mixture of natural lignin varieties. The development of this force field utilizes recent developments in parameterization methodology, and synthesizes them into a workflow that combines target data from multiple molecules simultaneously into a single consistent and comprehensive parameter set. The parameter set represents a significant improvement to alternatives for atomic modeling of diverse lignin topologies, more accurately reproducing experimental observables while also significantly reducing the error relative to quantum calculations. The improved energetics, as well as the rigid adherence to CHARMM parameterization philosophy, enables simulation of lignin within its biological context with greater accuracy than was previously possible. The lignin force field presented here is therefore a crucial first step towards modeling lignin structure across a broad range of environments, including within plant cell walls where lignin is complexed with carbohydrates and deconstructed by bacterial or fungal enzymes, or as it exists within industrial solvent mixtures. Future simulations enabled by this updated lignin force field will thus lead to better chemical and structural understanding of lignin, providing new insight into its role in biomass recalcitrance or probing the potential for lignin to be used within industrial processes.

09 BIOMASS FUELS↗
DOE OSTI2022

Impact of ferromagnetic electrode length and thickness on Magnetic Tunnel Junction-Based Molecular Spintronic Devices (MTJMSD)

A knowledge gap exists about the impact of variation in length and thickness of ferromagnetic(FM) electrodes on molecular spintronics devices’ ability to manifest molecular coupling impact. Magnetic Tunnel Junction-Based Molecular Spintronic Devices (MTJMSDs) are potential candidates for inventing highly correlated materials and devices and investigating the fundamental science of organic spintronics. This paper reports our experi- mental observations providing the dramatic impact of variation in ferromagnetic electrode length and thickness on paramagnetic molecule-based MTJMSD. Room temperature transport studies were performed to investigate the effect of FM electrode thickness. On the other hand, magnetic force microscopy measurements were con- ducted to understand the effect of FM electrode length extending beyond the molecular junction area, i.e., the site where paramagnetic molecules bridged between two FM. In the strong molecular coupling regime, transport study suggested thickness variation caused ~1000 to million-fold differences in junction conductivity. MFM study revealed near-zero magnetic contrast for pillar-shaped MTJMSD without any extended FM electrode. However, MFM images showed a multitude of microscopic magnetic phases on cross junction shaped MTJMSD where FM electrodes extended beyond the junction area. To understand the intriguing experimental results, we conducted an in-depth theoretical study using Monte Carlo Simulation (MCS) approach. MCS study utilized a Heisenberg atomic model of cross junction shaped MTJMSD to gain insights about room temperature transport and MFM experimental observations of microscopic MTJMSD. To make this study applicable for a wide variety of MTJMSDs, we systematically studied the effect of variation in molecular coupling strength between magnetic molecules and ferromagnetic (FM) electrodes of various dimensions. Here, our theoretical results suggest 25 atoms thick FM electrode show very weak molecular coupling impact and of the same order of experimentally studied FM electrode dimensions showing weak effect. Also, MCS results agree with experimentally observed multiple magnetic phases on lengthy FM electrodes of an MTJMSD.

42 ENGINEERING↗
DOE OSTI2019

Self-consistent charge embedding at very low cost, with application to symmetry-adapted perturbation theory

Extended symmetry-adapted perturbation theory (XSAPT) uses a self-consistent charge embedding to capture many-body polarization, in conjunction with a pairwise-additive SAPT calculation of intermolecular interaction energies. The original implementation of XSAPT is based on charges that are fit to reproduce molecular electrostatic potentials, but this becomes a computational bottleneck in large systems. Charge embedding based on modified Hirshfeld atomic charges is reported here, which dramatically reduces the computational cost without compromising accuracy. Exemplary calculations are presented for supramolecular complexes such as C 60 @C 60 H 28 , a DNA intercalation complex, and a 323-atom model of a drug molecule bound to an enzyme active site. The proposed charge embedding should be useful in other fragment-based quantum chemistry methods as well.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2018

Dynamics of Liquid Lithium Atoms. Pseudopotential and EAM-Type Potentials

It is generally accepted that the complicated character of the interparticle interaction in liquid metals is reproduced most correctly by many-particle potentials of the EAM-type (embedded atom model) interparticle interaction. It is shown that in the case of liquid lithium near the melting temperature (T{sub m} = 453.65 K), the spherical pseudopotential provides a better agreement with experimental data on elastic and inelastic X-ray scattering as compared to the known EAM potentials. The calculations of the dynamic structural factor and spectral densities of the longitudinal and transverse atomic currents lead to the conclusion that although the pseudopotential and EAM potentials generate a certain qualitative correspondence in the features of collective dynamics, the interparticle interaction of the spherical type reproduces correctly the general form of the dynamic structure factor in a certain wavenumber range, as well as the dispersion relation for collective excitations.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
NASA NTRS1976

Helium emission from model flare layers

The emission of visible and UV He I and He II line radiation from a plane-parallel model flare layer characterized by electron temperatures of 10,000 to 50,000 K and electron densities of 10 to the 10th power to 10 to the 15th power per cu cm is analyzed by solving the statistical-equilibrium equations for a 30-level He I-II-III system, using parametric representations of the line and continuum radiation fields. The atomic model was chosen to provide accurate solutions for the first two resonance lines of He I and He II as well as for the D3 and 10,830-A lines of He I. Reaction rates are discussed, and sample solutions to the steady-state population equations are given for a generally optically thin gas assumed to be irradiated over 2pi sr by a blackbody spectrum at 6000 K. Specific results are examined for ionization equilibrium, level populations, approximate optical depths of a 1000-km-thick flare layer, line intensities, and upper-level population rates.

Kulander, J. I.↗
DOE OSTI2021

Determining Partial Atomic Charges for Liquid Water: Assessing Electronic Structure and Charge Models

Partial atomic charges provide an intuitive and efficient way to describe the charge distribution and the resulting intermolecular electrostatic interactions in liquid water. Many charge models exist and it is unclear which model provides the best assignment of partial atomic charges in response to the local molecular environment. In this work, we systematically scrutinize various electronic structure methods and charge models (Mulliken, natural population analysis, CHelpG, RESP, Hirshfeld, Iterative Hirshfeld, and Bader) by evaluating their performance in predicting the dipole moments of isolated water, water clusters, and liquid water as well as charge transfer in the water dimer and liquid water. Although none of the seven charge models is capable of fully capturing the dipole moment increase from isolated water (1.85 D) to liquid water (about 2.9 D), the Iterative Hirshfeld method performs best for liquid water, reproducing its experimental average molecular dipole moment, yielding a reasonable amount of intermolecular charge transfer, and showing modest sensitivity to the local water environment. The performance of the charge model is dependent on the choice of the density functional and the quantum treatment of the environment. The computed molecular dipole moment of water generally increases with the percentage of the exact Hartree–Fock exchange in the functional, whereas the amount of charge transfer between molecules decreases. For liquid water, including two full solvation shells of surrounding water molecules (within about 5.5 Å of the central water) in the quantum chemical calculation converges the charges of the central water molecule. Furthermore, our final pragmatic quantum chemical charge-assigning protocol for liquid water is the Iterative Hirshfeld method with M06-HF/aug-cc-pVDZ and a quantum region cutoff radius of 5.5 Å.

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

Electrical and optical properties of warm dense beryllium along the principal Hugoniot

The electrical and optical properties of warm dense beryllium along the principal Hugoniot for temperatures from 0.95 eV to 10.65 eV and densities from 3.8 to 6.0 g/cm{sup 3} are investigated by using quantum molecular dynamics (QMD) simulations combined with the Kubo-Greenwood formulation. The dc conductivity σ{sub dc} and the ionization fraction are yielded by fitting the optical conductivity with the Drude-Smith model. The first-principles transport coefficients are compared with results of the Lee-More model and the Brysk model [Plasma Phys. 17, 473 (1975)]. Compared with the QMD result, the Lee-More model underestimates σ{sub dc} by 87% at low temperatures, approaches the QMD result gradually with the temperature rising, yet still underestimates σ{sub dc} by 49% corresponding to the temperature 10.65 eV. In the whole temperature range under investigation, the Brysk model overestimates the electronic thermal conductivity κ while the Lee-More model underestimates κ. The differences are reduced with the temperature increasing. At the temperature 10.65 eV, the Brysk κ is still around twice as large as the QMD result, and the Lee-More κ is smaller than the QMD data by about 40%. In addition, QMD Rosseland mean opacities are shown to be three orders of magnitude larger than results of the average-atom model.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

Uncertainties in Atomic Data for Modeling Astrophysical Charge Exchange Plasmas

Relevant uncertainties of theoretical atomic data are vital to determining the accuracy of plasma diagnostics in a number of areas, including, in particular, the astrophysical study. We present a new calculation of the uncertainties on the present theoretical ion-impact charge exchange atomic data and X-ray spectra, based on a set of comparisons with the existing laboratory data obtained in historical merged-beam, cold-target recoil-ion momentum spectroscopy, and electron beam ion traps experiments. The average systematic uncertainties are found to be 35–88% on the total cross sections, and 57–75% on the characteristic line ratios. The model deviation increases as the collision energy decreases. The errors on total cross sections further induce a significant uncertainty to the calculation of ionization balance for low-temperature collisional plasmas. Substantial improvements of the atomic database and dedicated laboratory measurements are needed to obtain the current models, ready for the X-ray spectra from the next X-ray spectroscopic mission.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2014

Simultaneous use of solution NMR and X-ray data in REFMAC5 for joint refinement/detection of structural differences

Paramagnetic NMR data (pseudocontact shifts and self-orientation residual dipolar couplings) and diamagnetic residual dipolar couplings can now be used in the program REFMAC5 from CCP4 as structural restraints together with X-ray crystallographic data. These NMR restraints can reveal differences between solid state and solution conformations of molecules or, in their absence, can be used together with X-ray crystallographic data for structural refinement. The program REFMAC5 from CCP4 was modified to allow the simultaneous use of X-ray crystallographic data and paramagnetic NMR data (pseudocontact shifts and self-orientation residual dipolar couplings) and/or diamagnetic residual dipolar couplings. Incorporation of these long-range NMR restraints in REFMAC5 can reveal differences between solid-state and solution conformations of molecules or, in their absence, can be used together with X-ray crystallographic data for structural refinement. Since NMR and X-ray data are complementary, when a single structure is consistent with both sets of data and still maintains reasonably ‘ideal’ geometries, the reliability of the derived atomic model is expected to increase. The program was tested on five different proteins: the catalytic domain of matrix metalloproteinase 1, GB3, ubiquitin, free calmodulin and calmodulin complexed with a peptide. In some cases the joint refinement produced a single model consistent with both sets of observations, while in other cases it indicated, outside the experimental uncertainty, the presence of different protein conformations in solution and in the solid state.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Modeling Molecules under Pressure with Gaussian Potentials

The computational modeling of molecules under high pressure is a growing research area that augments experimental high-pressure chemistry. Here, a new electronic structure method for modeling atoms and molecules under pressure, Gaussians On Surface Tesserae Simulate HYdrostatic Pressure (GOSTSHYP) approach, is introduced. In this method, a set of Gaussian potentials is distributed evenly on the van der Waals surface of the investigated chemical system, leading to a compression of the electron density and the atomic scaffold. Since no parameters other than pressure need to be specified, GOSTSHYP allows straightforward geometry optimizations and ab initio molecular dynamics simulations of chemical systems under pressure for nonexpert users. In this work, calculated energies, bond lengths, and dipole moments under pressure fall within the range of established computational methods for high-pressure chemistry. A Diels-Alder reaction and the cyclotrimerization of acetylene showcase the ability of GOSTSHYP to model pressure-induced chemical reactions. The connection to mechanochemistry is pointed out.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Expanding the Domain of Applicability of Machine Learning Models with Limited Data for Drug Property Prediction

Accurate machine learning models for predicting small molecule interactions with biological targets are essential for therapeutic discovery, biothreat response, and computational drug design, but their performance is often limited for understudied targets with sparse experimental data. To address this challenge, we developed and evaluated methods to improve molecular property prediction under low-data conditions, using the NimA-related kinase (NEK) family as a proof-of-concept. This work focused on two complementary goals within the ATOM Modeling PipeLine (AMPL) and the Generative Molecular Design (GMD) loop: expanding model applicability through transfer learning, representation learning, feature scaling, sampling strategies, and active-learning-inspired compound selection; and enabling efficient virtual screening to prioritize compounds that balance predicted activity, design objectives, and synthetic accessibility.

organic↗
DOE OSTI2026

Collisional stopping power of ions in warm dense matter

Here, a model for the collisional stopping of ions on free electrons in warm dense matter is developed and explored. It is based on plasma kinetic theory, but with modifications to address the warm dense matter regime. Specifically, it uses the Boltzmann-Uehling-Uhlenbeck kinetic equation to incorporate effects of Fermi degeneracy of electrons. The cross section is computed from quantum scattering of electrons and ions occurring via the potential of mean force derived from an average atom model, which incorporates effects of strong Coulomb correlations. Predictions from this model show comparable accuracy to results from time-dependent density functional theory calculations for deuterium near solid density and a temperature of several electronvolts, at a fraction of the computational cost. Further, the model captures the transition of a plasma from the classical limit to the degenerate limit, including qualitative behaviors of solid state theory.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2014

Analysis of simulation methodology for calculation of the heat of transport for vacancy thermodiffusion

Computation of the heat of transport Q{sub a}{sup *} in monatomic crystalline solids is investigated using the methodology first developed by Gillan [J. Phys. C: Solid State Phys. 11, 4469 (1978)] and further developed by Grout and coworkers [Philos. Mag. Lett. 74, 217 (1996)], referred to as the Grout-Gillan method. In the case of pair potentials, the hopping of a vacancy results in a heat wave that persists for up to 10 ps, consistent with previous studies. This leads to generally positive values for Q{sub a}{sup *} which can be quite large and are strongly dependent on the specific details of the pair potential. By contrast, when the interactions are described using the embedded atom model, there is no evidence of a heat wave, and Q{sub a}{sup *} is found to be negative. This demonstrates that the dynamics of vacancy hopping depends strongly on the details of the empirical potential. However, the results obtained here are in strong disagreement with experiment. Arguments are presented which demonstrate that there is a fundamental error made in the Grout-Gillan method due to the fact that the ensemble of states only includes successful atom hops and hence does not represent an equilibrium ensemble. This places the interpretation of the quantity computed in the Grout-Gillan method as the heat of transport in doubt. It is demonstrated that trajectories which do not yield hopping events are nevertheless relevant to computation of the heat of transport Q{sub a}{sup *}.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2013

From lows to highs: using low-resolution models to phase X-ray data

An unusual example of how virus structure determination pushes the limits of the molecular replacement method is presented. The study of virus structures has contributed to methodological advances in structural biology that are generally applicable (molecular replacement and noncrystallographic symmetry are just two of the best known examples). Moreover, structural virology has been instrumental in forging the more general concept of exploiting phase information derived from multiple structural techniques. This hybridization of structural methods, primarily electron microscopy (EM) and X-ray crystallography, but also small-angle X-ray scattering (SAXS) and nuclear magnetic resonance (NMR) spectroscopy, is central to integrative structural biology. Here, the interplay of X-ray crystallography and EM is illustrated through the example of the structural determination of the marine lipid-containing bacteriophage PM2. Molecular replacement starting from an ∼13 Å cryo-EM reconstruction, followed by cycling density averaging, phase extension and solvent flattening, gave the X-ray structure of the intact virus at 7 Å resolution This in turn served as a bridge to phase, to 2.5 Å resolution, data from twinned crystals of the major coat protein (P2), ultimately yielding a quasi-atomic model of the particle, which provided significant insights into virus evolution and viral membrane biogenesis.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Coordinate-based simulation of pair distance distribution functions for small and large molecular assemblies: implementation and applications

X-ray scattering has become a major tool in the structural characterization of nanoscale materials. Thanks to the widely available experimental and computational atomic models, coordinate-based X-ray scattering simulation has played a crucial role in data interpretation in the past two decades. However, simulation of real-space pair distance distribution functions (PDDFs) from small- and wide-angle X-ray scattering, SAXS/WAXS, has been relatively less exploited. This study presents a comparison of PDDF simulation methods, which are applied to molecular structures that range in size from β-cyclodextrin [1 kDa molecular weight (MW), 66 non-hydrogen atoms] to the satellite tobacco mosaic virus capsid (1.1 MDa MW, 81 960 non-hydrogen atoms). The results demonstrate the power of interpretation of experimental SAXS/WAXS from the real-space view, particularly by providing a more intuitive method for understanding of partial structure contributions. Furthermore, the computational efficiency of PDDF simulation algorithms makes them attractive as approaches for the analysis of large nanoscale materials and biological assemblies. The simulation methods demonstrated in this article have been implemented in stand-alone software, SolX 3.0 , which is available to download from https://12idb.xray.aps.anl.gov/solx.html.

Zuo, Xiaobing (ORCID:0000000201344804)↗