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DOE OSTI2017

Benchmarking the GW Approximation and Bethe–Salpeter Equation for Groups IB and IIB Atoms and Monoxides

Energies from the GW approximation and the Bethe–Salpeter equation (BSE) are benchmarked against the excitation energies of transition-metal (Cu, Zn, Ag, and Cd) single atoms and monoxide anions. We demonstrate that best estimates of GW quasiparticle energies at the complete basis set limit should be obtained via extrapolation or closure relations, while numerically converged GW -BSE eigenvalues can be obtained on a finite basis set. Calculations using real-space wave functions and pseudopotentials are shown to give best-estimate GW energies that agree (up to the extrapolation error) with calculations using all-electron Gaussian basis sets. We benchmark the effects of a vertex approximation (ΓLDA) and the mean-field starting point in GW and the BSE, performing computations using a real-space, transition-space basis and scalar-relativistic pseudopotentials. Here, while no variant of GW improves on perturbative G 0 W 0 at predicting ionization energies, G 0 W 0 Γ LDA -BSE computations give excellent agreement with experimental absorption spectra as long as off-diagonal self-energy terms are included. We also present G 0 W 0 quasiparticle energies for the CuO – , ZnO – , AgO – , and CdO – anions, in comparison to available anion photoelectron spectra.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2013

Self-consistent calculations of alpha-decay energies

On the basis of the self-consistent theory of finite Fermi systems, the energies of alphadecay chains were calculated for several new superheavy nuclei discovered recently in experiments of the Dubna-Livermore Collaboration headed by Yu.Ts. Oganessian. The approach in question is implemented on the basis of the generalized method of the density functional proposed by Fayans and his coauthors. The version used here relies on the functional DF3-a proposed recently for describing a wide array of nuclear data, including data on superheavy nuclei. A detailed comparison of the results obtained on this basis with the predictions of different approaches, including the self-consistent Skyrme-Hartree-Fock method, the micro-macro method in the version developed by Sobiczewski and his coauthors, and the phenomenological method of Liran and his coauthors, is performed. The resulting alpha-decay energies are used to calculate respective lifetimes with the aid of the phenomenological Parkhomenko-Sobiczewski formula.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2014

FDE-vdW: A van der Waals inclusive subsystem density-functional theory

We present a formally exact van der Waals inclusive electronic structure theory, called FDE-vdW, based on the Frozen Density Embedding formulation of subsystem Density-Functional Theory. In subsystem DFT, the energy functional is composed of subsystem additive and non-additive terms. We show that an appropriate definition of the long-range correlation energy is given by the value of the non-additive correlation functional. This functional is evaluated using the fluctuation–dissipation theorem aided by a formally exact decomposition of the response functions into subsystem contributions. FDE-vdW is derived in detail and several approximate schemes are proposed, which lead to practical implementations of the method. We show that FDE-vdW is Casimir-Polder consistent, i.e., it reduces to the generalized Casimir-Polder formula for asymptotic inter-subsystems separations. Pilot calculations of binding energies of 13 weakly bound complexes singled out from the S22 set show a dramatic improvement upon semilocal subsystem DFT, provided that an appropriate exchange functional is employed. The convergence of FDE-vdW with basis set size is discussed, as well as its dependence on the choice of associated density functional approximant.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2015

Functional reconstitution of Drosophila melanogaster NMJ glutamate receptors

The Drosophila larval neuromuscular junction (NMJ), at which glutamate acts as the excitatory neurotransmitter, is a widely used model for genetic analysis of synapse function and development. Despite decades of study, the inability to reconstitute NMJ glutamate receptor function using heterologous expression systems has complicated the analysis of receptor function, such that it is difficult to resolve the molecular basis for compound phenotypes observed in mutant flies. In this paper, we find that Drosophila Neto functions as an essential component required for the function of NMJ glutamate receptors, permitting analysis of glutamate receptor responses in Xenopus oocytes. Finally, in combination with a crystallographic analysis of the GluRIIB ligand binding domain, we use this system to characterize the subunit dependence of assembly, channel block, and ligand selectivity for Drosophila NMJ glutamate receptors.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1992

Forcing function effects on unsteady aerodynamic gust response. I - Forcing functions

The paper investigates the fundamental gust modeling assumption on the basis of a series of experiments performed in the Purdue Annular Cascade Research Facility. The measured unsteady flow fields are compared to linear-theory gust requirements. The perforated plate forcing functions closely resemble linear-theory forcing functions, with the static pressure fluctuations small and the periodic velocity vectors parallel to the downstream mean-relative flow angle over the entire periodic cycle. The airfoil forcing functions exhibit characteristics far from linear-theory gusts, with the alignment of the velocity vectors and the static pressure fluctuation amplitudes dependent on the rotor-loading condition, rotor solidity, and the inlet mean-relative flow angle. It is shown that airfoil wakes, both compressor and turbine, cannot be modeled with the boundary conditions of current state-of-the-art linear unsteady aerodynamic theory.

Henderson, Gregory H.↗

DOE OSTI2022

Harmonizing model organism data in the Alliance of Genome Resources

The Alliance of Genome Resources (the Alliance) is a combined effort of 7 knowledgebase projects: Saccharomyces Genome Database, WormBase, FlyBase, Mouse Genome Database, the Zebrafish Information Network, Rat Genome Database, and the Gene Ontology Resource. The Alliance seeks to provide several benefits: better service to the various communities served by these projects; a harmonized view of data for all biomedical researchers, bioinformaticians, clinicians, and students; and a more sustainable infrastructure. The Alliance has harmonized cross-organism data to provide useful comparative views of gene function, gene expression, and human disease relevance. The basis of the comparative views is shared calls of orthology relationships and the use of common ontologies. The key types of data are alleles and variants, gene function based on gene ontology annotations, phenotypes, association to human disease, gene expression, protein–protein and genetic interactions, and participation in pathways. The information is presented on uniform gene pages that allow facile summarization of information about each gene in each of the 7 organisms covered (budding yeast, roundworm Caenorhabditis elegans, fruit fly, house mouse, zebrafish, brown rat, and human). The harmonized knowledge is freely available on the alliancegenome.org portal, as downloadable files, and by APIs. We expect other existing and emerging knowledge bases to join in the effort to provide the union of useful data and features that each knowledge base currently provides.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2015

Fully self-consistent solution of the Dyson equation using a plane-wave basis set

Self-consistent solutions of the Dyson equation are obtained using a plane-wave basis set for seven small molecules. Such self-consistent solutions can help to unify the different GW self-consistent schemes, reduce the scatter of results in current GW calculations, and shed light on the true effects of GW self-consistency. Unlike other works of self-consistent GW calculations, in the present work the Green's function is expressed as a matrix under the plane-wave basis set. The algorithmic details which enable such calculations are presented. Finally, the ability to solve the full Green's function using a plane-wave basis set may open the door for future beyond- GW many-body perturbation theory calculations.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2016

A theoretical study on 2-amino-5-nitroprydinium trifluoroaceta

The geometry optimization of 2-amino-5-nitroprydinium trifluoroacetate molecule was carried out by using Becke’s three-parameter exchange functional in conjunction with the Lee-Yang-Parr correlation functional (B3LYP) level of density functional theory (DFT) and 6-311++G(d,p) basis set at GAUSSIAN 09 program. The vibration spectrum of the title compound was simulated to predict the presence of functional groups and their vibrational modes. The highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies were calculated at the same level, and the obtained small energy gap shows that charge transfer occurs in the title compound. The molecular dipole moment, polarizability and hyperpolarizability parameters were determined to evaluate nonlinear optical efficiency of the title compound. Finally, the {sup 13}C and {sup 1}H Nuclear Magnetic Resonance (NMR) chemical shift values were calculated by the application of the gauge independent atomic orbital (GIAO) method. All of the calculations were carried out by using GAUSSIAN 09 program.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

NASA NTRS1967

Theoretical studies on the relationship between the thermionic work functions of refractory-metal intermetallic compounds and their electronic and crystal structures Final summary report

The Group VIA-Re binary systems are characterized by the presence of several intermediate phases. The u phase is present in all of the systems, but the a-Mn phases occur in only the Mo-Re and W-Re systems. The occurrence of these intermediate phases appears to be governed largely by electronic factors and is predictable on the basis of electron/atom ratio. The thermionic work functions of the intermediate phase materials were experimentally determined. function and the screening of the outermost electrons in the Group VIA metals was found. A correlation between the work As might be expected for purely metallic substances, the work functions were relatively high, in the range 4. 5 to 5. 0 eV, and in each case were bracketed by the work functions of the pure constituents. A discontinuous change in the average work function with composition is proposed, based on a thermodynamical treatment of the electron vapor.

REFRACTORY METAL↗

DOE OSTI2018

Quantum Chemical Calculation of p K a s of Environmentally Relevant Functional Groups: Carboxylic Acids, Amines, and Thiols in Aqueous Solution

Developing accurate quantum chemical approaches for calculating p K a s is of broad interest. Useful accuracy can be obtained by using density functional theory (DFT) in combination with a polarizable continuum solvent model. However, some classes of molecules present problems for this approach, yielding errors greater than 5 p K units. Various methods have been developed to improve the accuracy of the combined strategy. These methods perform well but either do not generalize or introduce additional degrees of freedom, increasing the computational cost. The Solvation Model based on Density (SMD) has emerged as one of the most commonly used continuum solvent models. Nevertheless, for some classes of organic compounds, e.g., thiols, the p K a s calculated with the original SMD model show errors of 6–10 p K units, and we traced these errors to inaccuracies in the solvation free energies of the anions. To improve the accuracy of p K a s calculated with DFT and the SMD model, we developed a scaled solvent-accessible surface approach for constructing the solute–solvent boundary. By using a “direct” approach, in which all quantities are computed in the presence of the continuum solvent, the use of thermodynamic cycles is avoided. Furthermore, no explicit water molecules are required. Three benchmark data sets of experimentally measured p K a values, including 28 carboxylic acids, 10 aliphatic amines, and 45 thiols, were used to assess the optimized SMD model, which we call SMD with a scaled solvent-accessible surface (SMD sSAS ). Of the methods tested, the M06-2X density functional approximation, 6-31+G(d,p) basis set, and SMD sSAS solvent model provided the most accurate p K a s for each set, yielding mean unsigned errors of 0.9, 0.4, and 0.5 p K units, respectively, for carboxylic acids, aliphatic amines, and thiols. As a result, this approach is therefore useful for efficiently calculating the p K a s of environmentally relevant functional groups.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2016

ωB97M-V: A combinatorially optimized, range-separated hybrid, meta-GGA density functional with VV10 nonlocal correlation

A combinatorially optimized, range-separated hybrid, meta-GGA density functional with VV10 nonlocal correlation is presented in this paper. The final 12-parameter functional form is selected from approximately 10 × 10 9 candidate fits that are trained on a training set of 870 data points and tested on a primary test set of 2964 data points. The resulting density functional, ωB97M-V, is further tested for transferability on a secondary test set of 1152 data points. For comparison, ωB97M-V is benchmarked against 11 leading density functionals including M06-2X, ωB97X-D, M08-HX, M11, ωM05-D, ωB97X-V, and MN15. Encouragingly, the overall performance of ωB97M-V on nearly 5000 data points clearly surpasses that of all of the tested density functionals. Finally, in order to facilitate the use of ωB97M-V, its basis set dependence and integration grid sensitivity are thoroughly assessed, and recommendations that take into account both efficiency and accuracy are provided.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS1986

A generalized algorithm to design finite field normal basis multipliers

Finite field arithmetic logic is central in the implementation of some error-correcting coders and some cryptographic devices. There is a need for good multiplication algorithms which can be easily realized. Massey and Omura recently developed a new multiplication algorithm for finite fields based on a normal basis representation. Using the normal basis representation, the design of the finite field multiplier is simple and regular. The fundamental design of the Massey-Omura multiplier is based on a design of a product function. In this article, a generalized algorithm to locate a normal basis in a field is first presented. Using this normal basis, an algorithm to construct the product function is then developed. This design does not depend on particular characteristics of the generator polynomial of the field.

Wang, C. C.↗

DOE OSTI2011

High-Resolution Infrared Spectra of Spiropentane, C5H8

Infrared spectra of spiropentane (C{sub 5}H{sub 8}) have been recorded at a resolution (0.002 cm{sup -1}) sufficient to resolve for the first time individual rovibrational lines. This initial report presents the ground state constants for this molecule determined from the detailed analysis of the {nu}16 (b2) parallel band at 993 cm{sup -1}. In addition, the determination included more than 2000 ground state combination-differences deduced from partial analyses of four other infrared-allowed bands, the {nu}24(e) perpendicular band at 780 cm{sup -1} and three (b2) parallel bands at 1540 cm{sup -1} ({nu}14), 1568 cm{sup -1} ({nu}5+{nu}16), and 2098 cm{sup -1} ({nu}5+{nu}14). In each of the latter four cases, the spectra show complications; in the case of {nu}24, these complications are due to rotational l-type doublings, and in the case of the parallel bands, the spectral complexities are due to Fermi resonance and Coriolis interactions of the upper states with nearby levels. The unraveling of these is underway but the assignment of many of these transitions permit the confident use of the ground state differences in determining the following constants for the ground state (in units of cm{sup -1}): B0 = 0.1394736(2), DJ = 2.458(1) x 10{sup -8}, DJK = 8.28(3) x 10{sup -8}. For the unperturbed {nu}16 fundamental, more than 3000 transitions were fit and the band origin was found to be at 992.53793(2) cm{sup -1}. The numbers in parentheses are the uncertainties (two standard deviations) in the value of the last digit of the constants. Surprisingly, the very accurate B0 value measured here is lower than the value (0.1418 cm{sup -1}) calculated from an electron diffraction structure, instead of being higher, as expected. Where possible, the rovibrational results are compared with those computed at the anharmonic level using the B3LYP density functional method with a cc-pVTZ basis set. These too suggest that the electron diffraction results are in question.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2015

Metal cluster structures and properties from Born-Oppenheimer molecular dynamics

Density functional theory (DFT) Born-Oppenheimer molecular dynamics (BOMD) simulations of metal clusters are presented. The calculations have been performed with the deMon2k [1] code employing all-electron basis sets and local and non-local functionals. The capability to perform reasonable long (∼ 100 ps) first-principle BOMD simulations in order to explore potential energy landscape of metallic clusters will be presented [2,3]. The evolution of the cluster structures and properties, such as polarizability and heat capacity, with temperature is discussed.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2014

Simulating three-dimensional nonthermal high-energy photon emission in colliding-wind binaries

Massive stars in binary systems have long been regarded as potential sources of high-energy γ rays. The emission is principally thought to arise in the region where the stellar winds collide and accelerate relativistic particles which subsequently emit γ rays. On the basis of a three-dimensional distribution function of high-energy particles in the wind collision region—as obtained by a numerical hydrodynamics and particle transport model—we present the computation of the three-dimensional nonthermal photon emission for a given line of sight. Anisotropic inverse Compton emission is modeled using the target radiation field of both stars. Photons from relativistic bremsstrahlung and neutral pion decay are computed on the basis of local wind plasma densities. We also consider photon-photon opacity effects due to the dense radiation fields of the stars. Results are shown for different stellar separations of a given binary system comprising of a B star and a Wolf-Rayet star. The influence of orbital orientation with respect to the line of sight is also studied by using different orbital viewing angles. For the chosen electron-proton injection ratio of 10{sup –2}, we present the ensuing photon emission in terms of two-dimensional projections maps, spectral energy distributions, and integrated photon flux values in various energy bands. Here, we find a transition from hadron-dominated to lepton-dominated high-energy emission with increasing stellar separations. In addition, we confirm findings from previous analytic modeling that the spectral energy distribution varies significantly with orbital orientation.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2023

Effects of anisotropy and disorder on the superconducting properties of niobium

We report results for the superconducting transition temperature and anisotropic energy gap for pure niobium based on Eliashberg’s equations and electron and phonon band structures computed from density functional theory. The electronic band structure is used to construct the Fermi surface and calculate the Fermi velocity at each point on the Fermi surface. The phonon bands are in excellent agreement with inelastic neutron scattering data. The corresponding phonon density of states and electron–phonon coupling define the electron–phonon spectral function, α 2 F(p, p'; ω), and the corresponding electron–phonon pairing interaction, which is the basis for computing the superconducting properties. The electron–phonon spectral function is in good agreement with existing tunneling spectroscopy data except for the spectral weight of the longitudinal phonon peak at ℏω LO = 23 meV. We obtain an electron–phonon coupling constant of λ = 1.057, renormalized Coulomb interaction μ* = 0.218, and transition temperature T c = 9.33 K. The corresponding strong-coupling gap at T = 0 is modestly enhanced, Δ 0 = 1.55 meV, compared to the weak-coupling BCS value $Δ^{\text {wc}}_{0}$ = 1.78 k B T c = 1.43 meV. The superconducting gap function exhibits substantial anisotropy on the Fermi surface. We analyze the distribution of gap anisotropy and compute the suppression of the superconducting transition temperature using a self-consistent T-matrix theory for quasiparticle-impurity scattering to describe niobium doped with non-magnetic impurities. We compare these results with experimental results on niobium SRF cavities doped with nitrogen impurities.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

NASA NTRS1990

Toward modeling a dynamic biological neural network

The organization of a mammalian macular endorgan is interpreted on physical and engineering principles. Having accomplished this task, it is possible to mathematically and symbolically model information processing by the macular neural network. A complex symbolic model is produced through use of mathematical notations that describe the functioning system. The model, consisting of six tiers, is constructed to mimic the neural system. On the basis of initial simulations, it is concluded that the network functions best when some of the detecting elements (i.e., type I hair cells) are weakly inhibitory. The simulations also illustrate the importance of disinhibition of receptors located in the third tier in shaping nerve discharge patterns at the sixth tier in the model system.

Ross, M. D.↗

DOE OSTI2011

Scattering in multilayered structures: Diffraction from a nanohole

The spectral expansion of the Green's tensor for a planar multilayered structure allows us to semianalytically obtain the angular spectrum representation of the field scattered by an arbitrary dielectric perturbation present in the structure. In this paper we present a method to find the expansion coefficients of the scattered field, given that the electric field inside the perturbation is available. The method uses a complete set of orthogonal vector wave functions to solve the structure's vector wave equation. In the two semi-infinite bottom and top media, those vector wave functions coincide with the plane-wave basis vectors, including both propagating and evanescent components. The technique is used to obtain the complete angular spectrum of the field scattered by a nanohole in a metallic film under Gaussian illumination. We also show how the obtained formalism can easily be extended to spherically and cylindrically multilayered media. In those cases, the expansion coefficients would multiply the spherical and cylindrical vector wave functions.

36 MATERIALS SCIENCE↗