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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 883 records · Page 49
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

A high order characteristic discontinuous Galerkin scheme for advection on unstructured meshes

A new characteristic discontinuous Galerkin (CDG) advection scheme is presented. In contrast to standard discontinuous Galerkin schemes, the test functions themselves follow characteristics in order to ensure conservation and the edges of each element are also traced backwards along characteristics in order to create a swept region , which is integrated in order to determine the mass flux across the edge. Both the accuracy and performance of the scheme are greatly improved by the use of large Courant–Friedrichs–Lewy numbers for a shear flow test case and the scheme is shown to scale sublinearly with the number of tracers being advected, outperforming a standard flux corrected transport scheme for 10 or more tracers with a linear basis. Moreover the CDG scheme may be run to arbitrarily high order spatial accuracy and on unstructured grids, and is shown to give the correct order of error convergence for piecewise linear and quadratic bases on regular quadrilateral and hexahedral planar grids. Using a modal Taylor series basis, the scheme may be made monotone while preserving conservation with the use of a standard slope limiter, although this reduces the formal accuracy of the scheme to first order. The second order scheme is roughly as accurate as the incremental remap scheme with nonlocal gradient reconstruction at half the horizontal resolution. Furthermore, the scheme is being developed for implementation within the Model for Prediction Across Scales (MPAS) Ocean model, an unstructured grid finite volume ocean model.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Curating a comprehensive set of enzymatic reaction rules for efficient novel biosynthetic pathway design

Enzyme substrate promiscuity has significant implications for metabolic engineering. The ability to predict the space of possible enzymatic side reactions is crucial for elucidating underground metabolic networks in microorganisms, as well as harnessing novel biosynthetic capabilities of enzymes to produce desired chemicals. Reaction rule-based cheminformatics platforms have been implemented to computationally enumerate possible promiscuous reactions, relying on existing knowledge of enzymatic transformations to inform novel reactions. However, past versions of curated reaction rules have been limited by a lack of comprehensiveness in representing all possible transformations, as well as the need to prune rules to enhance computational efficiency in pathway expansion. To this end, we curated a set of 1224 most generalized reaction rules, automatically abstracted from atom-mapped MetaCyc reactions and verified to uniquely cover all common enzymatic transformations. Additionally, we developed a framework to systematically identify and correct redundancies and errors in the curation process, resulting in a minimal, yet comprehensive, rule set. These reaction rules were capable of reproducing more than 85% of all reactions in the KEGG and BRENDA databases, for which a large fraction of reactions is not present in MetaCyc. Our rules exceed all previously published rule sets for which reproduction was possible in this coverage analysis, which allows for the exploration of a larger space of known enzymatic transformations. By leveraging the entire knowledge of possible metabolic reactions through generalized enzymatic reaction rules, we are able to better utilize underground metabolic pathways and accelerate novel biosynthetic pathway design to enable bioproduction towards a wider range of new molecules.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Functional Independent Scaling Relation for ORR/OER Catalysts

A widely used adsorption energy scaling relation between OH* and OOH* intermediates in the oxygen reduction reaction (ORR) and oxygen evolution reaction (OER), has previously been determined using density functional theory and shown to dictate a minimum thermodynamic overpotential for both reactions. Here, we show that the oxygen–oxygen bond in the OOH* intermediate is, however, not well described with the previously used class of exchange-correlation functionals. By quantifying and correcting the systematic error, an improved description of gaseous peroxide species versus experimental data and a reduction in calculational uncertainty is obtained. For adsorbates, we find that the systematic error largely cancels the vdW interaction missing in the original determination of the scaling relation. An improved scaling relation, which is fully independent of the applied exchange–correlation functional, is obtained and found to differ by 0.1 eV from the original. Lastly, this largely confirms that, although obtained with a method suffering from systematic errors, the previously obtained scaling relation is applicable for predictions of catalytic activity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Investigation of Ethane Dehydrogenation and Hydrogenolysis on Pt(111), Pt(211), and Pt(100): Bayesian Quantification and Correction of DFT-Based Enthalpic and Entropic Uncertainties

Computational investigations of heterogeneously catalyzed reactions using density functional theory (DFT) are often inaccurate, largely due to uncertainties in the choice of DFT functional (enthalpic uncertainty) and approximations for modeling adsorbate movement along the catalyst surface (entropic uncertainty). This work illustrates that both uncertainties are significant in the investigation of ethane dehydrogenation (EDH) and hydrogenolysis on Pt catalysts by considering the complete deconstruction of ethane on Pt(111), Pt(211), and Pt(100) using microkinetic modeling (MKM). Hence, this work uses both noncalibrated and Bayesian-calibrated MKMs to quantify and correct inaccuracies in macroscopic properties due to both uncertainties. A Bayesian approach to the correction of entropic errors was introduced using a “Modified Fermi Function (MFF)” to calibrate between the two bounds of entropy represented by the harmonic oscillator (HO) and free translator (FT) approximations. Regardless of enthalpic and entropic uncertainties, all three surfaces are capable of ethane activation; however, Pt(211) was found to be the most active and is largely responsible for methane production. Next, Pt(111) is largely responsible for acetylene production, and Pt(100) has the highest ethylene selectivity but is most susceptible to coking. By comparison of different calibrated models, the FT entropy approximation was found to better describe EDH under typical experimental conditions. Statistical evidence was found to support Pt(111) as the active site for EDH, assuming that one single site is responsible for the chemistry. On the three surfaces, competing second dehydrogenations to CH 2 CH 2 and CH 3 CH were observed as well as isomerization of CH 3 CH back to CH 2 CH 2 and deeper dehydrogenation of CH 3 CH. In conclusion, C–C cleavage was found to largely proceed via the CH 3 C intermediate on Pt(100) and Pt(111), while on Pt(211), it was via both CHC and CH 3 C.

Bayesian model selection↗
DOE OSTI2017

Atomistic non-adiabatic dynamics of the LH2 complex with a GPU-accelerated ab initio exciton model

We recently outlined an efficient multi-tiered parallel ab initio excitonic framework that utilizes time dependent density functional theory (TDDFT) to calculate ground and excited state energies and gradients of large supramolecular complexes in atomistic detail – enabling us to undertake non-adiabatic simulations which explicitly account for the coupled anharmonic vibrational motion of all the constituent atoms in a supramolecular system. Here we apply that framework to the 27 coupled bacterio-chlorophyll-a chromophores which make up the LH2 complex, using it to compute an on-the-fly nonadiabatic surface-hopping (SH) trajectory of electronically excited LH2. Part one of this article is focussed on calibrating our ab initio exciton Hamiltonian using two key parameters: a shift δ, which corrects for the error in TDDFT vertical excitation energies; and an effective dielectric constant ε, which describes the average screening of the transition-dipole coupling between chromophores. Using snapshots obtained from equilibrium molecular dynamics simulations (MD) of LH2, we tune the values of both δ and ε through fitting to the thermally broadened experimental absorption spectrum, giving a linear absorption spectrum that agrees reasonably well with experiment. In part two of this article, we construct a time-resolved picture of the coupled vibrational and excitation energy transfer (EET) dynamics in the sub-picosecond regime following photo-excitation. Assuming Franck–Condon excitation of a narrow eigenstate band centred at 800 nm, we use surface hopping to follow a single nonadiabatic dynamics trajectory within the full eigenstate manifold. Consistent with experimental data, this trajectory gives timescales for B800→B850 population transfer (τ B800→B850 ) between 650–1050 fs, and B800 population decay (τ 800→ ) between 10–50 fs. The dynamical picture that emerges is one of rapidly fluctuating LH2 eigenstates that are delocalized over multiple chromophores and undergo frequent crossing on a femtosecond timescale as a result of the atomic vibrations of the constituent chromophores. The eigenstate fluctuations arise from disorder that is driven by vibrational dynamics with multiple characteristic timescales. The scalability of our ab initio excitonic computational framework across massively parallel architectures opens up the possibility of addressing a wide range of questions, including how specific dynamical motions impact both the pathways and efficiency of electronic energy-transfer within large supramolecular systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Real single ion solvation free energies with quantum mechanical simulation

Single ion solvation free energies are one of the most important properties of electrolyte solutions and yet there is ongoing debate about what these values are. Only the values for neutral ion pairs are known. Here, we use DFT interaction potentials with molecular dynamics simulation (DFT-MD) combined with a modified version of the quasi-chemical theory (QCT) to calculate these energies for the lithium and fluoride ions. A method to correct for the error in the DFT functional is developed and very good agreement with the experimental value for the lithium fluoride pair is obtained. Moreover, this method partitions the energies into physically intuitive terms such as surface potential, cavity and charging energies which are amenable to descriptions with reduced models. Here, our research suggests that lithium's solvation free energy is dominated by the free energetics of a charged hard sphere, whereas fluoride exhibits significant quantum mechanical behavior that cannot be simply described with a reduced model.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2011

The kinetics of homogeneous melting beyond the limit of superheating

Here, molecular dynamics simulation is used to study the time-scales involved in the homogeneous melting of a superheated crystal. The interaction model used is an embedded-atom model for Fe developed in previous work, and the melting process is simulated in the microcanonical (N, V, E) ensemble. We study periodically repeated systems containing from 96 to 7776 atoms, and the initial system is always the perfect crystal without free surfaces or other defects. For each chosen total energy E and number of atoms N, we perform several hundred statistically independent simulations, with each simulation lasting for between 500 ps and 10 ns, in order to gather statistics for the waiting time τ w before melting occurs. We find that the probability distribution of τ w is roughly exponential, and that the mean value $\langle$τ w $\rangle$ depends strongly on the excess of the initial steady temperature of the crystal above the superheating limit identified by other researchers. The mean $\langle$τ w $\rangle$ furthermore depends strongly on system size in a way that we have quantified. For very small systems of ~100 atoms, we observe a persistent alternation between the solid and liquid states, and we explain why this happens. Our results allow us to draw conclusions about the reliability of the recently proposed Z method for determining the melting properties of simulated materials and to suggest ways of correcting for the errors of the method.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2013

Plasma radiation dynamics with the upgraded Absolute Extreme Ultraviolet tomographical system in the Tokamak à Configuration Variable

We introduce an upgraded version of a tomographical system which is built up from Absolute Extreme Ultraviolet-type (AXUV) detectors and has been installed on the Tokamak à Configuration Variable (TCV). The system is suitable for the investigation of fast radiative processes usually observed in magnetically confined high-temperature plasmas. The upgrade consists in the detector protection by movable shutters, some modifications to correct original design errors and the improvement in the data evaluation techniques. The short-term sensitivity degradation of the detectors, which is caused by the plasma radiation itself, has been monitored and found to be severe. The results provided by the system are consistent with the measurements obtained with the usual plasma radiation diagnostics installed on TCV. Additionally, the coupling between core plasma radiation and plasma-wall interaction is revealed. This was impossible with other available diagnostics on TCV.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2014

Second-order many-body perturbation and coupled-cluster singles and doubles study of ice VIII

The structure, equation of state, IR, Raman, and inelastic neutron scattering (INS) spectra of high-pressure, proton-ordered phase VIII of ice are calculated by the second-order many-body perturbation and coupled-cluster singles and doubles methods. Nearly all the observed features of the pressure-dependence of the structures and spectra are reproduced computationally up to 60 GPa insofar as the anharmonic effects can be neglected. The calculations display no sign of the hypothetical isostructural transition in 2–3 GPa to phase VIII{sup ′}, the existence of which has been a matter of controversy for over a decade, while they do not contradict the interpretation of the spectral anomaly at 10–14 GPa as a precursor of the VIII-X phase transition. The calculated INS spectra correct a systematic error in the peak positions of the observed spectra.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2014

A new polarizable force field for alkali and halide ions

We developed transferable potentials for alkali and halide ions which are consistent with our recent model of water [P. T. Kiss and A. Baranyai, J. Chem. Phys. 138, 204507 (2013)]. Following the approach used for the water potential, we applied Gaussian charge distributions, exponential repulsion, and r{sup −6} attraction. One of the two charges of the ions is fixed to the center of the particle, while the other is connected to this charge by a harmonic spring to express polarization. Polarizability is taken from quantum chemical calculations. The repulsion between different species is expressed by the combining rule of Kong [J. Chem. Phys. 59, 2464 (1972)]. Our primary target was the hydration free energy of ions which is correct within the error of calculations. We calculated water-ion clusters up to 6 water molecules, and, as a crosscheck, we determined the density and internal energy of alkali-halide crystals at ambient conditions with acceptable accuracy. The structure of hydrated ions was also discussed.

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

X-ray Compton scattering experiments for fluid alkali metals at high temperatures and pressures

We have developed a high-pressure vessel and a cell for x-ray Compton scattering measurements of fluid alkali metals. Measurements have been successfully carried out for alkali metal rubidium at elevated temperatures and pressures using synchrotron radiation at SPring-8. The width of Compton profiles (CPs) of fluid rubidium becomes narrow with decreasing fluid density, which indicates that the CPs sensitively detect the effect of reduction in the valence electron density. At the request of all authors of the paper, and with the agreement of the Proceedings Editor, an updated version of this article was published on 10 September 2015. The original article supplied to AIP Publishing was not the final version and contained PDF conversion errors in Formulas (1) and (2). The errors have been corrected in the updated and re-published article.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2016

Beam dynamics simulations of post low energy beam transport section in RAON heavy ion accelerator

RAON (Rare isotope Accelerator Of Newness) heavy ion accelerator of the rare isotope science project in Daejeon, Korea, has been designed to accelerate multiple-charge-state beams to be used for various science programs. In the RAON accelerator, the rare isotope beams which are generated by an isotope separation on-line system with a wide range of nuclei and charges will be transported through the post Low Energy Beam Transport (LEBT) section to the Radio Frequency Quadrupole (RFQ). In order to transport many kinds of rare isotope beams stably to the RFQ, the post LEBT should be devised to satisfy the requirement of the RFQ at the end of post LEBT, simultaneously with the twiss parameters small. We will present the recent lattice design of the post LEBT in the RAON accelerator and the results of the beam dynamics simulations from it. In addition, the error analysis and correction in the post LEBT will be also described.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2016

Development and application of InAsP/InP quantum well infrared detector

InAs{sub x}P{sub 1-x}/InP quantum wells grown using metal organic vapor phase epitaxy are investigated for infrared detector applications. The structural parameters of the QWs are evaluated from high resolution x-ray diffraction. The electronic transition energies measured from surface photo voltage and photoconductivity confirms that these QWs can be used for fabricating IR detectors in the wide wavelength range, i.e. 0.9–1.46 µm by inter-band transitions and 7–18 µm by inter-sub-band transitions. Subsequently the functionality of one such fabricated InAs{sub x}P{sub 1-x}/InPQW detector is verified by measuring the photoluminescence of suitable semiconductor quantum well structure. At the request of all authors of the paper, and with the agreement of the Proceedings Editor, an updated version of this article was published on 24 June 2016. The original version supplied to AIP Publishing contained an error in the Figures 1 and 2 where the right side of the images were cutoff. The error has been corrected in the updated and re-published article.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2016

X-Ray diffraction on large single crystals using a powder diffractometer

Information on the lattice parameter of single crystals with known crystallographic structure allows for estimations of sample quality and composition. In many cases it is sufficient to determine one lattice parameter or the lattice spacing along a certain, high- symmetry direction, e.g. in order to determine the composition in a substitution series by taking advantage of Vegard’s rule. Here we present a guide to accurate measurements of single crystals with dimensions ranging from 200 μm up to several millimeter using a standard powder diffractometer in Bragg-Brentano geometry. The correction of the error introduced by the sample height and the optimization of the alignment are discussed in detail. Finally, in particular for single crystals with a plate-like habit, the described procedure allows for measurement of the lattice spacings normal to the plates with high accuracy on a timescale of minutes.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2011

C IV EMISSION AND THE ULTRAVIOLET THROUGH X-RAY SPECTRAL ENERGY DISTRIBUTION OF RADIO-QUIET QUASARS

In the rest-frame ultraviolet (UV), two of the parameters that best characterize the range of emission-line properties in quasar broad emission-line regions are the equivalent width and the blueshift of the C IV {lambda}1549 line relative to the quasar rest frame. We explore the connection between these emission-line properties and the UV through X-ray spectral energy distribution (SED) for radio-quiet (RQ) quasars. Our sample consists of a heterogeneous compilation of 406 quasars from the Sloan Digital Sky Survey (at z > 1.54) and Palomar-Green survey (at z < 0.4) that have well-measured C IV emission-line and X-ray properties (including 164 objects with measured {Gamma}). We find that RQ quasars with both strong C IV emission and small C IV blueshifts can be classified as 'hard-spectrum' sources that are (relatively) strong in the X-ray as compared to the UV. On the other hand, RQ quasars with both weak C IV emission and large C IV blueshifts are instead 'soft-spectrum' sources that are (relatively) weak in the X-ray as compared to the UV. This work helps to further bridge optical/soft X-ray 'eigenvector 1' relationships to the UV and hard X-ray. Based on these findings, we argue that future work should consider systematic errors in bolometric corrections (and thus accretion rates) that are derived from a single mean SED. Detailed analysis of the C IV emission line may allow for SED-dependent corrections to these quantities.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2014

THE SPECTRUM OF THORIUM FROM 250 nm TO 5500 nm: RITZ WAVELENGTHS AND OPTIMIZED ENERGY LEVELS

We have made precise observations of a thorium-argon hollow cathode lamp emission spectrum in the region between 350 nm and 1175 nm using a high-resolution Fourier transform spectrometer. Our measurements are combined with results from seven previously published thorium line lists to re-optimize the energy levels of neutral, singly, and doubly ionized thorium (Th I, Th II, and Th III). Using the optimized level values, we calculate accurate Ritz wavelengths for 19, 874 thorium lines between 250 nm and 5500 nm (40, 000 cm{sup –1} to 1800 cm{sup –1}). We have also found 102 new thorium energy levels. A systematic analysis of previous measurements in light of our new results allows us to identify and propose corrections for systematic errors in Palmer and Engleman and typographical errors and incorrect classifications in Kerber et al. We also found a large scatter with respect to the thorium line list of Lovis and Pepe. We anticipate that our Ritz wavelengths will lead to improved measurement accuracy for current and future spectrographs that make use of thorium-argon or thorium-neon lamps as calibration standards.

74 ATOMIC AND MOLECULAR PHYSICS↗