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At least 325 records · Page 18

Interpretable, extensible linear and symbolic regression models for charge density prediction using a hierarchy of many-body correlation descriptors

Here, density functional theory (DFT) is routinely used to make electronic structure predictions for high-throughput screening of materials and molecules for technologically relevant areas, like the identification of better catalysts, electronic materials, and drug discovery. However, the DFT formalism is limited by (a) its poor (quadratic-to-quartic) scaling, and (b) the need to perform repeated eigenvalue computations of the electronic Hamiltonian as part of its self-consistent field (SCF) iteration procedure to obtain the converged ground state electron density, ρ (r). Approaches that directly predict ρ (r) of a structure with high accuracy can accelerate conventional SCF calculations and can also be used in linearly scaling methods such as orbital-free DFT. To this end, we present a procedure to predict the ground state electron density of molecular and periodic three-dimensional systems directly from the atomic structure with a particular emphasis on physical interpretability. In our framework, ρ (r) is modeled using many-body correlation descriptors that accurately capture the effects of local atomic arrangements in the neighborhood of a grid point. Our use of a linear regression scheme to fit to charge density data enables transparent analysis of the relative contributions of various types of local atomic correlations. By systematically including increasingly complex correlations, our model is shown to accurately predict ρ (r) for a variety of chemically and electronically diverse systems — amorphous Ge, Al(001) slab, crystalline Ga 2 O 3 , molecular benzene, and polyethylene. We then demonstrate a symbolic regression-based protocol to construct easily computable, interpretable features from lower-order correlations that significantly improves our electron density predictions with effectively no increase in the computational cost.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Optical and Plasmonic Properties of High-Electron-Density Epitaxial and Oxidative Controlled Titanium Nitride Thin Films

The present paper reports on the fabrication, detailed structural characterizations, and theoretical modeling of titanium nitride (TiN) and its isostructural oxide derivative, titanium oxynitride (TiNO) thin films that have excellent plasmonic properties and that also have the potential to overcome the limitation of noble metal and refractory metals. The TiNO films deposited at 700 °C in high vacuum conditions have the highest reflectance (R = ~ 95%), largest negative dielectric constant (ε 1 = –161), and maximal plasmonic figure of merit (FoM = –ε 1 /ε 2 ) of 1.2, followed by the 600 °C samples deposited in a vacuum (R = ~ 85%, ε 1 = –145, FoM = 0.8) and 700 °C–5 mTorr sample (R = ~ 82%, ε 1 = –8, FoM = 0.3). To corroborate our experimental observations, we calculated the phonon dispersions and Raman active modes of TiNO by using the virtual crystal approximation. From the experimental and theoretical studies, a multilayer optical model has been proposed for the TiN/TiNO epitaxial thin films for obtaining individual complex dielectric functions from which many other optical parameters can be calculated. The advantages of oxide derivatives of TiN are the continuation of similar free electron density as in TiN and the acquisition of additional features such as oxygen-dependent semiconductivity with a tunable bandgap.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Investigation of the Failure of Marcus Theory for Hydrated Electron Reactions

Reactions of the hydrated electron with a wide variety of substrates have been found to exhibit unusually similar activation energies in a manner incompatible with Marcus electron transfer theory. Given the fundamental linear response assumption of Marcus theory, one possible explanation for this apparent failure is that the underlying free energy surfaces governing the reactions are not harmonic, i.e., hydrated electron structural fluctuations exhibit non-Gaussian behavior. In this work, we test this hypothesis by using simulations to calculate the hydrated electron vertical detachment energy distribution. Furthermore, we consider both cavity and non-cavity models for the hydrated electron, between which the actual hydrated electron behavior is expected to lie. Our results identify a possible origin for non-Gaussian behavior of the hydrated electron, but show that it is not of sufficient magnitude to explain the failure of Marcus theory to describe its reactions. Thus, other explanations must be sought.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Towards the spatial resolution of metalloprotein charge states by detailed modeling of XFEL crystallographic diffraction

Oxidation states of individual metal atoms within a metalloprotein can be assigned by examining X-ray absorption edges, which shift to higher energy for progressively more positive valence numbers. Indeed, X-ray crystallography is well suited for such a measurement, owing to its ability to spatially resolve the scattering contributions of individual metal atoms that have distinct electronic environments contributing to protein function. However, as the magnitude of the shift is quite small, about +2 eV per valence state for iron, it has only been possible to measure the effect when performed with monochromated X-ray sources at synchrotron facilities with energy resolutions in the range 2–3 × 10 −4 (Δ E / E ). This paper tests whether X-ray free-electron laser (XFEL) pulses, which have a broader bandpass (Δ E / E = 3 × 10 −3 ) when used without a monochromator, might also be useful for such studies. The program nanoBragg is used to simulate serial femtosecond crystallography (SFX) diffraction images with sufficient granularity to model the XFEL spectrum, the crystal mosaicity and the wavelength-dependent anomalous scattering factors contributed by two differently charged iron centers in the 110-amino-acid protein, ferredoxin. Bayesian methods are then used to deduce, from the simulated data, the most likely X-ray absorption curves for each metal atom in the protein, which agree well with the curves chosen for the simulation. The data analysis relies critically on the ability to measure the incident spectrum for each pulse, and also on the nanoBragg simulator to predict the size, shape and intensity profile of Bragg spots based on an underlying physical model that includes the absorption curves, which are then modified to produce the best agreement with the simulated data. This inference methodology potentially enables the use of SFX diffraction for the study of metalloenzyme mechanisms and, in general, offers a more detailed approach to Bragg spot data reduction.

59 BASIC BIOLOGICAL SCIENCES↗

Structure of the E. coli agmatinase, SPEB

Agmatine amidinohydrolase, or agmatinase, catalyzes the conversion of agmatine to putrescine and urea. This enzyme is found broadly across kingdoms of life and plays a critical role in polyamine biosynthesis and the regulation of agmatine concentrations. Here we describe the high-resolution X-ray crystal structure of the E . coli agmatinase, SPEB. The data showed a relatively high degree of pseudomerohedral twinning, was ultimately indexed in the P 3 1 space group and led to a final model with eighteen chains, corresponding to three full hexamers in the asymmetric unit. There was a solvent content of 38.5% and refined R/R free values of 0.166/0.216. The protein has the conserved fold characteristic of the agmatine ureohydrolase family and displayed a high degree of structural similarity among individual protomers. Two distinct peaks of electron density were observed in the active site of most of the eighteen chains of SPEB. As the activity of this protein is known to be dependent upon manganese and the fold is similar to other dinuclear metallohydrolases, these peaks were modeled as manganese ions. The orientation of the conserved active site residues, in particular those amino acids that participate in binding the metal ions and a pair of acidic residues (D153 and E274 in SPEB) that play a role in catalysis, are similar to other agmatinase and arginase enzymes and is consistent with a hydrolytic mechanism that proceeds via a metal-activated hydroxide ion.

59 BASIC BIOLOGICAL SCIENCES↗

Ab Initio modeling of Near-Edge EELS spectra for chemisorbed molecules

Abstract Electron energy loss spectroscopy (EELS) has recently been applied to probe chemisorbed molecules on metal nanostructures, but a fundamental understanding of the correlation between these spectra and the electronic structures of the adsorbates has been limited. We report here on the insights afforded by time-dependent density functional theory to decipher the energy loss near edge structure (ELNES) of EELS spectra associated with chemisorption. These first-principles calculations simulate the ELNES-EELS spectra for chemisorbed CO on various facets of Au and Pt. Computational predictions of key signatures such as the ‘red shift’ and reductions in the peak intensity of the 2 π * and 6 σ * peaks, as compared to free CO in the gas phase, are validated in comparison to experimentally collected EELS spectra. These signatures are revealed to arise from changes in the electronic structure in terms of unoccupied density of states associated with the chemisorption process. They are consistent with a Blyholder model that incorporates donation and back-donation of electrons. They are also characteristic of the chemisorption process, such as the choice of metal, site of adsorption and the coverage and distribution of adsorbates. Our simulations thus provide guidelines for the use of ELNES-EELS to characterize the atomic structure and adsorption property of nanostructured surfaces and facilitate the development of advanced nanomaterials for catalytic applications.

Materials Science↗

Microstructure and growth model for rice-hull-derived SiC whiskers

The microstructure of silicon carbide whiskers grown from rice hulls has been studied using methods of high-resolution analytical electron microscopy. Small, partially crystalline inclusions (about 10 nm) containing calcium, manganese, and oxygen are concentrated in whisker core regions, while peripheral regions are generally inclusion free. The distinct microphase distribution is evidence of a two-stage growth process in which the core region grows first, followed by normal growth toward whisker sides. Partial dislocations extend radially from the core region to the surface and tend to be paired in V-shaped configurations. Whisker surfaces exhibit microroughness due to a tendency to develop small facets on close-packed planes. The microstructural data obtained from TEM observations are used as a basis for discussion of the mechanisms involved in whisker growth, and a model of the growth process is proposed. The model includes a two-dimensional growth mechanism involving vapor, liquid, and solid phases, although it is significantly different from the classical vapor-liquid-solid (VLS) process of whisker growth.

Nutt, Steven R.↗

Quantum mechanical dataset of 836k neutral closed-shell molecules with up to 5 heavy atoms from C, N, O, F, Si, P, S, Cl, Br

Abstract We introduce the Vector-QM24 (VQM24) dataset comprehensively covering all possible neutral closed-shell small organic and inorganic molecules with up to five heavy (p-block) atoms: C, N, O, F, Si, P, S, Cl, Br. All valid stoichiometries, Lewis-rule-consistent graphs, and stable conformers (identified via GFN2-xTB) were enumerated combinatorially, yielding 577k conformational isomers spanning 258k constitutional isomers and 5,599 unique stoichiometries. DFT (ωB97X-D3/cc-pVDZ) optimizations were performed for all, and diffusion quantum Monte Carlo (DMC@PBE0(ccECP/cc-pVQZ)) energies are provided for 10,793 lowest-energy conformers with up to 4 heavy atoms. VQM24 includes structures, vibrational modes, rotational constants, thermodynamic properties (Gibbs free energies, enthalpies, ZPVEs, entropies, heat capacities), and electronic properties such as atomization, electron interaction, exchange-correlation, dispersion energies, multipole moments (dipole to hexadecapole), alchemical potentials, Mulliken charges, and wavefunctions. Machine learning models of atomization energies on this dataset reveal significantly higher complexity than QM9, with none achieving chemical accuracy. VQM24 offers a rigorous, high-fidelity benchmark for evaluating quantum machine learning models.

Science & Technology - Other Topics↗

Interplanetary propagation of flare-associated energetic particles

The basic propagation process of flare-associated energetic particles in interplanetary space is studied on the basis of a model which combines a Gaussian coronal injection profile and interplanetary particle densities found by a theory of focused diffusion. The model is used to describe 30 electron and proton events which originate from the western hemisphere of the sun. A comparison of calculated and observed density profiles shows that the scattering mean free path is 0.1-0.3 AU for 4-80 MeV protons. The value is two or three times smaller for 0.5-1.1 and 3-12 MeV electrons. Thus the scattering mean free path is only slightly rigidity-dependent, contrary to that predicted by the quasi-linear theory of pitch-angle scattering. The rms width is found to be less than an hour for most proton and electron events. This width, which decreases with velocity, is not rigidity-dependent.

Ma Sung, L. S.↗

The relationship of the lunar regolith less than 10-microns fraction and agglutinates. II - Chemical composition of agglutinate glass as a test of the 'fusion of the finest fraction' /F3/ model

Agglutinate glasses from nine Apollo soils have been studied using an automated electron microprobe technique in order to test the fusion of the finest fraction model proposed by Papike (1981). The nine average agglutinate glass compositions are compared with the calculated fused-soil-free compositions, the bulk compositions and the 90-20 micron fraction compositions of the soils in which they are found. It is found that the agglutinate glass data are consistent with the composition of most of the fractions finer than 10 microns, allowing for the volatile loss of K2O and Na2O; some inconsistencies that do arise may result from the degree of soil maturity and the amount of material finer than 10 microns. It is concluded that the fusion of the finest fraction model is a good first approximation of mechanisms affecting the formation of agglutinate glass.

Walker, R. J.↗

Modeling Carbon and Hydrocarbon Molecular Structures in EZTB

A software module that models the electronic and mechanical aspects of hydrocarbon molecules and carbon molecular structures on the basis of first principles has been written for incorporation into, and execution within, the Easy (Modular) Tight-Binding (EZTB) software infrastructure, which is summarized briefly in the immediately preceding article. Of particular interest, this module can model carbon crystals and nanotubes characterized by various coordinates and containing defects, without need to adjust parameters of the physical model. The module has been used to study the changes in electronic properties of carbon nanotubes, caused by bending of the nanotubes, for potential utility as the basis of a nonvolatile, electriccharge- free memory devices. For example, in one application of the module, it was found that an initially 50-nmlong carbon, (10,10)-chirality nanotube, which is a metallic conductor when straight, becomes a semiconductor with an energy gap of .3 meV when bent to a lateral displacement of 4 nm at the middle.

Lee, Seungwon↗

Bayesian Optimization of a Free-Electron Laser

The Linac Coherent Light Source X-ray free-electron laser is a complex scienti c apparatus which changes con gurations multiple times per day, necessitating fast tuning strategies to reduce setup time for successive experiments. To this end, we employ a Bayesian approach to maximizing X- ray laser pulse energy by controlling groups of quadrupole magnets. A Gaussian process model provides probabilistic predictions for the machine response with respect to control parameters, enabling a balance of exploration and exploitation in the search for the global optimum. We show that the model parameters can be learned from archived scans, and correlations between devices can be extracted from the beam transport. Furthermore, the result is a sample-e cient optimization routine, combining both historical data and knowledge of accelerator physics to signi cantly outperform existing optimizers.

47 OTHER INSTRUMENTATION↗

Understanding the field and frequency dependence of rf loss in SRF cavities

SRF cavities subjected to heat treatment below 200 °C in the presence of nitrogen showed an improvement in quality factor while maintaining an accelerating gradient above 25 MV/m. Here, we report the rf performance of several single-cell superconducting radio frequency cavities with frequency ranging from 0.75 - 3.0 GHz subjected to low temperature heat treatment in nitrogen environment. The cavities were treated at temperature 120 - 175 oC for 24 - 48 hours in low partial pressure of ultra-pure nitrogen gas. The improvement in Q? with Q-rise was observed when nitrogen gas was injected ~300 °C during the furnace treatment. The surface modification was confirmed by the change in electronic mean free path and near surface elemental analysis by SIMS. The field dependence of the rf losses is strongly correlated to the cavity frequency. The analysis of experimental data with available theoretical models as well as comparison with similar study on high temperature nitrogen doped cavities will be presented.

Ciovati, Gianluigi↗

Binary Amplitude Reflection Gratings for X-ray Shearing and Hartmann Wavefront Sensors

New, high-coherent-flux X-ray beamlines at synchrotron and free-electron laser light sources rely on wavefront sensors to achieve and maintain optimal alignment under dynamic operating conditions. This includes feedback to adaptive X-ray optics. We describe the design and modeling of a new class of binary-amplitude reflective gratings for shearing interferometry and Hartmann wavefront sensing. Compact arrays of deeply etched gratings illuminated at glancing incidence can withstand higher power densities than transmission membranes and can be designed to operate across a broad range of photon energies with a fixed grating-to-detector distance. Coherent wave-propagation is used to study the energy bandwidth of individual elements in an array and to set the design parameters. We observe that shearing operates well over a ±10% bandwidth, while Hartmann can be extended to ±30% or more, in our configuration. We apply this methodology to the design of a wavefront sensor for a soft X-ray beamline operating from 230 eV to 1400 eV and model shearing and Hartmann tests in the presence of varying wavefront aberration types and magnitudes.

47 OTHER INSTRUMENTATION↗

A possible common origin for the rare gases on Venus, earth, and Mars

The rare gas concentrations in the terrestrial planets and the carbonaceous chondrites could have been derived from a single source an early solar wind. The fractionation processes responsible for the varying concentration patterns in this model are differential ionization and the relative separation of neutrals from ions due to interaction with the solar magnetic field. If species dependent effects are small relative to radius dependent effects, this process can explain in detail both the relative and absolute abundances in the terrestrial planets and carbonaceous chondrites. The electron temperatures predicted by the data are consistent with astrophysical constraints previously derived for the solar nebula, and the timeline of events necessary for this model is consistent with accretion in a gas free environment. If species dependent fractionations are small, or approximately cancel each other, the earth is found to be outgassed by an order of magnitude more efficiently than Venus or Mars.

Hostetler, C. J.↗

Direct simulation of reentry flows with ionization

The Direct Simulation Monte Carlo (DSMC) method is applied in this paper to the study of rarefied hypersonic reentry flows. The assumptions and simplifications involved with the treatment of ionization, free electrons and the electric field are investigated. A new method is presented for the calculation of the electric field and handling of charged particles with DSMC. In addition, a two-step model for electron impact ionization is implemented. The flowfield representing a 10 km/sec shock at an altitude of 65 km is calculated. The effects of the new modeling techniques on the calculation results are presented and discussed.

Carlson, Ann B.↗

Heating and ionization of stellar chromospheres by nonthermal proton beams: Implications for impulsive phase, redshifted Lyman-alpha radiation in stellar flares

We investigate the physical basis for the timescale of impulsive-phase, redshifted Lyman-alpha emission in stellar flares on the assumption that it is determined by energy losses in a nonthermal proton beam that is penetrating the chromosphere from above. The temporal evolution of ionization and heating in representative model chromospheres subjected to such beams is calculated. The treatment of 'stopping' of beam protons takes into account their interactions with (1) electrons bound in neutral hydrogen, (2) nuclei of neutral hydrogen, (3) free electrons, and (4) ambient thermal protons. We find that, for constant incident beam flux, the system attains an equilibrium with the beam energy input to the chromosphere balanced by radiative losses. In equilibrium, the beam penetration depth is constant, and erosion of the chromosphere ceases. If the redshifted, impulsive-phase stellar flare Lyman-alpha emission is produced by downstreaming hydrogen formed through charge exchange between beam protons and ambient hydrogen, then the emission should end when the beam no longer reaches neutral hydrogen. The durations of representative emission events calculated on this assumption range from 0.1 to 14 s. The stronger the beam, the shorter the timescale over which the redshifted Lyman-alpha emission can be observed.

Brosius, Jeffrey W.↗

A correlated ab initio study of the A2 pi <-- X2 sigma+ transition in MgCCH

The A2 pi <-- X2 sigma+ transition in MgCCH was studied with correlation consistent basis sets and single- and multireference correlation methods. The A2 pi excited state was characterized in detail; the x2 sigma+ ground state has been described elsewhere recently. The estimated complete basis set (CBS) limits for valence correlation, including zero-point energy corrections, are 22668, 23191, and 22795 for the RCCSD(T), MRCI, and MRCI + Q methods, respectively. A core-valence correction of +162 cm-1 shifts the RCCSD(T) value to 22830 cm-1, in good agreement with the experimental result of 22807 cm-1.

Non-NASA Center↗