Theoretical investigation of gas-phase molecular complex formation between 2-hydroxy thiophenol and a water molecule.

PubMed

Kumar Deb, Debojit; Sarkar, Biplab

2017-01-18

The torsional potential of OH and SH rotations in 2-hydroxy thiophenol is systematically studied using the MP2 ab initio method. The outcome of state-of-the-art calculations is used in the investigation of the structures and conformational preferences of 2-hydroxy thiophenol and aims at further interaction studies with a gas phase water molecule. SCS-MP2 and CCSD(T) complete basis set (CBS) limit interaction energies for these complexes are presented. The SCS-MP2/CBS limit is achieved using various two-point extrapolation methods with aug-cc-pVDZ and aug-cc-pVTZ basis sets. The CCSD(T) correction term is determined as the difference between CCSD(T) and SCS-MP2 interaction energies calculated using a smaller basis set. The effect of counterpoise correction on the extrapolation to the CBS limit is discussed. The performance of DFT based wB97XD, M06-2X and B3LYP-D3 functionals is tested against the benchmark energy from ab initio calculations. Hydrogen bond interactions are characterized by carrying out QTAIM, NCIPLOT, NBO and SAPT analyses.

Genetic basis of climatic adaptation in scots pine by bayesian quantitative trait locus analysis.

PubMed Central

Hurme, P; Sillanpää, M J; Arjas, E; Repo, T; Savolainen, O

2000-01-01

We examined the genetic basis of large adaptive differences in timing of bud set and frost hardiness between natural populations of Scots pine. As a mapping population, we considered an "open-pollinated backcross" progeny by collecting seeds of a single F(1) tree (cross between trees from southern and northern Finland) growing in southern Finland. Due to the special features of the design (no marker information available on grandparents or the father), we applied a Bayesian quantitative trait locus (QTL) mapping method developed previously for outcrossed offspring. We found four potential QTL for timing of bud set and seven for frost hardiness. Bayesian analyses detected more QTL than ANOVA for frost hardiness, but the opposite was true for bud set. These QTL included alleles with rather large effects, and additionally smaller QTL were supported. The largest QTL for bud set date accounted for about a fourth of the mean difference between populations. Thus, natural selection during adaptation has resulted in selection of at least some alleles of rather large effect. PMID:11063704

The structure and energetics of Cr(CO)6 and Cr(CO)5

NASA Technical Reports Server (NTRS)

Barnes, Leslie A.; Liu, Bowen; Lindh, Roland

1992-01-01

The geometric structure of Cr(CO)6 is optimized at the modified coupled pair functional (MCPF), single and double excitation coupled-cluster (CCSD) and CCSD(T) levels of theory (including a perturbational estimate for connected triple excitations), and the force constants for the totally symmetric representation are determined. The geometry of Cr(CO)5 is partially optimized at the MCPF, CCSD, and CCSD(T) levels of theory. Comparison with experimental data shows that the CCSD(T) method gives the best results for the structures and force constants, and that remaining errors are probably due to deficiencies in the one-particle basis sets used for CO. The total binding energies of Cr(CO)6 and Cr(CO)5 are also determined at the MCPF, CCSD, and CCSD(T) levels of theory. The CCSD(T) method gives a much larger total binding energy than either the MCPF or CCSD methods. An analysis of the basis set superposition error (BSSE) at the MCPF level of treatment points out limitations in the one-particle basis used. Calculations using larger basis sets reduce the BSSE, but the total binding energy of Cr(CO)6 is still significantly smaller than the experimental value, although the first CO bond dissociation energy of Cr(CO)6 is well described. An investigation of 3s3p correlation reveals only a small effect. In the largest basis set, the total CO binding energy of Cr(CO)6 is estimated to be 140 kcal/mol at the CCSD(T) level of theory, or about 86 percent of the experimental value. The remaining discrepancy between the experimental and theoretical value is probably due to limitations in the one-particle basis, rather than limitations in the correlation treatment. In particular an additional d function and an f function on each C and O are needed to obtain quantitative results. This is underscored by the fact that even using a very large primitive set (1042 primitive functions contracted to 300 basis functions), the superposition error for the total binding energy of Cr(CO)6 is 22 kcal/mol at the MCPF level of treatment.

A DFT and ab initio benchmarking study of metal-alkane interactions and the activation of carbon-hydrogen bonds.

PubMed

Flener-Lovitt, Charity; Woon, David E; Dunning, Thom H; Girolami, Gregory S

2010-02-04

Density functional theory and ab initio methods have been used to calculate the structures and energies of minima and transition states for the reactions of methane coordinated to a transition metal. The reactions studied are reversible C-H bond activation of the coordinated methane ligand to form a transition metal methyl hydride complex and dissociation of the coordinated methane ligand. The reaction sequence can be summarized as L(x)M(CH(3))H <==> L(x)M(CH(4)) <==> L(x)M + CH(4), where L(x)M is the osmium-containing fragment (C(5)H(5))Os(R(2)PCH(2)PR(2))(+) and R is H or CH(3). Three-center metal-carbon-hydrogen interactions play an important role in this system. Both basis sets and functionals have been benchmarked in this work, including new correlation consistent basis sets for a third transition series element, osmium. Double zeta quality correlation consistent basis sets yield energies close to those from calculations with quadruple-zeta basis sets, with variations that are smaller than the differences between functionals. The energies of important species on the potential energy surface, calculated by using 10 DFT functionals, are compared both to experimental values and to CCSD(T) single point calculations. Kohn-Sham natural bond orbital descriptions are used to understand the differences between functionals. Older functionals favor electrostatic interactions over weak donor-acceptor interactions and, therefore, are not particularly well suited for describing systems--such as sigma-complexes--in which the latter are dominant. Newer kinetic and dispersion-corrected functionals such as MPW1K and M05-2X provide significantly better descriptions of the bonding interactions, as judged by their ability to predict energies closer to CCSD(T) values. Kohn-Sham and natural bond orbitals are used to differentiate between bonding descriptions. Our evaluations of these basis sets and DFT functionals lead us to recommend the use of dispersion corrected functionals in conjunction with double-zeta or larger basis sets with polarization functions for calculations involving weak interactions, such as those found in sigma-complexes with transition metals.

Solvation effects on chemical shifts by embedded cluster integral equation theory.

PubMed

Frach, Roland; Kast, Stefan M

2014-12-11

The accurate computational prediction of nuclear magnetic resonance (NMR) parameters like chemical shifts represents a challenge if the species studied is immersed in strongly polarizing environments such as water. Common approaches to treating a solvent in the form of, e.g., the polarizable continuum model (PCM) ignore strong directional interactions such as H-bonds to the solvent which can have substantial impact on magnetic shieldings. We here present a computational methodology that accounts for atomic-level solvent effects on NMR parameters by extending the embedded cluster reference interaction site model (EC-RISM) integral equation theory to the prediction of chemical shifts of N-methylacetamide (NMA) in aqueous solution. We examine the influence of various so-called closure approximations of the underlying three-dimensional RISM theory as well as the impact of basis set size and different treatment of electrostatic solute-solvent interactions. We find considerable and systematic improvement over reference PCM and gas phase calculations. A smaller basis set in combination with a simple point charge model already yields good performance which can be further improved by employing exact electrostatic quantum-mechanical solute-solvent interaction energies. A larger basis set benefits more significantly from exact over point charge electrostatics, which can be related to differences of the solvent's charge distribution.

Yielding physically-interpretable emulators - A Sparse PCA approach

NASA Astrophysics Data System (ADS)

Galelli, S.; Alsahaf, A.; Giuliani, M.; Castelletti, A.

2015-12-01

Projection-based techniques, such as Principal Orthogonal Decomposition (POD), are a common approach to surrogate high-fidelity process-based models by lower order dynamic emulators. With POD, the dimensionality reduction is achieved by using observations, or 'snapshots' - generated with the high-fidelity model -, to project the entire set of input and state variables of this model onto a smaller set of basis functions that account for most of the variability in the data. While reduction efficiency and variance control of POD techniques are usually very high, the resulting emulators are structurally highly complex and can hardly be given a physically meaningful interpretation as each basis is a projection of the entire set of inputs and states. In this work, we propose a novel approach based on Sparse Principal Component Analysis (SPCA) that combines the several assets of POD methods with the potential for ex-post interpretation of the emulator structure. SPCA reduces the number of non-zero coefficients in the basis functions by identifying a sparse matrix of coefficients. While the resulting set of basis functions may retain less variance of the snapshots, the presence of a few non-zero coefficients assists in the interpretation of the underlying physical processes. The SPCA approach is tested on the reduction of a 1D hydro-ecological model (DYRESM-CAEDYM) used to describe the main ecological and hydrodynamic processes in Tono Dam, Japan. An experimental comparison against a standard POD approach shows that SPCA achieves the same accuracy in emulating a given output variable - for the same level of dimensionality reduction - while yielding better insights of the main process dynamics.

Performance of an Optimally Tuned Range-Separated Hybrid Functional for 0-0 Electronic Excitation Energies.

PubMed

Jacquemin, Denis; Moore, Barry; Planchat, Aurélien; Adamo, Carlo; Autschbach, Jochen

2014-04-08

Using a set of 40 conjugated molecules, we assess the performance of an "optimally tuned" range-separated hybrid functional in reproducing the experimental 0-0 energies. The selected protocol accounts for the impact of solvation using a corrected linear-response continuum approach and vibrational corrections through calculations of the zero-point energies of both ground and excited-states and provides basis set converged data thanks to the systematic use of diffuse-containing atomic basis sets at all computational steps. It turns out that an optimally tuned long-range corrected hybrid form of the Perdew-Burke-Ernzerhof functional, LC-PBE*, delivers both the smallest mean absolute error (0.20 eV) and standard deviation (0.15 eV) of all tested approaches, while the obtained correlation (0.93) is large but remains slightly smaller than its M06-2X counterpart (0.95). In addition, the efficiency of two other recently developed exchange-correlation functionals, namely SOGGA11-X and ωB97X-D, has been determined in order to allow more complete comparisons with previously published data.

Computational studies of metal-metal and metal-ligand interactions

NASA Technical Reports Server (NTRS)

Barnes, Leslie A.

1992-01-01

The geometric structure of Cr(CO)6 is optimized at the modified coupled-pair functional (MCPF), single and double excitation coupled-cluster (CCSD) and CCSD(T) levels of theory (including a perturbational estimate for connected triple excitations), and the force constants for the totally symmetric representation are determined. The geometry of Cr(CO)5 is partially optimized at the MCPF, CCSD and CCSD(T) levels of theory. Comparison with experimental data shows that the CCSD(T) method gives the best results for the structures and force constants, and that remaining errors are probably due to deficiencies in the one-particle basis sets used for CO. A detailed comparison of the properties of free CO is therefore given, at both the MCPF and CCSD/CCSD(T) levels of treatment, using a variety of basis sets. With very large one-particle basis sets, the SSCD(T) method gives excellent results for the bond distance, dipole moment and harmonic frequency of free CO. The total binding energies of Cr(CO)6 and Cr(CO)5 are also determined at the MCPF, CCSD and CCSD(T) levels of theory. The CCSD(T) method gives a much larger total binding energy than either the MCPF or CCSD methods. An analysis of the basis set superposition error (BSSE) at the MCPF level of treatment points out limitations in the one-particle basis used here and in a previous study. Calculations using larger basis sets reduced the BSSE, but the total binding energy of Cr(CO)6 is still significantly smaller than the experimental value, although the first CO bond dissociation energy of Cr(CO)6 is well described. An investigation of 3s3p correlation reveals only a small effect. The remaining discrepancy between the experimental and theoretical total binding energy of Cr(CO)6 is probably due to limitations in the one-particle basis, rather than limitations in the correlation treatment. In particular an additional d function and an f function on each C and O are needed to obtain quantitative results. This is underscored by the fact that even using a very large primitive se (1042 primitive functions contracted to 300 basis functions), the superposition error for the total binding energy of Cr(CO)6 is 22 kcal/mol at the MCPF level of treatment.

The Pariser-Parr-Pople model for trans-polyenes. I. Ab initio and semiempirical study of the bond alternation in trans-butadiene

NASA Astrophysics Data System (ADS)

Förner, Wolfgang

1992-03-01

Ab initio investigations of the bond alternation in butadiene are presented. The atomic basis sets applied range from minimal to split valence plus polarization quality. With the latter one the Hartree-Fock limit for the bond alternation is reached. Correlation is considered on Møller-Plesset many-body perturbation theory of second order (MP2), linear coupled cluster doubles (L-CCD) and coupled cluster doubles (CCD) level. For the smaller basis sets it is shown that for the bond alternation π-π correlations are essential while the effects of σ-σ and σ-π correlations are, though large, nearly independent of bond alternation. On MP2 level the variation of σ-π correlation with bond alternation is surprisingly large. This is discussed as an artefact of MP2. Comparative Su-Schrieffer-Heeger (SSH) and Pariser-Parr-Pople (PPP) calculations show that these models in their usual parametrizations cannot reproduce the ab initio results.

The X40×10 Halogen Bonding Benchmark Revisited: Surprising Importance of (n-1)d Subvalence Correlation.

PubMed

Kesharwani, Manoj K; Manna, Debashree; Sylvetsky, Nitai; Martin, Jan M L

2018-03-01

We have re-evaluated the X40×10 benchmark for halogen bonding using conventional and explicitly correlated coupled cluster methods. For the aromatic dimers at small separation, improved CCSD(T)-MP2 "high-level corrections" (HLCs) cause substantial reductions in the dissociation energy. For the bromine and iodine species, (n-1)d subvalence correlation increases dissociation energies and turns out to be more important for noncovalent interactions than is generally realized; (n-1)sp subvalence correlation is much less important. The (n-1)d subvalence term is dominated by core-valence correlation; with the smaller cc-pVDZ-F12-PP and cc-pVTZ-F12-PP basis sets, basis set convergence for the core-core contribution becomes sufficiently erratic that it may compromise results overall. The two factors conspire to generate discrepancies of up to 0.9 kcal/mol (0.16 kcal/mol RMS) between the original X40×10 data and the present revision.

Monte Carlo explicitly correlated second-order many-body perturbation theory

NASA Astrophysics Data System (ADS)

Johnson, Cole M.; Doran, Alexander E.; Zhang, Jinmei; Valeev, Edward F.; Hirata, So

2016-10-01

A stochastic algorithm is proposed and implemented that computes a basis-set-incompleteness (F12) correction to an ab initio second-order many-body perturbation energy as a short sum of 6- to 15-dimensional integrals of Gaussian-type orbitals, an explicit function of the electron-electron distance (geminal), and its associated excitation amplitudes held fixed at the values suggested by Ten-no. The integrals are directly evaluated (without a resolution-of-the-identity approximation or an auxiliary basis set) by the Metropolis Monte Carlo method. Applications of this method to 17 molecular correlation energies and 12 gas-phase reaction energies reveal that both the nonvariational and variational formulas for the correction give reliable correlation energies (98% or higher) and reaction energies (within 2 kJ mol-1 with a smaller statistical uncertainty) near the complete-basis-set limits by using just the aug-cc-pVDZ basis set. The nonvariational formula is found to be 2-10 times less expensive to evaluate than the variational one, though the latter yields energies that are bounded from below and is, therefore, slightly but systematically more accurate for energy differences. Being capable of using virtually any geminal form, the method confirms the best overall performance of the Slater-type geminal among 6 forms satisfying the same cusp conditions. Not having to precompute lower-dimensional integrals analytically, to store them on disk, or to transform them in a nonscalable dense-matrix-multiplication algorithm, the method scales favorably with both system size and computer size; the cost increases only as O(n4) with the number of orbitals (n), and its parallel efficiency reaches 99.9% of the ideal case on going from 16 to 4096 computer processors.

LEAP into the Pfizer Global Virtual Library (PGVL) space: creation of readily synthesizable design ideas automatically.

PubMed

Hu, Qiyue; Peng, Zhengwei; Kostrowicki, Jaroslav; Kuki, Atsuo

2011-01-01

Pfizer Global Virtual Library (PGVL) of 10(13) readily synthesizable molecules offers a tremendous opportunity for lead optimization and scaffold hopping in drug discovery projects. However, mining into a chemical space of this size presents a challenge for the concomitant design informatics due to the fact that standard molecular similarity searches against a collection of explicit molecules cannot be utilized, since no chemical information system could create and manage more than 10(8) explicit molecules. Nevertheless, by accepting a tolerable level of false negatives in search results, we were able to bypass the need for full 10(13) enumeration and enabled the efficient similarity search and retrieval into this huge chemical space for practical usage by medicinal chemists. In this report, two search methods (LEAP1 and LEAP2) are presented. The first method uses PGVL reaction knowledge to disassemble the incoming search query molecule into a set of reactants and then uses reactant-level similarities into actual available starting materials to focus on a much smaller sub-region of the full virtual library compound space. This sub-region is then explicitly enumerated and searched via a standard similarity method using the original query molecule. The second method uses a fuzzy mapping onto candidate reactions and does not require exact disassembly of the incoming query molecule. Instead Basis Products (or capped reactants) are mapped into the query molecule and the resultant asymmetric similarity scores are used to prioritize the corresponding reactions and reactant sets. All sets of Basis Products are inherently indexed to specific reactions and specific starting materials. This again allows focusing on a much smaller sub-region for explicit enumeration and subsequent standard product-level similarity search. A set of validation studies were conducted. The results have shown that the level of false negatives for the disassembly-based method is acceptable when the query molecule can be recognized for exact disassembly, and the fuzzy reaction mapping method based on Basis Products has an even better performance in terms of lower false-negative rate because it is not limited by the requirement that the query molecule needs to be recognized by any disassembly algorithm. Both search methods have been implemented and accessed through a powerful desktop molecular design tool (see ref. (33) for details). The chapter will end with a comparison of published search methods against large virtual chemical space.

From cottage to community hospitals: Watlington Cottage Hospital and its regional context, 1874-2000.

PubMed

Hall, John

2012-01-01

The appearance in England from the 1850s of 'cottage hospitals' in considerable numbers constituted a new and distinctive form of hospital provision. The historiography of hospital care has emphasised the role of the large teaching hospitals, to the neglect of the smaller and general practitioner hospitals. This article inverts that attention, by examining their history and shift in function to 'community hospitals'within their regional setting in the period up to 2000. As the planning of hospitals on a regional basis began from the 1920s, the impact of NHS organisational and planning mechanisms on smaller hospitals is explored through case studies at two levels. The strategy for community hospitals of the Oxford NHS Region--one of the first Regions to formulate such a strategy--and the impact of that strategy on one hospital, Watlington Cottage Hospital, is critically examined through its existence from 1874 to 2000.

Electronic structure of stoichiometric and reduced ZnO from periodic relativistic all electron hybrid density functional calculations using numeric atom-centered orbitals.

PubMed

Viñes, Francesc; Illas, Francesc

2017-03-30

The atomic and electronic structure of stoichiometric and reduced ZnO wurtzite has been studied using a periodic relativistic all electron hybrid density functional (PBE0) approach and numeric atom-centered orbital basis set with quality equivalent to aug-cc-pVDZ. To assess the importance of relativistic effects, calculations were carried out without and with explicit inclusion of relativistic effects through the zero order regular approximation. The calculated band gap is ∼0.2 eV smaller than experiment, close to previous PBE0 results including relativistic calculation through the pseudopotential and ∼0.25 eV smaller than equivalent nonrelativistic all electron PBE0 calculations indicating possible sources of error in nonrelativistic all electron density functional calculations for systems containing elements with relatively high atomic number. The oxygen vacancy formation energy converges rather fast with the supercell size, the predicted value agrees with previously hybrid density functional calculations and analysis of the electronic structure evidences the presence of localized electrons at the vacancy site with a concomitant well localized peak in the density of states ∼0.5 eV above the top of the valence band and a significant relaxation of the Zn atoms near to the oxygen vacancy. Finally, present work shows that accurate results can be obtained in systems involving large supercells containing up to ∼450 atoms using a numeric atomic-centered orbital basis set within a full all electron description including scalar relativistic effects at an affordable cost. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Model's sparse representation based on reduced mixed GMsFE basis methods

NASA Astrophysics Data System (ADS)

Jiang, Lijian; Li, Qiuqi

2017-06-01

In this paper, we propose a model's sparse representation based on reduced mixed generalized multiscale finite element (GMsFE) basis methods for elliptic PDEs with random inputs. A typical application for the elliptic PDEs is the flow in heterogeneous random porous media. Mixed generalized multiscale finite element method (GMsFEM) is one of the accurate and efficient approaches to solve the flow problem in a coarse grid and obtain the velocity with local mass conservation. When the inputs of the PDEs are parameterized by the random variables, the GMsFE basis functions usually depend on the random parameters. This leads to a large number degree of freedoms for the mixed GMsFEM and substantially impacts on the computation efficiency. In order to overcome the difficulty, we develop reduced mixed GMsFE basis methods such that the multiscale basis functions are independent of the random parameters and span a low-dimensional space. To this end, a greedy algorithm is used to find a set of optimal samples from a training set scattered in the parameter space. Reduced mixed GMsFE basis functions are constructed based on the optimal samples using two optimal sampling strategies: basis-oriented cross-validation and proper orthogonal decomposition. Although the dimension of the space spanned by the reduced mixed GMsFE basis functions is much smaller than the dimension of the original full order model, the online computation still depends on the number of coarse degree of freedoms. To significantly improve the online computation, we integrate the reduced mixed GMsFE basis methods with sparse tensor approximation and obtain a sparse representation for the model's outputs. The sparse representation is very efficient for evaluating the model's outputs for many instances of parameters. To illustrate the efficacy of the proposed methods, we present a few numerical examples for elliptic PDEs with multiscale and random inputs. In particular, a two-phase flow model in random porous media is simulated by the proposed sparse representation method.

Model's sparse representation based on reduced mixed GMsFE basis methods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jiang, Lijian, E-mail: ljjiang@hnu.edu.cn; Li, Qiuqi, E-mail: qiuqili@hnu.edu.cn

2017-06-01

In this paper, we propose a model's sparse representation based on reduced mixed generalized multiscale finite element (GMsFE) basis methods for elliptic PDEs with random inputs. A typical application for the elliptic PDEs is the flow in heterogeneous random porous media. Mixed generalized multiscale finite element method (GMsFEM) is one of the accurate and efficient approaches to solve the flow problem in a coarse grid and obtain the velocity with local mass conservation. When the inputs of the PDEs are parameterized by the random variables, the GMsFE basis functions usually depend on the random parameters. This leads to a largemore » number degree of freedoms for the mixed GMsFEM and substantially impacts on the computation efficiency. In order to overcome the difficulty, we develop reduced mixed GMsFE basis methods such that the multiscale basis functions are independent of the random parameters and span a low-dimensional space. To this end, a greedy algorithm is used to find a set of optimal samples from a training set scattered in the parameter space. Reduced mixed GMsFE basis functions are constructed based on the optimal samples using two optimal sampling strategies: basis-oriented cross-validation and proper orthogonal decomposition. Although the dimension of the space spanned by the reduced mixed GMsFE basis functions is much smaller than the dimension of the original full order model, the online computation still depends on the number of coarse degree of freedoms. To significantly improve the online computation, we integrate the reduced mixed GMsFE basis methods with sparse tensor approximation and obtain a sparse representation for the model's outputs. The sparse representation is very efficient for evaluating the model's outputs for many instances of parameters. To illustrate the efficacy of the proposed methods, we present a few numerical examples for elliptic PDEs with multiscale and random inputs. In particular, a two-phase flow model in random porous media is simulated by the proposed sparse representation method.« less

Combining Accuracy and Efficiency: An Incremental Focal-Point Method Based on Pair Natural Orbitals.

PubMed

Fiedler, Benjamin; Schmitz, Gunnar; Hättig, Christof; Friedrich, Joachim

2017-12-12

In this work, we present a new pair natural orbitals (PNO)-based incremental scheme to calculate CCSD(T) and CCSD(T0) reaction, interaction, and binding energies. We perform an extensive analysis, which shows small incremental errors similar to previous non-PNO calculations. Furthermore, slight PNO errors are obtained by using T PNO = T TNO with appropriate values of 10 -7 to 10 -8 for reactions and 10 -8 for interaction or binding energies. The combination with the efficient MP2 focal-point approach yields chemical accuracy relative to the complete basis-set (CBS) limit. In this method, small basis sets (cc-pVDZ, def2-TZVP) for the CCSD(T) part are sufficient in case of reactions or interactions, while some larger ones (e.g., (aug)-cc-pVTZ) are necessary for molecular clusters. For these larger basis sets, we show the very high efficiency of our scheme. We obtain not only tremendous decreases of the wall times (i.e., factors >10 2 ) due to the parallelization of the increment calculations as well as of the total times due to the application of PNOs (i.e., compared to the normal incremental scheme) but also smaller total times with respect to the standard PNO method. That way, our new method features a perfect applicability by combining an excellent accuracy with a very high efficiency as well as the accessibility to larger systems due to the separation of the full computation into several small increments.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yu, Liang; Abild-Pedersen, Frank

On the basis of an extensive set of density functional theory calculations, it is shown that a simple scheme provides a fundamental understanding of variations in the transition state energies and structures of reaction intermediates on transition metal surfaces across the periodic table. The scheme is built on the bond order conservation principle and requires a limited set of input data, still achieving transition state energies as a function of simple descriptors with an error smaller than those of approaches based on linear fits to a set of calculated transition state energies. Here, we have applied this approach together withmore » linear scaling of adsorption energies to obtain the energetics of the NH 3 decomposition reaction on a series of stepped fcc(211) transition metal surfaces. Moreover, this information is used to establish a microkinetic model for the formation of N 2 and H 2, thus providing insight into the components of the reaction that determines the activity.« less

XZP + 1d and XZP + 1d-DKH basis sets for second-row elements: application to CCSD(T) zero-point vibrational energy and atomization energy calculations.

PubMed

Campos, Cesar T; Jorge, Francisco E; Alves, Júlia M A

2012-09-01

Recently, segmented all-electron contracted double, triple, quadruple, quintuple, and sextuple zeta valence plus polarization function (XZP, X = D, T, Q, 5, and 6) basis sets for the elements from H to Ar were constructed for use in conjunction with nonrelativistic and Douglas-Kroll-Hess Hamiltonians. In this work, in order to obtain a better description of some molecular properties, the XZP sets for the second-row elements were augmented with high-exponent d "inner polarization functions," which were optimized in the molecular environment at the second-order Møller-Plesset level. At the coupled cluster level of theory, the inclusion of tight d functions for these elements was found to be essential to improve the agreement between theoretical and experimental zero-point vibrational energies (ZPVEs) and atomization energies. For all of the molecules studied, the ZPVE errors were always smaller than 0.5 %. The atomization energies were also improved by applying corrections due to core/valence correlation and atomic spin-orbit effects. This led to estimates for the atomization energies of various compounds in the gaseous phase. The largest error (1.2 kcal mol(-1)) was found for SiH(4).

Consistent structures and interactions by density functional theory with small atomic orbital basis sets.

PubMed

Grimme, Stefan; Brandenburg, Jan Gerit; Bannwarth, Christoph; Hansen, Andreas

2015-08-07

A density functional theory (DFT) based composite electronic structure approach is proposed to efficiently compute structures and interaction energies in large chemical systems. It is based on the well-known and numerically robust Perdew-Burke-Ernzerhoff (PBE) generalized-gradient-approximation in a modified global hybrid functional with a relatively large amount of non-local Fock-exchange. The orbitals are expanded in Ahlrichs-type valence-double zeta atomic orbital (AO) Gaussian basis sets, which are available for many elements. In order to correct for the basis set superposition error (BSSE) and to account for the important long-range London dispersion effects, our well-established atom-pairwise potentials are used. In the design of the new method, particular attention has been paid to an accurate description of structural parameters in various covalent and non-covalent bonding situations as well as in periodic systems. Together with the recently proposed three-fold corrected (3c) Hartree-Fock method, the new composite scheme (termed PBEh-3c) represents the next member in a hierarchy of "low-cost" electronic structure approaches. They are mainly free of BSSE and account for most interactions in a physically sound and asymptotically correct manner. PBEh-3c yields good results for thermochemical properties in the huge GMTKN30 energy database. Furthermore, the method shows excellent performance for non-covalent interaction energies in small and large complexes. For evaluating its performance on equilibrium structures, a new compilation of standard test sets is suggested. These consist of small (light) molecules, partially flexible, medium-sized organic molecules, molecules comprising heavy main group elements, larger systems with long bonds, 3d-transition metal systems, non-covalently bound complexes (S22 and S66×8 sets), and peptide conformations. For these sets, overall deviations from accurate reference data are smaller than for various other tested DFT methods and reach that of triple-zeta AO basis set second-order perturbation theory (MP2/TZ) level at a tiny fraction of computational effort. Periodic calculations conducted for molecular crystals to test structures (including cell volumes) and sublimation enthalpies indicate very good accuracy competitive to computationally more involved plane-wave based calculations. PBEh-3c can be applied routinely to several hundreds of atoms on a single processor and it is suggested as a robust "high-speed" computational tool in theoretical chemistry and physics.

A fresh look at the photoelectron spectrum of bromobenzene: A third-order non-Dyson electron propagator study.

PubMed

Schneider, M; Soshnikov, D Yu; Holland, D M P; Powis, I; Antonsson, E; Patanen, M; Nicolas, C; Miron, C; Wormit, M; Dreuw, A; Trofimov, A B

2015-10-14

The valence-shell ionization spectrum of bromobenzene, as a representative halogen substituted aromatic, was studied using the non-Dyson third-order algebraic-diagrammatic construction [nD-ADC(3)] approximation for the electron propagator. This method, also referred to as IP-ADC(3), was implemented as a part of the Q-Chem program and enables large-scale calculations of the ionization spectra, where the computational effort scales as n(5) with respect to the number of molecular orbitals n. The IP-ADC(3) scheme is ideally suited for investigating low-lying ionization transitions, so fresh insight could be gained into the cationic state manifold of bromobenzene. In particular, the present IP-ADC(3) calculations with the cc-pVTZ basis reveal a whole class of low-lying low-intensity two-hole-one-particle (2h-1p) doublet and quartet states, which are relevant to various photoionization processes. The good qualitative agreement between the theoretical spectral profile for the valence-shell ionization transitions generated with the smaller cc-pVDZ basis set and the experimental photoelectron spectrum measured at a photon energy of 80 eV on the PLÉIADES beamline at the Soleil synchrotron radiation source allowed all the main features to be assigned. Some theoretical aspects of the ionization energy calculations concerning the use of various approximation schemes and basis sets are discussed.

Excited states from quantum Monte Carlo in the basis of Slater determinants

DOE Office of Scientific and Technical Information (OSTI.GOV)

Humeniuk, Alexander; Mitrić, Roland, E-mail: roland.mitric@uni-wuerzburg.de

2014-11-21

Building on the full configuration interaction quantum Monte Carlo (FCIQMC) algorithm introduced recently by Booth et al. [J. Chem. Phys. 131, 054106 (2009)] to compute the ground state of correlated many-electron systems, an extension to the computation of excited states (exFCIQMC) is presented. The Hilbert space is divided into a large part consisting of pure Slater determinants and a much smaller orthogonal part (the size of which is controlled by a cut-off threshold), from which the lowest eigenstates can be removed efficiently. In this way, the quantum Monte Carlo algorithm is restricted to the orthogonal complement of the lower excitedmore » states and projects out the next highest excited state. Starting from the ground state, higher excited states can be found one after the other. The Schrödinger equation in imaginary time is solved by the same population dynamics as in the ground state algorithm with modified probabilities and matrix elements, for which working formulae are provided. As a proof of principle, the method is applied to lithium hydride in the 3-21G basis set and to the helium dimer in the aug-cc-pVDZ basis set. It is shown to give the correct electronic structure for all bond lengths. Much more testing will be required before the applicability of this method to electron correlation problems of interesting size can be assessed.« less

A fresh look at the photoelectron spectrum of bromobenzene: A third-order non-Dyson electron propagator study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schneider, M.; Wormit, M.; Dreuw, A.

2015-10-14

The valence-shell ionization spectrum of bromobenzene, as a representative halogen substituted aromatic, was studied using the non-Dyson third-order algebraic-diagrammatic construction [nD-ADC(3)] approximation for the electron propagator. This method, also referred to as IP-ADC(3), was implemented as a part of the Q-Chem program and enables large-scale calculations of the ionization spectra, where the computational effort scales as n{sup 5} with respect to the number of molecular orbitals n. The IP-ADC(3) scheme is ideally suited for investigating low-lying ionization transitions, so fresh insight could be gained into the cationic state manifold of bromobenzene. In particular, the present IP-ADC(3) calculations with the cc-pVTZmore » basis reveal a whole class of low-lying low-intensity two-hole-one-particle (2h-1p) doublet and quartet states, which are relevant to various photoionization processes. The good qualitative agreement between the theoretical spectral profile for the valence-shell ionization transitions generated with the smaller cc-pVDZ basis set and the experimental photoelectron spectrum measured at a photon energy of 80 eV on the PLÉIADES beamline at the Soleil synchrotron radiation source allowed all the main features to be assigned. Some theoretical aspects of the ionization energy calculations concerning the use of various approximation schemes and basis sets are discussed.« less

Comparison of volume, security, and biomechanical strength of square and Aberdeen termination knots tied with 4-0 polyglyconate and used for termination of intradermal closures in canine cadavers.

PubMed

Regier, Penny J; Smeak, Daniel D; Coleman, Kristin; McGilvray, Kirk C

2015-08-01

To compare volumes of square knots and Aberdeen knots in vitro and evaluate security of these knot types when used as buried terminal knots for continuous intradermal wound closures in canine cadavers. Experimental study. 24 surgically closed, full-thickness, 4-cm, epidermal wounds in 4 canine cadavers and 80 knots tied in vitro. Continuous intradermal closures were performed with 4-0 polyglyconate and completed with a buried knot technique. Surgeon (intern or experienced surgeon) and termination knot type (4-throw square knot or 2 + 1 Aberdeen knot; 12 each) were randomly assigned. Closed wounds were excised, and a servohydraulic machine applied tensile load perpendicular to the long axis of the suture line. A load-displacement curve was generated for each sample; maximum load, displacement, stiffness, and mode of construct failure were recorded. Volumes of 2 + 1 Aberdeen (n = 40) and 4-throw square knots (40) tied on a suture board were measured on the basis of a cylindrical model. Aberdeen knots had a mean smaller volume (0.00045 mm(3)) than did square knots (0.003838 mm(3)). Maximum load and displacement did not differ between construct types. Mean stiffness of Aberdeen knot constructs was greater than that of square knots. The 2 + 1 Aberdeen knot had a smaller volume than the 4-throw square knot and was as secure. Although both knots may be reliably used in a clinical setting as the termination knot at the end of a continuous intradermal line, the authors advocate use of the Aberdeen terminal knot on the basis of ease of burying the smaller knot.

Set of Comparable Carbon Footprints for Highway Travel in Metropolitan America

DOE Office of Scientific and Technical Information (OSTI.GOV)

Southworth, Frank; Sonnenberg, Anthon

2011-01-01

The authors describe the development of a set of carbon dioxide emissions estimates for highway travel by automobile, truck, bus and other public transit vehicle movements within the nation s 100 largest metropolitan areas, in calendar year 2005. Considerable variability is found to exist across metropolitan areas when these greenhouse gas emissions are measured on a per capita and a per gross metropolitan product (GMP) basis. Least square regression modeling shows a relationship between emissions per capita and per GMP with truck traffic share, transit share, employment density, population dispersion within the metro area, and GMP per capita. As amore » result many of the nation s largest metropolitan areas tend to have lower CO2 emissions per capita and per GMP than smaller and more recently developed metro areas.« less

Optimization of Turbine Blade Design for Reusable Launch Vehicles

NASA Technical Reports Server (NTRS)

Shyy, Wei

1998-01-01

To facilitate design optimization of turbine blade shape for reusable launching vehicles, appropriate techniques need to be developed to process and estimate the characteristics of the design variables and the response of the output with respect to the variations of the design variables. The purpose of this report is to offer insight into developing appropriate techniques for supporting such design and optimization needs. Neural network and polynomial-based techniques are applied to process aerodynamic data obtained from computational simulations for flows around a two-dimensional airfoil and a generic three- dimensional wing/blade. For the two-dimensional airfoil, a two-layered radial-basis network is designed and trained. The performances of two different design functions for radial-basis networks, one based on the accuracy requirement, whereas the other one based on the limit on the network size. While the number of neurons needed to satisfactorily reproduce the information depends on the size of the data, the neural network technique is shown to be more accurate for large data set (up to 765 simulations have been used) than the polynomial-based response surface method. For the three-dimensional wing/blade case, smaller aerodynamic data sets (between 9 to 25 simulations) are considered, and both the neural network and the polynomial-based response surface techniques improve their performance as the data size increases. It is found while the relative performance of two different network types, a radial-basis network and a back-propagation network, depends on the number of input data, the number of iterations required for radial-basis network is less than that for the back-propagation network.

Coupled-cluster and explicitly correlated perturbation-theory calculations of the uracil anion.

PubMed

Bachorz, Rafał A; Klopper, Wim; Gutowski, Maciej

2007-02-28

A valence-type anion of the canonical tautomer of uracil has been characterized using explicitly correlated second-order Moller-Plesset perturbation theory (RI-MP2-R12) in conjunction with conventional coupled-cluster theory with single, double, and perturbative triple excitations. At this level of electron-correlation treatment and after inclusion of a zero-point vibrational energy correction, determined in the harmonic approximation at the RI-MP2 level of theory, the valence anion is adiabatically stable with respect to the neutral molecule by 40 meV. The anion is characterized by a vertical detachment energy of 0.60 eV. To obtain accurate estimates of the vertical and adiabatic electron binding energies, a scheme was applied in which electronic energy contributions from various levels of theory were added, each of them extrapolated to the corresponding basis-set limit. The MP2 basis-set limits were also evaluated using an explicitly correlated approach, and the results of these calculations are in agreement with the extrapolated values. A remarkable feature of the valence anionic state is that the adiabatic electron binding energy is positive but smaller than the adiabatic electron binding energy of the dipole-bound state.

Comparison of some dispersion-corrected and traditional functionals as applied to peptides and conformations of cyclohexane derivatives

NASA Astrophysics Data System (ADS)

Marianski, Mateusz; Asensio, Amparo; Dannenberg, J. J.

2012-07-01

We compare the energetic and structural properties of fully optimized α-helical and antiparallel β-sheet polyalanines and the energetic differences between axial and equatorial conformations of three cyclohexane derivatives (methyl, fluoro, and chloro) as calculated using several functionals designed to treat dispersion (B97-D, ωB97x-D, M06, M06L, and M06-2X) with other traditional functionals not specifically parametrized to treat dispersion (B3LYP, X3LYP, and PBE1PBE) and with experimental results. Those functionals developed to treat dispersion significantly overestimate interaction enthalpies of folding for the α-helix and predict unreasonable structures that contain Ramachandran ϕ and ψ and C = O…N H-bonding angles that are out of the bounds of databases compiled the β-sheets. These structures are consistent with overestimation of the interaction energies. For the cyclohexanes, these functionals overestimate the stabilities of the axial conformation, especially when used with smaller basis sets. Their performance improves when the basis set is improved from D95** to aug-cc-pVTZ (which would not be possible with systems as large as the peptides).

Comparison of some dispersion-corrected and traditional functionals as applied to peptides and conformations of cyclohexane derivatives

PubMed Central

Marianski, Mateusz; Asensio, Amparo; Dannenberg, J. J.

2012-01-01

We compare the energetic and structural properties of fully optimized α-helical and antiparallel β-sheet polyalanines and the energetic differences between axial and equatorial conformations of three cyclohexane derivatives (methyl, fluoro, and chloro) as calculated using several functionals designed to treat dispersion (B97-D, ωB97x-D, M06, M06L, and M06-2X) with other traditional functionals not specifically parametrized to treat dispersion (B3LYP, X3LYP, and PBE1PBE) and with experimental results. Those functionals developed to treat dispersion significantly overestimate interaction enthalpies of folding for the α-helix and predict unreasonable structures that contain Ramachandran ϕ and ψ and C = O…N H-bonding angles that are out of the bounds of databases compiled the β-sheets. These structures are consistent with overestimation of the interaction energies. For the cyclohexanes, these functionals overestimate the stabilities of the axial conformation, especially when used with smaller basis sets. Their performance improves when the basis set is improved from D95** to aug-cc-pVTZ (which would not be possible with systems as large as the peptides). PMID:22852599

Comparison of some dispersion-corrected and traditional functionals as applied to peptides and conformations of cyclohexane derivatives.

PubMed

Marianski, Mateusz; Asensio, Amparo; Dannenberg, J J

2012-07-28

We compare the energetic and structural properties of fully optimized α-helical and antiparallel β-sheet polyalanines and the energetic differences between axial and equatorial conformations of three cyclohexane derivatives (methyl, fluoro, and chloro) as calculated using several functionals designed to treat dispersion (B97-D, ωB97x-D, M06, M06L, and M06-2X) with other traditional functionals not specifically parametrized to treat dispersion (B3LYP, X3LYP, and PBE1PBE) and with experimental results. Those functionals developed to treat dispersion significantly overestimate interaction enthalpies of folding for the α-helix and predict unreasonable structures that contain Ramachandran φ and ψ and C = O...N H-bonding angles that are out of the bounds of databases compiled the β-sheets. These structures are consistent with overestimation of the interaction energies. For the cyclohexanes, these functionals overestimate the stabilities of the axial conformation, especially when used with smaller basis sets. Their performance improves when the basis set is improved from D95∗∗ to aug-cc-pVTZ (which would not be possible with systems as large as the peptides).

Bond Order Conservation Strategies in Catalysis Applied to the NH 3 Decomposition Reaction

DOE PAGES

Yu, Liang; Abild-Pedersen, Frank

2016-12-14

On the basis of an extensive set of density functional theory calculations, it is shown that a simple scheme provides a fundamental understanding of variations in the transition state energies and structures of reaction intermediates on transition metal surfaces across the periodic table. The scheme is built on the bond order conservation principle and requires a limited set of input data, still achieving transition state energies as a function of simple descriptors with an error smaller than those of approaches based on linear fits to a set of calculated transition state energies. Here, we have applied this approach together withmore » linear scaling of adsorption energies to obtain the energetics of the NH 3 decomposition reaction on a series of stepped fcc(211) transition metal surfaces. Moreover, this information is used to establish a microkinetic model for the formation of N 2 and H 2, thus providing insight into the components of the reaction that determines the activity.« less

Field data analysis of boar semen quality.

PubMed

Broekhuijse, M L W J; Feitsma, H; Gadella, B M

2011-09-01

This contribution provides an overview of approaches to correlate sow fertility data with boar semen quality characteristics. Large data sets of fertility data and ejaculate data are more suitable to analyse effects of semen quality characteristics on field fertility. Variation in fertility in sows is large. The effect of semen factors is relatively small and therefore impossible to find in smaller data sets. Large data sets allow for statistical corrections on both sow- and boar-related parameters. Remaining sow fertility variation can then be assigned to semen quality parameters, which is of huge interest to AI (artificial insemination) companies. Previous studies of Varkens KI Nederland to find the contribution to field fertility of (i) the number of sperm cells in an insemination dose, (ii) the sperm motility and morphological defects and (iii) the age of semen at the moment of insemination are discussed in context of the possibility to apply such knowledge to select boars on the basis of their sperm parameters for AI purposes. © 2011 Blackwell Verlag GmbH.

On-line diagnosis of sequential systems, 3

NASA Technical Reports Server (NTRS)

Sundstrom, R. J.

1975-01-01

A formal model is introduced which can serve as the basis for a theoretical investigation of on-line diagnosis. Within this model a fault of a system S is considered to be a transformation of S into another system S prime at some time tau. The resulting faulty system is taken to be the system which looks like S up to time tau and like S prime thereafter. The on-line diagnosis of systems which are structurally decomposed and represented as a network of smaller systems is also investigated. The fault set considered is the set of unrestricted component faults; namely, the set of faults which only affect one component of the network. A characterization of networks which can be diagnosed using a combinational detector is obtained. It is further shown that any network can be made diagnosable in the above sense through the addition of one component. In addition, a lower bound is obtained on the complexity of any component, the addition of which is sufficient to make a particular network combinationally diagnosable.

On the truncation of the number of excited states in density functional theory sum-over-states calculations of indirect spin spin coupling constants

NASA Astrophysics Data System (ADS)

Zarycz, M. Natalia C.; Provasi, Patricio F.; Sauer, Stephan P. A.

2015-12-01

It is investigated, whether the number of excited (pseudo)states can be truncated in the sum-over-states expression for indirect spin-spin coupling constants (SSCCs), which is used in the Contributions from Localized Orbitals within the Polarization Propagator Approach and Inner Projections of the Polarization Propagator (IPPP-CLOPPA) approach to analyzing SSCCs in terms of localized orbitals. As a test set we have studied the nine simple compounds, CH4, NH3, H2O, SiH4, PH3, SH2, C2H2, C2H4, and C2H6. The excited (pseudo)states were obtained from time-dependent density functional theory (TD-DFT) calculations with the B3LYP exchange-correlation functional and the specialized core-property basis set, aug-cc-pVTZ-J. We investigated both how the calculated coupling constants depend on the number of (pseudo)states included in the summation and whether the summation can be truncated in a systematic way at a smaller number of states and extrapolated to the total number of (pseudo)states for the given one-electron basis set. We find that this is possible and that for some of the couplings it is sufficient to include only about 30% of the excited (pseudo)states.

Decomposability and convex structure of thermal processes

NASA Astrophysics Data System (ADS)

Mazurek, Paweł; Horodecki, Michał

2018-05-01

We present an example of a thermal process (TP) for a system of d energy levels, which cannot be performed without an instant access to the whole energy space. This TP is uniquely connected with a transition between some states of the system, that cannot be performed without access to the whole energy space even when approximate transitions are allowed. Pursuing the question about the decomposability of TPs into convex combinations of compositions of processes acting non-trivially on smaller subspaces, we investigate transitions within the subspace of states diagonal in the energy basis. For three level systems, we determine the set of extremal points of these operations, as well as the minimal set of operations needed to perform an arbitrary TP, and connect the set of TPs with thermomajorization criterion. We show that the structure of the set depends on temperature, which is associated with the fact that TPs cannot increase deterministically extractable work from a state—the conclusion that holds for arbitrary d level system. We also connect the decomposability problem with detailed balance symmetry of an extremal TPs.

Three- and four-body nonadditivities in nucleic acid tetramers: a CCSD(T) study.

PubMed

Pitonák, M; Neogrády, P; Hobza, P

2010-02-14

Three- and four-body nonadditivities in the uracil tetramer (in DNA-like geometry) and the GC step (in crystal geometry) were investigated at various levels of the wave-function theory: HF, MP2, MP3, L-CCD, CCSD and CCSD(T). All of the calculations were performed using the 6-31G**(0.25,0.15) basis set, whereas the HF, MP2 and the MP3 nonadditivities were, for the sake of comparison, also determined with the much larger aug-cc-pVDZ basis set. The HF and MP2 levels do not provide reliable values for many-body terms, making it necessary to go beyond the MP2 level. The benchmark CCSD(T) three- and four-body nonadditivities are reasonably well reproduced at the MP3 level, and almost quantitative agreement is obtained (fortuitously) either on the L-CCD level or as an average of the MP3 and the CCSD results. Reliable values of many-body terms (especially their higher-order correlation contributions) are obtained already when the rather small 6-31G**(0.25,0.15) basis set is used. The four-body term is much smaller when compared to the three-body terms, but it is definitely not negligible, e.g. in the case of the GC step it represents about 16% of all of the three- and four-body terms. While investigating the geometry dependence of many-body terms for the GG step at the MP3/6-31G**(0.25,0.15) level, we found that it is necessary to include at least three-body terms in the determination of optimal geometry parameters.

Dynamical properties of liquid water from ab initio molecular dynamics performed in the complete basis set limit

NASA Astrophysics Data System (ADS)

Lee, Hee-Seung; Tuckerman, Mark E.

2007-04-01

Dynamical properties of liquid water were studied using Car-Parrinello [Phys. Rev. Lett. 55, 2471 (1985)] ab initio molecular dynamics (AIMD) simulations within the Kohn-Sham (KS) density functional theory employing the Becke-Lee-Yang-Parr exchange-correlation functional for the electronic structure. The KS orbitals were expanded in a discrete variable representation basis set, wherein the complete basis set limit can be easily reached and which, therefore, provides complete convergence of ionic forces. In order to minimize possible nonergodic behavior of the simulated water system in a constant energy (NVE) ensemble, a long equilibration run (30ps) preceded a 60ps long production run. The temperature drift during the entire 60ps trajectory was found to be minimal. The diffusion coefficient [0.055Å2/ps] obtained from the present work for 32 D2O molecules is a factor of 4 smaller than the most up to date experimental value, but significantly larger than those of other recent AIMD studies. Adjusting the experimental result so as to match the finite-sized system used in the present study brings the comparison between theory and experiment to within a factor of 3. More importantly, the system is not observed to become "glassy" as has been reported in previous AIMD studies. The computed infrared spectrum is in good agreement with experimental data, especially in the low frequency regime where the translational and librational motions of water are manifested. The long simulation length also made it possible to perform detailed studies of hydrogen bond dynamics. The relaxation dynamics of hydrogen bonds observed in the present AIMD simulation is slower than those of popular force fields, such as the TIP4P potential, but comparable to that of the TIP5P potential.

Dynamical properties of liquid water from ab initio molecular dynamics performed in the complete basis set limit.

PubMed

Lee, Hee-Seung; Tuckerman, Mark E

2007-04-28

Dynamical properties of liquid water were studied using Car-Parrinello [Phys. Rev. Lett. 55, 2471 (1985)] ab initio molecular dynamics (AIMD) simulations within the Kohn-Sham (KS) density functional theory employing the Becke-Lee-Yang-Parr exchange-correlation functional for the electronic structure. The KS orbitals were expanded in a discrete variable representation basis set, wherein the complete basis set limit can be easily reached and which, therefore, provides complete convergence of ionic forces. In order to minimize possible nonergodic behavior of the simulated water system in a constant energy (NVE) ensemble, a long equilibration run (30 ps) preceded a 60 ps long production run. The temperature drift during the entire 60 ps trajectory was found to be minimal. The diffusion coefficient [0.055 A2/ps] obtained from the present work for 32 D2O molecules is a factor of 4 smaller than the most up to date experimental value, but significantly larger than those of other recent AIMD studies. Adjusting the experimental result so as to match the finite-sized system used in the present study brings the comparison between theory and experiment to within a factor of 3. More importantly, the system is not observed to become "glassy" as has been reported in previous AIMD studies. The computed infrared spectrum is in good agreement with experimental data, especially in the low frequency regime where the translational and librational motions of water are manifested. The long simulation length also made it possible to perform detailed studies of hydrogen bond dynamics. The relaxation dynamics of hydrogen bonds observed in the present AIMD simulation is slower than those of popular force fields, such as the TIP4P potential, but comparable to that of the TIP5P potential.

Matching by linear programming and successive convexification.

PubMed

Jiang, Hao; Drew, Mark S; Li, Ze-Nian

2007-06-01

We present a novel convex programming scheme to solve matching problems, focusing on the challenging problem of matching in a large search range and with cluttered background. Matching is formulated as metric labeling with L1 regularization terms, for which we propose a novel linear programming relaxation method and an efficient successive convexification implementation. The unique feature of the proposed relaxation scheme is that a much smaller set of basis labels is used to represent the original label space. This greatly reduces the size of the searching space. A successive convexification scheme solves the labeling problem in a coarse to fine manner. Importantly, the original cost function is reconvexified at each stage, in the new focus region only, and the focus region is updated so as to refine the searching result. This makes the method well-suited for large label set matching. Experiments demonstrate successful applications of the proposed matching scheme in object detection, motion estimation, and tracking.

Basis sets for the calculation of core-electron binding energies

NASA Astrophysics Data System (ADS)

Hanson-Heine, Magnus W. D.; George, Michael W.; Besley, Nicholas A.

2018-05-01

Core-electron binding energies (CEBEs) computed within a Δ self-consistent field approach require large basis sets to achieve convergence with respect to the basis set limit. It is shown that supplementing a basis set with basis functions from the corresponding basis set for the element with the next highest nuclear charge (Z + 1) provides basis sets that give CEBEs close to the basis set limit. This simple procedure provides relatively small basis sets that are well suited for calculations where the description of a core-ionised state is important, such as time-dependent density functional theory calculations of X-ray emission spectroscopy.

Mutually unbiased bases in six dimensions: The four most distant bases

DOE Office of Scientific and Technical Information (OSTI.GOV)

Raynal, Philippe; Lue Xin; Englert, Berthold-Georg

2011-06-15

We consider the average distance between four bases in six dimensions. The distance between two orthonormal bases vanishes when the bases are the same, and the distance reaches its maximal value of unity when the bases are unbiased. We perform a numerical search for the maximum average distance and find it to be strictly smaller than unity. This is strong evidence that no four mutually unbiased bases exist in six dimensions. We also provide a two-parameter family of three bases which, together with the canonical basis, reach the numerically found maximum of the average distance, and we conduct a detailedmore » study of the structure of the extremal set of bases.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Papajak, Ewa; Truhlar, Donald G.

We present sets of convergent, partially augmented basis set levels corresponding to subsets of the augmented “aug-cc-pV(n+d)Z” basis sets of Dunning and co-workers. We show that for many molecular properties a basis set fully augmented with diffuse functions is computationally expensive and almost always unnecessary. On the other hand, unaugmented cc-pV(n+d)Z basis sets are insufficient for many properties that require diffuse functions. Therefore, we propose using intermediate basis sets. We developed an efficient strategy for partial augmentation, and in this article, we test it and validate it. Sequentially deleting diffuse basis functions from the “aug” basis sets yields the “jul”,more » “jun”, “may”, “apr”, etc. basis sets. Tests of these basis sets for Møller-Plesset second-order perturbation theory (MP2) show the advantages of using these partially augmented basis sets and allow us to recommend which basis sets offer the best accuracy for a given number of basis functions for calculations on large systems. Similar truncations in the diffuse space can be performed for the aug-cc-pVxZ, aug-cc-pCVxZ, etc. basis sets.« less

Intermolecular vibrations of (CH2)2O-HF and -DF hydrogen bonded complexes investigated by Fourier transform infrared spectroscopy and ab initio calculations.

PubMed

Cirtog, M; Asselin, P; Soulard, P; Madebène, B; Alikhani, M E

2010-10-14

A series of Fourier transform infrared spectra (FTIR) of the hydrogen bonded complexes (CH(2))(2)O-HF and -DF have been recorded in the 50-750 cm(-1) range up to 0.1 cm(-1) resolution in a static cell maintained at near room temperature. The direct observation of three intermolecular transitions enabled us to perform band contour analysis of congested cell spectra and to determine reliable rovibrational parameters such as intermolecular frequencies, rovibrational and anharmonic coupling constants involving two l(1) and l(2) librations and one σ stretching intermolecular motion. Inter-inter anharmonic couplings could be identified between ν(l(1)), ν(l(2)), ν(σ) and the two lowest frequency bending modes. The positive sign of coupling constants (opposite with respect to acid stretching intra-inter ones) reveals a weakening of the hydrogen bond upon intermolecular excitation. The four rovibrational parameters ν(σ) and x(σj) (j = σ, δ(1), δ(2)) derived in the present far-infrared study and also in a previous mid-infrared one [Phys. Chem. Chem. Phys. 2005, 1, 592] make deviations appear smaller than 1% for frequencies and 12% for coupling constants which gives confidence to the reliability of the data obtained. Anharmonic frequencies obtained at the MP2 level with Aug-cc-pvTZ basis set agree well with experimental values over a large set of frequencies and coupling constants. An estimated anharmonic corrected value of the dissociation energy D for both oxirane-HF (2424 cm(-1)) and -DF (2566 cm(-1)) has been derived using a level of theory as high as CCSD(T)/Aug-cc-pvQZ, refining the harmonic value previously calculated for oxirane-HF with the MP2 method and a smaller basis set. Finally, contrary to short predissociation lifetimes evidenced for acid stretching excited states, any homogeneous broadening related to vibrational dynamics of (CH(2))(2)O-HF and -DF has been observed within the three highest frequency intermolecular states, as expected with low excitation energies largely below the dissociation limit as well as a negligible IVR contribution.

Dissociative recombination of the ground state of N2(+)

NASA Technical Reports Server (NTRS)

Guberman, Steven L.

1991-01-01

Large-scale calculations of the dissociative recombination cross sections and rates for the v = 0 level of the N2(+) ground state are reported, and the important role played by vibrationally excited Rydberg states lying both below and above the v = 0 level of the ion is demonstrated. The large-scale electronic wave function calculations were done using triple zeta plus polarization nuclear-centered-valence Gaussian basis sets. The electronic widths were obtained using smaller wave functions, and the cross sections were calculated on the basis of the multichannel quantum defect theory. The DR rate is calculated at 1.6 x 10 to the -7th x (Te/300) to the -0.37 cu cm/sec for Te in the range of 100 to 1000 K, and is found to be in excellent agreement with prior microwave afterglow experiments but in disagreement with recent merged beam results. It is inferred that the dominant mechanism for DR imparts sufficient energy to the product atoms to allow for escape from the Martian atmosphere.

Estimating the CCSD basis-set limit energy from small basis sets: basis-set extrapolations vs additivity schemes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Spackman, Peter R.; Karton, Amir, E-mail: amir.karton@uwa.edu.au

Coupled cluster calculations with all single and double excitations (CCSD) converge exceedingly slowly with the size of the one-particle basis set. We assess the performance of a number of approaches for obtaining CCSD correlation energies close to the complete basis-set limit in conjunction with relatively small DZ and TZ basis sets. These include global and system-dependent extrapolations based on the A + B/L{sup α} two-point extrapolation formula, and the well-known additivity approach that uses an MP2-based basis-set-correction term. We show that the basis set convergence rate can change dramatically between different systems(e.g.it is slower for molecules with polar bonds and/ormore » second-row elements). The system-dependent basis-set extrapolation scheme, in which unique basis-set extrapolation exponents for each system are obtained from lower-cost MP2 calculations, significantly accelerates the basis-set convergence relative to the global extrapolations. Nevertheless, we find that the simple MP2-based basis-set additivity scheme outperforms the extrapolation approaches. For example, the following root-mean-squared deviations are obtained for the 140 basis-set limit CCSD atomization energies in the W4-11 database: 9.1 (global extrapolation), 3.7 (system-dependent extrapolation), and 2.4 (additivity scheme) kJ mol{sup –1}. The CCSD energy in these approximations is obtained from basis sets of up to TZ quality and the latter two approaches require additional MP2 calculations with basis sets of up to QZ quality. We also assess the performance of the basis-set extrapolations and additivity schemes for a set of 20 basis-set limit CCSD atomization energies of larger molecules including amino acids, DNA/RNA bases, aromatic compounds, and platonic hydrocarbon cages. We obtain the following RMSDs for the above methods: 10.2 (global extrapolation), 5.7 (system-dependent extrapolation), and 2.9 (additivity scheme) kJ mol{sup –1}.« less

Estimating the CCSD basis-set limit energy from small basis sets: basis-set extrapolations vs additivity schemes

NASA Astrophysics Data System (ADS)

Spackman, Peter R.; Karton, Amir

2015-05-01

Coupled cluster calculations with all single and double excitations (CCSD) converge exceedingly slowly with the size of the one-particle basis set. We assess the performance of a number of approaches for obtaining CCSD correlation energies close to the complete basis-set limit in conjunction with relatively small DZ and TZ basis sets. These include global and system-dependent extrapolations based on the A + B/Lα two-point extrapolation formula, and the well-known additivity approach that uses an MP2-based basis-set-correction term. We show that the basis set convergence rate can change dramatically between different systems(e.g.it is slower for molecules with polar bonds and/or second-row elements). The system-dependent basis-set extrapolation scheme, in which unique basis-set extrapolation exponents for each system are obtained from lower-cost MP2 calculations, significantly accelerates the basis-set convergence relative to the global extrapolations. Nevertheless, we find that the simple MP2-based basis-set additivity scheme outperforms the extrapolation approaches. For example, the following root-mean-squared deviations are obtained for the 140 basis-set limit CCSD atomization energies in the W4-11 database: 9.1 (global extrapolation), 3.7 (system-dependent extrapolation), and 2.4 (additivity scheme) kJ mol-1. The CCSD energy in these approximations is obtained from basis sets of up to TZ quality and the latter two approaches require additional MP2 calculations with basis sets of up to QZ quality. We also assess the performance of the basis-set extrapolations and additivity schemes for a set of 20 basis-set limit CCSD atomization energies of larger molecules including amino acids, DNA/RNA bases, aromatic compounds, and platonic hydrocarbon cages. We obtain the following RMSDs for the above methods: 10.2 (global extrapolation), 5.7 (system-dependent extrapolation), and 2.9 (additivity scheme) kJ mol-1.

Analysis of Hydrogen Atom Abstraction from Ethylbenzene by an FeVO(TAML) Complex.

PubMed

Shen, Longzhu Q; Kundu, Soumen; Collins, Terrence J; Bominaar, Emile L

2017-04-17

It was shown previously (Chem. Eur. J. 2015, 21, 1803) that the rate of hydrogen atom abstraction, k, from ethylbenzene (EB) by TAML complex [Fe V (O)B*] - (1) in acetonitrile exhibits a large kinetic isotope effect (KIE ∼ 26) in the experimental range 233-243 K. The extrapolated tangents of ln(k/T) vs T -1 plots for EB-d 10 and EB gave a large, negative intercept difference, Int(EB) - Int(EB-d 10 ) = -34.5 J mol -1 K -1 for T -1 → 0, which is shown to be exclusively due to an isotopic mass effect on tunneling. A decomposition of the apparent activation barrier in terms of electronic, ZPE, thermal enthalpic, tunneling, and entropic contributions is presented. Tunneling corrections to ΔH ⧧ and ΔS ⧧ are estimated to be large. The DFT prediction, using functional B3LYP and basis set 6-311G, for the electronic contribution is significantly smaller than suggested by experiment. However, the agreement improves after correction for the basis set superposition error in the interaction between EB and 1. The kinetic model employed has been used to predict rate constants outside the experimental temperature range, which enabled us to compare the reactivity of 1 with those of other hydrogen abstracting complexes.

Study on airflow characteristics in the semi-closed irregular narrow flow channel

NASA Astrophysics Data System (ADS)

Jin, Yuzhen; Hu, Xiaodong; Zhu, Linhang; Hu, Xudong; Jin, Yingzi

2016-04-01

The air-jet loom is widely used in the textile industry. The interaction mechanism of airflow and yarn is not clear in such a narrow flow channel, the gas consumption is relatively large, the yarn motion is unstable and the weft insertion is often interrupted during the operation. In order to study the characteristics of the semi-closed flow field in profiled dents, the momentum conservation equation is modified and the model parameters and boundary conditions are set. Compared with the different r, the ratio of profiled dent's thickness and gap, the results show that the smaller the r is, the smaller the velocity fluctuations of the airflow is. When the angle of profiled dents α is close to zero, the diffusion of the airflow will be less. The experiment is also conducted to verify the result of the simulation with a high-speed camera and pressure sensor in profiled dents. The airflow characteristics in the semi-closed irregular narrow flow channel in the paper would provide the theoretical basis for optimizing the weft insertion process of the air-jet loom.

A theoretical study of hydrogen complexes of the XH-pi type between propyne and HF, HCL or HCN.

PubMed

Tavares, Alessandra M; da Silva, Washington L V; Lopes, Kelson C; Ventura, Elizete; Araújo, Regiane C M U; do Monte, Silmar A; da Silva, João Bosco P; Ramos, Mozart N

2006-05-15

The present manuscript reports a systematic investigation of the basis set dependence of some properties of hydrogen-bonded (pi type) complexes formed by propyne and a HX molecule, where X=F, Cl and CN. The calculations have been performed at Hartree-Fock, MP2 and B3LYP levels. Geometries, H-bond energies and vibrational have been considered. The more pronounced effects on the structural parameters of the isolated molecules, as a result of complexation, are verified on RCtriple bondC and HX bond lengths. As compared to double-zeta (6-31G**), triple-zeta (6-311G**) basis set leads to an increase of RCtriple bondC bond distance, at all three computational levels. In the case where diffuse functions are added to both hydrogen and 'heavy' atoms, the effect is more pronounced. The propyne-HX structural parameters are quite similar to the corresponding parameters of acetylene-HX complexes, at all levels. The largest difference is obtained for hydrogen bond distance, RH, with a smaller value for propyne-HX complex, indicating a stronger bond. Concerning the electronic properties, the results yield the following ordering for H-bond energies, DeltaE: propynecdots, three dots, centeredHF>propynecdots, three dots, centeredHCl>propynecdots, three dots, centeredHCN. It is also important to point out that the inclusion of BSSE and zero-point energies (ZPE) corrections cause significant changes on DeltaE. The smaller effect of ZPE is obtained for propynecdots, three dots, centeredHCN at HF/6-311++G** level, while the greatest difference is obtained at MP2/6-31G** level for propynecdots, three dots, centeredHF system. Concerning the IR vibrational it was obtained that larger shift can be associated with stronger hydrogen bonds. The more pronounced effect on the normal modes of the isolated molecule after the complexation is obtained for HX stretching frequency, which is shifted downward.

A theoretical study of hydrogen complexes of the X sbnd H-π type between propyne and HF, HCL or HCN

NASA Astrophysics Data System (ADS)

Tavares, Alessandra M.; da Silva, Washington L. V.; Lopes, Kelson C.; Ventura, Elizete; Araújo, Regiane C. M. U.; do Monte, Silmar A.; da Silva, João Bosco P.; Ramos, Mozart N.

2006-05-01

The present manuscript reports a systematic investigation of the basis set dependence of some properties of hydrogen-bonded (π type) complexes formed by propyne and a HX molecule, where X = F, Cl and CN. The calculations have been performed at Hartree-Fock, MP2 and B3LYP levels. Geometries, H-bond energies and vibrational have been considered. The more pronounced effects on the structural parameters of the isolated molecules, as a result of complexation, are verified on RC tbnd C and HX bond lengths. As compared to double-ζ (6-31G **), triple-ζ (6-311G **) basis set leads to an increase of RC tbnd C bond distance, at all three computational levels. In the case where diffuse functions are added to both hydrogen and 'heavy' atoms, the effect is more pronounced. The propyne-HX structural parameters are quite similar to the corresponding parameters of acetylene-HX complexes, at all levels. The largest difference is obtained for hydrogen bond distance, RH, with a smaller value for propyne-HX complex, indicating a stronger bond. Concerning the electronic properties, the results yield the following ordering for H-bond energies, Δ E: propyne⋯HF > propyne⋯HCl > propyne⋯HCN. It is also important to point out that the inclusion of BSSE and zero-point energies (ZPE) corrections cause significant changes on Δ E. The smaller effect of ZPE is obtained for propyne⋯HCN at HF/6-311++G ** level, while the greatest difference is obtained at MP2/6-31G ** level for propyne⋯HF system. Concerning the IR vibrational it was obtained that larger shift can be associated with stronger hydrogen bonds. The more pronounced effect on the normal modes of the isolated molecule after the complexation is obtained for H sbnd X stretching frequency, which is shifted downward.

Zn Coordination Chemistry:  Development of Benchmark Suites for Geometries, Dipole Moments, and Bond Dissociation Energies and Their Use To Test and Validate Density Functionals and Molecular Orbital Theory.

PubMed

Amin, Elizabeth A; Truhlar, Donald G

2008-01-01

We present nonrelativistic and relativistic benchmark databases (obtained by coupled cluster calculations) of 10 Zn-ligand bond distances, 8 dipole moments, and 12 bond dissociation energies in Zn coordination compounds with O, S, NH3, H2O, OH, SCH3, and H ligands. These are used to test the predictions of 39 density functionals, Hartree-Fock theory, and seven more approximate molecular orbital theories. In the nonrelativisitic case, the M05-2X, B97-2, and mPW1PW functionals emerge as the most accurate ones for this test data, with unitless balanced mean unsigned errors (BMUEs) of 0.33, 0.38, and 0.43, respectively. The best local functionals (i.e., functionals with no Hartree-Fock exchange) are M06-L and τ-HCTH with BMUEs of 0.54 and 0.60, respectively. The popular B3LYP functional has a BMUE of 0.51, only slightly better than the value of 0.54 for the best local functional, which is less expensive. Hartree-Fock theory itself has a BMUE of 1.22. The M05-2X functional has a mean unsigned error of 0.008 Å for bond lengths, 0.19 D for dipole moments, and 4.30 kcal/mol for bond energies. The X3LYP functional has a smaller mean unsigned error (0.007 Å) for bond lengths but has mean unsigned errors of 0.43 D for dipole moments and 5.6 kcal/mol for bond energies. The M06-2X functional has a smaller mean unsigned error (3.3 kcal/mol) for bond energies but has mean unsigned errors of 0.017 Å for bond lengths and 0.37 D for dipole moments. The best of the semiempirical molecular orbital theories are PM3 and PM6, with BMUEs of 1.96 and 2.02, respectively. The ten most accurate functionals from the nonrelativistic benchmark analysis are then tested in relativistic calculations against new benchmarks obtained with coupled-cluster calculations and a relativistic effective core potential, resulting in M05-2X (BMUE = 0.895), PW6B95 (BMUE = 0.90), and B97-2 (BMUE = 0.93) as the top three functionals. We find significant relativistic effects (∼0.01 Å in bond lengths, ∼0.2 D in dipole moments, and ∼4 kcal/mol in Zn-ligand bond energies) that cannot be neglected for accurate modeling, but the same density functionals that do well in all-electron nonrelativistic calculations do well with relativistic effective core potentials. Although most tests are carried out with augmented polarized triple-ζ basis sets, we also carried out some tests with an augmented polarized double-ζ basis set, and we found, on average, that with the smaller basis set DFT has no loss in accuracy for dipole moments and only ∼10% less accurate bond lengths.

A partitioned correlation function interaction approach for describing electron correlation in atoms

NASA Astrophysics Data System (ADS)

Verdebout, S.; Rynkun, P.; Jönsson, P.; Gaigalas, G.; Froese Fischer, C.; Godefroid, M.

2013-04-01

The traditional multiconfiguration Hartree-Fock (MCHF) and configuration interaction (CI) methods are based on a single orthonormal orbital basis. For atoms with many closed core shells, or complicated shell structures, a large orbital basis is needed to saturate the different electron correlation effects such as valence, core-valence and correlation within the core shells. The large orbital basis leads to massive configuration state function (CSF) expansions that are difficult to handle, even on large computer systems. We show that it is possible to relax the orthonormality restriction on the orbital basis and break down the originally very large calculations into a series of smaller calculations that can be run in parallel. Each calculation determines a partitioned correlation function (PCF) that accounts for a specific correlation effect. The PCFs are built on optimally localized orbital sets and are added to a zero-order multireference (MR) function to form a total wave function. The expansion coefficients of the PCFs are determined from a low dimensional generalized eigenvalue problem. The interaction and overlap matrices are computed using a biorthonormal transformation technique (Verdebout et al 2010 J. Phys. B: At. Mol. Phys. 43 074017). The new method, called partitioned correlation function interaction (PCFI), converges rapidly with respect to the orbital basis and gives total energies that are lower than the ones from ordinary MCHF and CI calculations. The PCFI method is also very flexible when it comes to targeting different electron correlation effects. Focusing our attention on neutral lithium, we show that by dedicating a PCF to the single excitations from the core, spin- and orbital-polarization effects can be captured very efficiently, leading to highly improved convergence patterns for hyperfine parameters compared with MCHF calculations based on a single orthogonal radial orbital basis. By collecting separately optimized PCFs to correct the MR function, the variational degrees of freedom in the relative mixing coefficients of the CSFs building the PCFs are inhibited. The constraints on the mixing coefficients lead to small off-sets in computed properties such as hyperfine structure, isotope shift and transition rates, with respect to the correct values. By (partially) deconstraining the mixing coefficients one converges to the correct limits and keeps the tremendous advantage of improved convergence rates that comes from the use of several orbital sets. Reducing ultimately each PCF to a single CSF with its own orbital basis leads to a non-orthogonal CI approach. Various perspectives of the new method are given.

Quantum decimation in Hilbert space: Coarse graining without structure

NASA Astrophysics Data System (ADS)

Singh, Ashmeet; Carroll, Sean M.

2018-03-01

We present a technique to coarse grain quantum states in a finite-dimensional Hilbert space. Our method is distinguished from other approaches by not relying on structures such as a preferred factorization of Hilbert space or a preferred set of operators (local or otherwise) in an associated algebra. Rather, we use the data corresponding to a given set of states, either specified independently or constructed from a single state evolving in time. Our technique is based on principle component analysis (PCA), and the resulting coarse-grained quantum states live in a lower-dimensional Hilbert space whose basis is defined using the underlying (isometric embedding) transformation of the set of fine-grained states we wish to coarse grain. Physically, the transformation can be interpreted to be an "entanglement coarse-graining" scheme that retains most of the global, useful entanglement structure of each state, while needing fewer degrees of freedom for its reconstruction. This scheme could be useful for efficiently describing collections of states whose number is much smaller than the dimension of Hilbert space, or a single state evolving over time.

Correlation consistent basis sets for the atoms In–Xe

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mahler, Andrew; Wilson, Angela K., E-mail: akwilson@unt.edu

In this work, the correlation consistent family of Gaussian basis sets has been expanded to include all-electron basis sets for In–Xe. The methodology for developing these basis sets is described, and several examples of the performance and utility of the new sets have been provided. Dissociation energies and bond lengths for both homonuclear and heteronuclear diatomics demonstrate the systematic convergence behavior with respect to increasing basis set quality expected by the family of correlation consistent basis sets in describing molecular properties. Comparison with recently developed correlation consistent sets designed for use with the Douglas-Kroll Hamiltonian is provided.

On the physical basis of succussion.

PubMed

Torres, J L

2002-10-01

It is argued that succussion drives the homeopathic tincture undergoing potentisation to a turbulent regime, where vortices continually form and disappear, ranging in size from the linear extent of the container to a minimum scale determined by viscosity and the rate of energy dissipation. Input mechanical energy cascades down this population of eddies and becomes available at the microscopic level to perform work (chemical, electrical, etc). A structure generated in the tincture would be rupted by vortices smaller than it, and this sets definite limits on the strength of succussion, so the power input leads to larger vortices than the structures one is trying to create and preserve through potentisation. An experimental procedure to test this proposal is suggested, based on Rayleigh scattering.

Sparse representation of Gravitational Sound

NASA Astrophysics Data System (ADS)

Rebollo-Neira, Laura; Plastino, A.

2018-03-01

Gravitational Sound clips produced by the Laser Interferometer Gravitational-Wave Observatory (LIGO) and the Massachusetts Institute of Technology (MIT) are considered within the particular context of data reduction. We advance a procedure to this effect and show that these types of signals can be approximated with high quality using significantly fewer elementary components than those required within the standard orthogonal basis framework. Furthermore, a local measure sparsity is shown to render meaningful information about the variation of a signal along time, by generating a set of local sparsity values which is much smaller than the dimension of the signal. This point is further illustrated by recourse to a more complex signal, generated by Milde Science Communication to divulge Gravitational Sound in the form of a ring tone.

Push it to the limit: Characterizing the convergence of common sequences of basis sets for intermolecular interactions as described by density functional theory

NASA Astrophysics Data System (ADS)

Witte, Jonathon; Neaton, Jeffrey B.; Head-Gordon, Martin

2016-05-01

With the aim of systematically characterizing the convergence of common families of basis sets such that general recommendations for basis sets can be made, we have tested a wide variety of basis sets against complete-basis binding energies across the S22 set of intermolecular interactions—noncovalent interactions of small and medium-sized molecules consisting of first- and second-row atoms—with three distinct density functional approximations: SPW92, a form of local-density approximation; B3LYP, a global hybrid generalized gradient approximation; and B97M-V, a meta-generalized gradient approximation with nonlocal correlation. We have found that it is remarkably difficult to reach the basis set limit; for the methods and systems examined, the most complete basis is Jensen's pc-4. The Dunning correlation-consistent sequence of basis sets converges slowly relative to the Jensen sequence. The Karlsruhe basis sets are quite cost effective, particularly when a correction for basis set superposition error is applied: counterpoise-corrected def2-SVPD binding energies are better than corresponding energies computed in comparably sized Dunning and Jensen bases, and on par with uncorrected results in basis sets 3-4 times larger. These trends are exhibited regardless of the level of density functional approximation employed. A sense of the magnitude of the intrinsic incompleteness error of each basis set not only provides a foundation for guiding basis set choice in future studies but also facilitates quantitative comparison of existing studies on similar types of systems.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Witte, Jonathon; Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720; Neaton, Jeffrey B.

With the aim of systematically characterizing the convergence of common families of basis sets such that general recommendations for basis sets can be made, we have tested a wide variety of basis sets against complete-basis binding energies across the S22 set of intermolecular interactions—noncovalent interactions of small and medium-sized molecules consisting of first- and second-row atoms—with three distinct density functional approximations: SPW92, a form of local-density approximation; B3LYP, a global hybrid generalized gradient approximation; and B97M-V, a meta-generalized gradient approximation with nonlocal correlation. We have found that it is remarkably difficult to reach the basis set limit; for the methodsmore » and systems examined, the most complete basis is Jensen’s pc-4. The Dunning correlation-consistent sequence of basis sets converges slowly relative to the Jensen sequence. The Karlsruhe basis sets are quite cost effective, particularly when a correction for basis set superposition error is applied: counterpoise-corrected def2-SVPD binding energies are better than corresponding energies computed in comparably sized Dunning and Jensen bases, and on par with uncorrected results in basis sets 3-4 times larger. These trends are exhibited regardless of the level of density functional approximation employed. A sense of the magnitude of the intrinsic incompleteness error of each basis set not only provides a foundation for guiding basis set choice in future studies but also facilitates quantitative comparison of existing studies on similar types of systems.« less

Conformational stability, structural parameters and vibrational assignment from variable temperature infrared spectra of krypton solutions and ab initio calculations of ethylisothiocyanate.

PubMed

Durig, James R; Zheng, Chao

2007-11-01

Variable temperature (-105 to -150 degrees C) studies of the infrared spectra (3500-400 cm(-1)) of ethylisothiocyanate, CH(3)CH(2)NCS, dissolved in liquid krypton have been recorded. Additionally the infrared spectra of the gas and solid have been re-investigated. These spectroscopic data indicate a single conformer in all physical states with a large number of molecules in the gas phase at ambient temperature in excited states of the CN torsional mode which has a very low barrier to conformational interchange. To aid in the analyses of the vibrational and rotational spectra, ab initio calculations have been carried out by the perturbation method to the second order (MP2) with valence and core electron correlation using a variety of basis sets up to 6-311+G(2df,2pd). With the smaller basis sets up to 6-311+G(d,p) and cc-PVDZ, the cis conformer is indicated as a transition state with all larger basis sets the cis conformer is the only stable form. The predicted energy difference from these calculations between the cis form and the higher energy trans conformer is about 125 cm(-1) which represents essentially the barrier to internal rotation of the NCS group (rotation around NC axis). Density functional theory calculation by the B3LYP method with the same basis sets predicts this barrier to be about 25 cm(-1). By utilizing the previously reported microwave rotational constants with the structural parameters predicted by the ab initio MP2(full)/6-311+G(d,p) calculations, adjusted r(0) structural parameters have been obtained for the cis form. The determined heavy atom parameters are: r(NC)=1.196(5), r(CS)=1.579(5), r(CN)=1.439(5), r(CC)=1.519(5)A for the distances and angles of angleCCN=112.1(5), angleCNC=146.2(5), angleNCS=174.0(5) degrees . The centrifugal distortion constants, dipole moments, conformational stability, vibrational frequencies, infrared intensities and Raman activities have been predicted from ab initio calculations and compared to experimental quantities when available. These results are compared to the corresponding quantities of some similar molecules.

Structure and binding energy of the H2S dimer at the CCSD(T) complete basis set limit.

PubMed

Lemke, Kono H

2017-06-21

This study presents results for the binding energy and geometry of the H 2 S dimer which have been computed using Møller-Plesset perturbation theory (MP2, MP4) and coupled cluster (CCSD, CCSD(T)) calculations with basis sets up to aug-cc-pV5Z. Estimates of D e , E ZPE , D o , and dimer geometry have been obtained at each level of theory by taking advantage of the systematic convergence behavior toward the complete basis set (CBS) limit. The CBS limit binding energy values of D e are 1.91 (MP2), 1.75 (MP4), 1.41 (CCSD), and 1.69 kcal/mol (CCSD[T]). The most accurate values for the equilibrium S-S distance r SS (without counterpoise correction) are 4.080 (MP2/aug-cc-pV5Z), 4.131 (MP4/aug-cc-pVQZ), 4.225 (CCSD/aug-cc-pVQZ), and 4.146 Å (CCSD(T)/aug-cc-pVQZ). This study also evaluates the effect of counterpoise correction on the H 2 S dimer geometry and binding energy. As regards the structure of (H 2 S) 2 , MPn, CCSD, and CCSD(T) level values of r SS , obtained by performing geometry optimizations on the counterpoise-corrected potential energy surface, converge systematically to CBS limit values of 4.099 (MP2), 4.146 (MP4), 4.233 (CCSD), and 4.167 Å (CCSD(T)). The corresponding CBS limit values of the equilibrium binding energy D e are 1.88 (MP2), 1.76 (MP4), 1.41 (CCSD), and 1.69 kcal/mol (CCSD(T)), the latter in excellent agreement with the measured binding energy value of 1.68 ± 0.02 kcal/mol reported by Ciaffoni et al. [Appl. Phys. B 92, 627 (2008)]. Combining CBS electronic binding energies D e with E ZPE predicted by CCSD(T) vibrational second-order perturbation theory calculations yields D o = 1.08 kcal/mol, which is around 0.6 kcal/mol smaller than the measured value of 1.7 ± 0.3 kcal/mol. Overall, the results presented here demonstrate that the application of high level calculations, in particular CCSD(T), in combination with augmented correlation consistent basis sets provides valuable insight into the structure and energetics of the hydrogen sulfide dimer.

Structure and binding energy of the H2S dimer at the CCSD(T) complete basis set limit

NASA Astrophysics Data System (ADS)

Lemke, Kono H.

2017-06-01

This study presents results for the binding energy and geometry of the H2S dimer which have been computed using Møller-Plesset perturbation theory (MP2, MP4) and coupled cluster (CCSD, CCSD(T)) calculations with basis sets up to aug-cc-pV5Z. Estimates of De, EZPE, Do, and dimer geometry have been obtained at each level of theory by taking advantage of the systematic convergence behavior toward the complete basis set (CBS) limit. The CBS limit binding energy values of De are 1.91 (MP2), 1.75 (MP4), 1.41 (CCSD), and 1.69 kcal/mol (CCSD[T]). The most accurate values for the equilibrium S-S distance rSS (without counterpoise correction) are 4.080 (MP2/aug-cc-pV5Z), 4.131 (MP4/aug-cc-pVQZ), 4.225 (CCSD/aug-cc-pVQZ), and 4.146 Å (CCSD(T)/aug-cc-pVQZ). This study also evaluates the effect of counterpoise correction on the H2S dimer geometry and binding energy. As regards the structure of (H2S)2, MPn, CCSD, and CCSD(T) level values of rSS, obtained by performing geometry optimizations on the counterpoise-corrected potential energy surface, converge systematically to CBS limit values of 4.099 (MP2), 4.146 (MP4), 4.233 (CCSD), and 4.167 Å (CCSD(T)). The corresponding CBS limit values of the equilibrium binding energy De are 1.88 (MP2), 1.76 (MP4), 1.41 (CCSD), and 1.69 kcal/mol (CCSD(T)), the latter in excellent agreement with the measured binding energy value of 1.68 ± 0.02 kcal/mol reported by Ciaffoni et al. [Appl. Phys. B 92, 627 (2008)]. Combining CBS electronic binding energies De with EZPE predicted by CCSD(T) vibrational second-order perturbation theory calculations yields Do = 1.08 kcal/mol, which is around 0.6 kcal/mol smaller than the measured value of 1.7 ± 0.3 kcal/mol. Overall, the results presented here demonstrate that the application of high level calculations, in particular CCSD(T), in combination with augmented correlation consistent basis sets provides valuable insight into the structure and energetics of the hydrogen sulfide dimer.

Chemoinformatic expedition of the chemical space of fungal products.

PubMed

González-Medina, Mariana; Prieto-Martínez, Fernando D; Naveja, J Jesús; Méndez-Lucio, Oscar; El-Elimat, Tamam; Pearce, Cedric J; Oberlies, Nicholas H; Figueroa, Mario; Medina-Franco, José L

2016-08-01

Fungi are valuable resources for bioactive secondary metabolites. However, the chemical space of fungal secondary metabolites has been studied only on a limited basis. Herein, we report a comprehensive chemoinformatic analysis of a unique set of 207 fungal metabolites isolated and characterized in a USA National Cancer Institute funded drug discovery project. Comparison of the molecular complexity of the 207 fungal metabolites with approved anticancer and nonanticancer drugs, compounds in clinical studies, general screening compounds and molecules Generally Recognized as Safe revealed that fungal metabolites have high degree of complexity. Molecular fingerprints showed that fungal metabolites are as structurally diverse as other natural products and have, in general, drug-like physicochemical properties. Fungal products represent promising candidates to expand the medicinally relevant chemical space. This work is a significant expansion of an analysis reported years ago for a smaller set of compounds (less than half of the ones included in the present work) from filamentous fungi using different structural properties.

On-line diagnosis of sequential systems, 2

NASA Technical Reports Server (NTRS)

Sundstrom, R. J.

1974-01-01

The theory and techniques applicable to the on-line diagnosis of sequential systems, were investigated. A complete model for the study of on-line diagnosis is developed. First an appropriate class of system models is formulated which can serve as a basis for a theoretical study of on-line diagnosis. Then notions of realization, fault, fault-tolerance and diagnosability are formalized which have meaningful interpretations in the the context of on-line diagnosis. The diagnosis of systems which are structurally decomposed and are represented as a network of smaller systems is studied. The fault set considered is the set of faults which only affect one component system is the network. A characterization of those networks which can be diagnosed using a purely combinational detector is achieved. A technique is given which can be used to realize any network by a network which is diagnosable in the above sense. Limits are found on the amount of redundancy involved in any such technique.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grimme, Stefan, E-mail: grimme@thch.uni-bonn.de; Brandenburg, Jan Gerit; Bannwarth, Christoph

A density functional theory (DFT) based composite electronic structure approach is proposed to efficiently compute structures and interaction energies in large chemical systems. It is based on the well-known and numerically robust Perdew-Burke-Ernzerhoff (PBE) generalized-gradient-approximation in a modified global hybrid functional with a relatively large amount of non-local Fock-exchange. The orbitals are expanded in Ahlrichs-type valence-double zeta atomic orbital (AO) Gaussian basis sets, which are available for many elements. In order to correct for the basis set superposition error (BSSE) and to account for the important long-range London dispersion effects, our well-established atom-pairwise potentials are used. In the design ofmore » the new method, particular attention has been paid to an accurate description of structural parameters in various covalent and non-covalent bonding situations as well as in periodic systems. Together with the recently proposed three-fold corrected (3c) Hartree-Fock method, the new composite scheme (termed PBEh-3c) represents the next member in a hierarchy of “low-cost” electronic structure approaches. They are mainly free of BSSE and account for most interactions in a physically sound and asymptotically correct manner. PBEh-3c yields good results for thermochemical properties in the huge GMTKN30 energy database. Furthermore, the method shows excellent performance for non-covalent interaction energies in small and large complexes. For evaluating its performance on equilibrium structures, a new compilation of standard test sets is suggested. These consist of small (light) molecules, partially flexible, medium-sized organic molecules, molecules comprising heavy main group elements, larger systems with long bonds, 3d-transition metal systems, non-covalently bound complexes (S22 and S66×8 sets), and peptide conformations. For these sets, overall deviations from accurate reference data are smaller than for various other tested DFT methods and reach that of triple-zeta AO basis set second-order perturbation theory (MP2/TZ) level at a tiny fraction of computational effort. Periodic calculations conducted for molecular crystals to test structures (including cell volumes) and sublimation enthalpies indicate very good accuracy competitive to computationally more involved plane-wave based calculations. PBEh-3c can be applied routinely to several hundreds of atoms on a single processor and it is suggested as a robust “high-speed” computational tool in theoretical chemistry and physics.« less

Explicit correlation treatment of the six-dimensional potential energy surface and predicted infrared spectra for OCS-H2

NASA Astrophysics Data System (ADS)

Liu, Jing-Min; Zhai, Yu; Li, Hui

2017-07-01

An effective six-dimensional ab initio potential energy surface (PES) for H2-OCS which explicitly includes the intramolecular stretch normal modes of carbonyl sulfide (OCS) is presented. The electronic structure computations are carried out using the explicitly correlated coupled cluster [CCSD(T)-F12] method with the augmented correlation-consistent aug-cc-pVTZ basis set, and the accuracy is critically tested by performing a series of benchmark calculations. Analytic four-dimensional PESs are obtained by least-squares fitting vibrationally averaged interaction energies to the Morse/long-range potential model. These fits to 13 485 points have a root-mean-square deviation (RMSD) of 0.16 cm-1. The combined radial discrete variable representation/angular finite basis representation method and the Lanczos algorithm were employed to evaluate the rovibrational energy levels for five isotopic species of the OCS-hydrogen complexes. The predicted transition frequencies and intensities based on the resulting vibrationally averaged PESs are in good agreement with the available experimental values, whose RMSDs are smaller than 0.004 cm-1 for five different species of OCS-hydrogen complexes. The calculated infrared band origin shifts for all five species of OCS-hydrogen complexes are only 0.03 cm-1 smaller than the corresponding experimental values. These validate the high quality of our PESs which can be used for modeling OCS doped in hydrogen clusters to further study quantum solution and microscopic superfluidity. In addition, the analytic coordinate transformation functions between isotopologues are also derived due to the center of mass shifting of different isotope substitutes.

Optimization of selected molecular orbitals in group basis sets.

PubMed

Ferenczy, György G; Adams, William H

2009-04-07

We derive a local basis equation which may be used to determine the orbitals of a group of electrons in a system when the orbitals of that group are represented by a group basis set, i.e., not the basis set one would normally use but a subset suited to a specific electronic group. The group orbitals determined by the local basis equation minimize the energy of a system when a group basis set is used and the orbitals of other groups are frozen. In contrast, under the constraint of a group basis set, the group orbitals satisfying the Huzinaga equation do not minimize the energy. In a test of the local basis equation on HCl, the group basis set included only 12 of the 21 functions in a basis set one might ordinarily use, but the calculated active orbital energies were within 0.001 hartree of the values obtained by solving the Hartree-Fock-Roothaan (HFR) equation using all 21 basis functions. The total energy found was just 0.003 hartree higher than the HFR value. The errors with the group basis set approximation to the Huzinaga equation were larger by over two orders of magnitude. Similar results were obtained for PCl(3) with the group basis approximation. Retaining more basis functions allows an even higher accuracy as shown by the perfect reproduction of the HFR energy of HCl with 16 out of 21 basis functions in the valence basis set. When the core basis set was also truncated then no additional error was introduced in the calculations performed for HCl with various basis sets. The same calculations with fixed core orbitals taken from isolated heavy atoms added a small error of about 10(-4) hartree. This offers a practical way to calculate wave functions with predetermined fixed core and reduced base valence orbitals at reduced computational costs. The local basis equation can also be used to combine the above approximations with the assignment of local basis sets to groups of localized valence molecular orbitals and to derive a priori localized orbitals. An appropriately chosen localization and basis set assignment allowed a reproduction of the energy of n-hexane with an error of 10(-5) hartree, while the energy difference between its two conformers was reproduced with a similar accuracy for several combinations of localizations and basis set assignments. These calculations include localized orbitals extending to 4-5 heavy atoms and thus they require to solve reduced dimension secular equations. The dimensions are not expected to increase with increasing system size and thus the local basis equation may find use in linear scaling electronic structure calculations.

Accurate Methods for Large Molecular Systems (Preprint)

DTIC Science & Technology

2009-01-06

tensor, EFP calculations are basis set dependent. The smallest recommended basis set is 6- 31++G( d , p )52 The dependence of the computational cost of...and second order perturbation theory (MP2) levels with the 6-31G( d , p ) basis set. Additional SFM tests are presented for a small set of alpha...helices using the 6-31++G( d , p ) basis set. The larger 6-311++G(3df,2p) basis set is employed for creating all EFPs used for non- bonded interactions, since

Benchmark CCSD(T) and DFT study of binding energies in Be7 - 12: in search of reliable DFT functional for beryllium clusters

NASA Astrophysics Data System (ADS)

Labanc, Daniel; Šulka, Martin; Pitoňák, Michal; Černušák, Ivan; Urban, Miroslav; Neogrády, Pavel

2018-05-01

We present a computational study of the stability of small homonuclear beryllium clusters Be7 - 12 in singlet electronic states. Our predictions are based on highly correlated CCSD(T) coupled cluster calculations. Basis set convergence towards the complete basis set limit as well as the role of the 1s core electron correlation are carefully examined. Our CCSD(T) data for binding energies of Be7 - 12 clusters serve as a benchmark for performance assessment of several density functional theory (DFT) methods frequently used in beryllium cluster chemistry. We observe that, from Be10 clusters on, the deviation from CCSD(T) benchmarks is stable with respect to size, and fluctuating within 0.02 eV error bar for most examined functionals. This opens up the possibility of scaling the DFT binding energies for large Be clusters using CCSD(T) benchmark values for smaller clusters. We also tried to find analogies between the performance of DFT functionals for Be clusters and for the valence-isoelectronic Mg clusters investigated recently in Truhlar's group. We conclude that it is difficult to find DFT functionals that perform reasonably well for both beryllium and magnesium clusters. Out of 12 functionals examined, only the M06-2X functional gives reasonably accurate and balanced binding energies for both Be and Mg clusters.

Interaction energies for the purine inhibitor roscovitine with cyclin-dependent kinase 2: correlated ab initio quantum-chemical, DFT and empirical calculations.

PubMed

Dobes, Petr; Otyepka, Michal; Strnad, Miroslav; Hobza, Pavel

2006-05-24

The interaction between roscovitine and cyclin-dependent kinase 2 (cdk2) was investigated by performing correlated ab initio quantum-chemical calculations. The whole protein was fragmented into smaller systems consisting of one or a few amino acids, and the interaction energies of these fragments with roscovitine were determined by using the MP2 method with the extended aug-cc-pVDZ basis set. For selected complexes, the complete basis set limit MP2 interaction energies, as well as the coupled-cluster corrections with inclusion of single, double and noninteractive triples contributions [CCSD(T)], were also evaluated. The energies of interaction between roscovitine and small fragments and between roscovitine and substantial sections of protein (722 atoms) were also computed by using density-functional tight-binding methods covering dispersion energy (DFTB-D) and the Cornell empirical potential. Total stabilisation energy originates predominantly from dispersion energy and methods that do not account for the dispersion energy cannot, therefore, be recommended for the study of protein-inhibitor interactions. The Cornell empirical potential describes reasonably well the interaction between roscovitine and protein; therefore, this method can be applied in future thermodynamic calculations. A limited number of amino acid residues contribute significantly to the binding of roscovitine and cdk2, whereas a rather large number of amino acids make a negligible contribution.

Approaching the theoretical limit in periodic local MP2 calculations with atomic-orbital basis sets: the case of LiH.

PubMed

Usvyat, Denis; Civalleri, Bartolomeo; Maschio, Lorenzo; Dovesi, Roberto; Pisani, Cesare; Schütz, Martin

2011-06-07

The atomic orbital basis set limit is approached in periodic correlated calculations for solid LiH. The valence correlation energy is evaluated at the level of the local periodic second order Møller-Plesset perturbation theory (MP2), using basis sets of progressively increasing size, and also employing "bond"-centered basis functions in addition to the standard atom-centered ones. Extended basis sets, which contain linear dependencies, are processed only at the MP2 stage via a dual basis set scheme. The local approximation (domain) error has been consistently eliminated by expanding the orbital excitation domains. As a final result, it is demonstrated that the complete basis set limit can be reached for both HF and local MP2 periodic calculations, and a general scheme is outlined for the definition of high-quality atomic-orbital basis sets for solids. © 2011 American Institute of Physics

Optimized auxiliary basis sets for density fitted post-Hartree-Fock calculations of lanthanide containing molecules

NASA Astrophysics Data System (ADS)

Chmela, Jiří; Harding, Michael E.

2018-06-01

Optimised auxiliary basis sets for lanthanide atoms (Ce to Lu) for four basis sets of the Karlsruhe error-balanced segmented contracted def2 - series (SVP, TZVP, TZVPP and QZVPP) are reported. These auxiliary basis sets enable the use of the resolution-of-the-identity (RI) approximation in post Hartree-Fock methods - as for example, second-order perturbation theory (MP2) and coupled cluster (CC) theory. The auxiliary basis sets are tested on an enlarged set of about a hundred molecules where the test criterion is the size of the RI error in MP2 calculations. Our tests also show that the same auxiliary basis sets can be used together with different effective core potentials. With these auxiliary basis set calculations of MP2 and CC quality can now be performed efficiently on medium-sized molecules containing lanthanides.

Ab Initio Density Fitting: Accuracy Assessment of Auxiliary Basis Sets from Cholesky Decompositions.

PubMed

Boström, Jonas; Aquilante, Francesco; Pedersen, Thomas Bondo; Lindh, Roland

2009-06-09

The accuracy of auxiliary basis sets derived by Cholesky decompositions of the electron repulsion integrals is assessed in a series of benchmarks on total ground state energies and dipole moments of a large test set of molecules. The test set includes molecules composed of atoms from the first three rows of the periodic table as well as transition metals. The accuracy of the auxiliary basis sets are tested for the 6-31G**, correlation consistent, and atomic natural orbital basis sets at the Hartree-Fock, density functional theory, and second-order Møller-Plesset levels of theory. By decreasing the decomposition threshold, a hierarchy of auxiliary basis sets is obtained with accuracies ranging from that of standard auxiliary basis sets to that of conventional integral treatments.

Structural methodologies for auditing SNOMED.

PubMed

Wang, Yue; Halper, Michael; Min, Hua; Perl, Yehoshua; Chen, Yan; Spackman, Kent A

2007-10-01

SNOMED is one of the leading health care terminologies being used worldwide. As such, quality assurance is an important part of its maintenance cycle. Methodologies for auditing SNOMED based on structural aspects of its organization are presented. In particular, automated techniques for partitioning SNOMED into smaller groups of concepts based primarily on relationships patterns are defined. Two abstraction networks, the area taxonomy and p-area taxonomy, are derived from the partitions. The high-level views afforded by these abstraction networks form the basis for systematic auditing. The networks tend to highlight errors that manifest themselves as irregularities at the abstract level. They also support group-based auditing, where sets of purportedly similar concepts are focused on for review. The auditing methodologies are demonstrated on one of SNOMED's top-level hierarchies. Errors discovered during the auditing process are reported.

Quantifying entanglement of rotor chains using basis truncation: Application to dipolar endofullerene peapods.

PubMed

Halverson, Tom; Iouchtchenko, Dmitri; Roy, Pierre-Nicholas

2018-02-21

We propose a variational approach for the calculation of the quantum entanglement entropy of assemblies of rotating dipolar molecules. A basis truncation scheme based on the total angular momentum quantum number is proposed. The method is tested on hydrogen fluoride (HF) molecules confined in C 60 fullerene cages themselves trapped in a nanotube to form a carbon peapod. The rotational degrees of freedom of the HF molecules and dipolar interactions between neighboring molecules are considered in our model Hamiltonian. Both screened and unscreened dipoles are simulated and results are obtained for the ground state and one excited state that is expected to be accessible via a far-infrared collective excitation. The effect of basis truncation on energetic and entanglement properties is examined and discussed in terms of size extensivity. It is empirically found that for unscreened dipoles, a total angular momentum cutoff that increases linearly with the number of rotors is required in order to obtain proper system size scaling of the chemical potential and entanglement entropy. Recent experiments [A. Krachmalnicoff et al., Nat. Chem. 8, 953 (2016)] suggest substantial screening of the HF dipole moment, so much smaller basis sets are required to obtain converged results in this realistic case. Static correlation functions are also computed and are shown to decay much quicker in the case of screened dipoles. Our variational results are also used to test the accuracy of perturbative and pairwise ansatz treatments.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rossi, Tuomas P., E-mail: tuomas.rossi@alumni.aalto.fi; Sakko, Arto; Puska, Martti J.

We present an approach for generating local numerical basis sets of improving accuracy for first-principles nanoplasmonics simulations within time-dependent density functional theory. The method is demonstrated for copper, silver, and gold nanoparticles that are of experimental interest but computationally demanding due to the semi-core d-electrons that affect their plasmonic response. The basis sets are constructed by augmenting numerical atomic orbital basis sets by truncated Gaussian-type orbitals generated by the completeness-optimization scheme, which is applied to the photoabsorption spectra of homoatomic metal atom dimers. We obtain basis sets of improving accuracy up to the complete basis set limit and demonstrate thatmore » the performance of the basis sets transfers to simulations of larger nanoparticles and nanoalloys as well as to calculations with various exchange-correlation functionals. This work promotes the use of the local basis set approach of controllable accuracy in first-principles nanoplasmonics simulations and beyond.« less

Effective empirical corrections for basis set superposition error in the def2-SVPD basis: gCP and DFT-C

NASA Astrophysics Data System (ADS)

Witte, Jonathon; Neaton, Jeffrey B.; Head-Gordon, Martin

2017-06-01

With the aim of mitigating the basis set error in density functional theory (DFT) calculations employing local basis sets, we herein develop two empirical corrections for basis set superposition error (BSSE) in the def2-SVPD basis, a basis which—when stripped of BSSE—is capable of providing near-complete-basis DFT results for non-covalent interactions. Specifically, we adapt the existing pairwise geometrical counterpoise (gCP) approach to the def2-SVPD basis, and we develop a beyond-pairwise approach, DFT-C, which we parameterize across a small set of intermolecular interactions. Both gCP and DFT-C are evaluated against the traditional Boys-Bernardi counterpoise correction across a set of 3402 non-covalent binding energies and isomerization energies. We find that the DFT-C method represents a significant improvement over gCP, particularly for non-covalently-interacting molecular clusters. Moreover, DFT-C is transferable among density functionals and can be combined with existing functionals—such as B97M-V—to recover large-basis results at a fraction of the cost.

Surface-based morphometry reveals the neuroanatomical basis of the five-factor model of personality

PubMed Central

Riccelli, Roberta; Toschi, Nicola; Nigro, Salvatore; Terracciano, Antonio

2017-01-01

Abstract The five-factor model (FFM) is a widely used taxonomy of human personality; yet its neuro anatomical basis remains unclear. This is partly because past associations between gray-matter volume and FFM were driven by different surface-based morphometry (SBM) indices (i.e. cortical thickness, surface area, cortical folding or any combination of them). To overcome this limitation, we used Free-Surfer to study how variability in SBM measures was related to the FFM in n = 507 participants from the Human Connectome Project. Neuroticism was associated with thicker cortex and smaller area and folding in prefrontal–temporal regions. Extraversion was linked to thicker pre-cuneus and smaller superior temporal cortex area. Openness was linked to thinner cortex and greater area and folding in prefrontal–parietal regions. Agreeableness was correlated to thinner prefrontal cortex and smaller fusiform gyrus area. Conscientiousness was associated with thicker cortex and smaller area and folding in prefrontal regions. These findings demonstrate that anatomical variability in prefrontal cortices is linked to individual differences in the socio-cognitive dispositions described by the FFM. Cortical thickness and surface area/folding were inversely related each others as a function of different FFM traits (neuroticism, extraversion and consciousness vs openness), which may reflect brain maturational effects that predispose or protect against psychiatric disorders. PMID:28122961

Polarization functions for the modified m6-31G basis sets for atoms Ga through Kr.

PubMed

Mitin, Alexander V

2013-09-05

The 2df polarization functions for the modified m6-31G basis sets of the third-row atoms Ga through Kr (Int J Quantum Chem, 2007, 107, 3028; Int J. Quantum Chem, 2009, 109, 1158) are proposed. The performances of the m6-31G, m6-31G(d,p), and m6-31G(2df,p) basis sets were examined in molecular calculations carried out by the density functional theory (DFT) method with B3LYP hybrid functional, Møller-Plesset perturbation theory of the second order (MP2), quadratic configuration interaction method with single and double substitutions and were compared with those for the known 6-31G basis sets as well as with the other similar 641 and 6-311G basis sets with and without polarization functions. Obtained results have shown that the performances of the m6-31G, m6-31G(d,p), and m6-31G(2df,p) basis sets are better in comparison with the performances of the known 6-31G, 6-31G(d,p) and 6-31G(2df,p) basis sets. These improvements are mainly reached due to better approximations of different electrons belonging to the different atomic shells in the modified basis sets. Applicability of the modified basis sets in thermochemical calculations is also discussed. © 2013 Wiley Periodicals, Inc.

Approaching the basis set limit for DFT calculations using an environment-adapted minimal basis with perturbation theory: Formulation, proof of concept, and a pilot implementation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mao, Yuezhi; Horn, Paul R.; Mardirossian, Narbe

2016-07-28

Recently developed density functionals have good accuracy for both thermochemistry (TC) and non-covalent interactions (NC) if very large atomic orbital basis sets are used. To approach the basis set limit with potentially lower computational cost, a new self-consistent field (SCF) scheme is presented that employs minimal adaptive basis (MAB) functions. The MAB functions are optimized on each atomic site by minimizing a surrogate function. High accuracy is obtained by applying a perturbative correction (PC) to the MAB calculation, similar to dual basis approaches. Compared to exact SCF results, using this MAB-SCF (PC) approach with the same large target basis set producesmore » <0.15 kcal/mol root-mean-square deviations for most of the tested TC datasets, and <0.1 kcal/mol for most of the NC datasets. The performance of density functionals near the basis set limit can be even better reproduced. With further improvement to its implementation, MAB-SCF (PC) is a promising lower-cost substitute for conventional large-basis calculations as a method to approach the basis set limit of modern density functionals.« less

Efficient time-dependent density functional theory approximations for hybrid density functionals: analytical gradients and parallelization.

PubMed

Petrenko, Taras; Kossmann, Simone; Neese, Frank

2011-02-07

In this paper, we present the implementation of efficient approximations to time-dependent density functional theory (TDDFT) within the Tamm-Dancoff approximation (TDA) for hybrid density functionals. For the calculation of the TDDFT/TDA excitation energies and analytical gradients, we combine the resolution of identity (RI-J) algorithm for the computation of the Coulomb terms and the recently introduced "chain of spheres exchange" (COSX) algorithm for the calculation of the exchange terms. It is shown that for extended basis sets, the RIJCOSX approximation leads to speedups of up to 2 orders of magnitude compared to traditional methods, as demonstrated for hydrocarbon chains. The accuracy of the adiabatic transition energies, excited state structures, and vibrational frequencies is assessed on a set of 27 excited states for 25 molecules with the configuration interaction singles and hybrid TDDFT/TDA methods using various basis sets. Compared to the canonical values, the typical error in transition energies is of the order of 0.01 eV. Similar to the ground-state results, excited state equilibrium geometries differ by less than 0.3 pm in the bond distances and 0.5° in the bond angles from the canonical values. The typical error in the calculated excited state normal coordinate displacements is of the order of 0.01, and relative error in the calculated excited state vibrational frequencies is less than 1%. The errors introduced by the RIJCOSX approximation are, thus, insignificant compared to the errors related to the approximate nature of the TDDFT methods and basis set truncation. For TDDFT/TDA energy and gradient calculations on Ag-TB2-helicate (156 atoms, 2732 basis functions), it is demonstrated that the COSX algorithm parallelizes almost perfectly (speedup ~26-29 for 30 processors). The exchange-correlation terms also parallelize well (speedup ~27-29 for 30 processors). The solution of the Z-vector equations shows a speedup of ~24 on 30 processors. The parallelization efficiency for the Coulomb terms can be somewhat smaller (speedup ~15-25 for 30 processors), but their contribution to the total calculation time is small. Thus, the parallel program completes a Becke3-Lee-Yang-Parr energy and gradient calculation on the Ag-TB2-helicate in less than 4 h on 30 processors. We also present the necessary extension of the Lagrangian formalism, which enables the calculation of the TDDFT excited state properties in the frozen-core approximation. The algorithms described in this work are implemented into the ORCA electronic structure system.

Derivation of a formula for the resonance integral for a nonorthogonal basis set

PubMed Central

Yim, Yung-Chang; Eyring, Henry

1981-01-01

In a self-consistent field calculation, a formula for the off-diagonal matrix elements of the core Hamiltonian is derived for a nonorthogonal basis set by a polyatomic approach. A set of parameters is then introduced for the repulsion integral formula of Mataga-Nishimoto to fit the experimental data. The matrix elements computed for the nonorthogonal basis set in the π-electron approximation are transformed to those for an orthogonal basis set by the Löwdin symmetrical orthogonalization. PMID:16593009

Time-oriented hierarchical method for computation of principal components using subspace learning algorithm.

PubMed

Jankovic, Marko; Ogawa, Hidemitsu

2004-10-01

Principal Component Analysis (PCA) and Principal Subspace Analysis (PSA) are classic techniques in statistical data analysis, feature extraction and data compression. Given a set of multivariate measurements, PCA and PSA provide a smaller set of "basis vectors" with less redundancy, and a subspace spanned by them, respectively. Artificial neurons and neural networks have been shown to perform PSA and PCA when gradient ascent (descent) learning rules are used, which is related to the constrained maximization (minimization) of statistical objective functions. Due to their low complexity, such algorithms and their implementation in neural networks are potentially useful in cases of tracking slow changes of correlations in the input data or in updating eigenvectors with new samples. In this paper we propose PCA learning algorithm that is fully homogeneous with respect to neurons. The algorithm is obtained by modification of one of the most famous PSA learning algorithms--Subspace Learning Algorithm (SLA). Modification of the algorithm is based on Time-Oriented Hierarchical Method (TOHM). The method uses two distinct time scales. On a faster time scale PSA algorithm is responsible for the "behavior" of all output neurons. On a slower scale, output neurons will compete for fulfillment of their "own interests". On this scale, basis vectors in the principal subspace are rotated toward the principal eigenvectors. At the end of the paper it will be briefly analyzed how (or why) time-oriented hierarchical method can be used for transformation of any of the existing neural network PSA method, into PCA method.

Breakdown of Zero-Energy Quantum Hall State in Graphene in the Light of Current Fluctuations and Shot Noise

NASA Astrophysics Data System (ADS)

Laitinen, Antti; Kumar, Manohar; Elo, Teemu; Liu, Ying; Abhilash, T. S.; Hakonen, Pertti J.

2018-06-01

We have investigated the cross-over from Zener tunneling of single charge carriers to avalanche type of bunched electron transport in a suspended graphene Corbino disk in the zeroth Landau level. At low bias, we find a tunneling current that follows the gyrotropic Zener tunneling behavior. At larger bias, we find an avalanche type of transport that sets in at a smaller current the larger the magnetic field is. The low-frequency noise indicates strong bunching of the electrons in the avalanches. On the basis of the measured low-frequency switching noise power, we deduce the characteristic switching rates of the avalanche sequence. The simultaneous microwave shot noise measurement also reveals intrinsic correlations within the avalanche pulses and indicate a decrease in correlations with increasing bias.

To investigate the relation between pore size and twist angle in enhanced thermoelectric efficient porous armchair graphene nanoribbons

NASA Astrophysics Data System (ADS)

Kaur, Sukhdeep; Randhawa, Deep Kamal Kaur; Bindra Narang, Sukhleen

2018-05-01

Based on Non-Equilibrium Green’s function method, we demonstrate that the twisted deformation is an efficient method to improve the figure of merit ZT of porous armchair graphene nanoribbons AGNRs. The peak value of ZT can be obtained for a certain tunable twist angle. Further analysis shows that the tunable twist angle exhibits an inverse relationship with the pore size laying forth the designers a choice for the larger twists to be replaced by smaller ones simply by increasing the size of the pore. Ballistic transport regime and semi-empirical method using Huckel basis set is used to obtain the electrical properties while the Tersoff potential is employed for the phononic system. These interesting findings indicate that the twisted porous AGNRs can be utilized as designing materials for potential thermoelectric applications.

An accurate ab initio quartic force field for ammonia

NASA Technical Reports Server (NTRS)

Martin, J. M. L.; Lee, Timothy J.; Taylor, Peter R.

1992-01-01

The quartic force field of ammonia is computed using basis sets of spdf/spd and spdfg/spdf quality and an augmented coupled cluster method. After correcting for Fermi resonance, the computed fundamentals and nu 4 overtones agree on average to better than 3/cm with the experimental ones except for nu 2. The discrepancy for nu 2 is principally due to higher-order anharmonicity effects. The computed omega 1, omega 3, and omega 4 confirm the recent experimental determination by Lehmann and Coy (1988) but are associated with smaller error bars. The discrepancy between the computed and experimental omega 2 is far outside the expected error range, which is also attributed to higher-order anharmonicity effects not accounted for in the experimental determination. Spectroscopic constants are predicted for a number of symmetric and asymmetric top isotopomers of NH3.

Can the BMS Algorithm Decode Up to \\lfloor \\frac{d_G-g-1}{2}\\rfloor Errors? Yes, but with Some Additional Remarks

NASA Astrophysics Data System (ADS)

Sakata, Shojiro; Fujisawa, Masaya

It is a well-known fact [7], [9] that the BMS algorithm with majority voting can decode up to half the Feng-Rao designed distance dFR. Since dFR is not smaller than the Goppa designed distance dG, that algorithm can correct up to \\lfloor \\frac{d_G-1}{2}\\rfloor errors. On the other hand, it has been considered to be evident that the original BMS algorithm (without voting) [1], [2] can correct up to \\lfloor \\frac{d_G-g-1}{2}\\rfloor errors similarly to the basic algorithm by Skorobogatov-Vladut. But, is it true? In this short paper, we show that it is true, although we need a few remarks and some additional procedures for determining the Groebner basis of the error locator ideal exactly. In fact, as the basic algorithm gives a set of polynomials whose zero set contains the error locators as a subset, it cannot always give the exact error locators, unless the syndrome equation is solved to find the error values in addition.

Approximations to complete basis set-extrapolated, highly correlated non-covalent interaction energies.

PubMed

Mackie, Iain D; DiLabio, Gino A

2011-10-07

The first-principles calculation of non-covalent (particularly dispersion) interactions between molecules is a considerable challenge. In this work we studied the binding energies for ten small non-covalently bonded dimers with several combinations of correlation methods (MP2, coupled-cluster single double, coupled-cluster single double (triple) (CCSD(T))), correlation-consistent basis sets (aug-cc-pVXZ, X = D, T, Q), two-point complete basis set energy extrapolations, and counterpoise corrections. For this work, complete basis set results were estimated from averaged counterpoise and non-counterpoise-corrected CCSD(T) binding energies obtained from extrapolations with aug-cc-pVQZ and aug-cc-pVTZ basis sets. It is demonstrated that, in almost all cases, binding energies converge more rapidly to the basis set limit by averaging the counterpoise and non-counterpoise corrected values than by using either counterpoise or non-counterpoise methods alone. Examination of the effect of basis set size and electron correlation shows that the triples contribution to the CCSD(T) binding energies is fairly constant with the basis set size, with a slight underestimation with CCSD(T)∕aug-cc-pVDZ compared to the value at the (estimated) complete basis set limit, and that contributions to the binding energies obtained by MP2 generally overestimate the analogous CCSD(T) contributions. Taking these factors together, we conclude that the binding energies for non-covalently bonded systems can be accurately determined using a composite method that combines CCSD(T)∕aug-cc-pVDZ with energy corrections obtained using basis set extrapolated MP2 (utilizing aug-cc-pVQZ and aug-cc-pVTZ basis sets), if all of the components are obtained by averaging the counterpoise and non-counterpoise energies. With such an approach, binding energies for the set of ten dimers are predicted with a mean absolute deviation of 0.02 kcal/mol, a maximum absolute deviation of 0.05 kcal/mol, and a mean percent absolute deviation of only 1.7%, relative to the (estimated) complete basis set CCSD(T) results. Use of this composite approach to an additional set of eight dimers gave binding energies to within 1% of previously published high-level data. It is also shown that binding within parallel and parallel-crossed conformations of naphthalene dimer is predicted by the composite approach to be 9% greater than that previously reported in the literature. The ability of some recently developed dispersion-corrected density-functional theory methods to predict the binding energies of the set of ten small dimers was also examined. © 2011 American Institute of Physics

Communication: A novel implementation to compute MP2 correlation energies without basis set superposition errors and complete basis set extrapolation.

PubMed

Dixit, Anant; Claudot, Julien; Lebègue, Sébastien; Rocca, Dario

2017-06-07

By using a formulation based on the dynamical polarizability, we propose a novel implementation of second-order Møller-Plesset perturbation (MP2) theory within a plane wave (PW) basis set. Because of the intrinsic properties of PWs, this method is not affected by basis set superposition errors. Additionally, results are converged without relying on complete basis set extrapolation techniques; this is achieved by using the eigenvectors of the static polarizability as an auxiliary basis set to compactly and accurately represent the response functions involved in the MP2 equations. Summations over the large number of virtual states are avoided by using a formalism inspired by density functional perturbation theory, and the Lanczos algorithm is used to include dynamical effects. To demonstrate this method, applications to three weakly interacting dimers are presented.

Correlation consistent valence basis sets for use with the Stuttgart-Dresden-Bonn relativistic effective core potentials: The atoms Ga-Kr and In-Xe

NASA Astrophysics Data System (ADS)

Martin, Jan M. L.; Sundermann, Andreas

2001-02-01

We propose large-core correlation-consistent (cc) pseudopotential basis sets for the heavy p-block elements Ga-Kr and In-Xe. The basis sets are of cc-pVTZ and cc-pVQZ quality, and have been optimized for use with the large-core (valence-electrons only) Stuttgart-Dresden-Bonn (SDB) relativistic pseudopotentials. Validation calculations on a variety of third-row and fourth-row diatomics suggest them to be comparable in quality to the all-electron cc-pVTZ and cc-pVQZ basis sets for lighter elements. Especially the SDB-cc-pVQZ basis set in conjunction with a core polarization potential (CPP) yields excellent agreement with experiment for compounds of the later heavy p-block elements. For accurate calculations on Ga (and, to a lesser extent, Ge) compounds, explicit treatment of 13 valence electrons appears to be desirable, while it seems inevitable for In compounds. For Ga and Ge, we propose correlation consistent basis sets extended for (3d) correlation. For accurate calculations on organometallic complexes of interest to homogenous catalysis, we recommend a combination of the standard cc-pVTZ basis set for first- and second-row elements, the presently derived SDB-cc-pVTZ basis set for heavier p-block elements, and for transition metals, the small-core [6s5p3d] Stuttgart-Dresden basis set-relativistic effective core potential combination supplemented by (2f1g) functions with exponents given in the Appendix to the present paper.

Hybrid Grid and Basis Set Approach to Quantum Chemistry DMRG

NASA Astrophysics Data System (ADS)

Stoudenmire, Edwin Miles; White, Steven

We present a new approach for using DMRG for quantum chemistry that combines the advantages of a basis set with that of a grid approximation. Because DMRG scales linearly for quasi-one-dimensional systems, it is feasible to approximate the continuum with a fine grid in one direction while using a standard basis set approach for the transverse directions. Compared to standard basis set methods, we reach larger systems and achieve better scaling when approaching the basis set limit. The flexibility and reduced costs of our approach even make it feasible to incoporate advanced DMRG techniques such as simulating real-time dynamics. Supported by the Simons Collaboration on the Many-Electron Problem.

Distinguishing between natural and hatchery Snake River fall Chinook salmon subyearlings in the field using body morphology

USGS Publications Warehouse

Tiffan, K.F.; Connor, W.P.

2011-01-01

We used body morphology to distinguish between natural- and hatchery-origin subyearling fall Chinook salmon Oncorhynchus tshawytscha in rearing areas of the Snake River and at a downstream dam during seaward migration. Using subjective eye and body shape characteristics, field personnel correctly classified 88.9–100% of natural subyearlings (N = 626) and 90.0–100% of hatchery subyearlings (N = 867) in rearing areas from 2001 to 2008. The morphological characteristics used by these personnel proved to have a quantitative basis, as was shown by digital photography and principal components analysis. Natural subyearlings had smaller eyes and pupils, smaller heads, deeper bodies, and shorter caudal peduncles than their hatchery counterparts during rearing and at the dam. A discriminant function fitted from this set of morphological characteristics classified the origin of fish during rearing and at the dam with over 97% accuracy. We hypothesize that these morphological differences were primarily due to environmental influences during incubation and rearing because it is highly probable that a large portion of the natural juveniles we studied were the offspring of hatchery × hatchery mating in the wild. The findings in this paper might provide guidance for others seeking to differentiate between natural and hatchery fish.

Density functional theory calculations of the lowest energy quintet and triplet states of model hemes: role of functional, basis set, and zero-point energy corrections.

PubMed

Khvostichenko, Daria; Choi, Andrew; Boulatov, Roman

2008-04-24

We investigated the effect of several computational variables, including the choice of the basis set, application of symmetry constraints, and zero-point energy (ZPE) corrections, on the structural parameters and predicted ground electronic state of model 5-coordinate hemes (iron(II) porphines axially coordinated by a single imidazole or 2-methylimidazole). We studied the performance of B3LYP and B3PW91 with eight Pople-style basis sets (up to 6-311+G*) and B97-1, OLYP, and TPSS functionals with 6-31G and 6-31G* basis sets. Only hybrid functionals B3LYP, B3PW91, and B97-1 reproduced the quintet ground state of the model hemes. With a given functional, the choice of the basis set caused up to 2.7 kcal/mol variation of the quintet-triplet electronic energy gap (DeltaEel), in several cases, resulting in the inversion of the sign of DeltaEel. Single-point energy calculations with triple-zeta basis sets of the Pople (up to 6-311G++(2d,2p)), Ahlrichs (TZVP and TZVPP), and Dunning (cc-pVTZ) families showed the same trend. The zero-point energy of the quintet state was approximately 1 kcal/mol lower than that of the triplet, and accounting for ZPE corrections was crucial for establishing the ground state if the electronic energy of the triplet state was approximately 1 kcal/mol less than that of the quintet. Within a given model chemistry, effects of symmetry constraints and of a "tense" structure of the iron porphine fragment coordinated to 2-methylimidazole on DeltaEel were limited to 0.3 kcal/mol. For both model hemes the best agreement with crystallographic structural data was achieved with small 6-31G and 6-31G* basis sets. Deviation of the computed frequency of the Fe-Im stretching mode from the experimental value with the basis set decreased in the order: nonaugmented basis sets, basis sets with polarization functions, and basis sets with polarization and diffuse functions. Contraction of Pople-style basis sets (double-zeta or triple-zeta) affected the results insignificantly for iron(II) porphyrin coordinated with imidazole. Poor performance of a "locally dense" basis set with a large number of basis functions on the Fe center was observed in calculation of quintet-triplet gaps. Our results lead to a series of suggestions for density functional theory calculations of quintet-triplet energy gaps in ferrohemes with a single axial imidazole; these suggestions are potentially applicable for other transition-metal complexes.

Ab Initio and Analytic Intermolecular Potentials for Ar–CH3OH

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tasic, Uros; Alexeev, Yuri; Vayner, Grigoriy

2006-09-20

Ab initio calculations at the CCSD(T)/aug-cc-pVTZ level of theory were used to characterize the Ar–CH₃y6tOH intermolecular potential energy surface (PES). Potential energy curves were calculated for four different Ar + CH₃OH orientations and used to derive an analytic function for the intermolecular PES. A sum of Ar–C, Ar–O, Ar–H(C), and Ar–H(O) two-body potentials gives an excellent fit to these potential energy curves up to 100 kcal mol¯¹, and adding an additional r¯¹n term to the Buckingham two-body potential results in only a minor improvement in the fit. Three Ar–CH₃OH van der Waals minima were found from the CCSD(T)/aug-cc-pVTZ//MP2/aug-cc-pVTZ calculations. Themore » structure of the global minimum is in overall good agreement with experiment (X.-C. Tan, L. Sun and R. L. Kuczkowski, J. Mol. Spectrosc., 1995, 171, 248). It is T-shaped with the hydroxyl H-atom syn with respect to Ar. Extrapolated to the complete basis set (CBS) limit, the global minimum has a well depth of 0.72 kcal mol¯¹ with basis set superposition error (BSSE) correction. The aug-cc-pVTZ basis set gives a well depth only 0.10 kcal mol¯¹ smaller than this value. The well depths of the other two minima are within 0.16 kcal mol¯¹ of the global minimum. The analytic Ar–CH₃OH intermolecular potential also identifies these three minima as the only van der Waals minima and the structures predicted by the analytic potential are similar to the ab initio structures. The analytic potential identifies the same global minimum and the predicted well depths for the minima are within 0.05 kcal mol¯1 of the ab initio values. Combining this Ar–CH₃OH intermolecular potential with a potential for a OH-terminated alkylthiolate self-assembled monolayer surface (i.e., HO-SAM) provides a potential to model Ar + HO-SAM collisions.« less

Localized basis sets for unbound electrons in nanoelectronics.

PubMed

Soriano, D; Jacob, D; Palacios, J J

2008-02-21

It is shown how unbound electron wave functions can be expanded in a suitably chosen localized basis sets for any desired range of energies. In particular, we focus on the use of Gaussian basis sets, commonly used in first-principles codes. The possible usefulness of these basis sets in a first-principles description of field emission or scanning tunneling microscopy at large bias is illustrated by studying a simpler related phenomenon: The lifetime of an electron in a H atom subjected to a strong electric field.

Near Hartree-Fock quality GTO basis sets for the second-row atoms

NASA Technical Reports Server (NTRS)

Partridge, Harry

1987-01-01

Energy optimized, near Hartree-Fock quality Gaussian basis sets ranging in size from (17s12p) to (20s15p) are presented for the ground states of the second-row atoms for Na(2P), Na(+), Na(-), Mg(3P), P(-), S(-), and Cl(-). In addition, optimized supplementary functions are given for the ground state basis sets to describe the negative ions, and the excited Na(2P) and Mg(3P) atomic states. The ratios of successive orbital exponents describing the inner part of the 1s and 2p orbitals are found to be nearly independent of both nuclear charge and basis set size. This provides a method of obtaining good starting estimates for other basis set optimizations.

A rough set-based measurement model study on high-speed railway safety operation.

PubMed

Hu, Qizhou; Tan, Minjia; Lu, Huapu; Zhu, Yun

2018-01-01

Aiming to solve the safety problems of high-speed railway operation and management, one new method is urgently needed to construct on the basis of the rough set theory and the uncertainty measurement theory. The method should carefully consider every factor of high-speed railway operation that realizes the measurement indexes of its safety operation. After analyzing the factors that influence high-speed railway safety operation in detail, a rough measurement model is finally constructed to describe the operation process. Based on the above considerations, this paper redistricts the safety influence factors of high-speed railway operation as 16 measurement indexes which include staff index, vehicle index, equipment index and environment. And the paper also provides another reasonable and effective theoretical method to solve the safety problems of multiple attribute measurement in high-speed railway operation. As while as analyzing the operation data of 10 pivotal railway lines in China, this paper respectively uses the rough set-based measurement model and value function model (one model for calculating the safety value) for calculating the operation safety value. The calculation result shows that the curve of safety value with the proposed method has smaller error and greater stability than the value function method's, which verifies the feasibility and effectiveness.

Relativistic Prolapse-Free Gaussian Basis Sets of Quadruple-ζ Quality: (aug-)RPF-4Z. III. The f-Block Elements.

PubMed

Teodoro, Tiago Quevedo; Visscher, Lucas; da Silva, Albérico Borges Ferreira; Haiduke, Roberto Luiz Andrade

2017-03-14

The f-block elements are addressed in this third part of a series of prolapse-free basis sets of quadruple-ζ quality (RPF-4Z). Relativistic adapted Gaussian basis sets (RAGBSs) are used as primitive sets of functions while correlating/polarization (C/P) functions are chosen by analyzing energy lowerings upon basis set increments in Dirac-Coulomb multireference configuration interaction calculations with single and double excitations of the valence spinors. These function exponents are obtained by applying the RAGBS parameters in a polynomial expression. Moreover, through the choice of C/P characteristic exponents from functions of lower angular momentum spaces, a reduction in the computational demand is attained in relativistic calculations based on the kinetic balance condition. The present study thus complements the RPF-4Z sets for the whole periodic table (Z ≤ 118). The sets are available as Supporting Information and can also be found at http://basis-sets.iqsc.usp.br .

Combination of large and small basis sets in electronic structure calculations on large systems

NASA Astrophysics Data System (ADS)

Røeggen, Inge; Gao, Bin

2018-04-01

Two basis sets—a large and a small one—are associated with each nucleus of the system. Each atom has its own separate one-electron basis comprising the large basis set of the atom in question and the small basis sets for the partner atoms in the complex. The perturbed atoms in molecules and solids model is at core of the approach since it allows for the definition of perturbed atoms in a system. It is argued that this basis set approach should be particularly useful for periodic systems. Test calculations are performed on one-dimensional arrays of H and Li atoms. The ground-state energy per atom in the linear H array is determined versus bond length.

Validation of MODIS Dust Aerosol Retrieval and Development Ambient Dust Phase Function using PRIDE Data

NASA Technical Reports Server (NTRS)

Remer, Lorraine A.; Lau, William (Technical Monitor)

2002-01-01

The PRIDE data set of MODIS aerosol retrievals co-located with sunphotometer measurements provides the basis of MODIS validation in a dust environment. The sunphotometer measurements include AERONET automatic instruments, land-based Microtops instruments, ship-board Microtops instruments and the AATS-6 aboard the Navajo aircraft. Analysis of these data indicate that the MODIS retrieval is within pre-launch estimates of uncertainty within the spectral range of 600-900 nm. However, the MODIS algorithm consistently retrieves smaller particles than reality thus leading to incorrect spectral response outside of the 600-900 nm range and improper size information. Further analysis of MODIS retrievals in other dust environments shows the inconsistencies are due to nonspherical effects in the phase function. These data are used to develop an ambient phase function for dust aerosol to be used for remote sensing purposes.

Shape and energy consistent pseudopotentials for correlated electron systems

PubMed Central

Needs, R. J.

2017-01-01

A method is developed for generating pseudopotentials for use in correlated-electron calculations. The paradigms of shape and energy consistency are combined and defined in terms of correlated-electron wave-functions. The resulting energy consistent correlated electron pseudopotentials (eCEPPs) are constructed for H, Li–F, Sc–Fe, and Cu. Their accuracy is quantified by comparing the relaxed molecular geometries and dissociation energies which they provide with all electron results, with all quantities evaluated using coupled cluster singles, doubles, and triples calculations. Errors inherent in the pseudopotentials are also compared with those arising from a number of approximations commonly used with pseudopotentials. The eCEPPs provide a significant improvement in optimised geometries and dissociation energies for small molecules, with errors for the latter being an order-of-magnitude smaller than for Hartree-Fock-based pseudopotentials available in the literature. Gaussian basis sets are optimised for use with these pseudopotentials. PMID:28571391

Dynamical basis sets for algebraic variational calculations in quantum-mechanical scattering theory

NASA Technical Reports Server (NTRS)

Sun, Yan; Kouri, Donald J.; Truhlar, Donald G.; Schwenke, David W.

1990-01-01

New basis sets are proposed for linear algebraic variational calculations of transition amplitudes in quantum-mechanical scattering problems. These basis sets are hybrids of those that yield the Kohn variational principle (KVP) and those that yield the generalized Newton variational principle (GNVP) when substituted in Schlessinger's stationary expression for the T operator. Trial calculations show that efficiencies almost as great as that of the GNVP and much greater than the KVP can be obtained, even for basis sets with the majority of the members independent of energy.

On basis set superposition error corrected stabilization energies for large n-body clusters.

PubMed

Walczak, Katarzyna; Friedrich, Joachim; Dolg, Michael

2011-10-07

In this contribution, we propose an approximate basis set superposition error (BSSE) correction scheme for the site-site function counterpoise and for the Valiron-Mayer function counterpoise correction of second order to account for the basis set superposition error in clusters with a large number of subunits. The accuracy of the proposed scheme has been investigated for a water cluster series at the CCSD(T), CCSD, MP2, and self-consistent field levels of theory using Dunning's correlation consistent basis sets. The BSSE corrected stabilization energies for a series of water clusters are presented. A study regarding the possible savings with respect to computational resources has been carried out as well as a monitoring of the basis set dependence of the approximate BSSE corrections. © 2011 American Institute of Physics

High quality Gaussian basis sets for fourth-row atoms

NASA Technical Reports Server (NTRS)

Partridge, Harry; Faegri, Knut, Jr.

1992-01-01

Energy optimized Gaussian basis sets of triple-zeta quality for the atoms Rb-Xe have been derived. Two series of basis sets are developed: (24s 16p 10d) and (26s 16p 10d) sets which were expanded to 13d and 19p functions as the 4d and 5p shells become occupied. For the atoms lighter than Cd, the (24s 16p 10d) sets with triple-zeta valence distributions are higher in energy than the corresponding double-zeta distribution. To ensure a triple-zeta distribution and a global energy minimum, the (26s 16p 10d) sets were derived. Total atomic energies from the largest basis sets are between 198 and 284 (mu)E(sub H) above the numerical Hartree-Fock energies.

Structure of the alexithymic brain: A parametric coordinate-based meta-analysis.

PubMed

Xu, Pengfei; Opmeer, Esther M; van Tol, Marie-José; Goerlich, Katharina S; Aleman, André

2018-04-01

Alexithymia refers to deficiencies in identifying and expressing emotions. This might be related to changes in structural brain volumes, but its neuroanatomical basis remains uncertain as studies have shown heterogeneous findings. Therefore, we conducted a parametric coordinate-based meta-analysis. We identified seventeen structural neuroimaging studies (including a total of 2586 individuals with different levels of alexithymia) investigating the association between gray matter volume and alexithymia. Volumes of the left insula, left amygdala, orbital frontal cortex and striatum were consistently smaller in people with high levels of alexithymia. These areas are important for emotion perception and emotional experience. Smaller volumes in these areas might lead to deficiencies in appropriately identifying and expressing emotions. These findings provide the first quantitative integration of results pertaining to the structural neuroanatomical basis of alexithymia. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

Relativistic well-tempered Gaussian basis sets for helium through mercury

DOE Office of Scientific and Technical Information (OSTI.GOV)

Okada, S.; Matsuoka, O.

1989-10-01

Exponent parameters of the nonrelativistically optimized well-tempered Gaussian basis sets of Huzinaga and Klobukowski have been employed for Dirac--Fock--Roothaan calculations without their reoptimization. For light atoms He (atomic number {ital Z}=2)--Rh ({ital Z}=45), the number of exponent parameters used has been the same as the nonrelativistic basis sets and for heavier atoms Pd ({ital Z}=46)--Hg({ital Z}=80), two 2{ital p} (and three 3{ital d}) Gaussian basis functions have been augmented. The scheme of kinetic energy balance and the uniformly charged sphere model of atomic nuclei have been adopted. The qualities of the calculated basis sets are close to the Dirac--Fock limit.

Performance assessment of density functional methods with Gaussian and Slater basis sets using 7σ orbital momentum distributions of N2O

NASA Astrophysics Data System (ADS)

Wang, Feng; Pang, Wenning; Duffy, Patrick

2012-12-01

Performance of a number of commonly used density functional methods in chemistry (B3LYP, Bhandh, BP86, PW91, VWN, LB94, PBe0, SAOP and X3LYP and the Hartree-Fock (HF) method) has been assessed using orbital momentum distributions of the 7σ orbital of nitrous oxide (NNO), which models electron behaviour in a chemically significant region. The density functional methods are combined with a number of Gaussian basis sets (Pople's 6-31G*, 6-311G**, DGauss TZVP and Dunning's aug-cc-pVTZ as well as even-tempered Slater basis sets, namely, et-DZPp, et-QZ3P, et-QZ+5P and et-pVQZ). Orbital momentum distributions of the 7σ orbital in the ground electronic state of NNO, which are obtained from a Fourier transform into momentum space from single point electronic calculations employing the above models, are compared with experimental measurement of the same orbital from electron momentum spectroscopy (EMS). The present study reveals information on performance of (a) the density functional methods, (b) Gaussian and Slater basis sets, (c) combinations of the density functional methods and basis sets, that is, the models, (d) orbital momentum distributions, rather than a group of specific molecular properties and (e) the entire region of chemical significance of the orbital. It is found that discrepancies of this orbital between the measured and the calculated occur in the small momentum region (i.e. large r region). In general, Slater basis sets achieve better overall performance than the Gaussian basis sets. Performance of the Gaussian basis sets varies noticeably when combining with different Vxc functionals, but Dunning's augcc-pVTZ basis set achieves the best performance for the momentum distributions of this orbital. The overall performance of the B3LYP and BP86 models is similar to newer models such as X3LYP and SAOP. The present study also demonstrates that the combinations of the density functional methods and the basis sets indeed make a difference in the quality of the calculated orbitals.

On the validity of the basis set superposition error and complete basis set limit extrapolations for the binding energy of the formic acid dimer

NASA Astrophysics Data System (ADS)

Miliordos, Evangelos; Xantheas, Sotiris S.

2015-03-01

We report the variation of the binding energy of the Formic Acid Dimer with the size of the basis set at the Coupled Cluster with iterative Singles, Doubles and perturbatively connected Triple replacements [CCSD(T)] level of theory, estimate the Complete Basis Set (CBS) limit, and examine the validity of the Basis Set Superposition Error (BSSE)-correction for this quantity that was previously challenged by Kalescky, Kraka, and Cremer (KKC) [J. Chem. Phys. 140, 084315 (2014)]. Our results indicate that the BSSE correction, including terms that account for the substantial geometry change of the monomers due to the formation of two strong hydrogen bonds in the dimer, is indeed valid for obtaining accurate estimates for the binding energy of this system as it exhibits the expected decrease with increasing basis set size. We attribute the discrepancy between our current results and those of KKC to their use of a valence basis set in conjunction with the correlation of all electrons (i.e., including the 1s of C and O). We further show that the use of a core-valence set in conjunction with all electron correlation converges faster to the CBS limit as the BSSE correction is less than half than the valence electron/valence basis set case. The uncorrected and BSSE-corrected binding energies were found to produce the same (within 0.1 kcal/mol) CBS limits. We obtain CCSD(T)/CBS best estimates for De = - 16.1 ± 0.1 kcal/mol and for D0 = - 14.3 ± 0.1 kcal/mol, the later in excellent agreement with the experimental value of -14.22 ± 0.12 kcal/mol.

Characterizing and Understanding the Remarkably Slow Basis Set Convergence of Several Minnesota Density Functionals for Intermolecular Interaction Energies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mardirossian, Narbe; Head-Gordon, Martin

2013-08-22

For a set of eight equilibrium intermolecular complexes, it is discovered in this paper that the basis set limit (BSL) cannot be reached by aug-cc-pV5Z for three of the Minnesota density functionals: M06-L, M06-HF, and M11-L. In addition, the M06 and M11 functionals exhibit substantial, but less severe, difficulties in reaching the BSL. By using successively finer grids, it is demonstrated that this issue is not related to the numerical integration of the exchange-correlation functional. In addition, it is shown that the difficulty in reaching the BSL is not a direct consequence of the structure of the augmented functions inmore » Dunning’s basis sets, since modified augmentation yields similar results. By using a very large custom basis set, the BSL appears to be reached for the HF dimer for all of the functionals. As a result, it is concluded that the difficulties faced by several of the Minnesota density functionals are related to an interplay between the form of these functionals and the structure of standard basis sets. It is speculated that the difficulty in reaching the basis set limit is related to the magnitude of the inhomogeneity correction factor (ICF) of the exchange functional. A simple modification of the M06-L exchange functional that systematically reduces the basis set superposition error (BSSE) for the HF dimer in the aug-cc-pVQZ basis set is presented, further supporting the speculation that the difficulty in reaching the BSL is caused by the magnitude of the exchange functional ICF. In conclusion, the BSSE is plotted with respect to the internuclear distance of the neon dimer for two of the examined functionals.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Miliordos, Evangelos; Aprà, Edoardo; Xantheas, Sotiris S.

We establish a new estimate for the binding energy between two benzene molecules in the parallel-displaced (PD) conformation by systematically converging (i) the intra- and intermolecular geometry at the minimum, (ii) the expansion of the orbital basis set, and (iii) the level of electron correlation. The calculations were performed at the second-order Møller–Plesset perturbation (MP2) and the coupled cluster including singles, doubles, and a perturbative estimate of triples replacement [CCSD(T)] levels of electronic structure theory. At both levels of theory, by including results corrected for basis set superposition error (BSSE), we have estimated the complete basis set (CBS) limit bymore » employing the family of Dunning’s correlation-consistent polarized valence basis sets. The largest MP2 calculation was performed with the cc-pV6Z basis set (2772 basis functions), whereas the largest CCSD(T) calculation was with the cc-pV5Z basis set (1752 basis functions). The cluster geometries were optimized with basis sets up to quadruple-ζ quality, observing that both its intra- and intermolecular parts have practically converged with the triple-ζ quality sets. The use of converged geometries was found to play an important role for obtaining accurate estimates for the CBS limits. Our results demonstrate that the binding energies with the families of the plain (cc-pVnZ) and augmented (aug-cc-pVnZ) sets converge [within <0.01 kcal/mol for MP2 and <0.15 kcal/mol for CCSD(T)] to the same CBS limit. In addition, the average of the uncorrected and BSSE-corrected binding energies was found to converge to the same CBS limit much faster than either of the two constituents (uncorrected or BSSE-corrected binding energies). Due to the fact that the family of augmented basis sets (especially for the larger sets) causes serious linear dependency problems, the plain basis sets (for which no linear dependencies were found) are deemed as a more efficient and straightforward path for obtaining an accurate CBS limit. We considered extrapolations of the uncorrected (ΔE) and BSSE-corrected (ΔE cp) binding energies, their average value (ΔE ave), as well as the average of the latter over the plain and augmented sets (Δ~E ave) with the cardinal number of the basis set n. Our best estimate of the CCSD(T)/CBS limit for the π–π binding energy in the PD benzene dimer is D e = -2.65 ± 0.02 kcal/mol. The best CCSD(T)/cc-pV5Z calculated value is -2.62 kcal/mol, just 0.03 kcal/mol away from the CBS limit. For comparison, the MP2/CBS limit estimate is -5.00 ± 0.01 kcal/mol, demonstrating a 90% overbinding with respect to CCSD(T). Finally, the spin-component-scaled (SCS) MP2 variant was found to closely reproduce the CCSD(T) results for each basis set, while scaled opposite spin (SOS) MP2 yielded results that are too low when compared to CCSD(T).« less

Calculating Interaction Energies Using First Principle Theories: Consideration of Basis Set Superposition Error and Fragment Relaxation

ERIC Educational Resources Information Center

Bowen, J. Philip; Sorensen, Jennifer B.; Kirschner, Karl N.

2007-01-01

The analysis explains the basis set superposition error (BSSE) and fragment relaxation involved in calculating the interaction energies using various first principle theories. Interacting the correlated fragment and increasing the size of the basis set can help in decreasing the BSSE to a great extent.

Chimpanzees can point to smaller amounts of food to accumulate larger amounts but they still fail the reverse-reward contingency task.

PubMed

Beran, Michael J; James, Brielle T; Whitham, Will; Parrish, Audrey E

2016-10-01

The reverse-reward contingency task presents 2 food sets to an animal, and they are required to choose the smaller of the 2 sets in order to receive the larger food set. Intriguingly, the majority of species tested on the reverse-reward task fail to learn this contingency in the absence of large trial counts, correction trials, and punishment techniques. The unique difficulty of this seemingly simple task likely reflects a failure of inhibitory control which is required to point toward a smaller and less desirable reward rather than a larger and more desirable reward. This failure by chimpanzees and other primates to pass the reverse-reward task is striking given the self-control they exhibit in a variety of other paradigms. For example, chimpanzees have consistently demonstrated a high capacity for delay of gratification in order to maximize accumulating food rewards in which foods are added item-by-item to a growing set until the subject consumes the rewards. To study the mechanisms underlying success in the accumulation task and failure in the reverse-reward task, we presented chimpanzees with several combinations of these 2 tasks to determine when chimpanzees might succeed in pointing to smaller food sets over larger food sets and how the nature of the task might determine the animals' success or failure. Across experiments, 3 chimpanzees repeatedly failed to solve the reverse-reward task, whereas they accumulated nearly all food items across all instances of the accumulation self-control task, even when they had to point to small amounts of food to accumulate larger amounts. These data indicate that constraints of these 2 related but still different tasks of behavioral inhibition are dependent upon the animals' perceptions of the choice set, their sense of control over the contents of choice sets, and the nature of the task constraints. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

The effect of diffuse basis functions on valence bond structural weights

NASA Astrophysics Data System (ADS)

Galbraith, John Morrison; James, Andrew M.; Nemes, Coleen T.

2014-03-01

Structural weights and bond dissociation energies have been determined for H-F, H-X, and F-X molecules (-X = -OH, -NH2, and -CH3) at the valence bond self-consistent field (VBSCF) and breathing orbital valence bond (BOVB) levels of theory with the aug-cc-pVDZ and 6-31++G(d,p) basis sets. At the BOVB level, the aug-cc-pVDZ basis set yields a counterintuitive ordering of ionic structural weights when the initial heavy atom s-type basis functions are included. For H-F, H-OH, and F-X, the ordering follows chemical intuition when these basis functions are not included. These counterintuitive weights are shown to be a result of the diffuse polarisation function on one VB fragment being spatially located, in part, on the other VB fragment. Except in the case of F-CH3, this problem is corrected with the 6-31++G(d,p) basis set. The initial heavy atom s-type functions are shown to make an important contribution to the VB orbitals and bond dissociation energies and, therefore, should not be excluded. It is recommended to not use diffuse basis sets in valence bond calculations unless absolutely necessary. If diffuse basis sets are needed, the 6-31++G(d,p) basis set should be used with caution and the structural weights checked against VBSCF values which have been shown to follow the expected ordering in all cases.

Three-dimensional Models of Hydrothermal Circulation through a Seamount Network in Fast-spreading Crust

NASA Astrophysics Data System (ADS)

Fisher, A. T.; Lauer, R. M.; Winslow, D. M.

2015-12-01

There is a region of 20-24 M.y. old seafloor on the eastern flank of the East Pacific Rise, offshore of Costa Rica, where the advective heat loss from the crust is 60-85% of lithospheric. Much of this advective flux occurs through basement outcrops that penetrate regionally thick sediments, but rates and patterns of hydrothermal circulation in this area are poorly understood. We have run a series of numerical simulations of coupled fluid-heat transport to assess how crustal aquifer and outcrop properties and the distance(s) between outcrops control ridge-flank hydrothermal flows in this setting. Extracting a large fraction of lithospheric heat through this process requires crustal aquifer permeability on the order of 10-10 to 10-9 m2, values considerably higher than seen on other ridge flanks (where advective heat extraction is less efficient). In simulations using two crustal outcrops having a different size, vigorous discharge of outcrop-to-outcrop flow is favored through the smaller and/or less permeable outcrop. In addition, simulations with a larger grid (40 km square versus 20 km square) result in higher fluid flow rates, apparently because there is more heat to be mined by flow between the outcrops. For simulations matching regional heat extraction observations, the outcrop-to-outcrop flow rates from the smaller outcrops are 1,000-3,000 kg/s (for the smaller grids) and 2,000-10,000 kg/s (for larger grids), values consistent with predictions made on the basis of a regional heat flux budget. In many simulations, local convection in and out of individual, large outcrops also removes a significant fraction of lithospheric heat. Additional simulations were conducted with three or four outcrops per simulation grid, to further explore relationships between the geometry, properties, and advective heat extraction.

32 CFR 1800.33 - Allocation of resources; agreed extensions of time.

Code of Federal Regulations, 2010 CFR

2010-07-01

... strictly “first-in, first-out” basis and utilizing two or more processing queues to ensure that smaller as... Coordinator is responsible for management of the NACIC-wide program defined by this part and for establishing...

32 CFR 1801.33 - Allocation of resources; agreed extensions of time.

Code of Federal Regulations, 2010 CFR

2010-07-01

...” basis and utilizing two or more processing queues to ensure that smaller as well as larger (i.e... management of the NACIC-wide program defined by this part and for establishing priorities for cases...

On the effects of basis set truncation and electron correlation in conformers of 2-hydroxy-acetamide

NASA Astrophysics Data System (ADS)

Szarecka, A.; Day, G.; Grout, P. J.; Wilson, S.

Ab initio quantum chemical calculations have been used to study the differences in energy between two gas phase conformers of the 2-hydroxy-acetamide molecule that possess intramolecular hydrogen bonding. In particular, rotation around the central C-C bond has been considered as a factor determining the structure of the hydrogen bond and stabilization of the conformer. Energy calculations include full geometiy optimization using both the restricted matrix Hartree-Fock model and second-order many-body perturbation theory with a number of commonly used basis sets. The basis sets employed ranged from the minimal STO-3G set to [`]split-valence' sets up to 6-31 G. The effects of polarization functions were also studied. The results display a strong basis set dependence.

How food marketers can sell smaller portions: Consumer insights and product innovation.

PubMed

Riis, J; Fisher, J O; Rowe, S

2016-08-01

Food portion size has been shown to be an important driver of energy intake. Despite the well acknowledged role of portion control in weight management, large portion sizes remain ubiquitous in the marketplace. Moving consumers towards consumption of smaller portion sizes will require changes in consumer behavior as well as changes in products available to consumers in a variety of settings. This special supplement presents cutting edge research aimed at understanding consumer behavior around portion size and innovations in product design that may promote the selection and consumption of smaller portion sizes. We identify further research that will be needed to translate basic behavioral findings into real world settings and to viable product development. Copyright © 2016. Published by Elsevier Ltd.

On the optimization of Gaussian basis sets

NASA Astrophysics Data System (ADS)

Petersson, George A.; Zhong, Shijun; Montgomery, John A.; Frisch, Michael J.

2003-01-01

A new procedure for the optimization of the exponents, αj, of Gaussian basis functions, Ylm(ϑ,φ)rle-αjr2, is proposed and evaluated. The direct optimization of the exponents is hindered by the very strong coupling between these nonlinear variational parameters. However, expansion of the logarithms of the exponents in the orthonormal Legendre polynomials, Pk, of the index, j: ln αj=∑k=0kmaxAkPk((2j-2)/(Nprim-1)-1), yields a new set of well-conditioned parameters, Ak, and a complete sequence of well-conditioned exponent optimizations proceeding from the even-tempered basis set (kmax=1) to a fully optimized basis set (kmax=Nprim-1). The error relative to the exact numerical self-consistent field limit for a six-term expansion is consistently no more than 25% larger than the error for the completely optimized basis set. Thus, there is no need to optimize more than six well-conditioned variational parameters, even for the largest sets of Gaussian primitives.

Development of a database for the verification of trans-ionospheric remote sensing systems

NASA Astrophysics Data System (ADS)

Leitinger, R.

2005-08-01

Remote sensing systems need verification by means of in-situ data or by means of model data. In the case of ionospheric occultation inversion, ionosphere tomography and other imaging methods on the basis of satellite-to-ground or satellite-to-satellite electron content, the availability of in-situ data with adequate spatial and temporal co-location is a very rare case, indeed. Therefore the method of choice for verification is to produce artificial electron content data with realistic properties, subject these data to the inversion/retrieval method, compare the results with model data and apply a suitable type of “goodness of fit” classification. Inter-comparison of inversion/retrieval methods should be done with sets of artificial electron contents in a “blind” (or even “double blind”) way. The set up of a relevant database for the COST 271 Action is described. One part of the database will be made available to everyone interested in testing of inversion/retrieval methods. The artificial electron content data are calculated by means of large-scale models that are “modulated” in a realistic way to include smaller scale and dynamic structures, like troughs and traveling ionospheric disturbances.

In vivo growth of 60 non-screening detected lung cancers: a computed tomography study.

PubMed

Mets, Onno M; Chung, Kaman; Zanen, Pieter; Scholten, Ernst T; Veldhuis, Wouter B; van Ginneken, Bram; Prokop, Mathias; Schaefer-Prokop, Cornelia M; de Jong, Pim A

2018-04-01

Current pulmonary nodule management guidelines are based on nodule volume doubling time, which assumes exponential growth behaviour. However, this is a theory that has never been validated in vivo in the routine-care target population. This study evaluates growth patterns of untreated solid and subsolid lung cancers of various histologies in a non-screening setting.Growth behaviour of pathology-proven lung cancers from two academic centres that were imaged at least three times before diagnosis (n=60) was analysed using dedicated software. Random-intercept random-slope mixed-models analysis was applied to test which growth pattern most accurately described lung cancer growth. Individual growth curves were plotted per pathology subgroup and nodule type.We confirmed that growth in both subsolid and solid lung cancers is best explained by an exponential model. However, subsolid lesions generally progress slower than solid ones. Baseline lesion volume was not related to growth, indicating that smaller lesions do not grow slower compared to larger ones.By showing that lung cancer conforms to exponential growth we provide the first experimental basis in the routine-care setting for the assumption made in volume doubling time analysis. Copyright ©ERS 2018.

Structure, energetics and vibrational spectra of dimers, trimers, and tetramers of HX (X = Cl, Br, I)

NASA Astrophysics Data System (ADS)

Latajka, Zdzislaw; Scheiner, Steve

1997-03-01

The title complexes are studied by correlated ab initio methods using a pseudopotential double-ζ basis set, augmented by diffuse sp and two sets of polarization functions. The binding energies of the complexes decrease in the order HCl > HBr > HI. In the mixed HX…HX' dimers, the nature of the proton-donor molecule is more important than is the proton-acceptor with respect to the strength of the interaction. Only one minimum is found on the potential energy surface of the trimers and tetramers, which corresponds to the C nh cyclic structure. Enlargement of the complex leads to progressively greater individual H-bond energy and HX bond stretch, coupled with reduced intermolecular separation and smaller nonlinearity of each H-bond. Electron correlation makes a larger contribution as the atomic number of X increases. The highest degree of cooperativity is noted for oligomers of HCl and HBr, as compared to HI. The nonadditivity is dominated by terms present at the SCF level. The vibrational frequencies exhibit trends that generally parallel the energetics and geometry patterns, particularly the red shifts of the HX stretches and the intermolecular modes.

The application of midbond basis sets in efficient and accurate ab initio calculations on electron-deficient systems

NASA Astrophysics Data System (ADS)

Choi, Chu Hwan

2002-09-01

Ab initio chemistry has shown great promise in reproducing experimental results and in its predictive power. The many complicated computational models and methods seem impenetrable to an inexperienced scientist, and the reliability of the results is not easily interpreted. The application of midbond orbitals is used to determine a general method for use in calculating weak intermolecular interactions, especially those involving electron-deficient systems. Using the criteria of consistency, flexibility, accuracy and efficiency we propose a supermolecular method of calculation using the full counterpoise (CP) method of Boys and Bernardi, coupled with Moller-Plesset (MP) perturbation theory as an efficient electron-correlative method. We also advocate the use of the highly efficient and reliable correlation-consistent polarized valence basis sets of Dunning. To these basis sets, we add a general set of midbond orbitals and demonstrate greatly enhanced efficiency in the calculation. The H2-H2 dimer is taken as a benchmark test case for our method, and details of the computation are elaborated. Our method reproduces with great accuracy the dissociation energies of other previous theoretical studies. The added efficiency of extending the basis sets with conventional means is compared with the performance of our midbond-extended basis sets. The improvement found with midbond functions is notably superior in every case tested. Finally, a novel application of midbond functions to the BH5 complex is presented. The system is an unusual van der Waals complex. The interaction potential curves are presented for several standard basis sets and midbond-enhanced basis sets, as well as for two popular, alternative correlation methods. We report that MP theory appears to be superior to coupled-cluster (CC) in speed, while it is more stable than B3LYP, a widely-used density functional theory (DFT). Application of our general method yields excellent results for the midbond basis sets. Again they prove superior to conventional extended basis sets. Based on these results, we recommend our general approach as a highly efficient, accurate method for calculating weakly interacting systems.

Basis set limit and systematic errors in local-orbital based all-electron DFT

NASA Astrophysics Data System (ADS)

Blum, Volker; Behler, Jörg; Gehrke, Ralf; Reuter, Karsten; Scheffler, Matthias

2006-03-01

With the advent of efficient integration schemes,^1,2 numeric atom-centered orbitals (NAO's) are an attractive basis choice in practical density functional theory (DFT) calculations of nanostructured systems (surfaces, clusters, molecules). Though all-electron, the efficiency of practical implementations promises to be on par with the best plane-wave pseudopotential codes, while having a noticeably higher accuracy if required: Minimal-sized effective tight-binding like calculations and chemically accurate all-electron calculations are both possible within the same framework; non-periodic and periodic systems can be treated on equal footing; and the localized nature of the basis allows in principle for O(N)-like scaling. However, converging an observable with respect to the basis set is less straightforward than with competing systematic basis choices (e.g., plane waves). We here investigate the basis set limit of optimized NAO basis sets in all-electron calculations, using as examples small molecules and clusters (N2, Cu2, Cu4, Cu10). meV-level total energy convergence is possible using <=50 basis functions per atom in all cases. We also find a clear correlation between the errors which arise from underconverged basis sets, and the system geometry (interatomic distance). ^1 B. Delley, J. Chem. Phys. 92, 508 (1990), ^2 J.M. Soler et al., J. Phys.: Condens. Matter 14, 2745 (2002).

Basis set construction for molecular electronic structure theory: natural orbital and Gauss-Slater basis for smooth pseudopotentials.

PubMed

Petruzielo, F R; Toulouse, Julien; Umrigar, C J

2011-02-14

A simple yet general method for constructing basis sets for molecular electronic structure calculations is presented. These basis sets consist of atomic natural orbitals from a multiconfigurational self-consistent field calculation supplemented with primitive functions, chosen such that the asymptotics are appropriate for the potential of the system. Primitives are optimized for the homonuclear diatomic molecule to produce a balanced basis set. Two general features that facilitate this basis construction are demonstrated. First, weak coupling exists between the optimal exponents of primitives with different angular momenta. Second, the optimal primitive exponents for a chosen system depend weakly on the particular level of theory employed for optimization. The explicit case considered here is a basis set appropriate for the Burkatzki-Filippi-Dolg pseudopotentials. Since these pseudopotentials are finite at nuclei and have a Coulomb tail, the recently proposed Gauss-Slater functions are the appropriate primitives. Double- and triple-zeta bases are developed for elements hydrogen through argon. These new bases offer significant gains over the corresponding Burkatzki-Filippi-Dolg bases at various levels of theory. Using a Gaussian expansion of the basis functions, these bases can be employed in any electronic structure method. Quantum Monte Carlo provides an added benefit: expansions are unnecessary since the integrals are evaluated numerically.

Adaptive local basis set for Kohn–Sham density functional theory in a discontinuous Galerkin framework II: Force, vibration, and molecular dynamics calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Gaigong; Lin, Lin, E-mail: linlin@math.berkeley.edu; Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720

Recently, we have proposed the adaptive local basis set for electronic structure calculations based on Kohn–Sham density functional theory in a pseudopotential framework. The adaptive local basis set is efficient and systematically improvable for total energy calculations. In this paper, we present the calculation of atomic forces, which can be used for a range of applications such as geometry optimization and molecular dynamics simulation. We demonstrate that, under mild assumptions, the computation of atomic forces can scale nearly linearly with the number of atoms in the system using the adaptive local basis set. We quantify the accuracy of the Hellmann–Feynmanmore » forces for a range of physical systems, benchmarked against converged planewave calculations, and find that the adaptive local basis set is efficient for both force and energy calculations, requiring at most a few tens of basis functions per atom to attain accuracies required in practice. Since the adaptive local basis set has implicit dependence on atomic positions, Pulay forces are in general nonzero. However, we find that the Pulay force is numerically small and systematically decreasing with increasing basis completeness, so that the Hellmann–Feynman force is sufficient for basis sizes of a few tens of basis functions per atom. We verify the accuracy of the computed forces in static calculations of quasi-1D and 3D disordered Si systems, vibration calculation of a quasi-1D Si system, and molecular dynamics calculations of H{sub 2} and liquid Al–Si alloy systems, where we show systematic convergence to benchmark planewave results and results from the literature.« less

Adaptive local basis set for Kohn–Sham density functional theory in a discontinuous Galerkin framework II: Force, vibration, and molecular dynamics calculations

DOE PAGES

Zhang, Gaigong; Lin, Lin; Hu, Wei; ...

2017-01-27

Recently, we have proposed the adaptive local basis set for electronic structure calculations based on Kohn–Sham density functional theory in a pseudopotential framework. The adaptive local basis set is efficient and systematically improvable for total energy calculations. In this paper, we present the calculation of atomic forces, which can be used for a range of applications such as geometry optimization and molecular dynamics simulation. We demonstrate that, under mild assumptions, the computation of atomic forces can scale nearly linearly with the number of atoms in the system using the adaptive local basis set. We quantify the accuracy of the Hellmann–Feynmanmore » forces for a range of physical systems, benchmarked against converged planewave calculations, and find that the adaptive local basis set is efficient for both force and energy calculations, requiring at most a few tens of basis functions per atom to attain accuracies required in practice. Sin ce the adaptive local basis set has implicit dependence on atomic positions, Pulay forces are in general nonzero. However, we find that the Pulay force is numerically small and systematically decreasing with increasing basis completeness, so that the Hellmann–Feynman force is sufficient for basis sizes of a few tens of basis functions per atom. We verify the accuracy of the computed forces in static calculations of quasi-1D and 3D disordered Si systems, vibration calculation of a quasi-1D Si system, and molecular dynamics calculations of H 2 and liquid Al–Si alloy systems, where we show systematic convergence to benchmark planewave results and results from the literature.« less

Adaptive local basis set for Kohn–Sham density functional theory in a discontinuous Galerkin framework II: Force, vibration, and molecular dynamics calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Gaigong; Lin, Lin; Hu, Wei

Recently, we have proposed the adaptive local basis set for electronic structure calculations based on Kohn–Sham density functional theory in a pseudopotential framework. The adaptive local basis set is efficient and systematically improvable for total energy calculations. In this paper, we present the calculation of atomic forces, which can be used for a range of applications such as geometry optimization and molecular dynamics simulation. We demonstrate that, under mild assumptions, the computation of atomic forces can scale nearly linearly with the number of atoms in the system using the adaptive local basis set. We quantify the accuracy of the Hellmann–Feynmanmore » forces for a range of physical systems, benchmarked against converged planewave calculations, and find that the adaptive local basis set is efficient for both force and energy calculations, requiring at most a few tens of basis functions per atom to attain accuracies required in practice. Sin ce the adaptive local basis set has implicit dependence on atomic positions, Pulay forces are in general nonzero. However, we find that the Pulay force is numerically small and systematically decreasing with increasing basis completeness, so that the Hellmann–Feynman force is sufficient for basis sizes of a few tens of basis functions per atom. We verify the accuracy of the computed forces in static calculations of quasi-1D and 3D disordered Si systems, vibration calculation of a quasi-1D Si system, and molecular dynamics calculations of H 2 and liquid Al–Si alloy systems, where we show systematic convergence to benchmark planewave results and results from the literature.« less

Adaptive local basis set for Kohn-Sham density functional theory in a discontinuous Galerkin framework II: Force, vibration, and molecular dynamics calculations

NASA Astrophysics Data System (ADS)

Zhang, Gaigong; Lin, Lin; Hu, Wei; Yang, Chao; Pask, John E.

2017-04-01

Recently, we have proposed the adaptive local basis set for electronic structure calculations based on Kohn-Sham density functional theory in a pseudopotential framework. The adaptive local basis set is efficient and systematically improvable for total energy calculations. In this paper, we present the calculation of atomic forces, which can be used for a range of applications such as geometry optimization and molecular dynamics simulation. We demonstrate that, under mild assumptions, the computation of atomic forces can scale nearly linearly with the number of atoms in the system using the adaptive local basis set. We quantify the accuracy of the Hellmann-Feynman forces for a range of physical systems, benchmarked against converged planewave calculations, and find that the adaptive local basis set is efficient for both force and energy calculations, requiring at most a few tens of basis functions per atom to attain accuracies required in practice. Since the adaptive local basis set has implicit dependence on atomic positions, Pulay forces are in general nonzero. However, we find that the Pulay force is numerically small and systematically decreasing with increasing basis completeness, so that the Hellmann-Feynman force is sufficient for basis sizes of a few tens of basis functions per atom. We verify the accuracy of the computed forces in static calculations of quasi-1D and 3D disordered Si systems, vibration calculation of a quasi-1D Si system, and molecular dynamics calculations of H2 and liquid Al-Si alloy systems, where we show systematic convergence to benchmark planewave results and results from the literature.

Benchmark of Ab Initio Bethe-Salpeter Equation Approach with Numeric Atom-Centered Orbitals

NASA Astrophysics Data System (ADS)

Liu, Chi; Kloppenburg, Jan; Kanai, Yosuke; Blum, Volker

The Bethe-Salpeter equation (BSE) approach based on the GW approximation has been shown to be successful for optical spectra prediction of solids and recently also for small molecules. We here present an all-electron implementation of the BSE using numeric atom-centered orbital (NAO) basis sets. In this work, we present benchmark of BSE implemented in FHI-aims for low-lying excitation energies for a set of small organic molecules, the well-known Thiel's set. The difference between our implementation (using an analytic continuation of the GW self-energy on the real axis) and the results generated by a fully frequency dependent GW treatment on the real axis is on the order of 0.07 eV for the benchmark molecular set. We study the convergence behavior to the complete basis set limit for excitation spectra, using a group of valence correlation consistent NAO basis sets (NAO-VCC-nZ), as well as for standard NAO basis sets for ground state DFT with extended augmentation functions (NAO+aug). The BSE results and convergence behavior are compared to linear-response time-dependent DFT, where excellent numerical convergence is shown for NAO+aug basis sets.

Kinetic balance and variational bounds failure in the solution of the Dirac equation in a finite Gaussian basis set

NASA Technical Reports Server (NTRS)

Dyall, Kenneth G.; Faegri, Knut, Jr.

1990-01-01

The paper investigates bounds failure in calculations using Gaussian basis sets for the solution of the one-electron Dirac equation for the 2p1/2 state of Hg(79+). It is shown that bounds failure indicates inadequacies in the basis set, both in terms of the exponent range and the number of functions. It is also shown that overrepresentation of the small component space may lead to unphysical results. It is concluded that it is important to use matched large and small component basis sets with an adequate size and exponent range.

Ab Initio and Analytic Intermolecular Potentials for Ar-CF₄

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vayner, Grigoriy; Alexeev, Yuri; Wang, Jiangping

2006-03-09

Ab initio calculations at the CCSD(T) level of theory are performed to characterize the Ar + CF ₄ intermolecular potential. Extensive calculations, with and without a correction for basis set superposition error (BSSE), are performed with the cc-pVTZ basis set. Additional calculations are performed with other correlation consistent (cc) basis sets to extrapolate the Ar---CF₄potential energy minimum to the complete basis set (CBS) limit. Both the size of the basis set and BSSE have substantial effects on the Ar + CF₄ potential. Calculations with the cc-pVTZ basis set and without a BSSE correction, appear to give a good representation ofmore » the potential at the CBS limit and with a BSSE correction. In addition, MP2 theory is found to give potential energies in very good agreement with those determined by the much higher level CCSD(T) theory. Two analytic potential energy functions were determined for Ar + CF₄by fitting the cc-pVTZ calculations both with and without a BSSE correction. These analytic functions were written as a sum of two body potentials and excellent fits to the ab initio potentials were obtained by representing each two body interaction as a Buckingham potential.« less

On the performance of large Gaussian basis sets for the computation of total atomization energies

NASA Technical Reports Server (NTRS)

Martin, J. M. L.

1992-01-01

The total atomization energies of a number of molecules have been computed using an augmented coupled-cluster method and (5s4p3d2f1g) and 4s3p2d1f) atomic natural orbital (ANO) basis sets, as well as the correlation consistent valence triple zeta plus polarization (cc-pVTZ) correlation consistent valence quadrupole zeta plus polarization (cc-pVQZ) basis sets. The performance of ANO and correlation consistent basis sets is comparable throughout, although the latter can result in significant CPU time savings. Whereas the inclusion of g functions has significant effects on the computed Sigma D(e) values, chemical accuracy is still not reached for molecules involving multiple bonds. A Gaussian-1 (G) type correction lowers the error, but not much beyond the accuracy of the G1 model itself. Using separate corrections for sigma bonds, pi bonds, and valence pairs brings down the mean absolute error to less than 1 kcal/mol for the spdf basis sets, and about 0.5 kcal/mol for the spdfg basis sets. Some conclusions on the success of the Gaussian-1 and Gaussian-2 models are drawn.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shirkov, Leonid; Makarewicz, Jan, E-mail: jama@amu.edu.pl

An ab initio intermolecular potential energy surface (PES) has been constructed for the benzene-krypton (BKr) van der Waals (vdW) complex. The interaction energy has been calculated at the coupled cluster level of theory with single, double, and perturbatively included triple excitations using different basis sets. As a result, a few analytical PESs of the complex have been determined. They allowed a prediction of the complex structure and its vibrational vdW states. The vibrational energy level pattern exhibits a distinct polyad structure. Comparison of the equilibrium structure, the dipole moment, and vibrational levels of BKr with their experimental counterparts has allowedmore » us to design an optimal basis set composed of a small Dunning’s basis set for the benzene monomer, a larger effective core potential adapted basis set for Kr and additional midbond functions. Such a basis set yields vibrational energy levels that agree very well with the experimental ones as well as with those calculated from the available empirical PES derived from the microwave spectra of the BKr complex. The basis proposed can be applied to larger complexes including Kr because of a reasonable computational cost and accurate results.« less

Polarized atomic orbitals for self-consistent field electronic structure calculations

NASA Astrophysics Data System (ADS)

Lee, Michael S.; Head-Gordon, Martin

1997-12-01

We present a new self-consistent field approach which, given a large "secondary" basis set of atomic orbitals, variationally optimizes molecular orbitals in terms of a small "primary" basis set of distorted atomic orbitals, which are simultaneously optimized. If the primary basis is taken as a minimal basis, the resulting functions are termed polarized atomic orbitals (PAO's) because they are valence (or core) atomic orbitals which have distorted or polarized in an optimal way for their molecular environment. The PAO's derive their flexibility from the fact that they are formed from atom-centered linear-combinations of the larger set of secondary atomic orbitals. The variational conditions satisfied by PAO's are defined, and an iterative method for performing a PAO-SCF calculation is introduced. We compare the PAO-SCF approach against full SCF calculations for the energies, dipoles, and molecular geometries of various molecules. The PAO's are potentially useful for studying large systems that are currently intractable with larger than minimal basis sets, as well as offering potential interpretative benefits relative to calculations in extended basis sets.

Incomplete Gröbner basis as a preconditioner for polynomial systems

NASA Astrophysics Data System (ADS)

Sun, Yang; Tao, Yu-Hui; Bai, Feng-Shan

2009-04-01

Precondition plays a critical role in the numerical methods for large and sparse linear systems. It is also true for nonlinear algebraic systems. In this paper incomplete Gröbner basis (IGB) is proposed as a preconditioner of homotopy methods for polynomial systems of equations, which transforms a deficient system into a system with the same finite solutions, but smaller degree. The reduced system can thus be solved faster. Numerical results show the efficiency of the preconditioner.

Using an expanding nondirect product harmonic basis with an iterative eigensolver to compute vibrational energy levels with as many as seven atoms.

PubMed

Brown, James; Carrington, Tucker

2016-10-14

We demonstrate that it is possible to use a variational method to compute 50 vibrational levels of ethylene oxide (a seven-atom molecule) with convergence errors less than 0.01 cm -1 . This is done by beginning with a small basis and expanding it to include product basis functions that are deemed to be important. For ethylene oxide a basis with fewer than 3 × 10 6 functions is large enough. Because the resulting basis has no exploitable structure we use a mapping to evaluate the matrix-vector products required to use an iterative eigensolver. The expanded basis is compared to bases obtained from pre-determined pruning condition. Similar calculations are presented for molecules with 3, 4, 5, and 6 atoms. For the 6-atom molecule, CH 3 CH, the required expanded basis has about 106 000 functions and is about an order of magnitude smaller than bases made with a pre-determined pruning condition.

Ontology modularization to improve semantic medical image annotation.

PubMed

Wennerberg, Pinar; Schulz, Klaus; Buitelaar, Paul

2011-02-01

Searching for medical images and patient reports is a significant challenge in a clinical setting. The contents of such documents are often not described in sufficient detail thus making it difficult to utilize the inherent wealth of information contained within them. Semantic image annotation addresses this problem by describing the contents of images and reports using medical ontologies. Medical images and patient reports are then linked to each other through common annotations. Subsequently, search algorithms can more effectively find related sets of documents on the basis of these semantic descriptions. A prerequisite to realizing such a semantic search engine is that the data contained within should have been previously annotated with concepts from medical ontologies. One major challenge in this regard is the size and complexity of medical ontologies as annotation sources. Manual annotation is particularly time consuming labor intensive in a clinical environment. In this article we propose an approach to reducing the size of clinical ontologies for more efficient manual image and text annotation. More precisely, our goal is to identify smaller fragments of a large anatomy ontology that are relevant for annotating medical images from patients suffering from lymphoma. Our work is in the area of ontology modularization, which is a recent and active field of research. We describe our approach, methods and data set in detail and we discuss our results. Copyright © 2010 Elsevier Inc. All rights reserved.

A method of classification for multisource data in remote sensing based on interval-valued probabilities

NASA Technical Reports Server (NTRS)

Kim, Hakil; Swain, Philip H.

1990-01-01

An axiomatic approach to intervalued (IV) probabilities is presented, where the IV probability is defined by a pair of set-theoretic functions which satisfy some pre-specified axioms. On the basis of this approach representation of statistical evidence and combination of multiple bodies of evidence are emphasized. Although IV probabilities provide an innovative means for the representation and combination of evidential information, they make the decision process rather complicated. It entails more intelligent strategies for making decisions. The development of decision rules over IV probabilities is discussed from the viewpoint of statistical pattern recognition. The proposed method, so called evidential reasoning method, is applied to the ground-cover classification of a multisource data set consisting of Multispectral Scanner (MSS) data, Synthetic Aperture Radar (SAR) data, and digital terrain data such as elevation, slope, and aspect. By treating the data sources separately, the method is able to capture both parametric and nonparametric information and to combine them. Then the method is applied to two separate cases of classifying multiband data obtained by a single sensor. In each case a set of multiple sources is obtained by dividing the dimensionally huge data into smaller and more manageable pieces based on the global statistical correlation information. By a divide-and-combine process, the method is able to utilize more features than the conventional maximum likelihood method.

Auditory proactive interference in monkeys: the roles of stimulus set size and intertrial interval.

PubMed

Bigelow, James; Poremba, Amy

2013-09-01

We conducted two experiments to examine the influences of stimulus set size (the number of stimuli that are used throughout the session) and intertrial interval (ITI, the elapsed time between trials) in auditory short-term memory in monkeys. We used an auditory delayed matching-to-sample task wherein the animals had to indicate whether two sounds separated by a 5-s retention interval were the same (match trials) or different (nonmatch trials). In Experiment 1, we randomly assigned stimulus set sizes of 2, 4, 8, 16, 32, 64, or 192 (trial-unique) for each session of 128 trials. Consistent with previous visual studies, overall accuracy was consistently lower when smaller stimulus set sizes were used. Further analyses revealed that these effects were primarily caused by an increase in incorrect "same" responses on nonmatch trials. In Experiment 2, we held the stimulus set size constant at four for each session and alternately set the ITI at 5, 10, or 20 s. Overall accuracy improved when the ITI was increased from 5 to 10 s, but it was the same across the 10- and 20-s conditions. As in Experiment 1, the overall decrease in accuracy during the 5-s condition was caused by a greater number of false "match" responses on nonmatch trials. Taken together, Experiments 1 and 2 showed that auditory short-term memory in monkeys is highly susceptible to proactive interference caused by stimulus repetition. Additional analyses of the data from Experiment 1 suggested that monkeys may make same-different judgments on the basis of a familiarity criterion that is adjusted by error-related feedback.

42 CFR 415.170 - Conditions for payment on a fee schedule basis for physician services in a teaching setting.

Code of Federal Regulations, 2010 CFR

2010-10-01

... physician services in a teaching setting. 415.170 Section 415.170 Public Health CENTERS FOR MEDICARE... BY PHYSICIANS IN PROVIDERS, SUPERVISING PHYSICIANS IN TEACHING SETTINGS, AND RESIDENTS IN CERTAIN SETTINGS Physician Services in Teaching Settings § 415.170 Conditions for payment on a fee schedule basis...

Projected Hybrid Orbitals: A General QM/MM Method

PubMed Central

2015-01-01

A projected hybrid orbital (PHO) method was described to model the covalent boundary in a hybrid quantum mechanical and molecular mechanical (QM/MM) system. The PHO approach can be used in ab initio wave function theory and in density functional theory with any basis set without introducing system-dependent parameters. In this method, a secondary basis set on the boundary atom is introduced to formulate a set of hybrid atomic orbtials. The primary basis set on the boundary atom used for the QM subsystem is projected onto the secondary basis to yield a representation that provides a good approximation to the electron-withdrawing power of the primary basis set to balance electronic interactions between QM and MM subsystems. The PHO method has been tested on a range of molecules and properties. Comparison with results obtained from QM calculations on the entire system shows that the present PHO method is a robust and balanced QM/MM scheme that preserves the structural and electronic properties of the QM region. PMID:25317748

A novel Gaussian-Sinc mixed basis set for electronic structure calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jerke, Jonathan L.; Lee, Young; Tymczak, C. J.

2015-08-14

A Gaussian-Sinc basis set methodology is presented for the calculation of the electronic structure of atoms and molecules at the Hartree–Fock level of theory. This methodology has several advantages over previous methods. The all-electron electronic structure in a Gaussian-Sinc mixed basis spans both the “localized” and “delocalized” regions. A basis set for each region is combined to make a new basis methodology—a lattice of orthonormal sinc functions is used to represent the “delocalized” regions and the atom-centered Gaussian functions are used to represent the “localized” regions to any desired accuracy. For this mixed basis, all the Coulomb integrals are definablemore » and can be computed in a dimensional separated methodology. Additionally, the Sinc basis is translationally invariant, which allows for the Coulomb singularity to be placed anywhere including on lattice sites. Finally, boundary conditions are always satisfied with this basis. To demonstrate the utility of this method, we calculated the ground state Hartree–Fock energies for atoms up to neon, the diatomic systems H{sub 2}, O{sub 2}, and N{sub 2}, and the multi-atom system benzene. Together, it is shown that the Gaussian-Sinc mixed basis set is a flexible and accurate method for solving the electronic structure of atomic and molecular species.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hill, J. Grant, E-mail: grant.hill@sheffield.ac.uk, E-mail: kipeters@wsu.edu; Peterson, Kirk A., E-mail: grant.hill@sheffield.ac.uk, E-mail: kipeters@wsu.edu

New correlation consistent basis sets, cc-pVnZ-PP-F12 (n = D, T, Q), for all the post-d main group elements Ga–Rn have been optimized for use in explicitly correlated F12 calculations. The new sets, which include not only orbital basis sets but also the matching auxiliary sets required for density fitting both conventional and F12 integrals, are designed for correlation of valence sp, as well as the outer-core d electrons. The basis sets are constructed for use with the previously published small-core relativistic pseudopotentials of the Stuttgart-Cologne variety. Benchmark explicitly correlated coupled-cluster singles and doubles with perturbative triples [CCSD(T)-F12b] calculations of themore » spectroscopic properties of numerous diatomic molecules involving 4p, 5p, and 6p elements have been carried out and compared to the analogous conventional CCSD(T) results. In general the F12 results obtained with a n-zeta F12 basis set were comparable to conventional aug-cc-pVxZ-PP or aug-cc-pwCVxZ-PP basis set calculations obtained with x = n + 1 or even x = n + 2. The new sets used in CCSD(T)-F12b calculations are particularly efficient at accurately recovering the large correlation effects of the outer-core d electrons.« less

Pile construction

DOEpatents

Johnson, Alfred A.; Carleton, John T.

1978-05-02

A graphite-moderated, water-cooled nuclear reactor including graphite blocks disposed in transverse alternate layers, one set of alternate layers consisting of alternate full size blocks and smaller blocks through which cooling tubes containing fuel extend, said smaller blocks consisting alternately of tube bearing blocks and support block, the support blocks being smaller than the tube bearing blocks, the aperture of each support block being tapered so as to provide the tube extending therethrough with a narrow region of support while being elsewhere spaced therefrom.

Many-body calculations with deuteron based single-particle bases and their associated natural orbits

NASA Astrophysics Data System (ADS)

Puddu, G.

2018-06-01

We use the recently introduced single-particle states obtained from localized deuteron wave-functions as a basis for nuclear many-body calculations. We show that energies can be substantially lowered if the natural orbits (NOs) obtained from this basis are used. We use this modified basis for {}10{{B}}, {}16{{O}} and {}24{{Mg}} employing the bare NNLOopt nucleon–nucleon interaction. The lowering of the energies increases with the mass. Although in principle NOs require a full scale preliminary many-body calculation, we found that an approximate preliminary many-body calculation, with a marginal increase in the computational cost, is sufficient. The use of natural orbits based on an harmonic oscillator basis leads to a much smaller lowering of the energies for a comparable computational cost.

High-level ab initio calculations for the four low-lying families of minima of (H2O)(20): 1. Estimates of MP2/CBS binding energies and comparison with empirical potentials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fanourgakis, Georgios S.; Apra, Edoardo; Xantheas, Sotiris S.

2004-08-08

We report estimates of complete basis set (CBS) limits at the second-order Møller-Plesset perturbation level of theory (MP2) for the binding energies of the lowest lying isomers within each of the four major families of minima of (H2O)20. These were obtained by performing MP2 calculations with the family of correlation-consistent basis sets up to quadruple zeta quality, augmented with additional diffuse functions (aug-cc-pVnZ, n=D, T, Q). The MP2/CBS estimates are: -200.1 kcal/mol (dodecahedron, 30 hydrogen bonds), -212.6 kcal/mol (fused cubes, 36 hydrogen bonds), -215.0 (face-sharing pentagonal prisms, 35 hydrogen bonds) and –217.9 kcal/mol (edge-sharing pentagonal prisms, 34 hydrogen bonds). Themore » energetic ordering of the various (H2O)20 isomers does not follow monotonically the number of hydrogen bonds as in the case of smaller clusters such as the different isomers of the water hexamer. The dodecahedron lies ca. 18 kcal/mol higher in energy than the most stable edge-sharing pentagonal prism isomer. The TIP4P, ASP-W4, TTM2-R, AMOEBA and TTM2-F empirical potentials also predict the energetic stabilization of the edge-sharing pentagonal prisms with respect to the dodecahedron, albeit they universally underestimate the cluster binding energies with respect to the MP2/CBS result. Among them, the TTM2-F potential was found to predict the absolute cluster binding energies to within < 1% from the corresponding MP2/CBS values, whereas the error for the rest of the potentials considered in this study ranges from 3-5%.« less

Comparison of fMRI analysis methods for heterogeneous BOLD responses in block design studies

PubMed Central

Bernal-Casas, David; Fang, Zhongnan; Lee, Jin Hyung

2017-01-01

A large number of fMRI studies have shown that the temporal dynamics of evoked BOLD responses can be highly heterogeneous. Failing to model heterogeneous responses in statistical analysis can lead to significant errors in signal detection and characterization and alter the neurobiological interpretation. However, to date it is not clear that, out of a large number of options, which methods are robust against variability in the temporal dynamics of BOLD responses in block-design studies. Here, we used rodent optogenetic fMRI data with heterogeneous BOLD responses and simulations guided by experimental data as a means to investigate different analysis methods’ performance against heterogeneous BOLD responses. Evaluations are carried out within the general linear model (GLM) framework and consist of standard basis sets as well as independent component analysis (ICA). Analyses show that, in the presence of heterogeneous BOLD responses, conventionally used GLM with a canonical basis set leads to considerable errors in the detection and characterization of BOLD responses. Our results suggest that the 3rd and 4th order gamma basis sets, the 7th to 9th order finite impulse response (FIR) basis sets, the 5th to 9th order B-spline basis sets, and the 2nd to 5th order Fourier basis sets are optimal for good balance between detection and characterization, while the 1st order Fourier basis set (coherence analysis) used in our earlier studies show good detection capability. ICA has mostly good detection and characterization capabilities, but detects a large volume of spurious activation with the control fMRI data. PMID:27993672

Naturally Occurring Compound Can Protect Pines from the Southern Pine Beetle

Treesearch

B.L. Strom; R.A. Goyer; J.L. Hayes

1995-01-01

The southern pine beetle (SPB), Dendroctonus frontalis, is the most destructive insect pest of southern pine forests. This tiny insect, smaller than a grain of rice, is responsible for killing pine timber worth millions of dollars on a periodic basis in Louisiana.

Comparing the UK EQ-5D-3L and English EQ-5D-5L Value Sets.

PubMed

Mulhern, Brendan; Feng, Yan; Shah, Koonal; Janssen, Mathieu F; Herdman, Michael; van Hout, Ben; Devlin, Nancy

2018-06-01

Three EQ-5D value sets (EQ-5D-3L, crosswalk, and EQ-5D-5L) are now available for cost-utility analysis in the UK and/or England. The value sets' characteristics differ, and it is important to assess the implications of these differences. The aim of this paper is to compare the three value sets. We carried out analysis comparing the predicted values from each value set, and investigated how differences in health on the descriptive system is reflected in the utility score by assessing the value of adjacent states. We also assessed differences in values using data from patients who completed both EQ-5D-3L and EQ-5D-5L. The distribution of the value sets systematically differed. EQ-5D-5L values were higher than EQ-5D-3L/crosswalk values. The overall range and difference between adjacent states was smaller. In the patient data, the EQ-5D-5L produced higher values across all conditions and there was some evidence that the value sets rank different health conditions in a similar severity order. There are important differences between the value sets. Due to the smaller range of EQ-5D-5L values, the possible change in quality-adjusted life years (QALYs) might be reduced, but they will apply to both control and intervention groups, and will depend on whether the gain is in quality of life, survival, or both. The increased sensitivity of EQ-5D-5L may also favour QALY gains even if the changes in utility are smaller. Further work should assess the impact of the different value sets on cost effectiveness by repeating the analysis on clinical trial data.

Conventional and Explicitly Correlated ab Initio Benchmark Study on Water Clusters: Revision of the BEGDB and WATER27 Data Sets.

PubMed

Manna, Debashree; Kesharwani, Manoj K; Sylvetsky, Nitai; Martin, Jan M L

2017-07-11

Benchmark ab initio energies for BEGDB and WATER27 data sets have been re-examined at the MP2 and CCSD(T) levels with both conventional and explicitly correlated (F12) approaches. The basis set convergence of both conventional and explicitly correlated methods has been investigated in detail, both with and without counterpoise corrections. For the MP2 and CCSD-MP2 contributions, rapid basis set convergence observed with explicitly correlated methods is compared to conventional methods. However, conventional, orbital-based calculations are preferred for the calculation of the (T) term, since it does not benefit from F12. CCSD(F12*) converges somewhat faster with the basis set than CCSD-F12b for the CCSD-MP2 term. The performance of various DFT methods is also evaluated for the BEGDB data set, and results show that Head-Gordon's ωB97X-V and ωB97M-V functionals outperform all other DFT functionals. Counterpoise-corrected DSD-PBEP86 and raw DSD-PBEPBE-NL also perform well and are close to MP2 results. In the WATER27 data set, the anionic (deprotonated) water clusters exhibit unacceptably slow basis set convergence with the regular cc-pVnZ-F12 basis sets, which have only diffuse s and p functions. To overcome this, we have constructed modified basis sets, denoted aug-cc-pVnZ-F12 or aVnZ-F12, which have been augmented with diffuse functions on the higher angular momenta. The calculated final dissociation energies of BEGDB and WATER27 data sets are available in the Supporting Information. Our best calculated dissociation energies can be reproduced through n-body expansion, provided one pushes to the basis set and electron correlation limit for the two-body term; for the three-body term, post-MP2 contributions (particularly CCSD-MP2) are important for capturing the three-body dispersion effects. Terms beyond four-body can be adequately captured at the MP2-F12 level.

On the Use of a Mixed Gaussian/Finite-Element Basis Set for the Calculation of Rydberg States

NASA Technical Reports Server (NTRS)

Thuemmel, Helmar T.; Langhoff, Stephen (Technical Monitor)

1996-01-01

Configuration-interaction studies are reported for the Rydberg states of the helium atom using mixed Gaussian/finite-element (GTO/FE) one particle basis sets. Standard Gaussian valence basis sets are employed, like those, used extensively in quantum chemistry calculations. It is shown that the term values for high-lying Rydberg states of the helium atom can be obtained accurately (within 1 cm -1), even for a small GTO set, by augmenting the n-particle space with configurations, where orthonormalized interpolation polynomials are singly occupied.

77 FR 14574 - Self-Regulatory Organizations; Municipal Securities Rulemaking Board; Notice of Filing of...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-03-12

... consisting of twelve consecutive complete month data sets of the documents and related indexing information....\\11\\ The MSRB proposes to charge $10,000 for any twelve consecutive complete month data set for the... data set for the Continuing Disclosure Historical Data Product.\\12\\ In general, no smaller data sets...

Perturbation corrections to Koopmans' theorem. V - A study with large basis sets

NASA Technical Reports Server (NTRS)

Chong, D. P.; Langhoff, S. R.

1982-01-01

The vertical ionization potentials of N2, F2 and H2O were calculated by perturbation corrections to Koopmans' theorem using six different basis sets. The largest set used includes several sets of polarization functions. Comparison is made with measured values and with results of computations using Green's functions.

A new basis set for molecular bending degrees of freedom.

PubMed

Jutier, Laurent

2010-07-21

We present a new basis set as an alternative to Legendre polynomials for the variational treatment of bending vibrational degrees of freedom in order to highly reduce the number of basis functions. This basis set is inspired from the harmonic oscillator eigenfunctions but is defined for a bending angle in the range theta in [0:pi]. The aim is to bring the basis functions closer to the final (ro)vibronic wave functions nature. Our methodology is extended to complicated potential energy surfaces, such as quasilinearity or multiequilibrium geometries, by using several free parameters in the basis functions. These parameters allow several density maxima, linear or not, around which the basis functions will be mainly located. Divergences at linearity in integral computations are resolved as generalized Legendre polynomials. All integral computations required for the evaluation of molecular Hamiltonian matrix elements are given for both discrete variable representation and finite basis representation. Convergence tests for the low energy vibronic states of HCCH(++), HCCH(+), and HCCS are presented.

Assessing the utility of phase-space-localized basis functions: Exploiting direct product structure and a new basis function selection procedure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brown, James, E-mail: 9jhb3@queensu.ca; Carrington, Tucker, E-mail: Tucker.Carrington@queensu.ca

In this paper we show that it is possible to use an iterative eigensolver in conjunction with Halverson and Poirier’s symmetrized Gaussian (SG) basis [T. Halverson and B. Poirier, J. Chem. Phys. 137, 224101 (2012)] to compute accurate vibrational energy levels of molecules with as many as five atoms. This is done, without storing and manipulating large matrices, by solving a regular eigenvalue problem that makes it possible to exploit direct-product structure. These ideas are combined with a new procedure for selecting which basis functions to use. The SG basis we work with is orders of magnitude smaller than themore » basis made by using a classical energy criterion. We find significant convergence errors in previous calculations with SG bases. For sum-of-product Hamiltonians, SG bases large enough to compute accurate levels are orders of magnitude larger than even simple pruned bases composed of products of harmonic oscillator functions.« less

Highly Efficient Design-of-Experiments Methods for Combining CFD Analysis and Experimental Data

NASA Technical Reports Server (NTRS)

Anderson, Bernhard H.; Haller, Harold S.

2009-01-01

It is the purpose of this study to examine the impact of "highly efficient" Design-of-Experiments (DOE) methods for combining sets of CFD generated analysis data with smaller sets of Experimental test data in order to accurately predict performance results where experimental test data were not obtained. The study examines the impact of micro-ramp flow control on the shock wave boundary layer (SWBL) interaction where a complete paired set of data exist from both CFD analysis and Experimental measurements By combining the complete set of CFD analysis data composed of fifteen (15) cases with a smaller subset of experimental test data containing four/five (4/5) cases, compound data sets (CFD/EXP) were generated which allows the prediction of the complete set of Experimental results No statistical difference were found to exist between the combined (CFD/EXP) generated data sets and the complete Experimental data set composed of fifteen (15) cases. The same optimal micro-ramp configuration was obtained using the (CFD/EXP) generated data as obtained with the complete set of Experimental data, and the DOE response surfaces generated by the two data sets were also not statistically different.

An Alternate Set of Basis Functions for the Electromagnetic Solution of Arbitrarily-Shaped, Three-Dimensional, Closed, Conducting Bodies Using Method of Moments

NASA Technical Reports Server (NTRS)

Mackenzie, Anne I.; Baginski, Michael E.; Rao, Sadasiva M.

2008-01-01

In this work, we present an alternate set of basis functions, each defined over a pair of planar triangular patches, for the method of moments solution of electromagnetic scattering and radiation problems associated with arbitrarily-shaped, closed, conducting surfaces. The present basis functions are point-wise orthogonal to the pulse basis functions previously defined. The prime motivation to develop the present set of basis functions is to utilize them for the electromagnetic solution of dielectric bodies using a surface integral equation formulation which involves both electric and magnetic cur- rents. However, in the present work, only the conducting body solution is presented and compared with other data.

Correction of energy-dependent systematic errors in dual-energy X-ray CT using a basis material coefficients transformation method

NASA Astrophysics Data System (ADS)

Goh, K. L.; Liew, S. C.; Hasegawa, B. H.

1997-12-01

Computer simulation results from our previous studies showed that energy dependent systematic errors exist in the values of attenuation coefficient synthesized using the basis material decomposition technique with acrylic and aluminum as the basis materials, especially when a high atomic number element (e.g., iodine from radiographic contrast media) was present in the body. The errors were reduced when a basis set was chosen from materials mimicking those found in the phantom. In the present study, we employed a basis material coefficients transformation method to correct for the energy-dependent systematic errors. In this method, the basis material coefficients were first reconstructed using the conventional basis materials (acrylic and aluminum) as the calibration basis set. The coefficients were then numerically transformed to those for a more desirable set materials. The transformation was done at the energies of the low and high energy windows of the X-ray spectrum. With this correction method using acrylic and an iodine-water mixture as our desired basis set, computer simulation results showed that accuracy of better than 2% could be achieved even when iodine was present in the body at a concentration as high as 10% by mass. Simulation work had also been carried out on a more inhomogeneous 2D thorax phantom of the 3D MCAT phantom. The results of the accuracy of quantitation were presented here.

Dispersion corrected hartree-fock and density functional theory for organic crystal structure prediction.

PubMed

Brandenburg, Jan Gerit; Grimme, Stefan

2014-01-01

We present and evaluate dispersion corrected Hartree-Fock (HF) and Density Functional Theory (DFT) based quantum chemical methods for organic crystal structure prediction. The necessity of correcting for missing long-range electron correlation, also known as van der Waals (vdW) interaction, is pointed out and some methodological issues such as inclusion of three-body dispersion terms are discussed. One of the most efficient and widely used methods is the semi-classical dispersion correction D3. Its applicability for the calculation of sublimation energies is investigated for the benchmark set X23 consisting of 23 small organic crystals. For PBE-D3 the mean absolute deviation (MAD) is below the estimated experimental uncertainty of 1.3 kcal/mol. For two larger π-systems, the equilibrium crystal geometry is investigated and very good agreement with experimental data is found. Since these calculations are carried out with huge plane-wave basis sets they are rather time consuming and routinely applicable only to systems with less than about 200 atoms in the unit cell. Aiming at crystal structure prediction, which involves screening of many structures, a pre-sorting with faster methods is mandatory. Small, atom-centered basis sets can speed up the computation significantly but they suffer greatly from basis set errors. We present the recently developed geometrical counterpoise correction gCP. It is a fast semi-empirical method which corrects for most of the inter- and intramolecular basis set superposition error. For HF calculations with nearly minimal basis sets, we additionally correct for short-range basis incompleteness. We combine all three terms in the HF-3c denoted scheme which performs very well for the X23 sublimation energies with an MAD of only 1.5 kcal/mol, which is close to the huge basis set DFT-D3 result.

Comparison of fMRI analysis methods for heterogeneous BOLD responses in block design studies.

PubMed

Liu, Jia; Duffy, Ben A; Bernal-Casas, David; Fang, Zhongnan; Lee, Jin Hyung

2017-02-15

A large number of fMRI studies have shown that the temporal dynamics of evoked BOLD responses can be highly heterogeneous. Failing to model heterogeneous responses in statistical analysis can lead to significant errors in signal detection and characterization and alter the neurobiological interpretation. However, to date it is not clear that, out of a large number of options, which methods are robust against variability in the temporal dynamics of BOLD responses in block-design studies. Here, we used rodent optogenetic fMRI data with heterogeneous BOLD responses and simulations guided by experimental data as a means to investigate different analysis methods' performance against heterogeneous BOLD responses. Evaluations are carried out within the general linear model (GLM) framework and consist of standard basis sets as well as independent component analysis (ICA). Analyses show that, in the presence of heterogeneous BOLD responses, conventionally used GLM with a canonical basis set leads to considerable errors in the detection and characterization of BOLD responses. Our results suggest that the 3rd and 4th order gamma basis sets, the 7th to 9th order finite impulse response (FIR) basis sets, the 5th to 9th order B-spline basis sets, and the 2nd to 5th order Fourier basis sets are optimal for good balance between detection and characterization, while the 1st order Fourier basis set (coherence analysis) used in our earlier studies show good detection capability. ICA has mostly good detection and characterization capabilities, but detects a large volume of spurious activation with the control fMRI data. Copyright © 2016 Elsevier Inc. All rights reserved.

Chimpanzees Sometimes See Fuller as Better: Judgments of Food Quantities Based on Container Size and Fullness

PubMed Central

Parrish, Audrey E.; Beran, Michael J.

2014-01-01

The context in which food is presented can alter quantity judgments leading to sub-optimal choice behavior. Humans often over-estimate food quantity on the basis of how food is presented. Food appears larger if plated on smaller dishes than larger dishes and liquid volumes appear larger in taller cups than shorter cups. Moreover, smaller but fuller containers are preferred in comparison to larger, but less full containers with a truly larger quantity. Here, we assessed whether similar phenomena occur in chimpanzees. Four chimpanzees chose between two amounts of food presented in different sized containers, a large (2 oz.) and small (1 oz.) cup. When different quantities were presented in the same-sized cups or when the small cup contained the larger quantity, chimpanzees were highly accurate in choosing the larger food amount. However, when different-sized cups contained the same amount of food or the smaller cup contained the smaller amount of food (but looked relatively fuller), the chimpanzees often showed a bias to select the smaller but fuller cup. These findings contribute to our understanding of how quantity estimation and portion judgment is impacted by the surrounding context in which it is presented. PMID:24374384

DFT conformational studies of the HI-6 molecule

NASA Astrophysics Data System (ADS)

Silva, Gustavo R.; Borges, Itamar; Figueroa-Villar, Jose D.

A systematic study of the oxime HI-6 [1-(2-hydroxyiminomethyl-1-pyridinium)-1-(4-carboxy-aminopyridinium)dimethyl ether] hydrochloride, which is one of the most promising antidotes against soman intoxication, was carried out using density functional theory with the B3LYP (Becke, Lee, Yang, and Parr) method and the 6-31+G*, 6-31+G*, and 6-31+G** basis sets. Rotational barriers, equilibrium geometries, and charge distributions were calculated in order to investigate the role of the side chain for the larger oximes used as antidotes in the treatment of neurotoxic organophosphate poisoning. Also reported is the comparison between HI-6 and pralidoxime (2-PAM), a smaller oxime previously studied in our research group. It is shown that conformation minima for the protonated E isomer do not depend on the size of the side chain; on the other hand, this effect has a pronounced influence on the protonated Z isomer. For the unprotonated isomers, other effects, such as electrostatic interactions and resonance, should be taken into account in their conformational analysis.

Nuclear relaxation and vibrational contributions to the static electrical properties of polyatomic molecules: beyond the Hartree-Fock approximation

NASA Astrophysics Data System (ADS)

Luis, Josep M.; Martí, Josep; Duran, Miquel; Andrés, JoséL.

1997-04-01

Electronic and nuclear contributions to the static molecular electrical properties, along with the Stark tuning rate ( δνE ) and the infrared cross section changes ( δSE) have been calculated at the SCF level and at different correlated levels of theory, using a TZ2P basis set and finite field techniques. Nuclear contributions to these molecular properties have also been calculated using a recent analytical approach that allow both to check the accuracy of the finite field values, and to evaluate the importance of higher-order derivatives. The HF, CO, H 2O, H 2CO, and CH 4 molecules have been studied and the results compared to experimental date when available. The paper shows that nuclear relaxation and vibrational contributions must be included in order to obtain accurate values of the static electrical properties. Two different, combined approaches are proposed to predict experimental values of the electrical properties to an error smaller than 5%.

Volcanic rises on Venus: Geology, formation, and sequence of evolution

NASA Technical Reports Server (NTRS)

Senske, D. A.; Stofan, E. R.; Bindschadler, D. L.; Smrekar, S. E.

1993-01-01

Large centers of volcanism on Venus are concentrated primarily in the equatorial region of the planet and are associated with regional topographic rises. Analysis of both radar images and geophysical data suggest that these uplands are sites of mantle upwelling. Magellan radar imaging provides a globally contiguous data set from which the geology of these regions is evaluated and compared. In addition, high resolution gravity data currently being collected provide a basis to assess the relationship between these uplands and processes in the planet's interior. Studies of the geology of the three largest volcanic highlands (Beta Regio, Atla Regio, Western Eistla Regio) show them to be distinct, having a range of volcanic and tectonic characteristics. In addition to these large areas, a number of smaller uplands are identified and are being analyzed (Bell Regio, Imdr Regio, Dione Regio (Ushas, Innini, and Hathor Montes), and Themis Regio). To understand better the mechanisms by which these volcanic rises form and evolve, we assess their geologic and geophysical characteristics.

Point Set Denoising Using Bootstrap-Based Radial Basis Function.

PubMed

Liew, Khang Jie; Ramli, Ahmad; Abd Majid, Ahmad

2016-01-01

This paper examines the application of a bootstrap test error estimation of radial basis functions, specifically thin-plate spline fitting, in surface smoothing. The presence of noisy data is a common issue of the point set model that is generated from 3D scanning devices, and hence, point set denoising is one of the main concerns in point set modelling. Bootstrap test error estimation, which is applied when searching for the smoothing parameters of radial basis functions, is revisited. The main contribution of this paper is a smoothing algorithm that relies on a bootstrap-based radial basis function. The proposed method incorporates a k-nearest neighbour search and then projects the point set to the approximated thin-plate spline surface. Therefore, the denoising process is achieved, and the features are well preserved. A comparison of the proposed method with other smoothing methods is also carried out in this study.

Computational study of the electronic spectra of the rare gas fluorohydrides HRgF (Rg = Ar, Kr, Xe, Rn)

NASA Astrophysics Data System (ADS)

van Hoeve, Miriam D.; Klobukowski, Mariusz

2018-03-01

Simulation of the electronic spectra of HRgF (Rg = Ar, Kr, Xe, Rn) was carried out using the time-dependent density functional method, with the CAMB3LYP functional and several basis sets augmented with even-tempered diffuse functions. A full spectral assignment for the HRgF systems was done. The effect of the rare gas matrix on the HRgF (Rg = Ar and Kr) spectra was investigated and it was found that the matrix blue-shifted the spectra. Scalar relativistic effects on the spectra were also studied and it was found that while the excitation energies of HArF and HKrF were insignificantly affected by relativistic effects, most of the excitation energies of HXeF and HRnF were red-shifted. Spin-orbit coupling was found to significantly affect excitation energies in HRnF. Analysis of performance of the model core potential basis set relative to all-electron (AE) basis sets showed that the former basis set increased computational efficiency and gave results similar to those obtained with the AE basis set.

Midbond basis functions for weakly bound complexes

NASA Astrophysics Data System (ADS)

Shaw, Robert A.; Hill, J. Grant

2018-06-01

Weakly bound systems present a difficult problem for conventional atom-centred basis sets due to large separations, necessitating the use of large, computationally expensive bases. This can be remedied by placing a small number of functions in the region between molecules in the complex. We present compact sets of optimised midbond functions for a range of complexes involving noble gases, alkali metals and small molecules for use in high accuracy coupled -cluster calculations, along with a more robust procedure for their optimisation. It is shown that excellent results are possible with double-zeta quality orbital basis sets when a few midbond functions are added, improving both the interaction energy and the equilibrium bond lengths of a series of noble gas dimers by 47% and 8%, respectively. When used in conjunction with explicitly correlated methods, near complete basis set limit accuracy is readily achievable at a fraction of the cost that using a large basis would entail. General purpose auxiliary sets are developed to allow explicitly correlated midbond function studies to be carried out, making it feasible to perform very high accuracy calculations on weakly bound complexes.

Effect of iron content on the creep behavior of Olivine: 2. Hydrous conditions

NASA Astrophysics Data System (ADS)

Zhao, Yong-Hong; Zimmerman, Mark E.; Kohlstedt, David L.

2018-05-01

We have undertaken an experimental investigation of the effect of iron content on the viscosity of Fe-Mg olivine aggregates deformed under hydrous conditions in order to provide a basis for comparing convection models for the mantle of Earth with those for the more iron-rich mantle of Mars. Fine-grained samples of Fe-bearing olivine with fayalite contents, Fax, of x = 100, 75, 50, 30 and 10 were deformed in triaxial compressive creep primarily in the dislocation creep regime under water-saturated conditions at temperatures of 1273 to 1473 K and a confining pressure of 300 MPa. Nickel sleeves around the samples of Fa10, Fa30 and Fa50 set the oxygen fugacity at the Ni:NiO buffer and thus the water fugacity at ≲300 MPa, while Fe sleeves around samples of Fa75 and Fa100 set the oxygen fugacity at the Fe:FeO buffer and thus the water fugacity at ≲200 MPa. Samples were deformed in triaxial compression to a maximum strain of 0.2 at differential stresses from 10 to 300 MPa and strain rates from 10-7 to 10-3 s-1. In the dislocation creep field at a given temperature, the viscosity of samples of Fa50 is a factor of ∼10 smaller than the viscosity of samples of Fa30, while the viscosity of samples of Fa30 is a factor of ∼10 smaller than that of samples of Fa10. Our experimental results can be described by the flow law ε˙disl =Cdisl(σ/μ) ndisl XFa pdisl exp(-(Qdisl0 +αdislXFa)/RT) fH2Omdisl with Cdisl = 99.7 MPa-5/4 s-1, ndisl = 3.7, pdisl = 0.5, Qdisl0 = 510 kJ/mol, αdisl = -120 kJ/mol, and mdisl = 5/4. This flow law indicates that the viscosity of olivine of a specific Fe:Mg ratio is a factor of ∼10 smaller than its counterpart deformed under anhydrous conditions. In a hydrous environment at the same thermodynamic conditions, the viscosity of the more Fe-rich mantle (∼Fa19) of Mars is a factor of ∼5 lower than that of the mantle (∼Fa8) of Earth.

Møller-Plesset perturbation energies and distances for HeC(20) extrapolated to the complete basis set limit.

PubMed

Varandas, A J C

2009-02-01

The potential energy surface for the C(20)-He interaction is extrapolated for three representative cuts to the complete basis set limit using second-order Møller-Plesset perturbation calculations with correlation consistent basis sets up to the doubly augmented variety. The results both with and without counterpoise correction show consistency with each other, supporting that extrapolation without such a correction provides a reliable scheme to elude the basis-set-superposition error. Converged attributes are obtained for the C(20)-He interaction, which are used to predict the fullerene dimer ones. Time requirements show that the method can be drastically more economical than the counterpoise procedure and even competitive with Kohn-Sham density functional theory for the title system.

Exact exchange-correlation potentials of singlet two-electron systems

NASA Astrophysics Data System (ADS)

Ryabinkin, Ilya G.; Ospadov, Egor; Staroverov, Viktor N.

2017-10-01

We suggest a non-iterative analytic method for constructing the exchange-correlation potential, v XC ( r ) , of any singlet ground-state two-electron system. The method is based on a convenient formula for v XC ( r ) in terms of quantities determined only by the system's electronic wave function, exact or approximate, and is essentially different from the Kohn-Sham inversion technique. When applied to Gaussian-basis-set wave functions, the method yields finite-basis-set approximations to the corresponding basis-set-limit v XC ( r ) , whereas the Kohn-Sham inversion produces physically inappropriate (oscillatory and divergent) potentials. The effectiveness of the procedure is demonstrated by computing accurate exchange-correlation potentials of several two-electron systems (helium isoelectronic series, H2, H3 + ) using common ab initio methods and Gaussian basis sets.

A hybrid wavelet de-noising and Rank-Set Pair Analysis approach for forecasting hydro-meteorological time series.

PubMed

Wang, Dong; Borthwick, Alistair G; He, Handan; Wang, Yuankun; Zhu, Jieyu; Lu, Yuan; Xu, Pengcheng; Zeng, Xiankui; Wu, Jichun; Wang, Lachun; Zou, Xinqing; Liu, Jiufu; Zou, Ying; He, Ruimin

2018-01-01

Accurate, fast forecasting of hydro-meteorological time series is presently a major challenge in drought and flood mitigation. This paper proposes a hybrid approach, wavelet de-noising (WD) and Rank-Set Pair Analysis (RSPA), that takes full advantage of a combination of the two approaches to improve forecasts of hydro-meteorological time series. WD allows decomposition and reconstruction of a time series by the wavelet transform, and hence separation of the noise from the original series. RSPA, a more reliable and efficient version of Set Pair Analysis, is integrated with WD to form the hybrid WD-RSPA approach. Two types of hydro-meteorological data sets with different characteristics and different levels of human influences at some representative stations are used to illustrate the WD-RSPA approach. The approach is also compared to three other generic methods: the conventional Auto Regressive Integrated Moving Average (ARIMA) method, Artificial Neural Networks (ANNs) (BP-error Back Propagation, MLP-Multilayer Perceptron and RBF-Radial Basis Function), and RSPA alone. Nine error metrics are used to evaluate the model performance. Compared to three other generic methods, the results generated by WD-REPA model presented invariably smaller error measures which means the forecasting capability of the WD-REPA model is better than other models. The results show that WD-RSPA is accurate, feasible, and effective. In particular, WD-RSPA is found to be the best among the various generic methods compared in this paper, even when the extreme events are included within a time series. Copyright © 2017 Elsevier Inc. All rights reserved.

Let's Do It: Paper Dot Plates Give Numbers Meaning.

ERIC Educational Resources Information Center

Thompson, Charles S.; Van de Walle, John

1980-01-01

Described are activities using paper plates with dots drawn on them which place a heavy emphasis on matching and ordering sets, on developing mental images of sets, and on perceiving sets of a certain size as composed of smaller subsets. Also suggested are activities involving numerals. (Author/TG)

Calibration of GPS based high accuracy speed meter for vehicles

NASA Astrophysics Data System (ADS)

Bai, Yin; Sun, Qiao; Du, Lei; Yu, Mei; Bai, Jie

2015-02-01

GPS based high accuracy speed meter for vehicles is a special type of GPS speed meter which uses Doppler Demodulation of GPS signals to calculate the speed of a moving target. It is increasingly used as reference equipment in the field of traffic speed measurement, but acknowledged standard calibration methods are still lacking. To solve this problem, this paper presents the set-ups of simulated calibration, field test signal replay calibration, and in-field test comparison with an optical sensor based non-contact speed meter. All the experiments were carried out on particular speed values in the range of (40-180) km/h with the same GPS speed meter. The speed measurement errors of simulated calibration fall in the range of +/-0.1 km/h or +/-0.1%, with uncertainties smaller than 0.02% (k=2). The errors of replay calibration fall in the range of +/-0.1% with uncertainties smaller than 0.10% (k=2). The calibration results justify the effectiveness of the two methods. The relative deviations of the GPS speed meter from the optical sensor based noncontact speed meter fall in the range of +/-0.3%, which validates the use of GPS speed meter as reference instruments. The results of this research can provide technical basis for the establishment of internationally standard calibration methods of GPS speed meters, and thus ensures the legal status of GPS speed meters as reference equipment in the field of traffic speed metrology.

On the basis set convergence of electron–electron entanglement measures: helium-like systems

PubMed Central

Hofer, Thomas S.

2013-01-01

A systematic investigation of three different electron–electron entanglement measures, namely the von Neumann, the linear and the occupation number entropy at full configuration interaction level has been performed for the four helium-like systems hydride, helium, Li+ and Be2+ using a large number of different basis sets. The convergence behavior of the resulting energies and entropies revealed that the latter do in general not show the expected strictly monotonic increase upon increase of the one–electron basis. Overall, the three different entanglement measures show good agreement among each other, the largest deviations being observed for small basis sets. The data clearly demonstrates that it is important to consider the nature of the chemical system when investigating entanglement phenomena in the framework of Gaussian type basis sets: while in case of hydride the use of augmentation functions is crucial, the application of core functions greatly improves the accuracy in case of cationic systems such as Li+ and Be2+. In addition, numerical derivatives of the entanglement measures with respect to the nucleic charge have been determined, which proved to be a very sensitive probe of the convergence leading to qualitatively wrong results (i.e., the wrong sign) if too small basis sets are used. PMID:24790952

On the basis set convergence of electron-electron entanglement measures: helium-like systems.

PubMed

Hofer, Thomas S

2013-01-01

A systematic investigation of three different electron-electron entanglement measures, namely the von Neumann, the linear and the occupation number entropy at full configuration interaction level has been performed for the four helium-like systems hydride, helium, Li(+) and Be(2+) using a large number of different basis sets. The convergence behavior of the resulting energies and entropies revealed that the latter do in general not show the expected strictly monotonic increase upon increase of the one-electron basis. Overall, the three different entanglement measures show good agreement among each other, the largest deviations being observed for small basis sets. The data clearly demonstrates that it is important to consider the nature of the chemical system when investigating entanglement phenomena in the framework of Gaussian type basis sets: while in case of hydride the use of augmentation functions is crucial, the application of core functions greatly improves the accuracy in case of cationic systems such as Li(+) and Be(2+). In addition, numerical derivatives of the entanglement measures with respect to the nucleic charge have been determined, which proved to be a very sensitive probe of the convergence leading to qualitatively wrong results (i.e., the wrong sign) if too small basis sets are used.

Orbital-Dependent Density Functionals for Chemical Catalysis

DTIC Science & Technology

2014-10-17

noncollinear density functional theory to show that the low-spin state of Mn3 in a model of the oxygen -evolving complex of photosystem II avoids...DK, which denotes the cc-pV5Z-DK basis set for 3d metals and hydrogen and the ma-cc- pV5Z-DK basis set for oxygen ) and to nonrelativistic all...cc-pV5Z basis set for oxygen ). As compared to NCBS-DK results, all ECP calculations perform worse than def2-TZVP all-electron relativistic

Electric dipole moment of diatomic molecules by configuration interaction. IV.

NASA Technical Reports Server (NTRS)

Green, S.

1972-01-01

The theory of basis set dependence in configuration interaction calculations is discussed, taking into account a perturbation model which is valid for small changes in the self-consistent field orbitals. It is found that basis set corrections are essentially additive through first order. It is shown that an error found in a previously published dipole moment calculation by Green (1972) for the metastable first excited state of CO was indeed due to an inadequate basis set as claimed.

Antibiotic tolerance and the alternative lifestyles of Staphylococcus aureus.

PubMed

Bui, Long M G; Conlon, Brian P; Kidd, Stephen P

2017-02-28

Staphylococcus aureus has an incredible ability to survive, either by adapting to environmental conditions or defending against exogenous stress. Although there are certainly important genetic traits, in part this ability is provided by the breadth of modes of growth S. aureus can adopt. It has been proposed that while within their host, S. aureus survives host-generated and therapeutic antimicrobial stress via alternative lifestyles: a persister sub-population, through biofilm growth on host tissue or by growing as small colony variants (SCVs). Key to an understanding of chronic and relapsing S. aureus infections is determining the molecular basis for its switch to these quasi-dormant lifestyles. In a multicellular biofilm, the metabolically quiescent bacterial community additionally produces a highly protective extracellular polymeric substance (EPS). Furthermore, there are bacteria within a biofilm community that have an altered physiology potentially equivalent to persister cells. Recent studies have directly linked the cellular ATP production by persister cells as their key feature and the basis for their tolerance of a range of antibiotics. In clinical settings, SCVs of S. aureus have been observed for many years; when cultured, these cells form non-pigmented colonies and are approximately ten times smaller than their counterparts. Various genotypic factors have been identified in attempts to characterize S. aureus SCVs and different environmental stresses have been implicated as important inducers. © 2017 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

Edge reconstruction in armchair phosphorene nanoribbons revealed by discontinuous Galerkin density functional theory.

PubMed

Hu, Wei; Lin, Lin; Yang, Chao

2015-12-21

With the help of our recently developed massively parallel DGDFT (Discontinuous Galerkin Density Functional Theory) methodology, we perform large-scale Kohn-Sham density functional theory calculations on phosphorene nanoribbons with armchair edges (ACPNRs) containing a few thousands to ten thousand atoms. The use of DGDFT allows us to systematically achieve a conventional plane wave basis set type of accuracy, but with a much smaller number (about 15) of adaptive local basis (ALB) functions per atom for this system. The relatively small number of degrees of freedom required to represent the Kohn-Sham Hamiltonian, together with the use of the pole expansion the selected inversion (PEXSI) technique that circumvents the need to diagonalize the Hamiltonian, results in a highly efficient and scalable computational scheme for analyzing the electronic structures of ACPNRs as well as their dynamics. The total wall clock time for calculating the electronic structures of large-scale ACPNRs containing 1080-10,800 atoms is only 10-25 s per self-consistent field (SCF) iteration, with accuracy fully comparable to that obtained from conventional planewave DFT calculations. For the ACPNR system, we observe that the DGDFT methodology can scale to 5000-50,000 processors. We use DGDFT based ab initio molecular dynamics (AIMD) calculations to study the thermodynamic stability of ACPNRs. Our calculations reveal that a 2 × 1 edge reconstruction appears in ACPNRs at room temperature.

New Basis Functions for the Electromagnetic Solution of Arbitrarily-shaped, Three Dimensional Conducting Bodies Using Method of Moments

NASA Technical Reports Server (NTRS)

Mackenzie, Anne I.; Baginski, Michael E.; Rao, Sadasiva M.

2007-01-01

In this work, we present a new set of basis functions, de ned over a pair of planar triangular patches, for the solution of electromagnetic scattering and radiation problems associated with arbitrarily-shaped surfaces using the method of moments solution procedure. The basis functions are constant over the function subdomain and resemble pulse functions for one and two dimensional problems. Further, another set of basis functions, point-wise orthogonal to the first set, is also de ned over the same function space. The primary objective of developing these basis functions is to utilize them for the electromagnetic solution involving conducting, dielectric, and composite bodies. However, in the present work, only the conducting body solution is presented and compared with other data.

New Basis Functions for the Electromagnetic Solution of Arbitrarily-shaped, Three Dimensional Conducting Bodies using Method of Moments

NASA Technical Reports Server (NTRS)

Mackenzie, Anne I.; Baginski, Michael E.; Rao, Sadasiva M.

2008-01-01

In this work, we present a new set of basis functions, defined over a pair of planar triangular patches, for the solution of electromagnetic scattering and radiation problems associated with arbitrarily-shaped surfaces using the method of moments solution procedure. The basis functions are constant over the function subdomain and resemble pulse functions for one and two dimensional problems. Further, another set of basis functions, point-wise orthogonal to the first set, is also defined over the same function space. The primary objective of developing these basis functions is to utilize them for the electromagnetic solution involving conducting, dielectric, and composite bodies. However, in the present work, only the conducting body solution is presented and compared with other data.

Grid and basis adaptive polynomial chaos techniques for sensitivity and uncertainty analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Perkó, Zoltán, E-mail: Z.Perko@tudelft.nl; Gilli, Luca, E-mail: Gilli@nrg.eu; Lathouwers, Danny, E-mail: D.Lathouwers@tudelft.nl

2014-03-01

The demand for accurate and computationally affordable sensitivity and uncertainty techniques is constantly on the rise and has become especially pressing in the nuclear field with the shift to Best Estimate Plus Uncertainty methodologies in the licensing of nuclear installations. Besides traditional, already well developed methods – such as first order perturbation theory or Monte Carlo sampling – Polynomial Chaos Expansion (PCE) has been given a growing emphasis in recent years due to its simple application and good performance. This paper presents new developments of the research done at TU Delft on such Polynomial Chaos (PC) techniques. Our work ismore » focused on the Non-Intrusive Spectral Projection (NISP) approach and adaptive methods for building the PCE of responses of interest. Recent efforts resulted in a new adaptive sparse grid algorithm designed for estimating the PC coefficients. The algorithm is based on Gerstner's procedure for calculating multi-dimensional integrals but proves to be computationally significantly cheaper, while at the same it retains a similar accuracy as the original method. More importantly the issue of basis adaptivity has been investigated and two techniques have been implemented for constructing the sparse PCE of quantities of interest. Not using the traditional full PC basis set leads to further reduction in computational time since the high order grids necessary for accurately estimating the near zero expansion coefficients of polynomial basis vectors not needed in the PCE can be excluded from the calculation. Moreover the sparse PC representation of the response is easier to handle when used for sensitivity analysis or uncertainty propagation due to the smaller number of basis vectors. The developed grid and basis adaptive methods have been implemented in Matlab as the Fully Adaptive Non-Intrusive Spectral Projection (FANISP) algorithm and were tested on four analytical problems. These show consistent good performance both in terms of the accuracy of the resulting PC representation of quantities and the computational costs associated with constructing the sparse PCE. Basis adaptivity also seems to make the employment of PC techniques possible for problems with a higher number of input parameters (15–20), alleviating a well known limitation of the traditional approach. The prospect of larger scale applicability and the simplicity of implementation makes such adaptive PC algorithms particularly appealing for the sensitivity and uncertainty analysis of complex systems and legacy codes.« less

Atomic Cholesky decompositions: a route to unbiased auxiliary basis sets for density fitting approximation with tunable accuracy and efficiency.

PubMed

Aquilante, Francesco; Gagliardi, Laura; Pedersen, Thomas Bondo; Lindh, Roland

2009-04-21

Cholesky decomposition of the atomic two-electron integral matrix has recently been proposed as a procedure for automated generation of auxiliary basis sets for the density fitting approximation [F. Aquilante et al., J. Chem. Phys. 127, 114107 (2007)]. In order to increase computational performance while maintaining accuracy, we propose here to reduce the number of primitive Gaussian functions of the contracted auxiliary basis functions by means of a second Cholesky decomposition. Test calculations show that this procedure is most beneficial in conjunction with highly contracted atomic orbital basis sets such as atomic natural orbitals, and that the error resulting from the second decomposition is negligible. We also demonstrate theoretically as well as computationally that the locality of the fitting coefficients can be controlled by means of the decomposition threshold even with the long-ranged Coulomb metric. Cholesky decomposition-based auxiliary basis sets are thus ideally suited for local density fitting approximations.

Atomic Cholesky decompositions: A route to unbiased auxiliary basis sets for density fitting approximation with tunable accuracy and efficiency

NASA Astrophysics Data System (ADS)

Aquilante, Francesco; Gagliardi, Laura; Pedersen, Thomas Bondo; Lindh, Roland

2009-04-01

Cholesky decomposition of the atomic two-electron integral matrix has recently been proposed as a procedure for automated generation of auxiliary basis sets for the density fitting approximation [F. Aquilante et al., J. Chem. Phys. 127, 114107 (2007)]. In order to increase computational performance while maintaining accuracy, we propose here to reduce the number of primitive Gaussian functions of the contracted auxiliary basis functions by means of a second Cholesky decomposition. Test calculations show that this procedure is most beneficial in conjunction with highly contracted atomic orbital basis sets such as atomic natural orbitals, and that the error resulting from the second decomposition is negligible. We also demonstrate theoretically as well as computationally that the locality of the fitting coefficients can be controlled by means of the decomposition threshold even with the long-ranged Coulomb metric. Cholesky decomposition-based auxiliary basis sets are thus ideally suited for local density fitting approximations.

Electron correlation within the relativistic no-pair approximation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Almoukhalalati, Adel; Saue, Trond, E-mail: trond.saue@irsamc.ups-tlse.fr; Knecht, Stefan

This paper addresses the definition of correlation energy within 4-component relativistic atomic and molecular calculations. In the nonrelativistic domain the correlation energy is defined as the difference between the exact eigenvalue of the electronic Hamiltonian and the Hartree-Fock energy. In practice, what is reported is the basis set correlation energy, where the “exact” value is provided by a full Configuration Interaction (CI) calculation with some specified one-particle basis. The extension of this definition to the relativistic domain is not straightforward since the corresponding electronic Hamiltonian, the Dirac-Coulomb Hamiltonian, has no bound solutions. Present-day relativistic calculations are carried out within themore » no-pair approximation, where the Dirac-Coulomb Hamiltonian is embedded by projectors eliminating the troublesome negative-energy solutions. Hartree-Fock calculations are carried out with the implicit use of such projectors and only positive-energy orbitals are retained at the correlated level, meaning that the Hartree-Fock projectors are frozen at the correlated level. We argue that the projection operators should be optimized also at the correlated level and that this is possible by full Multiconfigurational Self-Consistent Field (MCSCF) calculations, that is, MCSCF calculations using a no-pair full CI expansion, but including orbital relaxation from the negative-energy orbitals. We show by variational perturbation theory that the MCSCF correlation energy is a pure MP2-like correlation expression, whereas the corresponding CI correlation energy contains an additional relaxation term. We explore numerically our theoretical analysis by carrying out variational and perturbative calculations on the two-electron rare gas atoms with specially tailored basis sets. In particular, we show that the correlation energy obtained by the suggested MCSCF procedure is smaller than the no-pair full CI correlation energy, in accordance with the underlying minmax principle and our theoretical analysis. We also show that the relativistic correlation energy, obtained from no-pair full MCSCF calculations, scales at worst as X{sup −2} with respect to the cardinal number X of our correlation-consistent basis sets optimized for the two-electron atoms. This is better than the X{sup −1} scaling suggested by previous studies, but worse than the X{sup −3} scaling observed in the nonrelativistic domain. The well-known 1/Z- expansion in nonrelativistic atomic theory follows from coordinate scaling. We point out that coordinate scaling for consistency should be accompanied by velocity scaling. In the nonrelativistic domain this comes about automatically, whereas in the relativistic domain an explicit scaling of the speed of light is required. This in turn explains why the relativistic correlation energy to the lowest order is not independent of nuclear charge, in contrast to nonrelativistic theory.« less

16 CFR § 1633.4 - Prototype testing requirements.

Code of Federal Regulations, 2013 CFR

2013-01-01

.../foundation length and width, not depth (e.g., twin, queen, king); (2) Ticking, unless the ticking of the... § 1633.3(b). (c) All tests must be conducted on specimens that are no smaller than a twin size, unless the largest size mattress set produced is smaller than a twin size, in which case the largest size...

16 CFR 1633.4 - Prototype testing requirements.

Code of Federal Regulations, 2014 CFR

2014-01-01

.../foundation length and width, not depth (e.g., twin, queen, king); (2) Ticking, unless the ticking of the... § 1633.3(b). (c) All tests must be conducted on specimens that are no smaller than a twin size, unless the largest size mattress set produced is smaller than a twin size, in which case the largest size...

16 CFR 1633.4 - Prototype testing requirements.

Code of Federal Regulations, 2011 CFR

2011-01-01

.../foundation length and width, not depth (e.g., twin, queen, king); (2) Ticking, unless the ticking of the... § 1633.3(b). (c) All tests must be conducted on specimens that are no smaller than a twin size, unless the largest size mattress set produced is smaller than a twin size, in which case the largest size...

16 CFR 1633.4 - Prototype testing requirements.

Code of Federal Regulations, 2012 CFR

2012-01-01

.../foundation length and width, not depth (e.g., twin, queen, king); (2) Ticking, unless the ticking of the... § 1633.3(b). (c) All tests must be conducted on specimens that are no smaller than a twin size, unless the largest size mattress set produced is smaller than a twin size, in which case the largest size...

Systematically convergent basis sets for transition metals. I. All-electron correlation consistent basis sets for the 3d elements Sc-Zn

NASA Astrophysics Data System (ADS)

Balabanov, Nikolai B.; Peterson, Kirk A.

2005-08-01

Sequences of basis sets that systematically converge towards the complete basis set (CBS) limit have been developed for the first-row transition metal elements Sc-Zn. Two families of basis sets, nonrelativistic and Douglas-Kroll-Hess (-DK) relativistic, are presented that range in quality from triple-ζ to quintuple-ζ. Separate sets are developed for the description of valence (3d4s) electron correlation (cc-pVnZ and cc-pVnZ-DK; n =T,Q, 5) and valence plus outer-core (3s3p3d4s) correlation (cc-pwCVnZ and cc-pwCVnZ-DK; n =T,Q, 5), as well as these sets augmented by additional diffuse functions for the description of negative ions and weak interactions (aug-cc-pVnZ and aug-cc-pVnZ-DK). Extensive benchmark calculations at the coupled cluster level of theory are presented for atomic excitation energies, ionization potentials, and electron affinities, as well as molecular calculations on selected hydrides (TiH, MnH, CuH) and other diatomics (TiF, Cu2). In addition to observing systematic convergence towards the CBS limits, both 3s3p electron correlation and scalar relativity are calculated to strongly impact many of the atomic and molecular properties investigated for these first-row transition metal species.

Gaussian basis sets for use in correlated molecular calculations. XI. Pseudopotential-based and all-electron relativistic basis sets for alkali metal (K-Fr) and alkaline earth (Ca-Ra) elements

NASA Astrophysics Data System (ADS)

Hill, J. Grant; Peterson, Kirk A.

2017-12-01

New correlation consistent basis sets based on pseudopotential (PP) Hamiltonians have been developed from double- to quintuple-zeta quality for the late alkali (K-Fr) and alkaline earth (Ca-Ra) metals. These are accompanied by new all-electron basis sets of double- to quadruple-zeta quality that have been contracted for use with both Douglas-Kroll-Hess (DKH) and eXact 2-Component (X2C) scalar relativistic Hamiltonians. Sets for valence correlation (ms), cc-pVnZ-PP and cc-pVnZ-(DK,DK3/X2C), in addition to outer-core correlation [valence + (m-1)sp], cc-p(w)CVnZ-PP and cc-pwCVnZ-(DK,DK3/X2C), are reported. The -PP sets have been developed for use with small-core PPs [I. S. Lim et al., J. Chem. Phys. 122, 104103 (2005) and I. S. Lim et al., J. Chem. Phys. 124, 034107 (2006)], while the all-electron sets utilized second-order DKH Hamiltonians for 4s and 5s elements and third-order DKH for 6s and 7s. The accuracy of the basis sets is assessed through benchmark calculations at the coupled-cluster level of theory for both atomic and molecular properties. Not surprisingly, it is found that outer-core correlation is vital for accurate calculation of the thermodynamic and spectroscopic properties of diatomic molecules containing these elements.

Ab initio calculation of reaction energies. III. Basis set dependence of relative energies on the FH2 and H2CO potential energy surfaces

NASA Astrophysics Data System (ADS)

Frisch, Michael J.; Binkley, J. Stephen; Schaefer, Henry F., III

1984-08-01

The relative energies of the stationary points on the FH2 and H2CO nuclear potential energy surfaces relevant to the hydrogen atom abstraction, H2 elimination and 1,2-hydrogen shift reactions have been examined using fourth-order Møller-Plesset perturbation theory and a variety of basis sets. The theoretical absolute zero activation energy for the F+H2→FH+H reaction is in better agreement with experiment than previous theoretical studies, and part of the disagreement between earlier theoretical calculations and experiment is found to result from the use of assumed rather than calculated zero-point vibrational energies. The fourth-order reaction energy for the elimination of hydrogen from formaldehyde is within 2 kcal mol-1 of the experimental value using the largest basis set considered. The qualitative features of the H2CO surface are unchanged by expansion of the basis set beyond the polarized triple-zeta level, but diffuse functions and several sets of polarization functions are found to be necessary for quantitative accuracy in predicted reaction and activation energies. Basis sets and levels of perturbation theory which represent good compromises between computational efficiency and accuracy are recommended.

Calculations of molecular multipole electric moments of a series of exo-insaturated four-membered heterocycles, Y = CCH2CH2X

NASA Astrophysics Data System (ADS)

Romero, Angel H.

2017-10-01

The influence of ring puckering angle on the multipole moments of sixteen four-membered heterocycles (1-16) was theoretically estimated using MP2 and different DFTs in combination with the 6-31+G(d,p) basis set. To obtain an accurate evaluation, CCSD/cc-pVDZ level and, the MP2 and PBE1PBE methods in combination with the aug-cc-pVDZ and aug-cc-pVTZ basis sets were performed on the planar geometries of 1-16. In general, the DFT and MP2 approaches provided an identical dependence of the electrical properties with the puckering angle for 1-16. Quantitatively, the quality of the level of theory and basis sets affects significant the predictions of the multipole moments, in particular for the heterocycles containing C=O and C=S bonds. Convergence basis sets within the MP2 and PBE1PBE approximations are reached in the dipole moment calculations when the aug-cc-pVTZ basis set is used, while the quadrupole and octupole moment computations require a larger basis set than aug-cc-pVTZ. On the other hand, the multipole moments showed a strong dependence with the molecular geometry and the nature of the carbon-heteroatom bonds. Specifically, the C-X bond determines the behavior of the μ(ϕ), θ(ϕ) and Ώ(ϕ) functions, while the C=Y bond plays an important role in the magnitude of the studied properties.

Interannual variability and climatic noise in satellite-observed outgoing longwave radiation

NASA Technical Reports Server (NTRS)

Short, D. A.; Cahalan, R. F.

1983-01-01

Upwelling-IR observations of the North Pacific by polar orbiters NOAA 3, 4, 5, and 6 and TIROS-N from 1974 to 1981 are analyzed statistically in terms of interannual variability (IAV) in monthly averages and climatic noise due to short-term weather fluctuations. It is found that although the daily variance in the observations is the same in summer and winter months, and although IAV in winter is smaller than that in summer, the climatic noise in winter is so much smaller that a greater fraction of winter anomalies are statistically significant. The smaller winter climatic noise level is shown to be due to shorter autocorrelation times. It is demonstrated that increasing averaging area does not reduce the climatic noise level, suggesting that continuing collection of high-resolution satellite IR data on a global basis is necessary if better models of short-term variability are to be constructed.

Straightening the Hierarchical Staircase for Basis Set Extrapolations: A Low-Cost Approach to High-Accuracy Computational Chemistry

NASA Astrophysics Data System (ADS)

Varandas, António J. C.

2018-04-01

Because the one-electron basis set limit is difficult to reach in correlated post-Hartree-Fock ab initio calculations, the low-cost route of using methods that extrapolate to the estimated basis set limit attracts immediate interest. The situation is somewhat more satisfactory at the Hartree-Fock level because numerical calculation of the energy is often affordable at nearly converged basis set levels. Still, extrapolation schemes for the Hartree-Fock energy are addressed here, although the focus is on the more slowly convergent and computationally demanding correlation energy. Because they are frequently based on the gold-standard coupled-cluster theory with single, double, and perturbative triple excitations [CCSD(T)], correlated calculations are often affordable only with the smallest basis sets, and hence single-level extrapolations from one raw energy could attain maximum usefulness. This possibility is examined. Whenever possible, this review uses raw data from second-order Møller-Plesset perturbation theory, as well as CCSD, CCSD(T), and multireference configuration interaction methods. Inescapably, the emphasis is on work done by the author's research group. Certain issues in need of further research or review are pinpointed.

Excitation spectra of aromatic molecules within a real-space G W -BSE formalism: Role of self-consistency and vertex corrections

DOE PAGES

Hung, Linda; da Jornada, Felipe H.; Souto-Casares, Jaime; ...

2016-08-15

Here, we present first-principles calculations on the vertical ionization potentials (IPs), electron affinities (EAs), and singlet excitation energies on an aromatic-molecule test set (benzene, thiophene, 1,2,5-thiadiazole, naphthalene, benzothiazole, and tetrathiafulvalene) within the GW and Bethe-Salpeter equation (BSE) formalisms. Our computational framework, which employs a real-space basis for ground-state and a transition-space basis for excited-state calculations, is well suited for high-accuracy calculations on molecules, as we show by comparing against G0W0 calculations within a plane-wave-basis formalism. We then generalize our framework to test variants of the GW approximation that include a local density approximation (LDA)–derived vertex function (Γ LDA ) andmore » quasiparticle-self-consistent (QS) iterations. We find that Γ LDA and quasiparticle self-consistency shift IPs and EAs by roughly the same magnitude, but with opposite sign for IPs and the same sign for EAs. G0W0 and QS GWΓ LDA are more accurate for IPs, while G 0W 0Γ LDA and QS GW are best for EAs. For optical excitations, we find that perturbative GW-BSE underestimates the singlet excitation energy, while self-consistent GW-BSE results in good agreement with previous best-estimate values for both valence and Rydberg excitations. Finally, our work suggests that a hybrid approach, in which G0W0 energies are used for occupied orbitals and G0W0Γ LDA for unoccupied orbitals, also yields optical excitation energies in good agreement with experiment but at a smaller computational cost.« less

Excitation spectra of aromatic molecules within a real-space G W -BSE formalism: Role of self-consistency and vertex corrections

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hung, Linda; da Jornada, Felipe H.; Souto-Casares, Jaime

Here, we present first-principles calculations on the vertical ionization potentials (IPs), electron affinities (EAs), and singlet excitation energies on an aromatic-molecule test set (benzene, thiophene, 1,2,5-thiadiazole, naphthalene, benzothiazole, and tetrathiafulvalene) within the GW and Bethe-Salpeter equation (BSE) formalisms. Our computational framework, which employs a real-space basis for ground-state and a transition-space basis for excited-state calculations, is well suited for high-accuracy calculations on molecules, as we show by comparing against G0W0 calculations within a plane-wave-basis formalism. We then generalize our framework to test variants of the GW approximation that include a local density approximation (LDA)–derived vertex function (Γ LDA ) andmore » quasiparticle-self-consistent (QS) iterations. We find that Γ LDA and quasiparticle self-consistency shift IPs and EAs by roughly the same magnitude, but with opposite sign for IPs and the same sign for EAs. G0W0 and QS GWΓ LDA are more accurate for IPs, while G 0W 0Γ LDA and QS GW are best for EAs. For optical excitations, we find that perturbative GW-BSE underestimates the singlet excitation energy, while self-consistent GW-BSE results in good agreement with previous best-estimate values for both valence and Rydberg excitations. Finally, our work suggests that a hybrid approach, in which G0W0 energies are used for occupied orbitals and G0W0Γ LDA for unoccupied orbitals, also yields optical excitation energies in good agreement with experiment but at a smaller computational cost.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

McKemmish, Laura K., E-mail: laura.mckemmish@gmail.com; Research School of Chemistry, Australian National University, Canberra

Algorithms for the efficient calculation of two-electron integrals in the newly developed mixed ramp-Gaussian basis sets are presented, alongside a Fortran90 implementation of these algorithms, RAMPITUP. These new basis sets have significant potential to (1) give some speed-up (estimated at up to 20% for large molecules in fully optimised code) to general-purpose Hartree-Fock (HF) and density functional theory quantum chemistry calculations, replacing all-Gaussian basis sets, and (2) give very large speed-ups for calculations of core-dependent properties, such as electron density at the nucleus, NMR parameters, relativistic corrections, and total energies, replacing the current use of Slater basis functions or verymore » large specialised all-Gaussian basis sets for these purposes. This initial implementation already demonstrates roughly 10% speed-ups in HF/R-31G calculations compared to HF/6-31G calculations for large linear molecules, demonstrating the promise of this methodology, particularly for the second application. As well as the reduction in the total primitive number in R-31G compared to 6-31G, this timing advantage can be attributed to the significant reduction in the number of mathematically complex intermediate integrals after modelling each ramp-Gaussian basis-function-pair as a sum of ramps on a single atomic centre.« less

Putting Institutional Research to Work in the Smaller College.

ERIC Educational Resources Information Center

Stivers, Earl R.

The aims of institutional research should be to: (1) provide a basis for future planning, e.g., enrollment projections and criteria for accepting applications, (2) determine the effectiveness of space utilization, such as use of each instructional room, free hours of each, comparisons of class sizes with designed room capacities, discovery of…

HEASD PM EXPOSURE FACTORS- IMPROVE UNDERSTANDING OF THE FACTORS WHICH DETERMINE HUMANS' EXPOSURE TO PARTICLES SMALLER THAN 2.5 MICRONS

EPA Science Inventory

In July 1997, the EPA Administrator issued a new Particulate Matter (PM-2.5) National Ambient Air Quality Standards (NAAQS) that had been developed largely on the basis of epidemiological studies. These studies found a consistent association between ambient PM concentrations and...

26 CFR 1.42-15 - Available unit rule.

Code of Federal Regulations, 2010 CFR

2010-04-01

... maintain five of the residential units as low-income units, the qualified basis in the building is reduced... low-income building that is comparably sized or smaller than an over-income unit or, for deep rent.... Current resident means a person who is living in the low-income building. Low-income unit is defined by...

The Art of Projecting: The Cost of Keeping Periodicals.

ERIC Educational Resources Information Center

Ketcham, Lee; Born, Kathleen

1993-01-01

Provides periodical prices for 1993 and projects 1994 costs. Trends and projections, cost by country of origin, the role of foreign publications, currency fluctuations, and the basis for forecasting are discussed. Cost histories are given by subject area and country of publication. Prices of interest to smaller and public libraries are also given.…

Neural Basis of Intrinsic Motivation: Evidence from Event-Related Potentials.

PubMed

Jin, Jia; Yu, Liping; Ma, Qingguo

2015-01-01

Human intrinsic motivation is of great importance in human behavior. However, although researchers have focused on this topic for decades, its neural basis was still unclear. The current study employed event-related potentials to investigate the neural disparity between an interesting stop-watch (SW) task and a boring watch-stop task (WS) to understand the neural mechanisms of intrinsic motivation. Our data showed that, in the cue priming stage, the cue of the SW task elicited smaller N2 amplitude than that of the WS task. Furthermore, in the outcome feedback stage, the outcome of the SW task induced smaller FRN amplitude and larger P300 amplitude than that of the WS task. These results suggested that human intrinsic motivation did exist and that it can be detected at the neural level. Furthermore, intrinsic motivation could be quantitatively indexed by the amplitude of ERP components, such as N2, FRN, and P300, in the cue priming stage or feedback stage. Quantitative measurements would also be convenient for intrinsic motivation to be added as a candidate social factor in the construction of a machine learning model.

Quantum Mechanical Calculations of Monoxides of Silicon Carbide Molecules

DTIC Science & Technology

2003-03-01

Data for CO Final Energy Charge Mult Basis Set (hart) EA (eV) ZPE (hart) EA (eV) w/ ZPE 0 1 DVZ -112.6850703739 2.02121 -1 2 DVZ...Energy Charge Mult Basis Set (hart) EA (eV) ZPE (hart) EA (eV) w/ ZPE 0 1 DVZ -363.7341927429 0.617643 -1 2 DVZ -363.7114852831 0 3 DVZ...Input Geometry Output Geometry Basis Set Final Energy (hart) EA (eV) ZPE (hart) EA (eV) w/ ZPE -1 2 O-C-Si Linear O-C-Si Linear DZV -401.5363

Relativistic well-tempered Gaussian basis sets for helium through mercury. Breit interaction included

DOE Office of Scientific and Technical Information (OSTI.GOV)

Okada, S.; Shinada, M.; Matsuoka, O.

1990-10-01

A systematic calculation of new relativistic Gaussian basis sets is reported. The new basis sets are similar to the previously reported ones (J. Chem. Phys. {bold 91}, 4193 (1989)), but, in the calculation, the Breit interaction has been explicitly included besides the Dirac--Coulomb Hamiltonian. They have been adopted for the calculation of the self-consistent field effect on the Breit interaction energies and are expected to be useful for the studies on higher-order effects such as the electron correlations and other quantum electrodynamical effects.

Parallel Douglas-Kroll Energy and Gradients in NWChem. Estimating Scalar Relativistic Effects Using Douglas-Kroll Contracted Basis Sets.

DOE Office of Scientific and Technical Information (OSTI.GOV)

De Jong, Wibe A.; Harrison, Robert J.; Dixon, David A.

A parallel implementation of the spin-free one-electron Douglas-Kroll(-Hess) Hamiltonian (DKH) in NWChem is discussed. An efficient and accurate method to calculate DKH gradients is introduced. It is shown that the use of standard (non-relativistic) contracted basis set can produce erroneous results for elements beyond the first row elements. The generation of DKH contracted cc-pVXZ (X = D, T, Q, 5) basis sets for H, He, B - Ne, Al - Ar, and Ga - Br will be discussed.

Support vector machine regression (LS-SVM)--an alternative to artificial neural networks (ANNs) for the analysis of quantum chemistry data?

PubMed

Balabin, Roman M; Lomakina, Ekaterina I

2011-06-28

A multilayer feed-forward artificial neural network (MLP-ANN) with a single, hidden layer that contains a finite number of neurons can be regarded as a universal non-linear approximator. Today, the ANN method and linear regression (MLR) model are widely used for quantum chemistry (QC) data analysis (e.g., thermochemistry) to improve their accuracy (e.g., Gaussian G2-G4, B3LYP/B3-LYP, X1, or W1 theoretical methods). In this study, an alternative approach based on support vector machines (SVMs) is used, the least squares support vector machine (LS-SVM) regression. It has been applied to ab initio (first principle) and density functional theory (DFT) quantum chemistry data. So, QC + SVM methodology is an alternative to QC + ANN one. The task of the study was to estimate the Møller-Plesset (MPn) or DFT (B3LYP, BLYP, BMK) energies calculated with large basis sets (e.g., 6-311G(3df,3pd)) using smaller ones (6-311G, 6-311G*, 6-311G**) plus molecular descriptors. A molecular set (BRM-208) containing a total of 208 organic molecules was constructed and used for the LS-SVM training, cross-validation, and testing. MP2, MP3, MP4(DQ), MP4(SDQ), and MP4/MP4(SDTQ) ab initio methods were tested. Hartree-Fock (HF/SCF) results were also reported for comparison. Furthermore, constitutional (CD: total number of atoms and mole fractions of different atoms) and quantum-chemical (QD: HOMO-LUMO gap, dipole moment, average polarizability, and quadrupole moment) molecular descriptors were used for the building of the LS-SVM calibration model. Prediction accuracies (MADs) of 1.62 ± 0.51 and 0.85 ± 0.24 kcal mol(-1) (1 kcal mol(-1) = 4.184 kJ mol(-1)) were reached for SVM-based approximations of ab initio and DFT energies, respectively. The LS-SVM model was more accurate than the MLR model. A comparison with the artificial neural network approach shows that the accuracy of the LS-SVM method is similar to the accuracy of ANN. The extrapolation and interpolation results show that LS-SVM is superior by almost an order of magnitude over the ANN method in terms of the stability, generality, and robustness of the final model. The LS-SVM model needs a much smaller numbers of samples (a much smaller sample set) to make accurate prediction results. Potential energy surface (PES) approximations for molecular dynamics (MD) studies are discussed as a promising application for the LS-SVM calibration approach. This journal is © the Owner Societies 2011

On the Usage of Locally Dense Basis Sets in the Calculation of NMR Indirect Nuclear Spin-Spin Coupling Constants

NASA Astrophysics Data System (ADS)

Sanchez, Marina; Provasi, Patricio F.; Aucar, Gustavo A.; Sauer, Stephan P. A.

Locally dense basis sets (

Near Hartree-Fock quality GTO basis sets for the first- and third-row atoms

NASA Technical Reports Server (NTRS)

Partridge, Harry

1989-01-01

Energy-optimized Gaussian-type-orbital (GTO) basis sets of accuracy approaching that of numerical Hartree-Fock computations are compiled for the elements of the first and third rows of the periodic table. The methods employed in calculating the sets are explained; the applicability of the sets to electronic-structure calculations is discussed; and the results are presented in tables and briefly characterized.

Computational tests of quantum chemical models for excited and ionized states of molecules with phosphorus and sulfur atoms.

PubMed

Hahn, David K; RaghuVeer, Krishans; Ortiz, J V

2014-05-15

Time-dependent density functional theory (TD-DFT) and electron propagator theory (EPT) are used to calculate the electronic transition energies and ionization energies, respectively, of species containing phosphorus or sulfur. The accuracy of TD-DFT and EPT, in conjunction with various basis sets, is assessed with data from gas-phase spectroscopy. TD-DFT is tested using 11 prominent exchange-correlation functionals on a set of 37 vertical and 19 adiabatic transitions. For vertical transitions, TD-CAM-B3LYP calculations performed with the MG3S basis set are lowest in overall error, having a mean absolute deviation from experiment of 0.22 eV, or 0.23 eV over valence transitions and 0.21 eV over Rydberg transitions. Using a larger basis set, aug-pc3, improves accuracy over the valence transitions via hybrid functionals, but improved accuracy over the Rydberg transitions is only obtained via the BMK functional. For adiabatic transitions, all hybrid functionals paired with the MG3S basis set perform well, and B98 is best, with a mean absolute deviation from experiment of 0.09 eV. The testing of EPT used the Outer Valence Green's Function (OVGF) approximation and the Partial Third Order (P3) approximation on 37 vertical first ionization energies. It is found that OVGF outperforms P3 when basis sets of at least triple-ζ quality in the polarization functions are used. The largest basis set used in this study, aug-pc3, obtained the best mean absolute error from both methods -0.08 eV for OVGF and 0.18 eV for P3. The OVGF/6-31+G(2df,p) level of theory is particularly cost-effective, yielding a mean absolute error of 0.11 eV.

No need for external orthogonality in subsystem density-functional theory.

PubMed

Unsleber, Jan P; Neugebauer, Johannes; Jacob, Christoph R

2016-08-03

Recent reports on the necessity of using externally orthogonal orbitals in subsystem density-functional theory (SDFT) [Annu. Rep. Comput. Chem., 8, 2012, 53; J. Phys. Chem. A, 118, 2014, 9182] are re-investigated. We show that in the basis-set limit, supermolecular Kohn-Sham-DFT (KS-DFT) densities can exactly be represented as a sum of subsystem densities, even if the subsystem orbitals are not externally orthogonal. This is illustrated using both an analytical example and in basis-set free numerical calculations for an atomic test case. We further show that even with finite basis sets, SDFT calculations using accurate reconstructed potentials can closely approach the supermolecular KS-DFT density, and that the deviations between SDFT and KS-DFT decrease as the basis-set limit is approached. Our results demonstrate that formally, there is no need to enforce external orthogonality in SDFT, even though this might be a useful strategy when developing projection-based DFT embedding schemes.

Open-ended recursive calculation of single residues of response functions for perturbation-dependent basis sets.

PubMed

Friese, Daniel H; Ringholm, Magnus; Gao, Bin; Ruud, Kenneth

2015-10-13

We present theory, implementation, and applications of a recursive scheme for the calculation of single residues of response functions that can treat perturbations that affect the basis set. This scheme enables the calculation of nonlinear light absorption properties to arbitrary order for other perturbations than an electric field. We apply this scheme for the first treatment of two-photon circular dichroism (TPCD) using London orbitals at the Hartree-Fock level of theory. In general, TPCD calculations suffer from the problem of origin dependence, which has so far been solved by using the velocity gauge for the electric dipole operator. This work now enables comparison of results from London orbital and velocity gauge based TPCD calculations. We find that the results from the two approaches both exhibit strong basis set dependence but that they are very similar with respect to their basis set convergence.

Core-core and core-valence correlation

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Taylor, Peter R.

1988-01-01

The effect of (1s) core correlation on properties and energy separations was analyzed using full configuration-interaction (FCI) calculations. The Be 1 S - 1 P, the C 3 P - 5 S and CH+ 1 Sigma + or - 1 Pi separations, and CH+ spectroscopic constants, dipole moment and 1 Sigma + - 1 Pi transition dipole moment were studied. The results of the FCI calculations are compared to those obtained using approximate methods. In addition, the generation of atomic natural orbital (ANO) basis sets, as a method for contracting a primitive basis set for both valence and core correlation, is discussed. When both core-core and core-valence correlation are included in the calculation, no suitable truncated CI approach consistently reproduces the FCI, and contraction of the basis set is very difficult. If the (nearly constant) core-core correlation is eliminated, and only the core-valence correlation is included, CASSCF/MRCI approached reproduce the FCI results and basis set contraction is significantly easier.

Numerical judgments by chimpanzees (Pan troglodytes) in a token economy.

PubMed

Beran, Michael J; Evans, Theodore A; Hoyle, Daniel

2011-04-01

We presented four chimpanzees with a series of tasks that involved comparing two token sets or comparing a token set to a quantity of food. Selected tokens could be exchanged for food items on a one-to-one basis. Chimpanzees successfully selected the larger numerical set for comparisons of 1 to 5 items when both sets were visible and when sets were presented through one-by-one addition of tokens into two opaque containers. Two of four chimpanzees used the number of tokens and food items to guide responding in all conditions, rather than relying on token color, size, total amount, or duration of set presentation. These results demonstrate that judgments of simultaneous and sequential sets of stimuli are made by some chimpanzees on the basis of the numerousness of sets rather than other non-numerical dimensions. The tokens were treated as equivalent to food items on the basis of their numerousness, and the chimpanzees maximized reward by choosing the larger number of items in all situations.

Segmented all-electron Gaussian basis sets of double and triple zeta qualities for Fr, Ra, and Ac

NASA Astrophysics Data System (ADS)

Campos, C. T.; de Oliveira, A. Z.; Ferreira, I. B.; Jorge, F. E.; Martins, L. S. C.

2017-05-01

Segmented all-electron basis sets of valence double and triple zeta qualities plus polarization functions for the elements Fr, Ra, and Ac are generated using non-relativistic and Douglas-Kroll-Hess (DKH) Hamiltonians. The sets are augmented with diffuse functions with the purpose to describe appropriately the electrons far from the nuclei. At the DKH-B3LYP level, first atomic ionization energies and bond lengths, dissociation energies, and polarizabilities of a sample of diatomics are calculated. Comparison with theoretical and experimental data available in the literature is carried out. It is verified that despite the small sizes of the basis sets, they are yet reliable.

Basis set and electron correlation effects on the polarizability and second hyperpolarizability of model open-shell π-conjugated systems

NASA Astrophysics Data System (ADS)

Champagne, Benoı̂t; Botek, Edith; Nakano, Masayoshi; Nitta, Tomoshige; Yamaguchi, Kizashi

2005-03-01

The basis set and electron correlation effects on the static polarizability (α) and second hyperpolarizability (γ) are investigated ab initio for two model open-shell π-conjugated systems, the C5H7 radical and the C6H8 radical cation in their doublet state. Basis set investigations evidence that the linear and nonlinear responses of the radical cation necessitate the use of a less extended basis set than its neutral analog. Indeed, double-zeta-type basis sets supplemented by a set of d polarization functions but no diffuse functions already provide accurate (hyper)polarizabilities for C6H8 whereas diffuse functions are compulsory for C5H7, in particular, p diffuse functions. In addition to the 6-31G*+pd basis set, basis sets resulting from removing not necessary diffuse functions from the augmented correlation consistent polarized valence double zeta basis set have been shown to provide (hyper)polarizability values of similar quality as more extended basis sets such as augmented correlation consistent polarized valence triple zeta and doubly augmented correlation consistent polarized valence double zeta. Using the selected atomic basis sets, the (hyper)polarizabilities of these two model compounds are calculated at different levels of approximation in order to assess the impact of including electron correlation. As a function of the method of calculation antiparallel and parallel variations have been demonstrated for α and γ of the two model compounds, respectively. For the polarizability, the unrestricted Hartree-Fock and unrestricted second-order Møller-Plesset methods bracket the reference value obtained at the unrestricted coupled cluster singles and doubles with a perturbative inclusion of the triples level whereas the projected unrestricted second-order Møller-Plesset results are in much closer agreement with the unrestricted coupled cluster singles and doubles with a perturbative inclusion of the triples values than the projected unrestricted Hartree-Fock results. Moreover, the differences between the restricted open-shell Hartree-Fock and restricted open-shell second-order Møller-Plesset methods are small. In what concerns the second hyperpolarizability, the unrestricted Hartree-Fock and unrestricted second-order Møller-Plesset values remain of similar quality while using spin-projected schemes fails for the charged system but performs nicely for the neutral one. The restricted open-shell schemes, and especially the restricted open-shell second-order Møller-Plesset method, provide for both compounds γ values close to the results obtained at the unrestricted coupled cluster level including singles and doubles with a perturbative inclusion of the triples. Thus, to obtain well-converged α and γ values at low-order electron correlation levels, the removal of spin contamination is a necessary but not a sufficient condition. Density-functional theory calculations of α and γ have also been carried out using several exchange-correlation functionals. Those employing hybrid exchange-correlation functionals have been shown to reproduce fairly well the reference coupled cluster polarizability and second hyperpolarizability values. In addition, inclusion of Hartree-Fock exchange is of major importance for determining accurate polarizability whereas for the second hyperpolarizability the gradient corrections are large.

Rational Density Functional Selection Using Game Theory.

PubMed

McAnanama-Brereton, Suzanne; Waller, Mark P

2018-01-22

Theoretical chemistry has a paradox of choice due to the availability of a myriad of density functionals and basis sets. Traditionally, a particular density functional is chosen on the basis of the level of user expertise (i.e., subjective experiences). Herein we circumvent the user-centric selection procedure by describing a novel approach for objectively selecting a particular functional for a given application. We achieve this by employing game theory to identify optimal functional/basis set combinations. A three-player (accuracy, complexity, and similarity) game is devised, through which Nash equilibrium solutions can be obtained. This approach has the advantage that results can be systematically improved by enlarging the underlying knowledge base, and the deterministic selection procedure mathematically justifies the density functional and basis set selections.

Assessment of multireference approaches to explicitly correlated full configuration interaction quantum Monte Carlo

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kersten, J. A. F., E-mail: jennifer.kersten@cantab.net; Alavi, Ali, E-mail: a.alavi@fkf.mpg.de; Max Planck Institute for Solid State Research, Heisenbergstraße 1, 70569 Stuttgart

2016-08-07

The Full Configuration Interaction Quantum Monte Carlo (FCIQMC) method has proved able to provide near-exact solutions to the electronic Schrödinger equation within a finite orbital basis set, without relying on an expansion about a reference state. However, a drawback to the approach is that being based on an expansion of Slater determinants, the FCIQMC method suffers from a basis set incompleteness error that decays very slowly with the size of the employed single particle basis. The FCIQMC results obtained in a small basis set can be improved significantly with explicitly correlated techniques. Here, we present a study that assesses andmore » compares two contrasting “universal” explicitly correlated approaches that fit into the FCIQMC framework: the [2]{sub R12} method of Kong and Valeev [J. Chem. Phys. 135, 214105 (2011)] and the explicitly correlated canonical transcorrelation approach of Yanai and Shiozaki [J. Chem. Phys. 136, 084107 (2012)]. The former is an a posteriori internally contracted perturbative approach, while the latter transforms the Hamiltonian prior to the FCIQMC simulation. These comparisons are made across the 55 molecules of the G1 standard set. We found that both methods consistently reduce the basis set incompleteness, for accurate atomization energies in small basis sets, reducing the error from 28 mE{sub h} to 3-4 mE{sub h}. While many of the conclusions hold in general for any combination of multireference approaches with these methodologies, we also consider FCIQMC-specific advantages of each approach.« less

Detailed Wave Function Analysis for Multireference Methods: Implementation in the Molcas Program Package and Applications to Tetracene.

PubMed

Plasser, Felix; Mewes, Stefanie A; Dreuw, Andreas; González, Leticia

2017-11-14

High-level multireference computations on electronically excited and charged states of tetracene are performed, and the results are analyzed using an extensive wave function analysis toolbox that has been newly implemented in the Molcas program package. Aside from verifying the strong effect of dynamic correlation, this study reveals an unexpected critical influence of the atomic orbital basis set. It is shown that different polarized double-ζ basis sets produce significantly different results for energies, densities, and overall wave functions, with the best performance obtained for the atomic natural orbital (ANO) basis set by Pierloot et al. Strikingly, the ANO basis set not only reproduces the energies but also performs exceptionally well in terms of describing the diffuseness of the different states and of their attachment/detachment densities. This study, thus, not only underlines the fact that diffuse basis functions are needed for an accurate description of the electronic wave functions but also shows that, at least for the present example, it is enough to include them implicitly in the contraction scheme.

Homogeneous and heterogeneous noncovalent dimers of formaldehyde and thioformaldehyde: structures, energetics, and vibrational frequencies.

PubMed

Van Dornshuld, Eric; Holy, Christina M; Tschumper, Gregory S

2014-05-08

This work provides the first characterization of five stationary points of the homogeneous thioformaldehyde dimer, (CH2S)2, and seven stationary points of the heterogeneous formaldehyde/thioformaldehyde dimer, CH2O/CH2S, with correlated ab initio electronic structure methods. Full geometry optimizations and corresponding harmonic vibrational frequencies were computed with second-order Møller-Plesset perturbation theory (MP2) and 13 different density functionals in conjunction with triple-ζ basis sets augmented with diffuse and multiple sets of polarization functions. The MP2 results indicate that the three stationary points of (CH2S)2 and four of CH2O/CH2S are minima, in contrast to two stationary points of the formaldehyde dimer, (CH2O)2. Single-point energies were also computed using the explicitly correlated MP2-F12 and CCSD(T)-F12 methods and basis sets as large as heavy-aug-cc-pVTZ. The (CH2O)2 and CH2O/CH2S MP2 and MP2-F12 binding energies deviated from the CCSD(T)-F12 binding energies by no more than 0.2 and 0.4 kcal mol(-1), respectively. The (CH2O)2 and CH2O/CH2S global minimum is the same at every level of theory. However, the MP2 methods overbind (CH2S)2 by as much as 1.1 kcal mol(-1), effectively altering the energetic ordering of the thioformaldehyde dimer minima relative to the CCSD(T)-F12 energies. The CCSD(T)-F12 binding energies of the (CH2O)2 and CH2O/CH2S stationary points are quite similar, with the former ranging from around -2.4 to -4.6 kcal mol(-1) and the latter from about -1.1 to -4.4 kcal mol(-1). Corresponding (CH2S)2 stationary points have appreciably smaller CCSD(T)-F12 binding energies ranging from ca. -1.1 to -3.4 kcal mol(-1). The vibrational frequency shifts upon dimerization are also reported for each minimum on the MP2 potential energy surfaces.

Effect of oscillation dynamics on long-range electron transfer in a helical peptide monolayer.

PubMed

Matsushita, Daisuke; Uji, Hirotaka; Kimura, Shunsaku

2018-06-06

Electron transfer (ET) reactions via helical peptides composed of -(Aib-Pro)n- were studied in self-assembled monolayers and compared with -(Ala-Aib)n- peptides. Short Aib-Pro peptides showed slightly higher ET rates due to the better electronic coupling of the Pro residue. But, the 24mer Aib-Pro peptide showed a smaller ET rate than the corresponding Ala-Aib peptide. On the basis of DFT calculations, the deceleration of the ET rate of the longer Aib-Pro peptide is considered to be due to the smaller number of active modes of accordion-like oscillations than the Ala-Aib peptide, which has a strong influence on a long-range ET reaction.

Convergence of third order correlation energy in atoms and molecules.

PubMed

Kahn, Kalju; Granovsky, Alex A; Noga, Jozef

2007-01-30

We have investigated the convergence of third order correlation energy within the hierarchies of correlation consistent basis sets for helium, neon, and water, and for three stationary points of hydrogen peroxide. This analysis confirms that singlet pair energies converge much slower than triplet pair energies. In addition, singlet pair energies with (aug)-cc-pVDZ and (aug)-cc-pVTZ basis sets do not follow a converging trend and energies with three basis sets larger than aug-cc-pVTZ are generally required for reliable extrapolations of third order correlation energies, making so the explicitly correlated R12 calculations preferable.

Symmetry of semi-reduced lattices.

PubMed

Stróż, Kazimierz

2015-05-01

The main result of this work is extension of the famous characterization of Bravais lattices according to their metrical, algebraic and geometric properties onto a wide class of primitive lattices (including Buerger-reduced, nearly Buerger-reduced and a substantial part of Delaunay-reduced) related to low-restricted semi-reduced descriptions (s.r.d.'s). While the `geometric' operations in Bravais lattices map the basis vectors into themselves, the `arithmetic' operators in s.r.d. transform the basis vectors into cell vectors (basis vectors, face or space diagonals) and are represented by matrices from the set {\\bb V} of all 960 matrices with the determinant ±1 and elements {0, ±1} of the matrix powers. A lattice is in s.r.d. if the moduli of off-diagonal elements in both the metric tensors M and M(-1) are smaller than corresponding diagonal elements sharing the same column or row. Such lattices are split into 379 s.r.d. types relative to the arithmetic holohedries. Metrical criteria for each type do not need to be explicitly given but may be modelled as linear derivatives {\\bb M}(p,q,r), where {\\bb M} denotes the set of 39 highest-symmetry metric tensors, and p,q,r describe changes of appropriate interplanar distances. A sole filtering of {\\bb V} according to an experimental s.r.d. metric and subsequent geometric interpretation of the filtered matrices lead to mathematically stable and rich information on the Bravais-lattice symmetry and deviations from the exact symmetry. The emphasis on the crystallographic features of lattices was obtained by shifting the focus (i) from analysis of a lattice metric to analysis of symmetry matrices [Himes & Mighell (1987). Acta Cryst. A43, 375-384], (ii) from the isometric approach and invariant subspaces to the orthogonality concept {some ideas in Le Page [J. Appl. Cryst. (1982), 15, 255-259]} and splitting indices [Stróż (2011). Acta Cryst. A67, 421-429] and (iii) from fixed cell transformations to transformations derivable via geometric information (Himes & Mighell, 1987; Le Page, 1982). It is illustrated that corresponding arithmetic and geometric holohedries share space distribution of symmetry elements. Moreover, completeness of the s.r.d. types reveals their combinatorial structure and simplifies the crystallographic description of structural phase transitions, especially those observed with the use of powder diffraction. The research proves that there are excellent theoretical and practical reasons for looking at crystal lattice symmetry from an entirely new and surprising point of view - the combinatorial set {\\bb V} of matrices, their semi-reduced lattice context and their geometric properties.

Sensitivity of the Properties of Ruthenium “Blue Dimer” to Method, Basis Set, and Continuum Model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ozkanlar, Abdullah; Clark, Aurora E.

2012-05-23

The ruthenium “blue dimer” [(bpy)2RuIIIOH2]2O4+ is best known as the first well-defined molecular catalyst for water oxidation. It has been subject to numerous computational studies primarily employing density functional theory. However, those studies have been limited in the functionals, basis sets, and continuum models employed. The controversy in the calculated electronic structure and the reaction energetics of this catalyst highlights the necessity of benchmark calculations that explore the role of density functionals, basis sets, and continuum models upon the essential features of blue-dimer reactivity. In this paper, we report Kohn-Sham complete basis set (KS-CBS) limit extrapolations of the electronic structuremore » of “blue dimer” using GGA (BPW91 and BP86), hybrid-GGA (B3LYP), and meta-GGA (M06-L) density functionals. The dependence of solvation free energy corrections on the different cavity types (UFF, UA0, UAHF, UAKS, Bondi, and Pauling) within polarizable and conductor-like polarizable continuum model has also been investigated. The most common basis sets of double-zeta quality are shown to yield results close to the KS-CBS limit; however, large variations are observed in the reaction energetics as a function of density functional and continuum cavity model employed.« less

Spin-orbit ZORA and four-component Dirac-Coulomb estimation of relativistic corrections to isotropic nuclear shieldings and chemical shifts of noble gas dimers.

PubMed

Jankowska, Marzena; Kupka, Teobald; Stobiński, Leszek; Faber, Rasmus; Lacerda, Evanildo G; Sauer, Stephan P A

2016-02-05

Hartree-Fock and density functional theory with the hybrid B3LYP and general gradient KT2 exchange-correlation functionals were used for nonrelativistic and relativistic nuclear magnetic shielding calculations of helium, neon, argon, krypton, and xenon dimers and free atoms. Relativistic corrections were calculated with the scalar and spin-orbit zeroth-order regular approximation Hamiltonian in combination with the large Slater-type basis set QZ4P as well as with the four-component Dirac-Coulomb Hamiltonian using Dyall's acv4z basis sets. The relativistic corrections to the nuclear magnetic shieldings and chemical shifts are combined with nonrelativistic coupled cluster singles and doubles with noniterative triple excitations [CCSD(T)] calculations using the very large polarization-consistent basis sets aug-pcSseg-4 for He, Ne and Ar, aug-pcSseg-3 for Kr, and the AQZP basis set for Xe. For the dimers also, zero-point vibrational (ZPV) corrections are obtained at the CCSD(T) level with the same basis sets were added. Best estimates of the dimer chemical shifts are generated from these nuclear magnetic shieldings and the relative importance of electron correlation, ZPV, and relativistic corrections for the shieldings and chemical shifts is analyzed. © 2015 Wiley Periodicals, Inc.

Comparison of one-particle basis set extrapolation to explicitly correlated methods for the calculation of accurate quartic force fields, vibrational frequencies, and spectroscopic constants: Application to H2O, N2H+, NO2+, and C2H2

NASA Astrophysics Data System (ADS)

Huang, Xinchuan; Valeev, Edward F.; Lee, Timothy J.

2010-12-01

One-particle basis set extrapolation is compared with one of the new R12 methods for computing highly accurate quartic force fields (QFFs) and spectroscopic data, including molecular structures, rotational constants, and vibrational frequencies for the H2O, N2H+, NO2+, and C2H2 molecules. In general, agreement between the spectroscopic data computed from the best R12 and basis set extrapolation methods is very good with the exception of a few parameters for N2H+ where it is concluded that basis set extrapolation is still preferred. The differences for H2O and NO2+ are small and it is concluded that the QFFs from both approaches are more or less equivalent in accuracy. For C2H2, however, a known one-particle basis set deficiency for C-C multiple bonds significantly degrades the quality of results obtained from basis set extrapolation and in this case the R12 approach is clearly preferred over one-particle basis set extrapolation. The R12 approach used in the present study was modified in order to obtain high precision electronic energies, which are needed when computing a QFF. We also investigated including core-correlation explicitly in the R12 calculations, but conclude that current approaches are lacking. Hence core-correlation is computed as a correction using conventional methods. Considering the results for all four molecules, it is concluded that R12 methods will soon replace basis set extrapolation approaches for high accuracy electronic structure applications such as computing QFFs and spectroscopic data for comparison to high-resolution laboratory or astronomical observations, provided one uses a robust R12 method as we have done here. The specific R12 method used in the present study, CCSD(T)R12, incorporated a reformulation of one intermediate matrix in order to attain machine precision in the electronic energies. Final QFFs for N2H+ and NO2+ were computed, including basis set extrapolation, core-correlation, scalar relativity, and higher-order correlation and then used to compute highly accurate spectroscopic data for all isotopologues. Agreement with high-resolution experiment for 14N2H+ and 14N2D+ was excellent, but for 14N16O2+ agreement for the two stretching fundamentals is outside the expected residual uncertainty in the theoretical values, and it is concluded that there is an error in the experimental quantities. It is hoped that the highly accurate spectroscopic data presented for the minor isotopologues of N2H+ and NO2+ will be useful in the interpretation of future laboratory or astronomical observations.

Achievement Flourishes in Larger Classes: Secondary School Students in Most Countries Achieved Better Literacy in Larger Classes

ERIC Educational Resources Information Center

Alharbi, Abeer A.; Stoet, Gijsbert

2017-01-01

There is no consensus among academics about whether children benefit from smaller classes. We analysed the data from the 2012 Programme for International Student Assessment (PISA) to test if smaller classes lead to higher performance. Advantages of using this data set are not only its size (478,120 15-year old students in 63 nations) and…

Toward a W4-F12 approach: Can explicitly correlated and orbital-based ab initio CCSD(T) limits be reconciled?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sylvetsky, Nitai, E-mail: gershom@weizmann.ac.il; Martin, Jan M. L., E-mail: gershom@weizmann.ac.il; Peterson, Kirk A., E-mail: kipeters@wsu.edu

2016-06-07

In the context of high-accuracy computational thermochemistry, the valence coupled cluster with all singles and doubles (CCSD) correlation component of molecular atomization energies presents the most severe basis set convergence problem, followed by the (T) component. In the present paper, we make a detailed comparison, for an expanded version of the W4-11 thermochemistry benchmark, between, on the one hand, orbital-based CCSD/AV{5,6}Z + d and CCSD/ACV{5,6}Z extrapolation, and on the other hand CCSD-F12b calculations with cc-pVQZ-F12 and cc-pV5Z-F12 basis sets. This latter basis set, now available for H–He, B–Ne, and Al–Ar, is shown to be very close to the basis setmore » limit. Apparent differences (which can reach 0.35 kcal/mol for systems like CCl{sub 4}) between orbital-based and CCSD-F12b basis set limits disappear if basis sets with additional radial flexibility, such as ACV{5,6}Z, are used for the orbital calculation. Counterpoise calculations reveal that, while total atomization energies with V5Z-F12 basis sets are nearly free of BSSE, orbital calculations have significant BSSE even with AV(6 + d)Z basis sets, leading to non-negligible differences between raw and counterpoise-corrected extrapolated limits. This latter problem is greatly reduced by switching to ACV{5,6}Z core-valence basis sets, or simply adding an additional zeta to just the valence orbitals. Previous reports that all-electron approaches like HEAT (high-accuracy extrapolated ab-initio thermochemistry) lead to different CCSD(T) limits than “valence limit + CV correction” approaches like Feller-Peterson-Dixon and Weizmann-4 (W4) theory can be rationalized in terms of the greater radial flexibility of core-valence basis sets. For (T) corrections, conventional CCSD(T)/AV{Q,5}Z + d calculations are found to be superior to scaled or extrapolated CCSD(T)-F12b calculations of similar cost. For a W4-F12 protocol, we recommend obtaining the Hartree-Fock and valence CCSD components from CCSD-F12b/cc-pV{Q,5}Z-F12 calculations, but the (T) component from conventional CCSD(T)/aug’-cc-pV{Q,5}Z + d calculations using Schwenke’s extrapolation; post-CCSD(T), core-valence, and relativistic corrections are to be obtained as in the original W4 theory. W4-F12 is found to agree slightly better than W4 with ATcT (active thermochemical tables) data, at a substantial saving in computation time and especially I/O overhead. A W4-F12 calculation on benzene is presented as a proof of concept.« less

Laboratory agonistic interactions demonstrate failure of an introduced crayfish to dominate two imperiled endemic crayfishes

USGS Publications Warehouse

Rahm, E.J.; Griffith, S.A.; Noltie, Douglas B.; DiStefano, R.J.

2005-01-01

Following its introduction into the St. Francis River drainage, Missouri, U.S.A., the woodland crayfish, Orconectes hylas has expanded its range there; simultaneously populations of two imperiled endemic species, the Big Creek crayfish, O. peruncus, and the St. Francis River crayfish, O. quadruncus have declined therein. In seeking a basis for this decline, our study objective was to test whether the outcome of aggressive inter-specific interactions would favor O. hylas. We studied agonistic encounters between size-matched pairs of same-sex individuals of the introduced and the endemic species in a laboratory setting, first with juveniles and then with adults. Within each life stage, we conducted four sets of laboratory experiments, with approximately 20 trials in each set: (1) O. hylas males versus O. peruncus males, (2) O. hylas males versus O. quadruncus males, (3) O. hylas females versus O. peruncus females, and (4) O. hylas females versus O. quadruncus females. In addition, these same four experiment sets were repeated using larger adult O. hylas crayfish matched with smaller-sized adult endemics, mimicking the mismatch in adult sizes that occurs in the wild. Within each experiment, every trial was analysed to quantify the frequency of occurrence of three initiation behaviors and to determine the overall outcome of the trial. Results did not show O. hylas (juveniles or adults) to be behaviorally dominant over either endemic species. Orconectes hylas displayed the majority of one of the initiation behaviors significantly more often than did the endemic species in only two of the twelve experiments. Because direct aggressive interaction was not demonstrated to be the mechanism whereby O. peruncus and O. quadruncus are being replaced by O. hylas, other life history and ecological factors will require investigation. ?? Koninklijke Brill NV, 2005.

German Women Today: What Some German Newspapers Say. Inter Nationes Basis-Info 4-2000/Society. In Press.

ERIC Educational Resources Information Center

Born, Sigrid, Ed.

This document contains eight articles from German newspapers that feature women who have achieved career success in very diverse economic sectors, while simultaneously highlighting the discrimination and other problems (including lower income, fewer promotions to executive positions, and smaller pensions) that many other German women continue to…

Develop the Worker: Develop the Business. A Guide for Smaller Businesses.

ERIC Educational Resources Information Center

McGivney, Veronica

This document, which was developed on the basis of recent research and testimony of small business owners, managers and employees, and training providers, is a basic practical manual for those owners and managers of British small and medium-sized enterprises (SMEs) who want to initiate or improve staff training and development activities. The…

Challenges in Disseminating Model Programs: A Qualitative Analysis of the Strengthening Washington DC Families Program

ERIC Educational Resources Information Center

Fox, Danielle Polizzi; Gottfredson, Denise C.; Kumpfer, Karol K.; Beatty, Penny D.

2004-01-01

This article discusses the challenges faced when a popular model program, the Strengthening Families Program, which in the past has been implemented on a smaller scale in single organizations, moves to a larger, multiorganization endeavor. On the basis of 42 interviews conducted with program staff, the results highlight two main themes that…

A converged calculation of the energy barrier to internal rotation in the ethylene-sulfur dioxide dimer

NASA Astrophysics Data System (ADS)

Resende, Stella M.; De Almeida, Wagner B.; van Duijneveldt-van de Rijdt, Jeanne G. C. M.; van Duijneveldt, Frans B.

2001-08-01

Geometrical parameters for the equilibrium (MIN) and lowest saddle-point (TS) geometries of the C2H4⋯SO2 dimer, and the corresponding binding energies, were calculated using the Hartree-Fock and correlated levels of ab initio theory, in basis sets ranging from the D95(d,p) double-zeta basis set to the aug-cc-pVQZ correlation consistent basis set. An assessment of the effect of the basis set superposition error (BSSE) on these results was made. The dissociation energy from the lowest vibrational state was estimated to be 705±100 cm-1 at the basis set limit, which is well within the range expected from experiment. The barrier to internal rotation was found to be 53±5 cm-1, slightly higher than the (revised) experimental result of 43 cm-1, probably due to zero-point vibrational effects. Our results clearly show that, in direct contrast with recent ideas, the BSSE correction affects differentially the MIN and TS binding energies and so has to be included in the calculation of small energy barriers such as that in the C2H4⋯SO2 dimer. Previous reports of positive MP2 frozen-core binding energies for this complex in basis D95(d,p) are confirmed. The anomalies are shown to be an artifact arising from an incorrect removal of virtual orbitals by the default frozen-core option in the GAUSSIAN program.

Influence maximization in complex networks through optimal percolation

NASA Astrophysics Data System (ADS)

Morone, Flaviano; Makse, Hernan; CUNY Collaboration; CUNY Collaboration

The whole frame of interconnections in complex networks hinges on a specific set of structural nodes, much smaller than the total size, which, if activated, would cause the spread of information to the whole network, or, if immunized, would prevent the diffusion of a large scale epidemic. Localizing this optimal, that is, minimal, set of structural nodes, called influencers, is one of the most important problems in network science. Here we map the problem onto optimal percolation in random networks to identify the minimal set of influencers, which arises by minimizing the energy of a many-body system, where the form of the interactions is fixed by the non-backtracking matrix of the network. Big data analyses reveal that the set of optimal influencers is much smaller than the one predicted by previous heuristic centralities. Remarkably, a large number of previously neglected weakly connected nodes emerges among the optimal influencers. Reference: F. Morone, H. A. Makse, Nature 524,65-68 (2015)

Stereochemical analysis of (+)-limonene using theoretical and experimental NMR and chiroptical data

NASA Astrophysics Data System (ADS)

Reinscheid, F.; Reinscheid, U. M.

2016-02-01

Using limonene as test molecule, the success and the limitations of three chiroptical methods (optical rotatory dispersion (ORD), electronic and vibrational circular dichroism, ECD and VCD) could be demonstrated. At quite low levels of theory (mpw1pw91/cc-pvdz, IEFPCM (integral equation formalism polarizable continuum model)) the experimental ORD values differ by less than 10 units from the calculated values. The modelling in the condensed phase still represents a challenge so that experimental NMR data were used to test for aggregation and solvent-solute interactions. After establishing a reasonable structural model, only the ECD spectra prediction showed a decisive dependence on the basis set: only augmented (in the case of Dunning's basis sets) or diffuse (in the case of Pople's basis sets) basis sets predicted the position and shape of the ECD bands correctly. Based on these result we propose a procedure to assign the absolute configuration (AC) of an unknown compound using the comparison between experimental and calculated chiroptical data.

First-principles investigation on Rydberg and resonance excitations: A case study of the firefly luciferin anion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Noguchi, Yoshifumi, E-mail: y.noguchi@issp.u-tokyo.ac.jp; Hiyama, Miyabi; Akiyama, Hidefumi

2014-07-28

The optical properties of an isolated firefly luciferin anion are investigated by using first-principles calculations, employing the many-body perturbation theory to take into account the excitonic effect. The calculated photoabsorption spectra are compared with the results obtained using the time-dependent density functional theory (TDDFT) employing the localized atomic orbital (AO) basis sets and a recent experiment in vacuum. The present method well reproduces the line shape at the photon energy corresponding to the Rydberg and resonance excitations but overestimates the peak positions by about 0.5 eV. However, the TDDFT-calculated positions of some peaks are closer to those of the experiment.more » We also investigate the basis set dependency in describing the free electron states above vacuum level and the excitons involving the transitions to the free electron states and conclude that AO-only basis sets are inaccurate for free electron states and the use of a plane wave basis set is required.« less

Basis set study of classical rotor lattice dynamics.

PubMed

Witkoskie, James B; Wu, Jianlan; Cao, Jianshu

2004-03-22

The reorientational relaxation of molecular systems is important in many phenomenon and applications. In this paper, we explore the reorientational relaxation of a model Brownian rotor lattice system with short range interactions in both the high and low temperature regimes. In this study, we use a basis set expansion to capture collective motions of the system. The single particle basis set is used in the high temperature regime, while the spin wave basis is used in the low temperature regime. The equations of motion derived in this approach are analogous to the generalized Langevin equation, but the equations render flexibility by allowing nonequilibrium initial conditions. This calculation shows that the choice of projection operators in the generalized Langevin equation (GLE) approach corresponds to defining a specific inner-product space, and this inner-product space should be chosen to reveal the important physics of the problem. The basis set approach corresponds to an inner-product and projection operator that maintain the orthogonality of the spherical harmonics and provide a convenient platform for analyzing GLE expansions. The results compare favorably with numerical simulations, and the formalism is easily extended to more complex systems. (c) 2004 American Institute of Physics

Bonded Radii and the Contraction of the Electron Density of the Oxygen Atom by Bonded Interactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gibbs, Gerald V.; Ross, Nancy L.; Cox, David F.

2013-02-21

The bonded radii for more than 550 bonded pairs of atoms, comprising more than 50 crystals, determined from experimental and theoretical electron density distributions, are compared with the effective ionic, ri(M), and crystal radii, rc(M), for metal atoms, M, bonded to O atoms. At odds with the fixed ionic radius of 1.40 Å, assumed for the O atom in the compilation of the ionic radii, the bonded radius for the atom, rb(O), is not fixed but displays a relatively wide range of values as the O atom is progressively polarized by the M-O bonded interactions: as such, rb(O) decreases systematicallymore » from 1.40 Å (the Pauling radius of the oxide anion) as bond lengths decrease when bonded to an electropositive atom like sodium, to 0.64 Å (Bragg’s atomic radius of the O atom) when bonded to an electronegative atom like nitrogen. Both rb(M) and rb(O) increase in tandum with the increasing coordination number of the M atom. The bonded radii of the M atoms are highly correlated with both ri(M) and rc(M), but they both depart systematically from rb(M) and become smaller as the electronegativity of the M atom increases and the M-O bond length decreases. The well-developed correlations between both sets of radii and rb(M) testifies to the relative precision of both sets of radii and the fact that both sets are highly correlated the M-O bond 1 lengths. On the other hand, the progressive departure of rb(O) from the fixed ionic radius of the O atom with the increasing electronegativity of the bonded M atom indicates that any compilation of sets of ionic radii, assuming that the radius for the oxygen atom is fixed in value, is problematical and impacts on the accuracy of the resulting sets of ionic and crystal radii thus compiled. The assumption of a fixed O atom radius not only results in a negative ionic radii for several atoms, but it also results in values of rb(M) that are much as ~ 0.6 Å larger than the ri(M) and rc(M) values, respectively, particularly for the more electronegative M atoms. On the other hand, the ionic radii are in closer agreement with rb(M) for the more electropositive atoms. Notwithstanding that ionic radii are typically smaller than bonded radii, particularly for the more electronegative atoms, they have been used with considerable success in understanding and rationalizing problems and properties in crystal chemistry primarily because both ionic and crystal radii are highly correlated on a one-to-one basis with both the bonded radii and the associated M-O bond lengths. The lack of agreement between the effective ionic and crystal radii and the bonded radii for the more shared bonded interactions is ascribed to the progressive increase in the polarization of the O atom by the bonded atoms with a concomitant decrease in its radius, a factor that was neglected in the compilation of ionic and crystal radii for fluorides, oxides, sulfides and nitrides. This accounts for ionic radii for these materials being smaller than the bonded radii for the more electronegative atoms.« less

MP estimation applied to platykurtic sets of geodetic observations

NASA Astrophysics Data System (ADS)

Wiśniewski, Zbigniew

2017-06-01

MP estimation is a method which concerns estimating of the location parameters when the probabilistic models of observations differ from the normal distributions in the kurtosis or asymmetry. The system of Pearson's distributions is the probabilistic basis for the method. So far, such a method was applied and analyzed mostly for leptokurtic or mesokurtic distributions (Pearson's distributions of types IV or VII), which predominate practical cases. The analyses of geodetic or astronomical observations show that we may also deal with sets which have moderate asymmetry or small negative excess kurtosis. Asymmetry might result from the influence of many small systematic errors, which were not eliminated during preprocessing of data. The excess kurtosis can be related with bigger or smaller (in relations to the Hagen hypothesis) frequency of occurrence of the elementary errors which are close to zero. Considering that fact, this paper focuses on the estimation with application of the Pearson platykurtic distributions of types I or II. The paper presents the solution of the corresponding optimization problem and its basic properties. Although platykurtic distributions are rare in practice, it was an interesting issue to find out what results can be provided by MP estimation in the case of such observation distributions. The numerical tests which are presented in the paper are rather limited; however, they allow us to draw some general conclusions.

StrBioLib: a Java library for development of custom computationalstructural biology applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chandonia, John-Marc

2007-05-14

Summary: StrBioLib is a library of Java classes useful fordeveloping software for computational structural biology research.StrBioLib contains classes to represent and manipulate proteinstructures, biopolymer sequences, sets of biopolymer sequences, andalignments between biopolymers based on either sequence or structure.Interfaces are provided to interact with commonly used bioinformaticsapplications, including (PSI)-BLAST, MODELLER, MUSCLE, and Primer3, andtools are provided to read and write many file formats used to representbioinformatic data. The library includes a general-purpose neural networkobject with multiple training algorithms, the Hooke and Jeeves nonlinearoptimization algorithm, and tools for efficient C-style string parsingand formatting. StrBioLib is the basis for the Pred2ary secondarystructure predictionmore » program, is used to build the ASTRAL compendium forsequence and structure analysis, and has been extensively tested throughuse in many smaller projects. Examples and documentation are available atthe site below.Availability: StrBioLib may be obtained under the terms ofthe GNU LGPL license from http://strbio.sourceforge.net/Contact:JMChandonia@lbl.gov« less

Structural, electronic, vibrational and optical properties of Bin clusters

NASA Astrophysics Data System (ADS)

Liang, Dan; Shen, Wanting; Zhang, Chunfang; Lu, Pengfei; Wang, Shumin

2017-10-01

The neutral, anionic and cationic bismuth clusters with the size n up to 14 are investigated by using B3LYP functional within the regime of density functional theory and the LAN2DZ basis set. By analysis of the geometries of the Bin (n = 2-14) clusters, where cationic and anionic bismuth clusters are largely similar to those of neutral ones, a periodic effect by adding units with one to four atoms into smaller cluster to form larger cluster is drawn for the stable structures of bismuth clusters. An even-odd alteration is shown for the properties of the clusters, such as the calculated binding energies and dissociation energies, as well as frontier orbital energies, electron affinities, ionization energies. All the properties indicate that the Bi4 cluster is the most possible existence in bismuth-containing materials, which supports the most recent experiment. The orbital compositions, infrared and Raman activities and the ultraviolet absorption of the most possible tetramer bismuth cluster are given in detail to reveal the periodic tendency of adding bismuth atoms and the stability of tetramer bismuth cluster.

Disentangling the triadic interactions in Navier-Stokes equations.

PubMed

Sahoo, Ganapati; Biferale, Luca

2015-10-01

We study the role of helicity in the dynamics of energy transfer in a modified version of the Navier-Stokes equations with explicit breaking of the mirror symmetry. We select different set of triads participating in the dynamics on the basis of their helicity content. In particular, we remove the negative helically polarized Fourier modes at all wave numbers except for those falling on a localized shell of wave number, |k| ~ k(m). Changing k(m) to be above or below the forcing scale, k(f), we are able to assess the energy transfer of triads belonging to different interaction classes. We observe that when the negative helical modes are present only at a wave number smaller than the forced wave numbers, an inverse energy cascade develops with an accumulation of energy on a stationary helical condensate. Vice versa, when negative helical modes are present only at a wave number larger than the forced wave numbers, a transition from backward to forward energy transfer is observed in the regime when the minority modes become energetic enough.

StrBioLib: a Java library for development of custom computational structural biology applications.

PubMed

Chandonia, John-Marc

2007-08-01

StrBioLib is a library of Java classes useful for developing software for computational structural biology research. StrBioLib contains classes to represent and manipulate protein structures, biopolymer sequences, sets of biopolymer sequences, and alignments between biopolymers based on either sequence or structure. Interfaces are provided to interact with commonly used bioinformatics applications, including (psi)-blast, modeller, muscle and Primer3, and tools are provided to read and write many file formats used to represent bioinformatic data. The library includes a general-purpose neural network object with multiple training algorithms, the Hooke and Jeeves non-linear optimization algorithm, and tools for efficient C-style string parsing and formatting. StrBioLib is the basis for the Pred2ary secondary structure prediction program, is used to build the astral compendium for sequence and structure analysis, and has been extensively tested through use in many smaller projects. Examples and documentation are available at the site below. StrBioLib may be obtained under the terms of the GNU LGPL license from http://strbio.sourceforge.net/

Can Technology Capture the Signals That Certain Sites May Be Generating Electromagnetically, Which Some Traditional Cultures May Have Incorporated Into Their World-views?

NASA Astrophysics Data System (ADS)

Hedge, Jonathan S.; Mc Leod, Roger D.

2002-10-01

Electromagnetic field (EMF) signals may be associated with certain "artifacts" of N.E., such as N.H.'s "Old Man of the Mountain," or its possible "equivalents," as on the Penley Hill ledge at Mexico, ME, or the "enhanced" smaller versions at Mashamocket Brook State Park, CT, Potato Cave at Acton, MA, and especially a site in Lowell, MA, which may date to AD1069. Without physical evidence, they could be dismissed as figments of the imagination. Can electromagnetic signals be correlated with the Lowell site, which RDM observed as it tipped over a 27" TV set? It seems to generate somewhat periodic signals and may stimulate certain nerve endings, like the Psychiatrist Guirdham's "pins and needles," and could evoke "tinnitus." Can solenoids detect "elastic" EMFs "breaking and reconnecting" as hypothesized by RDM, where EMF lines may be running from the equivalent of "N" to "S" rotating poles? Is there a physical correlation with psychophysically detected phenomena, with cultural, religious, and historic implications on a worldwide basis?

Latent hardening size effect in small-scale plasticity

NASA Astrophysics Data System (ADS)

Bardella, Lorenzo; Segurado, Javier; Panteghini, Andrea; Llorca, Javier

2013-07-01

We aim at understanding the multislip behaviour of metals subject to irreversible deformations at small-scales. By focusing on the simple shear of a constrained single-crystal strip, we show that discrete Dislocation Dynamics (DD) simulations predict a strong latent hardening size effect, with smaller being stronger in the range [1.5 µm, 6 µm] for the strip height. We attempt to represent the DD pseudo-experimental results by developing a flow theory of Strain Gradient Crystal Plasticity (SGCP), involving both energetic and dissipative higher-order terms and, as a main novelty, a strain gradient extension of the conventional latent hardening. In order to discuss the capability of the SGCP theory proposed, we implement it into a Finite Element (FE) code and set its material parameters on the basis of the DD results. The SGCP FE code is specifically developed for the boundary value problem under study so that we can implement a fully implicit (Backward Euler) consistent algorithm. Special emphasis is placed on the discussion of the role of the material length scales involved in the SGCP model, from both the mechanical and numerical points of view.

From Data to Knowledge – Promising Analytical Tools and Techniques for Capture and Reuse of Corporate Knowledge and to Aid in the State Evaluation Process

DOE Office of Scientific and Technical Information (OSTI.GOV)

Danielson, Gary R.; Augustenborg, Elsa C.; Beck, Andrew E.

2010-10-29

The IAEA is challenged with limited availability of human resources for inspection and data analysis while proliferation threats increase. PNNL has a variety of IT solutions and techniques (at varying levels of maturity and development) that take raw data closer to useful knowledge, thereby assisting with and standardizing the analytical processes. This paper highlights some PNNL tools and techniques which are applicable to the international safeguards community, including: • Intelligent in-situ triage of data prior to reliable transmission to an analysis center resulting in the transmission of smaller and more relevant data sets • Capture of expert knowledge in re-usablemore » search strings tailored to specific mission outcomes • Image based searching fused with text based searching • Use of gaming to discover unexpected proliferation scenarios • Process modeling (e.g. Physical Model) as the basis for an information integration portal, which links to data storage locations along with analyst annotations, categorizations, geographic data, search strings and visualization outputs.« less

Absolute proper motions to B approximately 22.5: Evidence for kimematical substructure in halo field stars

NASA Technical Reports Server (NTRS)

Majewski, Steven R.; Munn, Jeffrey A.; Hawley, Suzanne L.

1994-01-01

Radial velocities have been obtained for six of nine stars identified on the basis of similar distances and common, extreme transverse velocities in the proper motion survey of Majewski (1992) as a candidate halo moving group at the north Galactic pole. These radial velocities correspond to velocities perpendicular to the Galactic plane which span the range -48 +/- 21 to -128 +/- 9 km/sec (but a smaller range, -48 +/- 21 to -86 +/- 19 km/sec, when only our own measurements are considered), significantly different than the expected distribution, with mean 0 km/sec, for a random sample of either halo or thick disk stars. The probability of picking such a set of radial velocities at random is less than 1%. Thus the radial velocity data support the hypothesis that these stars constitute part of a halo moving group or star stream at a distance of approximately 4-5 kpc above the Galactic plane. If real, this moving group is evidence for halo phase space substructure which may be the fossil remains of a destroyed globular cluster, Galactic satellite, or Searle & Zinn (1978) 'fragment.'

Abstract-Reasoning Software for Coordinating Multiple Agents

NASA Technical Reports Server (NTRS)

Clement, Bradley; Barrett, Anthony; Rabideau, Gregg; Knight, Russell

2003-01-01

A computer program for scheduling the activities of multiple agents that share limited resources has been incorporated into the Automated Scheduling and Planning Environment (ASPEN) software system, aspects of which have been reported in several previous NASA Tech Briefs articles. In the original intended application, the agents would be multiple spacecraft and/or robotic vehicles engaged in scientific exploration of distant planets. The program could also be used on Earth in such diverse settings as production lines and military maneuvers. This program includes a planning/scheduling subprogram of the iterative repair type that reasons about the activities of multiple agents at abstract levels in order to greatly improve the scheduling of their use of shared resources. The program summarizes the information about the constraints on, and resource requirements of, abstract activities on the basis of the constraints and requirements that pertain to their potential refinements (decomposition into less-abstract and ultimately to primitive activities). The advantage of reasoning about summary information is that time needed to find consistent schedules is exponentially smaller than the time that would be needed for reasoning about the same tasks at the primitive level.

Fabrication of a New Lineage of Artificial Luciferases from Natural Luciferase Pools.

PubMed

Kim, Sung Bae; Nishihara, Ryo; Citterio, Daniel; Suzuki, Koji

2017-09-11

The fabrication of artificial luciferases (ALucs) with unique optical properties has a fundamental impact on bioassays and molecular imaging. In this study, we developed a new lineage of ALucs with unique substrate preferences by extracting consensus amino acids from the alignment of 25 copepod luciferase sequences available in natural luciferase pools. The primary sequence was first created with a sequence logo generator resulting in a total of 11 sibling sequences. Phylogenetic analysis shows that the newly fabricated ALucs form an independent branch, genetically isolated from the natural luciferases, and from a prior series of ALucs produced by our laboratory using a smaller basis set. The new lineage of ALucs were strongly luminescent in living mammalian cells with specific substrate selectivity to native coelenterazine. A single-residue-level comparison of the C-terminal sequences of new ALucs reveals that some amino acids in the C-terminal ends are greatly influential on the optical intensities but limited in the color variance. The success of this approach guides on how to engineer and functionalize marine luciferases for bioluminescence imaging and assays.

Theoretical study of the XP3 (X = Al, B, Ga) clusters

NASA Astrophysics Data System (ADS)

Ueno, Leonardo T.; Lopes, Cinara; Malaspina, Thaciana; Roberto-Neto, Orlando; Canuto, Sylvio; Machado, Francisco B. C.

2012-05-01

The lowest singlet and triplet states of AlP3, GaP3 and BP3 molecules with Cs, C2v and C3v symmetries were characterized using the B3LYP functional and the aug-cc-pVTZ and aug-cc-pVQZ correlated consistent basis sets. Geometrical parameters and vibrational frequencies were calculated and compared to existent experimental and theoretical data. Relative energies were obtained with single point CCSD(T) calculations using the aug-cc-pVTZ, aug-cc-pVQZ and aug-cc-pV5Z basis sets, and then extrapolating to the complete basis set (CBS) limit.

How to compute isomerization energies of organic molecules with quantum chemical methods.

PubMed

Grimme, Stefan; Steinmetz, Marc; Korth, Martin

2007-03-16

The reaction energies for 34 typical organic isomerizations including oxygen and nitrogen heteroatoms are investigated with modern quantum chemical methods that have the perspective of also being applicable to large systems. The experimental reaction enthalpies are corrected for vibrational and thermal effects, and the thus derived "experimental" reaction energies are compared to corresponding theoretical data. A series of standard AO basis sets in combination with second-order perturbation theory (MP2, SCS-MP2), conventional density functionals (e.g., PBE, TPSS, B3-LYP, MPW1K, BMK), and new perturbative functionals (B2-PLYP, mPW2-PLYP) are tested. In three cases, obvious errors of the experimental values could be detected, and accurate coupled-cluster [CCSD(T)] reference values have been used instead. It is found that only triple-zeta quality AO basis sets provide results close enough to the basis set limit and that sets like the popular 6-31G(d) should be avoided in accurate work. Augmentation of small basis sets with diffuse functions has a notable effect in B3-LYP calculations that is attributed to intramolecular basis set superposition error and covers basic deficiencies of the functional. The new methods based on perturbation theory (SCS-MP2, X2-PLYP) are found to be clearly superior to many other approaches; that is, they provide mean absolute deviations of less than 1.2 kcal mol-1 and only a few (<10%) outliers. The best performance in the group of conventional functionals is found for the highly parametrized BMK hybrid meta-GGA. Contrary to accepted opinion, hybrid density functionals offer no real advantage over simple GGAs. For reasonably large AO basis sets, results of poor quality are obtained with the popular B3-LYP functional that cannot be recommended for thermochemical applications in organic chemistry. The results of this study are complementary to often used benchmarks based on atomization energies and should guide chemists in their search for accurate and efficient computational thermochemistry methods.

Development of a database of organ doses for paediatric and young adult CT scans in the United Kingdom

PubMed Central

Kim, K. P.; Berrington de González, A.; Pearce, M. S.; Salotti, J. A.; Parker, L.; McHugh, K.; Craft, A. W.; Lee, C.

2012-01-01

Despite great potential benefits, there are concerns about the possible harm from medical imaging including the risk of radiation-related cancer. There are particular concerns about computed tomography (CT) scans in children because both radiation dose and sensitivity to radiation for children are typically higher than for adults undergoing equivalent procedures. As direct empirical data on the cancer risks from CT scans are lacking, the authors are conducting a retrospective cohort study of over 240 000 children in the UK who underwent CT scans. The main objective of the study is to quantify the magnitude of the cancer risk in relation to the radiation dose from CT scans. In this paper, the methods used to estimate typical organ-specific doses delivered by CT scans to children are described. An organ dose database from Monte Carlo radiation transport-based computer simulations using a series of computational human phantoms from newborn to adults for both male and female was established. Organ doses vary with patient size and sex, examination types and CT technical settings. Therefore, information on patient age, sex and examination type from electronic radiology information systems and technical settings obtained from two national surveys in the UK were used to estimate radiation dose. Absorbed doses to the brain, thyroid, breast and red bone marrow were calculated for reference male and female individuals with the ages of newborns, 1, 5, 10, 15 and 20 y for a total of 17 different scan types in the pre- and post-2001 time periods. In general, estimated organ doses were slightly higher for females than males which might be attributed to the smaller body size of the females. The younger children received higher doses in pre-2001 period when adult CT settings were typically used for children. Paediatric-specific adjustments were assumed to be used more frequently after 2001, since then radiation doses to children have often been smaller than those to adults. The database here is the first detailed organ-specific paediatric CT scan database for the UK. As well as forming the basis for the UK study, the results and description of the methods will also serve as a key resource for paediatric CT scan studies currently underway in other countries. PMID:22228685

Development of a database of organ doses for paediatric and young adult CT scans in the United Kingdom.

PubMed

Kim, K P; Berrington de González, A; Pearce, M S; Salotti, J A; Parker, L; McHugh, K; Craft, A W; Lee, C

2012-07-01

Despite great potential benefits, there are concerns about the possible harm from medical imaging including the risk of radiation-related cancer. There are particular concerns about computed tomography (CT) scans in children because both radiation dose and sensitivity to radiation for children are typically higher than for adults undergoing equivalent procedures. As direct empirical data on the cancer risks from CT scans are lacking, the authors are conducting a retrospective cohort study of over 240,000 children in the UK who underwent CT scans. The main objective of the study is to quantify the magnitude of the cancer risk in relation to the radiation dose from CT scans. In this paper, the methods used to estimate typical organ-specific doses delivered by CT scans to children are described. An organ dose database from Monte Carlo radiation transport-based computer simulations using a series of computational human phantoms from newborn to adults for both male and female was established. Organ doses vary with patient size and sex, examination types and CT technical settings. Therefore, information on patient age, sex and examination type from electronic radiology information systems and technical settings obtained from two national surveys in the UK were used to estimate radiation dose. Absorbed doses to the brain, thyroid, breast and red bone marrow were calculated for reference male and female individuals with the ages of newborns, 1, 5, 10, 15 and 20 y for a total of 17 different scan types in the pre- and post-2001 time periods. In general, estimated organ doses were slightly higher for females than males which might be attributed to the smaller body size of the females. The younger children received higher doses in pre-2001 period when adult CT settings were typically used for children. Paediatric-specific adjustments were assumed to be used more frequently after 2001, since then radiation doses to children have often been smaller than those to adults. The database here is the first detailed organ-specific paediatric CT scan database for the UK. As well as forming the basis for the UK study, the results and description of the methods will also serve as a key resource for paediatric CT scan studies currently underway in other countries.

Comment on “Rethinking first-principles electron transport theories with projection operators: The problems caused by partitioning the basis set” [J. Chem. Phys. 139, 114104 (2013)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brandbyge, Mads, E-mail: mads.brandbyge@nanotech.dtu.dk

2014-05-07

In a recent paper Reuter and Harrison [J. Chem. Phys. 139, 114104 (2013)] question the widely used mean-field electron transport theories, which employ nonorthogonal localized basis sets. They claim these can violate an “implicit decoupling assumption,” leading to wrong results for the current, different from what would be obtained by using an orthogonal basis, and dividing surfaces defined in real-space. We argue that this assumption is not required to be fulfilled to get exact results. We show how the current/transmission calculated by the standard Greens function method is independent of whether or not the chosen basis set is nonorthogonal, andmore » that the current for a given basis set is consistent with divisions in real space. The ambiguity known from charge population analysis for nonorthogonal bases does not carry over to calculations of charge flux.« less

Morphometrics within dog breeds are highly reproducible and dispute Rensch’s rule

PubMed Central

Sutter, Nathan B.; Mosher, Dana S.; Gray, Melissa M.

2009-01-01

Using 27 body measurements, we have identified 13 breed-defining metrics for 109 of 159 domestic dog breeds, most of which are recognized by the American Kennel Club (AKC). The data set included 1,155 dogs at least 1 year old (average 5.4 years), and for 53 breed populations, complete measurement data were collected from at least three males and three females. We demonstrate, first, that AKC breed standards are rigorously adhered to for most domestic breeds with little variation observed within breeds. Second, Rensch’s rule, which describes a scaling among taxa such that sexual dimorphism is greater among larger species if males are the larger sex, with less pronounced differences in male versus female body size in smaller species, is not maintained in domestic dog breeds because the proportional size difference between males and females of small and large breeds is essentially the same. Finally, principal components (PCs) analysis describes both the overall body size (PC1) and the shape (length versus width) of the skeleton (PC2). That the integrity of the data set is sufficiently rich to discern PCs has strong implications for mapping studies, suggesting that individual measurements may not be needed for genetic studies of morphologic traits, particularly in the case of breed-defining traits that are typically under strong selection. Rather, phenotypes derived from data sets such as these, collected at a fraction of the effort and cost, may be used to direct whole-genome association studies aimed at understanding the genetic basis of fixed morphologic phenotypes defining distinct dog breeds. PMID:19020935

RESEARCH: Influence of Social, Biophysical, and Managerial Conditions on Tourism Experiences Within the Great Barrier Reef World Heritage Area.

PubMed

Shafer; Inglis

2000-07-01

/ Managing protected areas involves balancing the enjoyment of visitors with the protection of a variety of cultural and biophysical resources. Tourism pressures in the Great Barrier Reef World Heritage Area (GBRWHA) are creating concerns about how to strike this balance in a marine environment. Terrestrial-based research has led to conceptual planning and management frameworks that address issues of human use and resource protection. The limits of acceptable change (LAC) framework was used as a conceptual basis for a study of snorkeling at reef sites in the GBRWHA. The intent was to determine if different settings existed among tourism operators traveling to the reef and, if so, to identify specific conditions relating to those settings. Snorkelers (N = 1475) traveling with tourism operations of different sizes who traveled to different sites completed surveys. Results indicated that snorkelers who traveled with larger operations (more people and infrastructure) differed from those traveling with smaller operations (few people and little on-site infrastructure) on benefits received and in the way that specific conditions influenced their enjoyment. Benefits related to nature, escape, and family helped to define reef experiences. Conditions related to coral, fish, and operator staff had a positive influence on the enjoyment of most visitors but, number of people on the trip and site infrastructure may have the greatest potential as setting indicators. Data support the potential usefulness of visitor input in applying the LAC concept to a marine environment where tourism and recreational uses are rapidly changing.

Ab initio coupled-cluster and multi-reference configuration interaction studies of the low-lying electronic states of 1,2,3,4-cyclobutanetetraone

DOE PAGES

Hansen, Jared A.; Bauman, Nicholas P.; Shen, Jun; ...

2015-12-09

In this paper, the four, closely spaced, lowest energy electronic states of the challenging, D 4h-symmetric, 1,2,3,4-cyclobutanetetraone (C 4O 4) molecule have been investigated using high-level ab initio methods. The calculated states include the closed-shell singlet 8π( 1A 1g) state, the singlet 10π( 1A 1g) state, in which the π-type lowest unoccupied molecular orbital (LUMO) of the 8π( 1A 1g) reference is doubly occupied and the σ-type highest occupied molecular orbital (HOMO) is empty, and the open-shell singlet and triplet states, designated as 9π( 1B 2u) and 9π( 3B 2u), respectively, originating from single occupancy of the HOMO and LUMO.more » Our focus is on single-reference coupled-cluster (CC) approaches capable of handling electronic near-degeneracies in diradicals, especially the completely renormalised CR-CC(2,3) and active-space CCSDt methods, along with their CCSD and EOMCCSD counterparts. The internally contracted multi-reference configuration interaction calculations with a quasi-degenerate Davidson correction are performed as well. Our computations demonstrate that the state ordering is 9π( 3B 2u) < 8π( 1A 1g) < 9π( 1B 2u) < 10π( 1A 1g) and that the 8π( 1A 1g) - 9π( 3B 2u) gap is in the 7–11 kJ/mol range, in reasonable agreement with the negative ion photoelectron spectroscopy measurements, which give 6.27 ± 0.5 kJ/mol. Finally, in addition to the theory level used, geometry relaxation and basis set play a significant role in determining the state ordering and energy spacings. In particular, it is unsafe to use lower level, non-CC geometries and smaller basis sets.« less

Some considerations about Gaussian basis sets for electric property calculations

NASA Astrophysics Data System (ADS)

Arruda, Priscilla M.; Canal Neto, A.; Jorge, F. E.

Recently, segmented contracted basis sets of double, triple, and quadruple zeta valence quality plus polarization functions (XZP, X = D, T, and Q, respectively) for the atoms from H to Ar were reported. In this work, with the objective of having a better description of polarizabilities, the QZP set was augmented with diffuse (s and p symmetries) and polarization (p, d, f, and g symmetries) functions that were chosen to maximize the mean dipole polarizability at the UHF and UMP2 levels, respectively. At the HF and B3LYP levels of theory, electric dipole moment and static polarizability for a sample of molecules were evaluated. Comparison with experimental data and results obtained with a similar size basis set, whose diffuse functions were optimized for the ground state energy of the anion, was done.

A Simplified Approach to the Basis Functions of Symmetry Operations and Terms of Metal Complexes in an Octahedral Field with d[superscript 1] to d[superscript 9] Configurations

ERIC Educational Resources Information Center

Lee, Liangshiu

2010-01-01

The basis sets for symmetry operations of d[superscript 1] to d[superscript 9] complexes in an octahedral field and the resulting terms are derived for the ground states and spin-allowed excited states. The basis sets are of fundamental importance in group theory. This work addresses such a fundamental issue, and the results are pedagogically…

DOE Office of Scientific and Technical Information (OSTI.GOV)

Makhov, Dmitry V.; Shalashilin, Dmitrii V.; Glover, William J.

We present a new algorithm for ab initio quantum nonadiabatic molecular dynamics that combines the best features of ab initio Multiple Spawning (AIMS) and Multiconfigurational Ehrenfest (MCE) methods. In this new method, ab initio multiple cloning (AIMC), the individual trajectory basis functions (TBFs) follow Ehrenfest equations of motion (as in MCE). However, the basis set is expanded (as in AIMS) when these TBFs become sufficiently mixed, preventing prolonged evolution on an averaged potential energy surface. We refer to the expansion of the basis set as “cloning,” in analogy to the “spawning” procedure in AIMS. This synthesis of AIMS and MCEmore » allows us to leverage the benefits of mean-field evolution during periods of strong nonadiabatic coupling while simultaneously avoiding mean-field artifacts in Ehrenfest dynamics. We explore the use of time-displaced basis sets, “trains,” as a means of expanding the basis set for little cost. We also introduce a new bra-ket averaged Taylor expansion (BAT) to approximate the necessary potential energy and nonadiabatic coupling matrix elements. The BAT approximation avoids the necessity of computing electronic structure information at intermediate points between TBFs, as is usually done in saddle-point approximations used in AIMS. The efficiency of AIMC is demonstrated on the nonradiative decay of the first excited state of ethylene. The AIMC method has been implemented within the AIMS-MOLPRO package, which was extended to include Ehrenfest basis functions.« less

A review of methods for monitoring streamflow for sustainable water resource management

NASA Astrophysics Data System (ADS)

Dobriyal, Pariva; Badola, Ruchi; Tuboi, Chongpi; Hussain, Syed Ainul

2017-10-01

Monitoring of streamflow may help to determine the optimum levels of its use for sustainable water management in the face of climate change. We reviewed available methods for monitoring streamflow on the basis of six criteria viz. their applicability across different terrains and size of the streams, operational ease, time effectiveness, accuracy, environmental impact that they may cause and cost involve in it. On the basis of the strengths and weaknesses of each of the methods reviewed, we conclude that the timed volume method is apt for hilly terrain having smaller streams due to its operational ease and accuracy of results. Although comparatively expensive, the weir and flume methods are suitable for long term studies of small hill streams, since once the structure is put in place, it yields accurate results. In flat terrain, the float method is best suited for smaller streams for its operational ease and cost effectiveness, whereas, for larger streams, the particle image velocimetry may be used for its accuracy. Our review suggests that the selection of a method for monitoring streamflow may be based on volume of the stream, accuracy of the method, accessibility of the terrain and financial and physical resources available.

Asymptotic behavior and interpretation of virtual states: The effects of confinement and of basis sets

NASA Astrophysics Data System (ADS)

Boffi, Nicholas M.; Jain, Manish; Natan, Amir

2016-02-01

A real-space high order finite difference method is used to analyze the effect of spherical domain size on the Hartree-Fock (and density functional theory) virtual eigenstates. We show the domain size dependence of both positive and negative virtual eigenvalues of the Hartree-Fock equations for small molecules. We demonstrate that positive states behave like a particle in spherical well and show how they approach zero. For the negative eigenstates, we show that large domains are needed to get the correct eigenvalues. We compare our results to those of Gaussian basis sets and draw some conclusions for real-space, basis-sets, and plane-waves calculations.

Exact solution for the hydrogen atom confined by a dielectric continuum and the correct basis set to study many-electron atoms under similar confinements

NASA Astrophysics Data System (ADS)

Martínez-Sánchez, Michael-Adán; Aquino, Norberto; Vargas, Rubicelia; Garza, Jorge

2017-12-01

The Schrödinger equation associated to the hydrogen atom confined by a dielectric continuum is solved exactly and suggests the appropriate basis set to be used when an atom is immersed in a dielectric continuum. Exact results show that this kind of confinement spread the electron density, which is confirmed through the Shannon entropy. The basis set suggested by the exact results is similar to Slater type orbitals and it was applied on two-electron atoms, where the H- ion ejects one electron for moderate confinements for distances much larger than those commonly used to generate cavities in solvent models.

CCSD(T) potential energy and induced dipole surfaces for N2–H2(D2): retrieval of the collision-induced absorption integrated intensities in the regions of the fundamental and first overtone vibrational transitions.

PubMed

Buryak, Ilya; Lokshtanov, Sergei; Vigasin, Andrey

2012-09-21

The present work aims at ab initio characterization of the integrated intensity temperature variation of collision-induced absorption (CIA) in N(2)-H(2)(D(2)). Global fits of potential energy surface (PES) and induced dipole moment surface (IDS) were made on the basis of CCSD(T) (coupled cluster with single and double and perturbative triple excitations) calculations with aug-cc-pV(T,Q)Z basis sets. Basis set superposition error correction and extrapolation to complete basis set (CBS) limit techniques were applied to both energy and dipole moment. Classical second cross virial coefficient calculations accounting for the first quantum correction were employed to prove the quality of the obtained PES. The CIA temperature dependence was found in satisfactory agreement with available experimental data.

Fragment approach to constrained density functional theory calculations using Daubechies wavelets

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ratcliff, Laura E.; Genovese, Luigi; Mohr, Stephan

2015-06-21

In a recent paper, we presented a linear scaling Kohn-Sham density functional theory (DFT) code based on Daubechies wavelets, where a minimal set of localized support functions are optimized in situ and therefore adapted to the chemical properties of the molecular system. Thanks to the systematically controllable accuracy of the underlying basis set, this approach is able to provide an optimal contracted basis for a given system: accuracies for ground state energies and atomic forces are of the same quality as an uncontracted, cubic scaling approach. This basis set offers, by construction, a natural subset where the density matrix ofmore » the system can be projected. In this paper, we demonstrate the flexibility of this minimal basis formalism in providing a basis set that can be reused as-is, i.e., without reoptimization, for charge-constrained DFT calculations within a fragment approach. Support functions, represented in the underlying wavelet grid, of the template fragments are roto-translated with high numerical precision to the required positions and used as projectors for the charge weight function. We demonstrate the interest of this approach to express highly precise and efficient calculations for preparing diabatic states and for the computational setup of systems in complex environments.« less

77 FR 53781 - Safety Standard for Magnet Sets

Federal Register 2010, 2011, 2012, 2013, 2014

2012-09-04

... preliminarily that there may be an unreasonable risk of injury associated with children ingesting high-powered... during the eight months after it. A high percentage of the injuries resulted in surgeries or other... exception of the smaller sets, are sold with a container, such as a square plastic cube, a metal tin, and/or...

78 FR 61113 - Acquisition Process: Task and Delivery Order Contracts, Bundling, Consolidation

Federal Register 2010, 2011, 2012, 2013, 2014

2013-10-02

... that a total set-aside is not appropriate but the procurement can be broken up into smaller discrete... discrete components to support a partial set-aside and market research shows that either: at least two... could divide a multiple award contract for divergent goods and services into discrete categories (which...

Narrowing the error in electron correlation calculations by basis set re-hierarchization and use of the unified singlet and triplet electron-pair extrapolation scheme: Application to a test set of 106 systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Varandas, A. J. C., E-mail: varandas@uc.pt; Departamento de Física, Universidade Federal do Espírito Santo, 29075-910 Vitória; Pansini, F. N. N.

2014-12-14

A method previously suggested to calculate the correlation energy at the complete one-electron basis set limit by reassignment of the basis hierarchical numbers and use of the unified singlet- and triplet-pair extrapolation scheme is applied to a test set of 106 systems, some with up to 48 electrons. The approach is utilized to obtain extrapolated correlation energies from raw values calculated with second-order Møller-Plesset perturbation theory and the coupled-cluster singles and doubles excitations method, some of the latter also with the perturbative triples corrections. The calculated correlation energies have also been used to predict atomization energies within an additive scheme.more » Good agreement is obtained with the best available estimates even when the (d, t) pair of hierarchical numbers is utilized to perform the extrapolations. This conceivably justifies that there is no strong reason to exclude double-zeta energies in extrapolations, especially if the basis is calibrated to comply with the theoretical model.« less

The convergence of complete active space self-consistent-field configuration interaction including all single and double excitation energies to the complete basis set limit

NASA Astrophysics Data System (ADS)

Petersson, George A.; Malick, David K.; Frisch, Michael J.; Braunstein, Matthew

2006-07-01

Examination of the convergence of full valence complete active space self-consistent-field configuration interaction including all single and double excitation (CASSCF-CISD) energies with expansion of the one-electron basis set reveals a pattern very similar to the convergence of single determinant energies. Calculations on the lowest four singlet states and the lowest four triplet states of N2 with the sequence of n-tuple-ζ augmented polarized (nZaP) basis sets (n =2, 3, 4, 5, and 6) are used to establish the complete basis set limits. Full configuration-interaction (CI) and core electron contributions must be included for very accurate potential energy surfaces. However, a simple extrapolation scheme that has no adjustable parameters and requires nothing more demanding than CAS(10e -,8orb)-CISD/3ZaP calculations gives the Re, ωe, ωeXe, Te, and De for these eight states with rms errors of 0.0006Å, 4.43cm-1, 0.35cm-1, 0.063eV, and 0.018eV, respectively.

48 CFR 25.504-4 - Group award basis.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 48 Federal Acquisition Regulations System 1 2011-10-01 2011-10-01 false Group award basis. 25.504... SOCIOECONOMIC PROGRAMS FOREIGN ACQUISITION Evaluating Foreign Offers-Supply Contracts 25.504-4 Group award basis... a group basis. Assume the Buy American Act applies and the acquisition cannot be set aside for small...

48 CFR 25.504-4 - Group award basis.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 48 Federal Acquisition Regulations System 1 2013-10-01 2013-10-01 false Group award basis. 25.504... SOCIOECONOMIC PROGRAMS FOREIGN ACQUISITION Evaluating Foreign Offers-Supply Contracts 25.504-4 Group award basis... a group basis. Assume the Buy American Act applies and the acquisition cannot be set aside for small...

48 CFR 25.504-4 - Group award basis.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 48 Federal Acquisition Regulations System 1 2014-10-01 2014-10-01 false Group award basis. 25.504... SOCIOECONOMIC PROGRAMS FOREIGN ACQUISITION Evaluating Foreign Offers-Supply Contracts 25.504-4 Group award basis... a group basis. Assume the Buy American statute applies and the acquisition cannot be set aside for...

48 CFR 25.504-4 - Group award basis.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 48 Federal Acquisition Regulations System 1 2012-10-01 2012-10-01 false Group award basis. 25.504... SOCIOECONOMIC PROGRAMS FOREIGN ACQUISITION Evaluating Foreign Offers-Supply Contracts 25.504-4 Group award basis... a group basis. Assume the Buy American Act applies and the acquisition cannot be set aside for small...

48 CFR 25.504-4 - Group award basis.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 48 Federal Acquisition Regulations System 1 2010-10-01 2010-10-01 false Group award basis. 25.504... SOCIOECONOMIC PROGRAMS FOREIGN ACQUISITION Evaluating Foreign Offers-Supply Contracts 25.504-4 Group award basis... a group basis. Assume the Buy American Act applies and the acquisition cannot be set aside for small...

A geometrical correction for the inter- and intra-molecular basis set superposition error in Hartree-Fock and density functional theory calculations for large systems

NASA Astrophysics Data System (ADS)

Kruse, Holger; Grimme, Stefan

2012-04-01

A semi-empirical counterpoise-type correction for basis set superposition error (BSSE) in molecular systems is presented. An atom pair-wise potential corrects for the inter- and intra-molecular BSSE in supermolecular Hartree-Fock (HF) or density functional theory (DFT) calculations. This geometrical counterpoise (gCP) denoted scheme depends only on the molecular geometry, i.e., no input from the electronic wave-function is required and hence is applicable to molecules with ten thousands of atoms. The four necessary parameters have been determined by a fit to standard Boys and Bernadi counterpoise corrections for Hobza's S66×8 set of non-covalently bound complexes (528 data points). The method's target are small basis sets (e.g., minimal, split-valence, 6-31G*), but reliable results are also obtained for larger triple-ζ sets. The intermolecular BSSE is calculated by gCP within a typical error of 10%-30% that proves sufficient in many practical applications. The approach is suggested as a quantitative correction in production work and can also be routinely applied to estimate the magnitude of the BSSE beforehand. The applicability for biomolecules as the primary target is tested for the crambin protein, where gCP removes intramolecular BSSE effectively and yields conformational energies comparable to def2-TZVP basis results. Good mutual agreement is also found with Jensen's ACP(4) scheme, estimating the intramolecular BSSE in the phenylalanine-glycine-phenylalanine tripeptide, for which also a relaxed rotational energy profile is presented. A variety of minimal and double-ζ basis sets combined with gCP and the dispersion corrections DFT-D3 and DFT-NL are successfully benchmarked on the S22 and S66 sets of non-covalent interactions. Outstanding performance with a mean absolute deviation (MAD) of 0.51 kcal/mol (0.38 kcal/mol after D3-refit) is obtained at the gCP-corrected HF-D3/(minimal basis) level for the S66 benchmark. The gCP-corrected B3LYP-D3/6-31G* model chemistry yields MAD=0.68 kcal/mol, which represents a huge improvement over plain B3LYP/6-31G* (MAD=2.3 kcal/mol). Application of gCP-corrected B97-D3 and HF-D3 on a set of large protein-ligand complexes prove the robustness of the method. Analytical gCP gradients make optimizations of large systems feasible with small basis sets, as demonstrated for the inter-ring distances of 9-helicene and most of the complexes in Hobza's S22 test set. The method is implemented in a freely available FORTRAN program obtainable from the author's website.

Flat bases of invariant polynomials and P-matrices of E{sub 7} and E{sub 8}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Talamini, Vittorino

2010-02-15

Let G be a compact group of linear transformations of a Euclidean space V. The G-invariant C{sup {infinity}} functions can be expressed as C{sup {infinity}} functions of a finite basic set of G-invariant homogeneous polynomials, sometimes called an integrity basis. The mathematical description of the orbit space V/G depends on the integrity basis too: it is realized through polynomial equations and inequalities expressing rank and positive semidefiniteness conditions of the P-matrix, a real symmetric matrix determined by the integrity basis. The choice of the basic set of G-invariant homogeneous polynomials forming an integrity basis is not unique, so it ismore » not unique the mathematical description of the orbit space too. If G is an irreducible finite reflection group, Saito et al. [Commun. Algebra 8, 373 (1980)] characterized some special basic sets of G-invariant homogeneous polynomials that they called flat. They also found explicitly the flat basic sets of invariant homogeneous polynomials of all the irreducible finite reflection groups except of the two largest groups E{sub 7} and E{sub 8}. In this paper the flat basic sets of invariant homogeneous polynomials of E{sub 7} and E{sub 8} and the corresponding P-matrices are determined explicitly. Using the results here reported one is able to determine easily the P-matrices corresponding to any other integrity basis of E{sub 7} or E{sub 8}. From the P-matrices one may then write down the equations and inequalities defining the orbit spaces of E{sub 7} and E{sub 8} relatively to a flat basis or to any other integrity basis. The results here obtained may be employed concretely to study analytically the symmetry breaking in all theories where the symmetry group is one of the finite reflection groups E{sub 7} and E{sub 8} or one of the Lie groups E{sub 7} and E{sub 8} in their adjoint representations.« less

Spectroscopic properties of Arx-Zn and Arx-Ag+ (x = 1,2) van der Waals complexes

NASA Astrophysics Data System (ADS)

Oyedepo, Gbenga A.; Peterson, Charles; Schoendorff, George; Wilson, Angela K.

2013-03-01

Potential energy curves have been constructed using coupled cluster with singles, doubles, and perturbative triple excitations (CCSD(T)) in combination with all-electron and pseudopotential-based multiply augmented correlation consistent basis sets [m-aug-cc-pV(n + d)Z; m = singly, doubly, triply, n = D,T,Q,5]. The effect of basis set superposition error on the spectroscopic properties of Ar-Zn, Ar2-Zn, Ar-Ag+, and Ar2-Ag+ van der Waals complexes was examined. The diffuse functions of the doubly and triply augmented basis sets have been constructed using the even-tempered expansion. The a posteriori counterpoise scheme of Boys and Bernardi and its generalized variant by Valiron and Mayer has been utilized to correct for basis set superposition error (BSSE) in the calculated spectroscopic properties for diatomic and triatomic species. It is found that even at the extrapolated complete basis set limit for the energetic properties, the pseudopotential-based calculations still suffer from significant BSSE effects unlike the all-electron basis sets. This indicates that the quality of the approximations used in the design of pseudopotentials could have major impact on a seemingly valence-exclusive effect like BSSE. We confirm the experimentally determined equilibrium internuclear distance (re), binding energy (De), harmonic vibrational frequency (ωe), and C1Π ← X1Σ transition energy for ArZn and also predict the spectroscopic properties for the low-lying excited states of linear Ar2-Zn (X1Σg, 3Πg, 1Πg), Ar-Ag+ (X1Σ, 3Σ, 3Π, 3Δ, 1Σ, 1Π, 1Δ), and Ar2-Ag+ (X1Σg, 3Σg, 3Πg, 3Δg, 1Σg, 1Πg, 1Δg) complexes, using the CCSD(T) and MR-CISD + Q methods, to aid in their experimental characterizations.

A projection-free method for representing plane-wave DFT results in an atom-centered basis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dunnington, Benjamin D.; Schmidt, J. R., E-mail: schmidt@chem.wisc.edu

2015-09-14

Plane wave density functional theory (DFT) is a powerful tool for gaining accurate, atomic level insight into bulk and surface structures. Yet, the delocalized nature of the plane wave basis set hinders the application of many powerful post-computation analysis approaches, many of which rely on localized atom-centered basis sets. Traditionally, this gap has been bridged via projection-based techniques from a plane wave to atom-centered basis. We instead propose an alternative projection-free approach utilizing direct calculation of matrix elements of the converged plane wave DFT Hamiltonian in an atom-centered basis. This projection-free approach yields a number of compelling advantages, including strictmore » orthonormality of the resulting bands without artificial band mixing and access to the Hamiltonian matrix elements, while faithfully preserving the underlying DFT band structure. The resulting atomic orbital representation of the Kohn-Sham wavefunction and Hamiltonian provides a gateway to a wide variety of analysis approaches. We demonstrate the utility of the approach for a diverse set of chemical systems and example analysis approaches.« less

Pixel Dynamics Analysis of Photospheric Spectral Data

DTIC Science & Technology

2014-11-13

absorption lines centered at 6301.5 Å and 6302.5 Å. The two smaller absorption lines are telluric lines. The analysis is carried out for a range of...cadence and consist of 251 scan lines. These two new sets of SOLIS VSM data also revealed more inconsistent instrument movements between scans, forcing us...SOLIS VSM instrument. The wavelength range shows two photospheric absorption lines, Fe I 6301.5 Å and Fe I 6302.5 Å ), and two smaller telluric

Density functional theory study of the interaction of vinyl radical, ethyne, and ethene with benzene, aimed to define an affordable computational level to investigate stability trends in large van der Waals complexes

NASA Astrophysics Data System (ADS)

Maranzana, Andrea; Giordana, Anna; Indarto, Antonius; Tonachini, Glauco; Barone, Vincenzo; Causà, Mauro; Pavone, Michele

2013-12-01

Our purpose is to identify a computational level sufficiently dependable and affordable to assess trends in the interaction of a variety of radical or closed shell unsaturated hydro-carbons A adsorbed on soot platelet models B. These systems, of environmental interest, would unavoidably have rather large sizes, thus prompting to explore in this paper the performances of relatively low-level computational methods and compare them with higher-level reference results. To this end, the interaction of three complexes between non-polar species, vinyl radical, ethyne, or ethene (A) with benzene (B) is studied, since these species, involved themselves in growth processes of polycyclic aromatic hydrocarbons (PAHs) and soot particles, are small enough to allow high-level reference calculations of the interaction energy ΔEAB. Counterpoise-corrected interaction energies ΔEAB are used at all stages. (1) Density Functional Theory (DFT) unconstrained optimizations of the A-B complexes are carried out, using the B3LYP-D, ωB97X-D, and M06-2X functionals, with six basis sets: 6-31G(d), 6-311 (2d,p), and 6-311++G(3df,3pd); aug-cc-pVDZ and aug-cc-pVTZ; N07T. (2) Then, unconstrained optimizations by Møller-Plesset second order Perturbation Theory (MP2), with each basis set, allow subsequent single point Coupled Cluster Singles Doubles and perturbative estimate of the Triples energy computations with the same basis sets [CCSD(T)//MP2]. (3) Based on an additivity assumption of (i) the estimated MP2 energy at the complete basis set limit [EMP2/CBS] and (ii) the higher-order correlation energy effects in passing from MP2 to CCSD(T) at the aug-cc-pVTZ basis set, ΔECC-MP, a CCSD(T)/CBS estimate is obtained and taken as a computational energy reference. At DFT, variations in ΔEAB with basis set are not large for the title molecules, and the three functionals perform rather satisfactorily even with rather small basis sets [6-31G(d) and N07T], exhibiting deviation from the computational reference of less than 1 kcal mol-1. The zero-point vibrational energy corrected estimates Δ(EAB+ZPE), obtained with the three functionals and the 6-31G(d) and N07T basis sets, are compared with experimental D0 measures, when available. In particular, this comparison is finally extended to the naphthalene and coronene dimers and to three π-π associations of different PAHs (R, made by 10, 16, or 24 C atoms) and P (80 C atoms).

Density functional theory study of the interaction of vinyl radical, ethyne, and ethene with benzene, aimed to define an affordable computational level to investigate stability trends in large van der Waals complexes.

PubMed

Maranzana, Andrea; Giordana, Anna; Indarto, Antonius; Tonachini, Glauco; Barone, Vincenzo; Causà, Mauro; Pavone, Michele

2013-12-28

Our purpose is to identify a computational level sufficiently dependable and affordable to assess trends in the interaction of a variety of radical or closed shell unsaturated hydro-carbons A adsorbed on soot platelet models B. These systems, of environmental interest, would unavoidably have rather large sizes, thus prompting to explore in this paper the performances of relatively low-level computational methods and compare them with higher-level reference results. To this end, the interaction of three complexes between non-polar species, vinyl radical, ethyne, or ethene (A) with benzene (B) is studied, since these species, involved themselves in growth processes of polycyclic aromatic hydrocarbons (PAHs) and soot particles, are small enough to allow high-level reference calculations of the interaction energy ΔEAB. Counterpoise-corrected interaction energies ΔEAB are used at all stages. (1) Density Functional Theory (DFT) unconstrained optimizations of the A-B complexes are carried out, using the B3LYP-D, ωB97X-D, and M06-2X functionals, with six basis sets: 6-31G(d), 6-311 (2d,p), and 6-311++G(3df,3pd); aug-cc-pVDZ and aug-cc-pVTZ; N07T. (2) Then, unconstrained optimizations by Møller-Plesset second order Perturbation Theory (MP2), with each basis set, allow subsequent single point Coupled Cluster Singles Doubles and perturbative estimate of the Triples energy computations with the same basis sets [CCSD(T)//MP2]. (3) Based on an additivity assumption of (i) the estimated MP2 energy at the complete basis set limit [EMP2/CBS] and (ii) the higher-order correlation energy effects in passing from MP2 to CCSD(T) at the aug-cc-pVTZ basis set, ΔECC-MP, a CCSD(T)/CBS estimate is obtained and taken as a computational energy reference. At DFT, variations in ΔEAB with basis set are not large for the title molecules, and the three functionals perform rather satisfactorily even with rather small basis sets [6-31G(d) and N07T], exhibiting deviation from the computational reference of less than 1 kcal mol(-1). The zero-point vibrational energy corrected estimates Δ(EAB+ZPE), obtained with the three functionals and the 6-31G(d) and N07T basis sets, are compared with experimental D0 measures, when available. In particular, this comparison is finally extended to the naphthalene and coronene dimers and to three π-π associations of different PAHs (R, made by 10, 16, or 24 C atoms) and P (80 C atoms).

Design of a Multi-Pinhole Collimator for I-123 DaTscan Imaging on Dual-Headed SPECT Systems in Combination with a Fan-Beam Collimator.

PubMed

King, Michael A; Mukherjee, Joyeeta M; Könik, Arda; Zubal, I George; Dey, Joyoni; Licho, Robert

2016-02-01

For the 2011 FDA approved Parkinson's Disease (PD) SPECT imaging agent I-123 labeled DaTscan, the volume of interest (VOI) is the interior portion of the brain. However imaging of the occipital lobe is also required with PD for calculation of the striatal binding ratio (SBR), a parameter of significance in early diagnosis, differentiation of PD from other disorders with similar clinical presentations, and monitoring progression. Thus we propose the usage of a combination of a multi-pinhole (MPH) collimator on one head of the SPECT system and a fan-beam on the other. The MPH would be designed to provide high resolution and sensitivity for imaging of the interior portion of the brain. The fan-beam collimator would provide lower resolution but complete sampling of the brain addressing data sufficiency and allowing a volume-of-interest to be defined over the occipital lobe for calculation of SBR's. Herein we focus on the design of the MPH component of the combined system. Combined reconstruction will be addressed in a subsequent publication. An analysis of 46 clinical DaTscan studies was performed to provide information to define the VOI, and design of a MPH collimator to image this VOI. The system spatial resolution for the MPH was set to 4.7 mm, which is comparable to that of clinical PET systems, and significantly smaller than that of fan-beam collimators employed in SPECT. With this set, we compared system sensitivities for three aperture array designs, and selected the 3 × 3 array due to it being the highest of the three. The combined sensitivity of the apertures for it was similar to that of an ultra-high resolution fan-beam (LEUHRF) collimator, but smaller than that of a high-resolution fan-beam collimator (LEHRF). On the basis of these results we propose the further exploration of this design through simulations, and the development of combined MPH and fan-beam reconstruction.

The role of Euler buckling instability in the fabrication of nanoelectromechanical systems on the basis of GaAs/AlGaAs heterostructures

NASA Astrophysics Data System (ADS)

Shevyrin, A. A.; Pogosov, A. G.; Budantsev, M. V.; Bakarov, A. K.; Toropov, A. I.; Ishutkin, S. V.; Shesterikov, E. V.; Kozhukhov, A. S.; Kosolobov, S. S.; Gavrilova, T. A.

2012-12-01

Mechanical stresses are investigated in suspended nanowires made on the basis of GaAs/AlGaAs heterostructures. Though there are no intentionally introduced stressor layers in the heterostructure, the nanowires are subject to Euler buckling instability. In the wide nanowires, the out-of-plane buckling is observed at length significantly smaller (3 times) than the theoretically estimated critical value, while in the narrow nanowires, the experimentally measured critical length of the in-plane buckling coincides with the theoretical estimation. The possible reasons for the obtained discrepancy are considered. The observed peculiarities should be taken into account in the fabrication of nanomechanical and nanoelectromechanical systems.

Orthonormal vector polynomials in a unit circle, Part I: Basis set derived from gradients of Zernike polynomials.

PubMed

Zhao, Chunyu; Burge, James H

2007-12-24

Zernike polynomials provide a well known, orthogonal set of scalar functions over a circular domain, and are commonly used to represent wavefront phase or surface irregularity. A related set of orthogonal functions is given here which represent vector quantities, such as mapping distortion or wavefront gradient. These functions are generated from gradients of Zernike polynomials, made orthonormal using the Gram- Schmidt technique. This set provides a complete basis for representing vector fields that can be defined as a gradient of some scalar function. It is then efficient to transform from the coefficients of the vector functions to the scalar Zernike polynomials that represent the function whose gradient was fit. These new vector functions have immediate application for fitting data from a Shack-Hartmann wavefront sensor or for fitting mapping distortion for optical testing. A subsequent paper gives an additional set of vector functions consisting only of rotational terms with zero divergence. The two sets together provide a complete basis that can represent all vector distributions in a circular domain.

Employing general fit-bases for construction of potential energy surfaces with an adaptive density-guided approach

NASA Astrophysics Data System (ADS)

Klinting, Emil Lund; Thomsen, Bo; Godtliebsen, Ian Heide; Christiansen, Ove

2018-02-01

We present an approach to treat sets of general fit-basis functions in a single uniform framework, where the functional form is supplied on input, i.e., the use of different functions does not require new code to be written. The fit-basis functions can be used to carry out linear fits to the grid of single points, which are generated with an adaptive density-guided approach (ADGA). A non-linear conjugate gradient method is used to optimize non-linear parameters if such are present in the fit-basis functions. This means that a set of fit-basis functions with the same inherent shape as the potential cuts can be requested and no other choices with regards to the fit-basis functions need to be taken. The general fit-basis framework is explored in relation to anharmonic potentials for model systems, diatomic molecules, water, and imidazole. The behaviour and performance of Morse and double-well fit-basis functions are compared to that of polynomial fit-basis functions for unsymmetrical single-minimum and symmetrical double-well potentials. Furthermore, calculations for water and imidazole were carried out using both normal coordinates and hybrid optimized and localized coordinates (HOLCs). Our results suggest that choosing a suitable set of fit-basis functions can improve the stability of the fitting routine and the overall efficiency of potential construction by lowering the number of single point calculations required for the ADGA. It is possible to reduce the number of terms in the potential by choosing the Morse and double-well fit-basis functions. These effects are substantial for normal coordinates but become even more pronounced if HOLCs are used.

Analytical energy gradients for explicitly correlated wave functions. I. Explicitly correlated second-order Møller-Plesset perturbation theory

NASA Astrophysics Data System (ADS)

Győrffy, Werner; Knizia, Gerald; Werner, Hans-Joachim

2017-12-01

We present the theory and algorithms for computing analytical energy gradients for explicitly correlated second-order Møller-Plesset perturbation theory (MP2-F12). The main difficulty in F12 gradient theory arises from the large number of two-electron integrals for which effective two-body density matrices and integral derivatives need to be calculated. For efficiency, the density fitting approximation is used for evaluating all two-electron integrals and their derivatives. The accuracies of various previously proposed MP2-F12 approximations [3C, 3C(HY1), 3*C(HY1), and 3*A] are demonstrated by computing equilibrium geometries for a set of molecules containing first- and second-row elements, using double-ζ to quintuple-ζ basis sets. Generally, the convergence of the bond lengths and angles with respect to the basis set size is strongly improved by the F12 treatment, and augmented triple-ζ basis sets are sufficient to closely approach the basis set limit. The results obtained with the different approximations differ only very slightly. This paper is the first step towards analytical gradients for coupled-cluster singles and doubles with perturbative treatment of triple excitations, which will be presented in the second part of this series.

Simplified DFT methods for consistent structures and energies of large systems

NASA Astrophysics Data System (ADS)

Caldeweyher, Eike; Gerit Brandenburg, Jan

2018-05-01

Kohn–Sham density functional theory (DFT) is routinely used for the fast electronic structure computation of large systems and will most likely continue to be the method of choice for the generation of reliable geometries in the foreseeable future. Here, we present a hierarchy of simplified DFT methods designed for consistent structures and non-covalent interactions of large systems with particular focus on molecular crystals. The covered methods are a minimal basis set Hartree–Fock (HF-3c), a small basis set screened exchange hybrid functional (HSE-3c), and a generalized gradient approximated functional evaluated in a medium-sized basis set (B97-3c), all augmented with semi-classical correction potentials. We give an overview on the methods design, a comprehensive evaluation on established benchmark sets for geometries and lattice energies of molecular crystals, and highlight some realistic applications on large organic crystals with several hundreds of atoms in the primitive unit cell.

A practical radial basis function equalizer.

PubMed

Lee, J; Beach, C; Tepedelenlioglu, N

1999-01-01

A radial basis function (RBF) equalizer design process has been developed in which the number of basis function centers used is substantially fewer than conventionally required. The reduction of centers is accomplished in two-steps. First an algorithm is used to select a reduced set of centers that lie close to the decision boundary. Then the centers in this reduced set are grouped, and an average position is chosen to represent each group. Channel order and delay, which are determining factors in setting the initial number of centers, are estimated from regression analysis. In simulation studies, an RBF equalizer with more than 2000-to-1 reduction in centers performed as well as the RBF equalizer without reduction in centers, and better than a conventional linear equalizer.

The Topological Basis Realization for Six Qubits and the Corresponding Heisenberg Spin -{1/2} Chain Model

NASA Astrophysics Data System (ADS)

Yang, Qi; Cao, Yue; Chen, Shiyin; Teng, Yue; Meng, Yanli; Wang, Gangcheng; Sun, Chunfang; Xue, Kang

2018-03-01

In this paper, we construct a new set of orthonormal topological basis states for six qubits with the topological single loop d = 2. By acting on the subspace, we get a new five-dimensional (5D) reduced matrix. In addition, it is shown that the Heisenberg XXX spin-1/2 chain of six qubits can be constructed from the Temperley-Lieb algebra (TLA) generator, both the energy ground state and the spin singlet states of the system can be described by the set of topological basis states.

Use of an auxiliary basis set to describe the polarization in the fragment molecular orbital method

NASA Astrophysics Data System (ADS)

Fedorov, Dmitri G.; Kitaura, Kazuo

2014-03-01

We developed a dual basis approach within the fragment molecular orbital formalism enabling efficient and accurate use of large basis sets. The method was tested on water clusters and polypeptides and applied to perform geometry optimization of chignolin (PDB: 1UAO) in solution at the level of DFT/6-31++G∗∗, obtaining a structure in agreement with experiment (RMSD of 0.4526 Å). The polarization in polypeptides is discussed with a comparison of the α-helix and β-strand.

The Topological Basis Realization for Six Qubits and the Corresponding Heisenberg Spin-1/2 Chain Model

NASA Astrophysics Data System (ADS)

Yang, Qi; Cao, Yue; Chen, Shiyin; Teng, Yue; Meng, Yanli; Wang, Gangcheng; Sun, Chunfang; Xue, Kang

2018-06-01

In this paper, we construct a new set of orthonormal topological basis states for six qubits with the topological single loop d = 2. By acting on the subspace, we get a new five-dimensional (5 D) reduced matrix. In addition, it is shown that the Heisenberg XXX spin-1/2 chain of six qubits can be constructed from the Temperley-Lieb algebra (TLA) generator, both the energy ground state and the spin singlet states of the system can be described by the set of topological basis states.

[Estimates of Target Population for Pneumococcal Vaccination in People over 50 years in Catalonia and Spain].

PubMed

Vila-Córcoles, Angel; Ochoa-Gondar, Olga; Satué, Eva; de Diego, Cinta; Vila-Rovira, Marc; Jariod, Manel

2017-03-15

Published data about prevalence of distinct risk condictions for pneumococcal disease is scarce. This study investigated the prevalence of distinct risk conditions for pneumococal disease in Catalonian adults and stimated the potential size of target population for pneumococcal vaccination in Catalonia and Spain. Cross-sectional population-based study that included 2,033,465 individuals older than 49 years-old assigned to the Catalonian Health Institute (Catalonia, Spain) at 01/01/2015. The Catalonian Health Institute Information System for the Development of Research in Primary Care (SIDIAP) was used to identify comorbidities and/or underlying conditions in each subject and establish potential target population for pneumococcal vaccination on the basis of their risk for suffering pneumococcal infections: 1) immunocompromised subjects; 2) immunocompetents subjects with any risk condition; 3) immunocompetents subjects without risk conditions. Of the 2,033,465 study subjects, 1,053,155 (51.8%) had no risk conditions, 649,014 (31.9%) had one risk condition and 331,296 (16.3%) had multiple risk conditions (11.4% in 50-64 years vs 21.2% in people older than 65 years, p smaller than 0.001; 21.8% in men vs 11.6% in women, p smaller than 0.001). Overall, 176,600 (8.7%) and 803,710 (39.5%) were classified in risk stratum 1 and 2, respectively. According to distinct risk strata considered, the target population for pneumococcal vaccination varied between 0.2-1.9 million in Catalonia and 1.5-2.3 million in Spain. In our setting, almost fifty percent of people ≥50 years have at least one risk condition to suffert pneumococcal disease. Adult population susceptible for pneumococal vaccination largely varies depending on the risk stratum considered as targeted people for pneumococcal vaccination.

Counting or Chunking?

PubMed Central

Spotorno, Nicola; McMillan, Corey T.; Powers, John P.; Clark, Robin; Grossman, Murray

2014-01-01

A growing amount of empirical data is showing that the ability to manipulate quantities in a precise and efficient fashion is rooted in cognitive mechanisms devoted to specific aspects of numbers processing. The Analog number system (ANS) has a reasonable representation of quantities up to about 4, and represents larger quantities on the basis of a numerical ratio between quantities. In order to represent the precise cardinality of a number, the ANS may be supported by external algorithms such as language, leading to a “Precise Number System”. In the setting of limited language, other number-related systems can appear. For example the Parallel Individuation system (PIS) supports a “chunking mechanism” that clusters units of larger numerosities into smaller subsets. In the present study we investigated number processing in non-aphasic patients with Corticobasal Syndrome (CBS) and Posterior Cortical Atrophy (PCA), two neurodegenerative conditions that are associated with progressive parietal atrophy. The present study investigated these number systems in CBS and PCA by assessing the property of the ANS associated with smaller and larger numerosities, and the chunking property of the PIS. The results revealed that CBS/PCA patients are impaired in simple calculations (e.g., addition and subtraction) and that their performance strongly correlates with the size of the numbers involved in these calculations, revealing a clear magnitude effect. This magnitude effect correlated with gray matter atrophy in parietal regions. Moreover, a numeral-dots transcoding task showed that CBS/PCA patients are able to take advantage of clustering in the spatial distribution of the dots of the array. The relative advantage associated with chunking compared to a random spatial distribution correlated with both parietal and prefrontal regions. These results shed light on the properties of systems for representing number knowledge in non-aphasic patients with CBS and PCA. PMID:25278132

MEMS Louvers for Thermal Control

NASA Technical Reports Server (NTRS)

Champion, J. L.; Osiander, R.; Darrin, M. A. Garrison; Swanson, T. D.

1998-01-01

Mechanical louvers have frequently been used for spacecraft and instrument thermal control purposes. These devices typically consist of parallel or radial vanes, which can be opened or closed to vary the effective emissivity of the underlying surface. This project demonstrates the feasibility of using Micro-Electromechanical Systems (MEMS) technology to miniaturize louvers for such purposes. This concept offers the possibility of substituting the smaller, lighter weight, more rugged, and less costly MEMS devices for such mechanical louvers. In effect, a smart skin that self adjusts in response to environmental influences could be developed composed of arrays of thousands of miniaturized louvers. Several orders of magnitude size, weight, and volume decreases are potentially achieved using micro-electromechanical techniques. The use of this technology offers substantial benefits in spacecraft/instrument design, integration and testing, and flight operations. It will be particularly beneficial for the emerging smaller spacecraft and instruments of the future. In addition, this MEMS thermal louver technology can form the basis for related spacecraft instrument applications. The specific goal of this effort was to develop a preliminary MEMS device capable of modulating the effective emissivity of radiators on spacecraft. The concept pursued uses hinged panels, or louvers, in a manner such that heat emitted from the radiators is a function of louver angle. An electrostatic comb drive or other such actuator can control the louver position. The initial design calls for the louvers to be gold coated while the underlying surface is of high emissivity. Since, the base MEMS material, silicon, is transparent in the InfraRed (IR) spectrum, the device has a minimum emissivity when closed and a maximum emissivity when open. An initial set of polysilicon louver devices was designed at the Johns Hopkins Applied Physics Laboratory in conjunction with the Thermal Engineering Branch at NASA's Goddard Space Flight Center.

Large Stratospheric IDPs: Chemical Compostion and Comparison with Smaller Stratospheric IDPs

NASA Astrophysics Data System (ADS)

Flynn, G. J.; Bajt, S.; Sutton, S. R.; Klock, W.

1995-09-01

Six large stratospheric IDPs, each greater than 35 microns, previously analyzed using the X-Ray Microprobe at the National Synchrotron Light Source showed an average volatile content consistent with CI or CM meteorites [1]. Seven additional large IDPs, ranging from 37x33 to 50x44 microns in size and having chondritic major element abundances, have been analyzed using the same instrument. Each of these 7 IDPs is depleted in Ca compared to CI (Avg. Ca = 0.48xCI), a feature also observed in the first set of 6, suggesting most or all of these IDPs are hydrated. The average trace element content of these 7 large IDPs is similar to the previous set of 6 (see Figure 1), though Mn and Cu are about 70% higher in this set. The average composition of these large IDPs is distinctly different from that of smaller IDPs (generally 10 to 20 microns), which show enrichments of the volatiles Cu, Zn, Ga, Ge, and Se by factors of 1.5 to 3 over CI [2]. This suggests large IDPs which are strong enough to resist fragmentation on collection are chemically different from typical smaller IDPs. This may reflect a difference in the source(s) being sampled by the two types of IDPs. A subgroup of the smaller IDPs (9 of 51 particles) have a composition similar to CI meteorites and these large IDPs [2]. Bromine is enriched in most of these large IDPs. Two Br-rich IDPs (Br >300 ppm) and one Br-poor IDP (Br ~5 ppm) were each analyzed twice. The two Br-rich IDPs showed about a factor of two Br loss between the first and second analyses, presumably due to sample heating during the first analysis. This suggests some of the Br is very weakly bound in these Br-rich IDPs, a possible signature of Br surface contamination. However, the Br contents measured in the second analyses were still ~50xCI. No loss of Cu, Zn, Ga, Ge or Se was detected in these IDPs, suggesting these elements are in more retentive sites. The Br-poor IDP (Br ~1.5xCI) showed no Br loss in the second analysis. Only one of these IDPs, L2008G10, showed a large Zn depletion (Zn/Fe <0.01xCI). This was accompanied by low contents of Ga, Ge and Br (see Figure 1). This pattern of Zn, Ge, Br and Ga depletions was previously seen in smaller IDPs which were severely heated, presumably on atmospheric entry [2]. Sulfur and K are also low in L2008G10, suggesting these elements are also lost during heating, but the Se content is 0.8xCI. A second particle, L2009C8, has a Zn/Fe=0.26xCI, possibly indicating less severe heating. The low fraction of severely heated IDPs, only one in this set of 7 and none in the set of 6 [1] suggests a very low atmospheric entry velocity for these large IDPs [3]. References: [1] Flynn G. J. et al. (1995) LPS XXVI, 407-408. [2] Flynn G. J. et al. (1993) LPS XXIV, 495-496. [3] Flynn G. J., this volume. Figure 1: Average Fe and CI normalized element abundances in 7 large IDPs, 6 different large IDPs [1], 51 smaller IDPs [2], and the single low-Zn IDP, L2008G10, included in the set of 7 large IDPs.

An area model for on-chip memories and its application

NASA Technical Reports Server (NTRS)

Mulder, Johannes M.; Quach, Nhon T.; Flynn, Michael J.

1991-01-01

An area model suitable for comparing data buffers of different organizations and arbitrary sizes is described. The area model considers the supplied bandwidth of a memory cell and includes such buffer overhead as control logic, driver logic, and tag storage. The model gave less than 10 percent error when verified against real caches and register files. It is shown that, comparing caches and register files in terms of area for the same storage capacity, caches generally occupy more area per bit than register files for small caches because the overhead dominates the cache area at these sizes. For larger caches, the smaller storage cells in the cache provide a smaller total cache area per bit than the register set. Studying cache performance (traffic ratio) as a function of area, it is shown that, for small caches, direct-mapped caches perform significantly better than four-way set-associative caches and, for caches of medium areas, both direct-mapped and set-associative caches perform better than fully associative caches.

A Study of Preferred Conflict-Management Behaviors among Small-School Principals: Effects of Gender and Experience

ERIC Educational Resources Information Center

Vestal, Brad; Torres, Mario

2016-01-01

It cannot be overstated the broad skill set managers must have to manage conflict in modern organizations (Lang, 2009; Ramani & Zhimin, 2010). Few studies have explored this topic in smaller organizational settings where leaders often assume a greater number of roles and responsibilities. For this reason, this study analyzed preferred conflict…

Tile Patterns with LOGO--Part III: Tile Patterns from Mult Tiles Using Logo.

ERIC Educational Resources Information Center

Clason, Robert G.

1991-01-01

A mult tile is a set of polygons each of which can be dissected into smaller polygons similar to the original set of polygons. Using a recursive LOGO method that requires solutions to various geometry and trigonometry problems, dissections of mult tiles are carried out repeatedly to produce tile patterns. (MDH)

Do Practical Standard Coupled Cluster Calculations Agree Better than Kohn–Sham Calculations with Currently Available Functionals When Compared to the Best Available Experimental Data for Dissociation Energies of Bonds to 3d Transition Metals?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, Xuefei; Zhang, Wenjing; Tang, Mingsheng

2015-05-12

Coupled-cluster (CC) methods have been extensively used as the high-level approach in quantum electronic structure theory to predict various properties of molecules when experimental results are unavailable. It is often assumed that CC methods, if they include at least up to connected-triple-excitation quasiperturbative corrections to a full treatment of single and double excitations (in particular, CCSD(T)), and a very large basis set, are more accurate than Kohn–Sham (KS) density functional theory (DFT). In the present work, we tested and compared the performance of standard CC and KS methods on bond energy calculations of 20 3d transition metal-containing diatomic molecules againstmore » the most reliable experimental data available, as collected in a database called 3dMLBE20. It is found that, although the CCSD(T) and higher levels CC methods have mean unsigned deviations from experiment that are smaller than most exchange-correlation functionals for metal–ligand bond energies of transition metals, the improvement is less than one standard deviation of the mean unsigned deviation. Furthermore, on average, almost half of the 42 exchange-correlation functionals that we tested are closer to experiment than CCSD(T) with the same extended basis set for the same molecule. The results show that, when both relativistic and core–valence correlation effects are considered, even the very high-level (expensive) CC method with single, double, triple, and perturbative quadruple cluster operators, namely, CCSDT(2)Q, averaged over 20 bond energies, gives a mean unsigned deviation (MUD(20) = 4.7 kcal/mol when one correlates only valence, 3p, and 3s electrons of transition metals and only valence electrons of ligands, or 4.6 kcal/mol when one correlates all core electrons except for 1s shells of transition metals, S, and Cl); and that is similar to some good xc functionals (e.g., B97-1 (MUD(20) = 4.5 kcal/mol) and PW6B95 (MUD(20) = 4.9 kcal/mol)) when the same basis set is used. We found that, for both coupled cluster calculations and KS calculations, the T1 diagnostics correlate the errors better than either the M diagnostics or the B1 DFT-based diagnostics. The potential use of practical standard CC methods as a benchmark theory is further confounded by the finding that CC and DFT methods usually have different signs of the error. We conclude that the available experimental data do not provide a justification for using conventional single-reference CC theory calculations to validate or test xc functionals for systems involving 3d transition metals.« less

Cardiovascular anatomy and physiology in the female.

PubMed

Wingate, S

1997-12-01

Important differences in male and female cardiovascular anatomy and physiology may account for many of the gender differences seen in various cardiac disease states. Predominant influences on female disease manifestations include (1) women's smaller body size, hence smaller hearts and smaller coronary vessels and (2) women's fluctuating levels of estrogen throughout their lifespan. Understanding these critical anatomic and physiologic differences allows the clinician to better predict and plan care for women. For example, knowing that women generally have a smaller body surface area than men allows one to better understand why men have higher creatine kinase (CK) values than do women--an important distinction when interpreting these values in the acute care setting. The fact that women's hearts and coronary vessels are generally smaller than men's also helps one understand why women have a higher in-hospital mortality than men post-coronary artery bypass graft surgery (see article by Allen in this issue for more detailed information on revascularization). These are only a few examples of the many opportunities that acute care nurses have to integrate their knowledge of anatomy and physiology into proactive planning for their female cardiac patients.

Setting practical conservation priorities for birds in the Western Andes of Colombia.

PubMed

Ocampo-Peñuela, Natalia; Pimm, Stuart L

2014-10-01

We aspired to set conservation priorities in ways that lead to direct conservation actions. Very large-scale strategic mapping leads to familiar conservation priorities exemplified by biodiversity hotspots. In contrast, tactical conservation actions unfold on much smaller geographical extents and they need to reflect the habitat loss and fragmentation that have sharply restricted where species now live. Our aspirations for direct, practical actions were demanding. First, we identified the global, strategic conservation priorities and then downscaled to practical local actions within the selected priorities. In doing this, we recognized the limitations of incomplete information. We started such a process in Colombia and used the results presented here to implement reforestation of degraded land to prevent the isolation of a large area of cloud forest. We used existing range maps of 171 bird species to identify priority conservation areas that would conserve the greatest number of species at risk in Colombia. By at risk species, we mean those that are endemic and have small ranges. The Western Andes had the highest concentrations of such species-100 in total-but the lowest densities of national parks. We then adjusted the priorities for this region by refining these species ranges by selecting only areas of suitable elevation and remaining habitat. The estimated ranges of these species shrank by 18-100% after accounting for habitat and suitable elevation. Setting conservation priorities on the basis of currently available range maps excluded priority areas in the Western Andes and, by extension, likely elsewhere and for other taxa. By incorporating detailed maps of remaining natural habitats, we made practical recommendations for conservation actions. One recommendation was to restore forest connections to a patch of cloud forest about to become isolated from the main Andes. © 2014 Society for Conservation Biology.

Dimensional analysis using toric ideals: primitive invariants.

PubMed

Atherton, Mark A; Bates, Ronald A; Wynn, Henry P

2014-01-01

Classical dimensional analysis in its original form starts by expressing the units for derived quantities, such as force, in terms of power products of basic units [Formula: see text] etc. This suggests the use of toric ideal theory from algebraic geometry. Within this the Graver basis provides a unique primitive basis in a well-defined sense, which typically has more terms than the standard Buckingham approach. Some textbook examples are revisited and the full set of primitive invariants found. First, a worked example based on convection is introduced to recall the Buckingham method, but using computer algebra to obtain an integer [Formula: see text] matrix from the initial integer [Formula: see text] matrix holding the exponents for the derived quantities. The [Formula: see text] matrix defines the dimensionless variables. But, rather than this integer linear algebra approach it is shown how, by staying with the power product representation, the full set of invariants (dimensionless groups) is obtained directly from the toric ideal defined by [Formula: see text]. One candidate for the set of invariants is a simple basis of the toric ideal. This, although larger than the rank of [Formula: see text], is typically not unique. However, the alternative Graver basis is unique and defines a maximal set of invariants, which are primitive in a simple sense. In addition to the running example four examples are taken from: a windmill, convection, electrodynamics and the hydrogen atom. The method reveals some named invariants. A selection of computer algebra packages is used to show the considerable ease with which both a simple basis and a Graver basis can be found.

Approaching the new reality. [changes in NASA space programs due to US economy

NASA Technical Reports Server (NTRS)

Diaz, Al V.

1993-01-01

The focus on more frequent access to space through smaller, less costly missions, and on NASA's role as a source of technological advance within the U.S. economy is discussed. The Pluto fast flyby mission is examined as an illustration of this approach. Testbeds are to be developed to survive individual programs, becoming permanent facilities, to allow for technological upgrades on an ongoing basis.

The Molecular Basis of Cardiac Mechanics: Regulation of Motor Unit Recruitment

DTIC Science & Technology

2001-10-25

sensitivity, Cooperativity. I. INTRODUCTION The biological linear motor, that produces cardiac and skeletal muscle contraction , is by far smaller than...who have described the role of the mechanical initial loading condition (Preload) on muscle contraction and by Fenn (1923) who has showed that the...2437, 1982. [4] E. Eisenberg, and T. L. Hill. Muscle contraction and energy transduction in biological system. Science 227: 999-1006, 1985. [5

42 CFR 457.700 - Basis, scope, and applicability.

Code of Federal Regulations, 2010 CFR

2010-10-01

... Strategic Planning, Reporting, and Evaluation § 457.700 Basis, scope, and applicability. (a) Statutory basis... strategic planning, reports, and program budgets; and (2) Section 2108 of the Act, which sets forth... strategic planning, monitoring, reporting and evaluation under title XXI. (c) Applicability. The...

42 CFR 457.700 - Basis, scope, and applicability.

Code of Federal Regulations, 2011 CFR

2011-10-01

... Strategic Planning, Reporting, and Evaluation § 457.700 Basis, scope, and applicability. (a) Statutory basis... strategic planning, reports, and program budgets; and (2) Section 2108 of the Act, which sets forth... strategic planning, monitoring, reporting and evaluation under title XXI. (c) Applicability. The...

50 CFR 403.04 - Determinations and hearings under section 109(c) of the MMPA.

Code of Federal Regulations, 2010 CFR

2010-10-01

... management program the state must provide for a process, consistent with section 109(c) of the Act, to... must include the elements set forth below. (b) Basis, purpose, and scope. The process set forth in this... made solely on the basis of the record developed at the hearing. The state agency in making its final...

Time Domain Propagation of Quantum and Classical Systems using a Wavelet Basis Set Method

NASA Astrophysics Data System (ADS)

Lombardini, Richard; Nowara, Ewa; Johnson, Bruce

2015-03-01

The use of an orthogonal wavelet basis set (Optimized Maximum-N Generalized Coiflets) to effectively model physical systems in the time domain, in particular the electromagnetic (EM) pulse and quantum mechanical (QM) wavefunction, is examined in this work. Although past research has demonstrated the benefits of wavelet basis sets to handle computationally expensive problems due to their multiresolution properties, the overlapping supports of neighboring wavelet basis functions poses problems when dealing with boundary conditions, especially with material interfaces in the EM case. Specifically, this talk addresses this issue using the idea of derivative matching creating fictitious grid points (T.A. Driscoll and B. Fornberg), but replaces the latter element with fictitious wavelet projections in conjunction with wavelet reconstruction filters. Two-dimensional (2D) systems are analyzed, EM pulse incident on silver cylinders and the QM electron wave packet circling the proton in a hydrogen atom system (reduced to 2D), and the new wavelet method is compared to the popular finite-difference time-domain technique.

Maps showing mineral resource assessment for vein and replacement deposits of base and precious metals, barite, and fluorspar, Dillon 1 degree by 2 degrees Quadrangle, Idaho and Montana

USGS Publications Warehouse

Pearson, R.C.; Trautwein, C.M.; Berger, B.R.; Hanna, W.F.; Jenson, S.K.; Loen, J.S.; Moll, S.H.; Purdy, T.L.; Rowan, L.C.; Ruppel, E.T.; Segal, D.B.

1992-01-01

This report is one of several that assess the mineral resources in the Dillon quadrangle. For the purpose of the assessment, the deposits that are known in the quadrangle, or suspected to be present from a knowledge of the geologic setting, have been grouped into 30 deposit types on the basis of the mineralogy or commodity in the ore and the structural or depositional setting of the deposit. The emphasis in these assessment reports is on metallic minerals, but some important nonmetallic minerals are also considered. Fossil fuels are beyond the scope of this investigation, phosphate and uranium have been investigated previously (Swanson, 1970; Wodzicki and Krason, 1981 ), and certain nonmetallic minerals, including bulk commodities such as sand and gravel, are in large supply and thus are not considered. The mineral resource assessment discussed in this report concentrates on a single deposit type (of the total of 30 types) that we call "vein and replacement deposits of base and precious metals." Base and precious metals produced from such deposits are copper, lead, zinc, gold, and silver. Vein deposits of barite and fluorspar are also discussed, but because they seem to be of minor importance, they are treated briefly. Vein and replacement deposits of base and precious metals are classified as a single deposit type rather than as numerous possible subordinate types that might be distinguished on the basis of mineralogy, metal content, or other factors, because the characteristics of the ore, the ore bodies, and the structural setting are not sufficiently well known to yield a consistent detailed classification for the entire quadrangle. Furthermore, the criteria used here to explain the localization of deposits are too general to allow discrimination among subordinate types at a scale of 1 :250,000 or smaller. In assessing mineral resources, we have adopted a general philosophy similar to that of Harrison and others ( 1986). We attempt to identify parts of the quadrangle that are favorable for the occurrence of mineral resources, and we make an assignment of the relative resource potential of all parts of the quadrangle. We do not attempt to locate specific exploration targets nor to determine the quantity of reserves or resources present.

On the use of the exact exchange optimized effective potential method for static response properties

NASA Astrophysics Data System (ADS)

Krykunov, Mykhaylo; Ziegler, Tom

In the present work, we question the notion that the modified Kohn-Sham orbital energies and smaller HOMO-LUMO gaps, produced from the exact exchange optimized effective potential (EXX-OEP) method, might significantly improve the paramagnetic contribution to the NMR chemical shifts compared with the regular Hartree-Fock (HF) scheme. First of all, it is shown analytically that if there is such a local potential that produces the HF energy, and the Kohn-Sham orbitals are obtained as a result of separate rotations of the occupied and virtual HF orbitals, any static magnetic property obtained from the coupled perturbed HF method will be identical to that obtained from the EXX-OEP approach. In fact the EXX-OEP method is equivalent to the improved virtual orbitals (IVO) scheme in which the energies of the virtual orbitals are modified by an effective potential. It is shown that the IVO procedure leaves static response properties unchanged. To test our analysis numerically we have employed several variants of the EXX-OEP method, based on the expansion of the local exchange potential into a linear combination of fit functions. The different EXX-OEP schemes have been used to calculate the NMR chemical shifts for a set of small molecules containing C, H, N, O, and F atoms. Comparison of the deviation between experimental and calculated chemical shifts from the HF, the EXX-OEP, and the common energy denominator approximation (CEDA) approximation to the EXX-OEP methods has shown that for carbon, hydrogen, and fluorine the EXX-OEP methods do not yield any improvement over the HF method. For nitrogen and oxygen we have found that the EXX-OEP performs better than the HF method. However, in the limit of infinite fit basis set and, as a consequence of it, a perfect fit of the HF potential the EXX-OEP and the HF methods would afford the same chemical shifts according to our theoretical analysis. Unfortunately, without a perfect fit the chemical shifts from the EXX-OEP method strongly depend on the fit convergence. In our opinion, the EXX-OEP method should not be used for response properties as it is numerically unstable. Thus, any apparent improvement of the EXX-OEP method over the HF scheme for a finite fit basis set must be considered spurious.

Unbiased analysis of geomagnetic data sets and comparison of historical data with paleomagnetic and archeomagnetic records

NASA Astrophysics Data System (ADS)

Arneitz, Patrick; Egli, Ramon; Leonhardt, Roman

2017-03-01

Reconstructions of the past geomagnetic field provide fundamental constraints for understanding the dynamics of the Earth's interior, as well as serving as basis for magnetostratigraphic and archeomagnetic dating tools. Such reconstructions, when extending over epochs that precede the advent of instrumental measurements, rely exclusively on magnetic records from archeological artifacts, and, further in the past, from rocks and sediments. The most critical component of such indirect records is field intensity because of possible biases introduced by material properties and by laboratory protocols, which do not reproduce exactly the original field recording conditions. Large biases are usually avoided by the use of appropriate checking procedures; however, smaller ones can remain undetected in individual studies and might significantly affect field reconstructions. We introduce a new general approach for analyzing geomagnetic databases in order to investigate the reliability of indirect records. This approach is based on the comparison of historical records with archeomagnetic and volcanic data, considering temporal and spatial mismatches with adequate weighting functions and error estimation. A good overall agreement is found between indirect records and historical measurements, while for several subsets systematic bias is detected (e.g., inclination shallowing of lava records). We also demonstrate that simple approaches to analyzing highly inhomogeneous and internally correlated paleomagnetic data sets can lead to incorrect conclusions about the efficiency of quality checks and corrections. Consistent criteria for selecting and weighting data are presented in this review and can be used to improve current geomagnetic field modeling techniques.

Full-dimensional quantum dynamics study on the mode-specific unimolecular dissociation reaction of HFCO

NASA Astrophysics Data System (ADS)

Yamamoto, Takeshi; Kato, Shigeki

2000-05-01

The mode specificity of the unimolecular reaction of HFCO is studied by six-dimensional quantum dynamics calculations. The energy and mode dependency of the dissociation rate is examined by propagating a number of wave packets with a small energy dispersion representing highly excited states with respect to a specific vibrational mode. The wave packets are generated by applying a set of filter operators onto a source vibrational state. All the information necessary for propagating the wave packets is obtained from a single propagation of the source state, thus allowing a significant decrease of computational effort. The relevant spectral peaks are assigned using the three-dimensional CH chromophore Hamiltonian. The resulting dissociation rate of the CH stretching excited state is in agreement with that obtained from a statistical theory, while the rates of the out-of-plane bending excited states are about one order of magnitude smaller than the statistical rates. A local-mode analysis also shows that the relaxation of the out-of-plane excitation proceeds very slowly within 3 ps. These results clearly indicate weak couplings of the out-of-plane bending excited states with other in-plane vibrational states, which is in qualitative agreement with experimental findings. From a computational point of view, a parallel supercomputer is utilized efficiently to handle an ultra large basis set of an order of 108, and 200 Gflops rate on average is achieved in the dynamics calculations.

Precipitation-runoff, suspended-sediment, and flood-frequency characteristics for urbanized areas of Elmendorf Air Force Base, Alaska

USGS Publications Warehouse

Brabets, Timothy P.

1999-01-01

The developed part of Elmendorf Air Force Base near Anchorage, Alaska, consists of two basins with drainage areas of 4.0 and 0.64 square miles, respectively. Runoff and suspended-sediment data were collected from August 1996 to March 1998 to gain a basic understanding of the surface-water hydrology of these areas and to estimate flood-frequency characteristics. Runoff from the larger basin averaged 6 percent of rainfall, whereas runoff from the smaller basin averaged 13 percent of rainfall. During rainfall periods, the suspended-sediment load transported from the larger watershed ranged from 179 to 21,000 pounds and that from the smaller watershed ranged from 23 to 18,200 pounds. On a yield basis, suspended sediment from the larger watershed was 78 pounds per inch of runoff and from the smaller basin was 100 pounds per inch of runoff. Suspended-sediment loads and yields were generally lower during snowmelt periods than during rainfall periods. At each outfall of the two watersheds, water flows into steep natural channels. Suspended-sediment loads measured approximately 1,000 feet downstream from the outfalls during rainfall periods ranged from 8,450 to 530,000 pounds. On a yield basis, suspended sediment averaged 705 pounds per inch of runoff, more than three times as much as the combined sediment yield from the two watersheds. The increase in suspended sediment is most likely due to natural erosion of the streambanks. Streamflow data, collected in 1996 and 1997, were used to calibrate and verify a U.S. Geological Survey computer model?the Distributed Routing Rainfall Runoff Model-Version II (DR3M-II). The model was then used to simulate annual peak discharges and runoff volumes for 1981 to 1995 using historical rainfall records. Because the model indicated that surcharging (or ponding) would occur, no flood-frequency analysis was done for peak discharges. A flood-frequency analysis of flood volumes indicated that a 10-year flood would result in 0.39 inch of runoff (averaged over the entire drainage basin) from the larger watershed and 1.1 inches of runoff from the smaller watershed.

Kohn-Sham potentials from electron densities using a matrix representation within finite atomic orbital basis sets

NASA Astrophysics Data System (ADS)

Zhang, Xing; Carter, Emily A.

2018-01-01

We revisit the static response function-based Kohn-Sham (KS) inversion procedure for determining the KS effective potential that corresponds to a given target electron density within finite atomic orbital basis sets. Instead of expanding the potential in an auxiliary basis set, we directly update the potential in its matrix representation. Through numerical examples, we show that the reconstructed density rapidly converges to the target density. Preliminary results are presented to illustrate the possibility of obtaining a local potential in real space from the optimized potential in its matrix representation. We have further applied this matrix-based KS inversion approach to density functional embedding theory. A proof-of-concept study of a solvated proton transfer reaction demonstrates the method's promise.

Neural Mechanisms Underlying the Cost of Task Switching: An ERP Study

PubMed Central

Li, Ling; Wang, Meng; Zhao, Qian-Jing; Fogelson, Noa

2012-01-01

Background When switching from one task to a new one, reaction times are prolonged. This phenomenon is called switch cost (SC). Researchers have recently used several kinds of task-switching paradigms to uncover neural mechanisms underlying the SC. Task-set reconfiguration and passive dissipation of a previously relevant task-set have been reported to contribute to the cost of task switching. Methodology/Principal Findings An unpredictable cued task-switching paradigm was used, during which subjects were instructed to switch between a color and an orientation discrimination task. Electroencephalography (EEG) and behavioral measures were recorded in 14 subjects. Response-stimulus interval (RSI) and cue-stimulus interval (CSI) were manipulated with short and long intervals, respectively. Switch trials delayed reaction times (RTs) and increased error rates compared with repeat trials. The SC of RTs was smaller in the long CSI condition. For cue-locked waveforms, switch trials generated a larger parietal positive event-related potential (ERP), and a larger slow parietal positivity compared with repeat trials in the short and long CSI condition. Neural SC of cue-related ERP positivity was smaller in the long RSI condition. For stimulus-locked waveforms, a larger switch-related central negative ERP component was observed, and the neural SC of the ERP negativity was smaller in the long CSI. Results of standardized low resolution electromagnetic tomography (sLORETA) for both ERP positivity and negativity showed that switch trials evoked larger activation than repeat trials in dorsolateral prefrontal cortex (DLPFC) and posterior parietal cortex (PPC). Conclusions/Significance The results provide evidence that both RSI and CSI modulate the neural activities in the process of task-switching, but that these have a differential role during task-set reconfiguration and passive dissipation of a previously relevant task-set. PMID:22860090

The effect of sampling techniques used in the multiconfigurational Ehrenfest method

NASA Astrophysics Data System (ADS)

Symonds, C.; Kattirtzi, J. A.; Shalashilin, D. V.

2018-05-01

In this paper, we compare and contrast basis set sampling techniques recently developed for use in the ab initio multiple cloning method, a direct dynamics extension to the multiconfigurational Ehrenfest approach, used recently for the quantum simulation of ultrafast photochemistry. We demonstrate that simultaneous use of basis set cloning and basis function trains can produce results which are converged to the exact quantum result. To demonstrate this, we employ these sampling methods in simulations of quantum dynamics in the spin boson model with a broad range of parameters and compare the results to accurate benchmarks.

The effect of sampling techniques used in the multiconfigurational Ehrenfest method.

PubMed

Symonds, C; Kattirtzi, J A; Shalashilin, D V

2018-05-14

In this paper, we compare and contrast basis set sampling techniques recently developed for use in the ab initio multiple cloning method, a direct dynamics extension to the multiconfigurational Ehrenfest approach, used recently for the quantum simulation of ultrafast photochemistry. We demonstrate that simultaneous use of basis set cloning and basis function trains can produce results which are converged to the exact quantum result. To demonstrate this, we employ these sampling methods in simulations of quantum dynamics in the spin boson model with a broad range of parameters and compare the results to accurate benchmarks.

An Empirical Comparison of Five Linear Equating Methods for the NEAT Design

ERIC Educational Resources Information Center

Suh, Youngsuk; Mroch, Andrew A.; Kane, Michael T.; Ripkey, Douglas R.

2009-01-01

In this study, a data base containing the responses of 40,000 candidates to 90 multiple-choice questions was used to mimic data sets for 50-item tests under the "nonequivalent groups with anchor test" (NEAT) design. Using these smaller data sets, we evaluated the performance of five linear equating methods for the NEAT design with five levels of…

Suggestions for getting more forestry in the logging plan.

Treesearch

Robert H. Ruth; Roy R. Silen

1950-01-01

The staggered-setting system of clear-cutting is fast becoming prevailing practice in the Douglas-fir region. The trend is away from large, continuous clear cuts to clear-cutting smaller units of timber of less than 80 acres. These are called staggered settings because the surrounding stand is left uncut to provide seed and serve as a firebreak. Major aims of this...

Long-Term Changes in the Appearance of the Sky

NASA Astrophysics Data System (ADS)

Ruggles, Clive L. N.

Precession - the precession of the equinoxes - causes the rising and setting positions of the stars to change significantly over the centuries, but does not affect the rising and setting positions of the sun, moon, and planets. These change by a much smaller amount, significant over timescales of millennia, owing to a gradual change in the obliquity of the ecliptic.

Accurate energetics of small molecules containing third-row atoms Ga-Kr: A comparison of advanced ab initio and density functional theory

NASA Astrophysics Data System (ADS)

Yockel, Scott; Mintz, Benjamin; Wilson, Angela K.

2004-07-01

Advanced ab initio [coupled cluster theory through quasiperturbative triple excitations (CCSD(T))] and density functional (B3LYP) computational chemistry approaches were used in combination with the standard and augmented correlation consistent polarized valence basis sets [cc-pVnZ and aug-cc-pVnZ, where n=D(2), T(3), Q(4), and 5] to investigate the energetic and structural properties of small molecules containing third-row (Ga-Kr) atoms. These molecules were taken from the Gaussian-2 (G2) extended test set for third-row atoms. Several different schemes were used to extrapolate the calculated energies to the complete basis set (CBS) limit for CCSD(T) and the Kohn-Sham (KS) limit for B3LYP. Zero point energy and spin orbital corrections were included in the results. Overall, CCSD(T) atomization energies, ionization energies, proton affinities, and electron affinities are in good agreement with experiment, within 1.1 kcal/mol when the CBS limit has been determined using a series of two basis sets of at least triple zeta quality. For B3LYP, the overall mean absolute deviation from experiment for the three properties and the series of molecules is more significant at the KS limit, within 2.3 and 2.6 kcal/mol for the cc-pVnZ and aug-cc-pVnZ basis set series, respectively.

Optimization of metabolite basis sets prior to quantitation in magnetic resonance spectroscopy: an approach based on quantum mechanics

NASA Astrophysics Data System (ADS)

Lazariev, A.; Allouche, A.-R.; Aubert-Frécon, M.; Fauvelle, F.; Piotto, M.; Elbayed, K.; Namer, I.-J.; van Ormondt, D.; Graveron-Demilly, D.

2011-11-01

High-resolution magic angle spinning (HRMAS) nuclear magnetic resonance (NMR) is playing an increasingly important role for diagnosis. This technique enables setting up metabolite profiles of ex vivo pathological and healthy tissue. The need to monitor diseases and pharmaceutical follow-up requires an automatic quantitation of HRMAS 1H signals. However, for several metabolites, the values of chemical shifts of proton groups may slightly differ according to the micro-environment in the tissue or cells, in particular to its pH. This hampers the accurate estimation of the metabolite concentrations mainly when using quantitation algorithms based on a metabolite basis set: the metabolite fingerprints are not correct anymore. In this work, we propose an accurate method coupling quantum mechanical simulations and quantitation algorithms to handle basis-set changes. The proposed algorithm automatically corrects mismatches between the signals of the simulated basis set and the signal under analysis by maximizing the normalized cross-correlation between the mentioned signals. Optimized chemical shift values of the metabolites are obtained. This method, QM-QUEST, provides more robust fitting while limiting user involvement and respects the correct fingerprints of metabolites. Its efficiency is demonstrated by accurately quantitating 33 signals from tissue samples of human brains with oligodendroglioma, obtained at 11.7 tesla. The corresponding chemical shift changes of several metabolites within the series are also analyzed.

Geophysical Evidence to Link Terrestrial Insect Diversity and Groundwater Availability in Non-Riparian Ecosystems

NASA Astrophysics Data System (ADS)

Pehringer, M.; Carr, G.; Long, H.; Parsekian, A.

2015-12-01

Wyoming, the third driest state in the United States, is home to a high level of biodiversity. In many cases, ecosystems are dependent on the vast systems of water resting just below the surface. This groundwater supports a variety of organisms that live far from surface water and its surrounding riparian zone, where more than 70% of species reside. In order to observe the correlation of groundwater presence and biodiversity in non-riparian ecosystems, a study was conducted to look specifically at terrestrial insect species linked to groundwater in Bighorn National Forest, WY. It was hypothesized that the more groundwater present, the greater the diversity of insects would be. Sample areas were randomly selected in non-riparian zones and groundwater was evaluated using a transient electromagnetic (TEM) geophysical instrument. Electrical pulses were transmitted through a 40m by 40m square of wire to measure levels of resistivity from near the surface to several hundred meters below ground. Pulses are echoed back to the surface and received by a smaller 10m by 10m square of wire, and an even smaller 1m by 1m square of wire set inside the larger transmitting wire. An insect population and species count was then conducted within the perimeter set by the outer transmitting wire. The results were not as hypothesized. More inferred groundwater below the surface resulted in a smaller diversity of species. Inversely, the areas with a smaller diversity held a larger total population of terrestrial insects.

A new parallel algorithm of MP2 energy calculations.

PubMed

Ishimura, Kazuya; Pulay, Peter; Nagase, Shigeru

2006-03-01

A new parallel algorithm has been developed for second-order Møller-Plesset perturbation theory (MP2) energy calculations. Its main projected applications are for large molecules, for instance, for the calculation of dispersion interaction. Tests on a moderate number of processors (2-16) show that the program has high CPU and parallel efficiency. Timings are presented for two relatively large molecules, taxol (C(47)H(51)NO(14)) and luciferin (C(11)H(8)N(2)O(3)S(2)), the former with the 6-31G* and 6-311G** basis sets (1,032 and 1,484 basis functions, 164 correlated orbitals), and the latter with the aug-cc-pVDZ and aug-cc-pVTZ basis sets (530 and 1,198 basis functions, 46 correlated orbitals). An MP2 energy calculation on C(130)H(10) (1,970 basis functions, 265 correlated orbitals) completed in less than 2 h on 128 processors.

Efficient method for computing the maximum-likelihood quantum state from measurements with additive Gaussian noise.

PubMed

Smolin, John A; Gambetta, Jay M; Smith, Graeme

2012-02-17

We provide an efficient method for computing the maximum-likelihood mixed quantum state (with density matrix ρ) given a set of measurement outcomes in a complete orthonormal operator basis subject to Gaussian noise. Our method works by first changing basis yielding a candidate density matrix μ which may have nonphysical (negative) eigenvalues, and then finding the nearest physical state under the 2-norm. Our algorithm takes at worst O(d(4)) for the basis change plus O(d(3)) for finding ρ where d is the dimension of the quantum state. In the special case where the measurement basis is strings of Pauli operators, the basis change takes only O(d(3)) as well. The workhorse of the algorithm is a new linear-time method for finding the closest probability distribution (in Euclidean distance) to a set of real numbers summing to one.

A machine learning approach for efficient uncertainty quantification using multiscale methods

NASA Astrophysics Data System (ADS)

Chan, Shing; Elsheikh, Ahmed H.

2018-02-01

Several multiscale methods account for sub-grid scale features using coarse scale basis functions. For example, in the Multiscale Finite Volume method the coarse scale basis functions are obtained by solving a set of local problems over dual-grid cells. We introduce a data-driven approach for the estimation of these coarse scale basis functions. Specifically, we employ a neural network predictor fitted using a set of solution samples from which it learns to generate subsequent basis functions at a lower computational cost than solving the local problems. The computational advantage of this approach is realized for uncertainty quantification tasks where a large number of realizations has to be evaluated. We attribute the ability to learn these basis functions to the modularity of the local problems and the redundancy of the permeability patches between samples. The proposed method is evaluated on elliptic problems yielding very promising results.

Slater-type geminals in explicitly-correlated perturbation theory: application to n-alkanols and analysis of errors and basis-set requirements.

PubMed

Höfener, Sebastian; Bischoff, Florian A; Glöss, Andreas; Klopper, Wim

2008-06-21

In the recent years, Slater-type geminals (STGs) have been used with great success to expand the first-order wave function in an explicitly-correlated perturbation theory. The present work reports on this theory's implementation in the framework of the Turbomole suite of programs. A formalism is presented for evaluating all of the necessary molecular two-electron integrals by means of the Obara-Saika recurrence relations, which can be applied when the STG is expressed as a linear combination of a small number (n) of Gaussians (STG-nG geminal basis). In the Turbomole implementation of the theory, density fitting is employed and a complementary auxiliary basis set (CABS) is used for the resolution-of-the-identity (RI) approximation of explicitly-correlated theory. By virtue of this RI approximation, the calculation of molecular three- and four-electron integrals is avoided. An approximation is invoked to avoid the two-electron integrals over the commutator between the operators of kinetic energy and the STG. This approximation consists of computing commutators between matrices in place of operators. Integrals over commutators between operators would have occurred if the theory had been formulated and implemented as proposed originally. The new implementation in Turbomole was tested by performing a series of calculations on rotational conformers of the alkanols n-propanol through n-pentanol. Basis-set requirements concerning the orbital basis, the auxiliary basis set for density fitting and the CABS were investigated. Furthermore, various (constrained) optimizations of the amplitudes of the explicitly-correlated double excitations were studied. These amplitudes can be optimized in orbital-variant and orbital-invariant manners, or they can be kept fixed at the values governed by the rational generator approach, that is, by the electron cusp conditions. Electron-correlation effects beyond the level of second-order perturbation theory were accounted for by conventional coupled-cluster calculations with single, double and perturbative triple excitations [CCSD(T)]. The explicitly-correlated perturbation theory results were combined with CCSD(T) results and compared with literature data obtained by basis-set extrapolation.

Segmented Hoop as a Physical Pendulum

NASA Astrophysics Data System (ADS)

Layton, William; Rodriguez, Nuria

2013-10-01

An interesting demonstration with a surprising result is to suspend a hoop from a point near its edge and set it swinging in a vertical plane as a pendulum. If a simple pendulum of length equal to the diameter of the hoop is set oscillating at the same time, the two will have nearly the same period. However, the real surprise is if the pendulum is segmented horizontally (as illustrated in Fig. 1) into smaller pieces that are symmetrical about the point of suspension, each smaller segment will also have the same period. Constructing such a demonstration can be difficult, but thanks to a suggestion from a fellow physics teacher a dissectible hula hoop can be purchased that serves well in this demonstration.2 A setup that has been repeated many times at various physics teacher meetings in Southern California is illustrated below.

Transforming a large-class lecture course to a smaller-group interactive course.

PubMed

Persky, Adam M; Pollack, Gary M

2010-11-10

To transition a large pharmacokinetics course that was delivered using a traditional lecture format into a smaller-group course with a discussion format. An e-book and Web-based multimedia learning modules were utilized to facilitate students' independent learning which allowed the number of classes they were required to attend to be reduced from 3 to 1 per week. Students were assigned randomly to 1 of 3 weekly class sessions. The majority of lecture time was replaced with active-learning activities including discussion, problem solving, and case studies to encourage higher-order learning. Changes in course delivery were assessed over a 4-year period by comparing students' grades and satisfaction ratings on course evaluations. Although student satisfaction with the course did not improve significantly, students preferred the smaller-group setting to a large lecture-based class. The resources and activities designed to shift responsibility for learning to the students did not affect examination grades even though a larger portion of examination questions focused on higher orders of learning (eg, application) in the smaller-group format. Transitioning to a smaller-group discussion format is possible in a pharmacokinetics course by increasing student accountability for acquiring factual content outside of the classroom. Students favored the smaller-class format over a large lecture-based class.

Appropriate description of intermolecular interactions in the methane hydrates: an assessment of DFT methods.

PubMed

Liu, Yuan; Zhao, Jijun; Li, Fengyu; Chen, Zhongfang

2013-01-15

Accurate description of hydrogen-bonding energies between water molecules and van der Waals interactions between guest molecules and host water cages is crucial for study of methane hydrates (MHs). Using high-level ab initio MP2 and CCSD(T) results as the reference, we carefully assessed the performance of a variety of exchange-correlation functionals and various basis sets in describing the noncovalent interactions in MH. The functionals under investigation include the conventional GGA, meta-GGA, and hybrid functionals (PBE, PW91, TPSS, TPSSh, B3LYP, and X3LYP), long-range corrected functionals (ωB97X, ωB97, LC-ωPBE, CAM-B3LYP, and LC-TPSS), the newly developed Minnesota class functionals (M06-L, M06-HF, M06, and M06-2X), and the dispersion-corrected density functional theory (DFT) (DFT-D) methods (B97-D, ωB97X-D, PBE-TS, PBE-Grimme, and PW91-OBS). We found that the conventional functionals are not suitable for MH, notably, the widely used B3LYP functional even predicts repulsive interaction between CH(4) and (H(2)O)(6) cluster. M06-2X is the best among the M06-Class functionals. The ωB97X-D outperforms the other DFT-D methods and is recommended for accurate first-principles calculations of MH. B97-D is also acceptable as a compromise of computational cost and precision. Considering both accuracy and efficiency, B97-D, ωB97X-D, and M06-2X functional with 6-311++G(2d,2p) basis set without basis set superposition error (BSSE) correction are recommended. Though a fairly large basis set (e.g., aug-cc-pVTZ) and BSSE correction are necessary for a reliable MP2 calculation, DFT methods are less sensitive to the basis set and BSSE correction if the basis set is sufficient (e.g., 6-311++G(2d,2p)). These assessments provide useful guidance for choosing appropriate methodology of first-principles simulation of MH and related systems. © 2012 Wiley Periodicals, Inc. Copyright © 2012 Wiley Periodicals, Inc.

The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus)

PubMed Central

Ming, Ray; Hou, Shaobin; Feng, Yun; Yu, Qingyi; Dionne-Laporte, Alexandre; Saw, Jimmy H.; Senin, Pavel; Wang, Wei; Ly, Benjamin V.; Lewis, Kanako L. T.; Salzberg, Steven L.; Feng, Lu; Jones, Meghan R.; Skelton, Rachel L.; Murray, Jan E.; Chen, Cuixia; Qian, Wubin; Shen, Junguo; Du, Peng; Eustice, Moriah; Tong, Eric; Tang, Haibao; Lyons, Eric; Paull, Robert E.; Michael, Todd P.; Wall, Kerr; Rice, Danny W.; Albert, Henrik; Wang, Ming-Li; Zhu, Yun J.; Schatz, Michael; Nagarajan, Niranjan; Acob, Ricelle A.; Guan, Peizhu; Blas, Andrea; Wai, Ching Man; Ackerman, Christine M.; Ren, Yan; Liu, Chao; Wang, Jianmei; Wang, Jianping; Na, Jong-Kuk; Shakirov, Eugene V.; Haas, Brian; Thimmapuram, Jyothi; Nelson, David; Wang, Xiyin; Bowers, John E.; Gschwend, Andrea R.; Delcher, Arthur L.; Singh, Ratnesh; Suzuki, Jon Y.; Tripathi, Savarni; Neupane, Kabi; Wei, Hairong; Irikura, Beth; Paidi, Maya; Jiang, Ning; Zhang, Wenli; Presting, Gernot; Windsor, Aaron; Navajas-Pérez, Rafael; Torres, Manuel J.; Feltus, F. Alex; Porter, Brad; Li, Yingjun; Burroughs, A. Max; Luo, Ming-Cheng; Liu, Lei; Christopher, David A.; Mount, Stephen M.; Moore, Paul H.; Sugimura, Tak; Jiang, Jiming; Schuler, Mary A.; Friedman, Vikki; Mitchell-Olds, Thomas; Shippen, Dorothy E.; dePamphilis, Claude W.; Palmer, Jeffrey D.; Freeling, Michael; Paterson, Andrew H.; Gonsalves, Dennis; Wang, Lei; Alam, Maqsudul

2010-01-01

Papaya, a fruit crop cultivated in tropical and subtropical regions, is known for its nutritional benefits and medicinal applications. Here we report a 3× draft genome sequence of ‘SunUp’ papaya, the first commercial virus-resistant transgenic fruit tree1 to be sequenced. The papaya genome is three times the size of the Arabidopsis genome, but contains fewer genes, including significantly fewer disease-resistance gene analogues. Comparison of the five sequenced genomes suggests a minimal angiosperm gene set of 13,311. A lack of recent genome duplication, atypical of other angiosperm genomes sequenced so far2–5, may account for the smaller papaya gene number in most functional groups. Nonetheless, striking amplifications in gene number within particular functional groups suggest roles in the evolution of tree-like habit, deposition and remobilization of starch reserves, attraction of seed dispersal agents, and adaptation to tropical daylengths. Transgenesis at three locations is closely associated with chloroplast insertions into the nuclear genome, and with topoisomerase I recognition sites. Papaya offers numerous advantages as a system for fruit-tree functional genomics, and this draft genome sequence provides the foundation for revealing the basis of Carica's distinguishing morpho-physiological, medicinal and nutritional properties. PMID:18432245

The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus).

PubMed

Ming, Ray; Hou, Shaobin; Feng, Yun; Yu, Qingyi; Dionne-Laporte, Alexandre; Saw, Jimmy H; Senin, Pavel; Wang, Wei; Ly, Benjamin V; Lewis, Kanako L T; Salzberg, Steven L; Feng, Lu; Jones, Meghan R; Skelton, Rachel L; Murray, Jan E; Chen, Cuixia; Qian, Wubin; Shen, Junguo; Du, Peng; Eustice, Moriah; Tong, Eric; Tang, Haibao; Lyons, Eric; Paull, Robert E; Michael, Todd P; Wall, Kerr; Rice, Danny W; Albert, Henrik; Wang, Ming-Li; Zhu, Yun J; Schatz, Michael; Nagarajan, Niranjan; Acob, Ricelle A; Guan, Peizhu; Blas, Andrea; Wai, Ching Man; Ackerman, Christine M; Ren, Yan; Liu, Chao; Wang, Jianmei; Wang, Jianping; Na, Jong-Kuk; Shakirov, Eugene V; Haas, Brian; Thimmapuram, Jyothi; Nelson, David; Wang, Xiyin; Bowers, John E; Gschwend, Andrea R; Delcher, Arthur L; Singh, Ratnesh; Suzuki, Jon Y; Tripathi, Savarni; Neupane, Kabi; Wei, Hairong; Irikura, Beth; Paidi, Maya; Jiang, Ning; Zhang, Wenli; Presting, Gernot; Windsor, Aaron; Navajas-Pérez, Rafael; Torres, Manuel J; Feltus, F Alex; Porter, Brad; Li, Yingjun; Burroughs, A Max; Luo, Ming-Cheng; Liu, Lei; Christopher, David A; Mount, Stephen M; Moore, Paul H; Sugimura, Tak; Jiang, Jiming; Schuler, Mary A; Friedman, Vikki; Mitchell-Olds, Thomas; Shippen, Dorothy E; dePamphilis, Claude W; Palmer, Jeffrey D; Freeling, Michael; Paterson, Andrew H; Gonsalves, Dennis; Wang, Lei; Alam, Maqsudul

2008-04-24

Papaya, a fruit crop cultivated in tropical and subtropical regions, is known for its nutritional benefits and medicinal applications. Here we report a 3x draft genome sequence of 'SunUp' papaya, the first commercial virus-resistant transgenic fruit tree to be sequenced. The papaya genome is three times the size of the Arabidopsis genome, but contains fewer genes, including significantly fewer disease-resistance gene analogues. Comparison of the five sequenced genomes suggests a minimal angiosperm gene set of 13,311. A lack of recent genome duplication, atypical of other angiosperm genomes sequenced so far, may account for the smaller papaya gene number in most functional groups. Nonetheless, striking amplifications in gene number within particular functional groups suggest roles in the evolution of tree-like habit, deposition and remobilization of starch reserves, attraction of seed dispersal agents, and adaptation to tropical daylengths. Transgenesis at three locations is closely associated with chloroplast insertions into the nuclear genome, and with topoisomerase I recognition sites. Papaya offers numerous advantages as a system for fruit-tree functional genomics, and this draft genome sequence provides the foundation for revealing the basis of Carica's distinguishing morpho-physiological, medicinal and nutritional properties.

Insights into Corona Formation through Statistical Analyses

NASA Technical Reports Server (NTRS)

Glaze, L. S.; Stofan, E. R.; Smrekar, S. E.; Baloga, S. M.

2002-01-01

Statistical analysis of an expanded database of coronae on Venus indicates that the populations of Type 1 (with fracture annuli) and 2 (without fracture annuli) corona diameters are statistically indistinguishable, and therefore we have no basis for assuming different formation mechanisms. Analysis of the topography and diameters of coronae shows that coronae that are depressions, rimmed depressions, and domes tend to be significantly smaller than those that are plateaus, rimmed plateaus, or domes with surrounding rims. This is consistent with the model of Smrekar and Stofan and inconsistent with predictions of the spreading drop model of Koch and Manga. The diameter range for domes, the initial stage of corona formation, provides a broad constraint on the buoyancy of corona-forming plumes. Coronae are only slightly more likely to be topographically raised than depressions, with Type 1 coronae most frequently occurring as rimmed depressions and Type 2 coronae most frequently occuring with flat interiors and raised rims. Most Type 1 coronae are located along chasmata systems or fracture belts, while Type 2 coronas are found predominantly as isolated features in the plains. Coronae at hotspot rises tend to be significantly larger than coronae in other settings, consistent with a hotter upper mantle at hotspot rises and their active state.

Step styles of pedestrians at different densities

NASA Astrophysics Data System (ADS)

Wang, Jiayue; Weng, Wenguo; Boltes, Maik; Zhang, Jun; Tordeux, Antoine; Ziemer, Verena

2018-02-01

Stepping locomotion is the basis of human movement. The investigation of stepping locomotion and its affecting factors is necessary for a more realistic knowledge of human movement, which is usually referred to as walking with equal step lengths for the right and left leg. To study pedestrians’ stepping locomotion, a set of single-file movement experiments involving 39 participants of the same age walking on a highly curved oval course is conducted. The microscopic characteristics of the pedestrians including 1D Voronoi density, speed, and step length are calculated based on a projected coordinate. The influence of the projection lines with different radii on the measurement of these quantities is investigated. The step lengths from the straight and curved parts are compared using the Kolmogorov-Smirnov test. During the experiments, six different step styles are observed and the proportions of different step styles change with the density. At low density, the main step style is the stable-large step style and the step lengths of one pedestrian are almost constant. At high density, some pedestrians adjust and decrease their step lengths. Some pedestrians take relatively smaller and larger steps alternately to adapt to limited space.

Left-Right Non-Linear Dynamical Higgs

NASA Astrophysics Data System (ADS)

Jing, Shu; Juan, Yepes

2016-12-01

All the possible CP-conserving non-linear operators up to the p4-order in the Lagrangian expansion are analysed here for the left-right symmetric model in the non-linear electroweak chiral context coupled to a light dynamical Higgs. The low energy effects will be triggered by an emerging new physics field content in the nature, more specifically, from spin-1 resonances sourced by the straightforward extension of the SM local gauge symmetry to the larger local group SU(2)L × SU(2)R × U(1)B-L. Low energy phenomenology will be altered by integrating out the resonances from the physical spectrum, being manifested through induced corrections onto the left handed operators. Such modifications are weighted by powers of the scales ratio implied by the symmetries of the model and will determine the size of the effective operator basis to be used. The recently observed diboson excess around the invariant mass 1.8 TeV-2 TeV entails a scale suppression that suggests to encode the low energy effects via a much smaller set of effective operators. J. Y. also acknowledges KITPC financial support during the completion of this work

The transfer of movement sequences: effects of decreased and increased load.

PubMed

Muehlbauer, Thomas; Panzer, Stefan; Shea, Charles H

2007-06-01

A number of recent experiments have demonstrated that a movement structure develops during the course of learning a movement sequence that provides the basis for transfer. After learning a movement sequence participants have been shown to be able to effectively produce the sequence when movement demands require that the sequence be rescaled in amplitude or produced with an unpractised set of effectors. The purpose of the present experiment was to determine whether participants, after learning a complex 16-element movement sequence with a 0.567-kg load, could also effectively produce the sequence when the load was decreased (0.0 kg) or increased (1.134 kg). The results indicated that participants were able to effectively compensate for decreased and increased load with virtually no changes in performance characteristics (displacement, velocity, acceleration, and pattern of element durations) while electromyographic (EMG) signals demonstrated that smaller (reduced load) or larger forces (increased load) were spontaneously generated to compensate for the change in load. The muscle activation patterns of the biceps and triceps as well as the level of coactivation appeared to be generally upscaled to generate and dissipate the changes in force requirement needed to compensate for the increased load.

Support System for Mental Health Professionals*

PubMed Central

Dandekar, Ajit

2015-01-01

This paper talks of support systems for mental health professionals wherein the Bombay Psychiatric Society (BPS) should devote some meetings exclusively to problems pertaining to the profession, e.g., long and odd working hours leading to potentially hazardous practice schedules, unhealthy competitive attitudes and culture. A crash course in self-defence against potentially psychotic patients and drug addicts is advocated as also awareness of the potential hazards in dealing with the litigious paranoid patients, erotomaniacs and some of the difficult hysterical patients. Potential medicolegal problems arise in treating an uncooperative patient without his knowledge and consent on an outpatient department basis, admitting such an uncooperative patient to a nursing home or a hospital, administering electroconvulsive therapies, maintaining detailed clinical records of patients, and legal issues involving smaller psychiatric private nursing homes. This paper stresses on the use of Yoga as a recognised psycho-physiological therapy. Furthermore, it suggests on the need for BPS, as a professional body, to have a cell to guide and help aspiring young professionals in setting up private practice. It points out the need to evolve some concrete programmes that in the long run should help alleviate stresses and strains and promote positive comprehensive health amongst mental health professionals. PMID:25838730

Higher order alchemical derivatives from coupled perturbed self-consistent field theory.

PubMed

Lesiuk, Michał; Balawender, Robert; Zachara, Janusz

2012-01-21

We present an analytical approach to treat higher order derivatives of Hartree-Fock (HF) and Kohn-Sham (KS) density functional theory energy in the Born-Oppenheimer approximation with respect to the nuclear charge distribution (so-called alchemical derivatives). Modified coupled perturbed self-consistent field theory is used to calculate molecular systems response to the applied perturbation. Working equations for the second and the third derivatives of HF/KS energy are derived. Similarly, analytical forms of the first and second derivatives of orbital energies are reported. The second derivative of Kohn-Sham energy and up to the third derivative of Hartree-Fock energy with respect to the nuclear charge distribution were calculated. Some issues of practical calculations, in particular the dependence of the basis set and Becke weighting functions on the perturbation, are considered. For selected series of isoelectronic molecules values of available alchemical derivatives were computed and Taylor series expansion was used to predict energies of the "surrounding" molecules. Predicted values of energies are in unexpectedly good agreement with the ones computed using HF/KS methods. Presented method allows one to predict orbital energies with the error less than 1% or even smaller for valence orbitals. © 2012 American Institute of Physics

Photodissociation Dynamics of Phenol: Multistate Trajectory Simulations including Tunneling

DOE PAGES

Xu, Xuefei; Zheng, Jingjing; Yang, Ke R.; ...

2014-10-27

We report multistate trajectory simulations, including coherence, decoherence, and multidimensional tunneling, of phenol photodissociation dynamics. The calculations are based on full-dimensional anchor-points reactive potential surfaces and state couplings fit to electronic structure calculations including dynamical correlation with an augmented correlation-consistent polarized valence double-ζ basis set. The calculations successfully reproduce the experimentally observed bimodal character of the total kinetic energy release spectra and confirm the interpretation of the most recent experiments that the photodissociation process is dominated by tunneling. Analysis of the trajectories uncovers an unexpected dissociation pathway for one quantum excitation of the O–H stretching mode of the S 1more » state, namely, tunneling in a coherent mixture of states starting in a smaller R OH (~0.9–1.0 Å) region than has previously been invoked. The simulations also show that most trajectories do not pass close to the S 1–S 2 conical intersection (they have a minimum gap greater than 0.6 eV), they provide statistics on the out-of-plane angles at the locations of the minimum energy adiabatic gap, and they reveal information about which vibrational modes are most highly activated in the products.« less

H∞ filter design for nonlinear systems with quantised measurements in finite frequency domain

NASA Astrophysics Data System (ADS)

El Hellani, D.; El Hajjaji, A.; Ceschi, R.

2017-04-01

This paper deals with the problem of finite frequency (FF) H∞ full-order fuzzy filter design for nonlinear discrete-time systems with quantised measurements, described by Takagi-Sugeno models. The measured signals are assumed to be quantised with a logarithmic quantiser. Using a fuzzy-basis-dependent Lyapunov function, the finite frequency ℓ2 gain definition, the generalised S-procedure, and Finsler's lemma, a set of sufficient conditions are established in terms of matrix inequalities, ensuring that the filtering error system is stable and the H∞ attenuation level, from disturbance to the estimation error, is smaller than a given value over a prescribed finite frequency domain of the external disturbances. With the aid of Finsler's lemma, a large number of slack variables are introduced to the design conditions, which provides extra degrees of freedom in optimising the guaranteed H∞ performance. This directly leads to performance improvement and reduction of conservatism. Finally, we give a simulation example to demonstrate the efficiency of the proposed design method, and we show that a lower H∞ attenuation level can be obtained by our developed approach in comparison with another result in the literature.

SLUDGE TREATMENT PROJECT KOP DISPOSITION - THERMAL AND GAS ANALYSIS FOR THE COLD VACUUM DRYING FACILITY

DOE Office of Scientific and Technical Information (OSTI.GOV)

SWENSON JA; CROWE RD; APTHORPE R

2010-03-09

The purpose of this document is to present conceptual design phase thermal process calculations that support the process design and process safety basis for the cold vacuum drying of K Basin KOP material. This document is intended to demonstrate that the conceptual approach: (1) Represents a workable process design that is suitable for development in preliminary design; and (2) Will support formal safety documentation to be prepared during the definitive design phase to establish an acceptable safety basis. The Sludge Treatment Project (STP) is responsible for the disposition of Knock Out Pot (KOP) sludge within the 105-K West (KW) Basin.more » KOP sludge consists of size segregated material (primarily canister particulate) from the fuel and scrap cleaning process used in the Spent Nuclear Fuel process at K Basin. The KOP sludge will be pre-treated to remove fines and some of the constituents containing chemically bound water, after which it is referred to as KOP material. The KOP material will then be loaded into a Multi-Canister Overpack (MCO), dried at the Cold Vacuum Drying Facility (CVDF) and stored in the Canister Storage Building (CSB). This process is patterned after the successful drying of 2100 metric tons of spent fuel, and uses the same facilities and much of the same equipment that was used for drying fuel and scrap. Table ES-l present similarities and differences between KOP material and fuel and between MCOs loaded with these materials. The potential content of bound water bearing constituents limits the mass ofKOP material in an MCO load to a fraction of that in an MCO containing fuel and scrap; however, the small particle size of the KOP material causes the surface area to be significantly higher. This relatively large reactive surface area represents an input to the KOP thermal calculations that is significantly different from the calculations for fuel MCOs. The conceptual design provides for a copper insert block that limits the volume available to receive KOP material, enhances heat conduction, and functions as a heat source and sink during drying operations. This use of the copper insert represents a significant change to the thermal model compared to that used for the fuel calculations. A number of cases were run representing a spectrum of normal and upset conditions for the drying process. Dozens of cases have been run on cold vacuum drying of fuel MCOs. Analysis of these previous calculations identified four cases that provide a solid basis for judgments on the behavior of MCO in drying operations. These four cases are: (1) Normal Process; (2) Degraded vacuum pumping; (3) Open MCO with loss of annulus water; and (4) Cool down after vacuum drying. The four cases were run for two sets of input parameters for KOP MCOs: (1) a set of parameters drawn from safety basis values from the technical data book and (2) a sensitivity set using parameters selected to evaluate the impact of lower void volume and smaller particle size on MCO behavior. Results of the calculations for the drying phase cases are shown in Table ES-2. Cases using data book safety basis values showed dry out in 9.7 hours and heat rejection sufficient to hold temperature rise to less than 25 C. Sensitivity cases which included unrealistically small particle sizes and corresponding high reactive surface area showed higher temperature increases that were limited by water consumption. In this document and in the attachment (Apthorpe, R. and M.G. Plys, 2010) cases using Technical Databook safety basis values are referred to as nominal cases. In future calculations such cases will be called safety basis cases. Also in these documents cases using parameters that are less favorable to acceptable performance than databook safety values are referred to as safety cases. In future calculations such cases will be called sensitivity cases or sensitivity evaluations Calculations to be performed in support of the detailed design and formal safety basis documentation will expand the calculations presented in this document to include: additional features of the drying cycle, more realistic treatment of uranium metal consumption during oxidation, larger water inventory, longer time scales, and graphing of results of hydrogen gas concentration.« less

47 CFR 4.1 - Scope, basis and purpose.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 47 Telecommunication 1 2010-10-01 2010-10-01 false Scope, basis and purpose. 4.1 Section 4.1 Telecommunication FEDERAL COMMUNICATIONS COMMISSION GENERAL DISRUPTIONS TO COMMUNICATIONS General § 4.1 Scope, basis and purpose. In this part, the Federal Communications Commission is setting forth requirements...

47 CFR 4.1 - Scope, basis and purpose.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 47 Telecommunication 1 2012-10-01 2012-10-01 false Scope, basis and purpose. 4.1 Section 4.1 Telecommunication FEDERAL COMMUNICATIONS COMMISSION GENERAL DISRUPTIONS TO COMMUNICATIONS General § 4.1 Scope, basis and purpose. In this part, the Federal Communications Commission is setting forth requirements...

Projective limits of state spaces IV. Fractal label sets

NASA Astrophysics Data System (ADS)

Lanéry, Suzanne; Thiemann, Thomas

2018-01-01

Instead of formulating the state space of a quantum field theory over one big Hilbert space, it has been proposed by Kijowski (1977) to represent quantum states as projective families of density matrices over a collection of smaller, simpler Hilbert spaces (see Lanéry (2016) [1] for a concise introduction to this formalism). One can thus bypass the need to select a vacuum state for the theory, and still be provided with an explicit and constructive description of the quantum state space, at least as long as the label set indexing the projective structure is countable. Because uncountable label sets are much less practical in this context, we develop in the present article a general procedure to trim an originally uncountable label set down to countable cardinality. In particular, we investigate how to perform this tightening of the label set in a way that preserves both the physical content of the algebra of observables and its symmetries. This work is notably motivated by applications to the holonomy-flux algebra underlying Loop Quantum Gravity. Building on earlier work by Okołów (2013), a projective state space was introduced for this algebra in Lanéry and Thiemann (2016). However, the non-trivial structure of the holonomy-flux algebra prevents the construction of satisfactory semi-classical states (Lanéry and Thiemann, 2017). Implementing the general procedure just mentioned in the case of a one-dimensional version of this algebra, we show how a discrete subalgebra can be extracted without destroying universality nor diffeomorphism invariance. On this subalgebra, quantum states can then be constructed which are more regular than was possible on the original algebra. In particular, this allows the design of semi-classical states whose semi-classicality is enforced step by step, starting from collective, macroscopic degrees of freedom and going down progressively toward smaller and smaller scales.

Apo adenylate kinase encodes its holo form: a principal component and varimax analysis.

PubMed

Cukier, Robert I

2009-02-12

Adenylate kinase undergoes large-scale motions of its LID and AMP-binding (AMPbd) domains when its apo, open form closes over its substrates, AMP and Mg2+-ATP. It may be an example of an enzyme that provides an ensemble of conformations in its apo state from which its substrates can select and bind to produce catalytically competent conformations. In this work, the fluctuations of the enzyme apo Escherichia coli adenylate kinase (AKE) are obtained with molecular dynamics. The resulting trajectory is analyzed with principal component analysis (PCA) that decomposes the atom motions into orthogonal modes ordered by their decreasing contributions to the total protein fluctuation. In apo AKE, a small set of the PCA modes describes the bulk of the fluctuations. Identification of the atom motions that are important contributors to these modes is improved with the use of a varimax rotation method that rotates the PCA modes to a new mode set that concentrates the atom contributions to a smaller set of atoms in these new modes. In this way, the nature of the important motions of the LID and AMPbd domains are clarified. The dominant PCA modes are used to investigate if apo AKE can fluctuate to conformations that are holo-like, even though the apo trajectory is mainly confined to a region around the initial apo structure. This is accomplished by expressing the difference between the protein coordinates, obtained from the holo and apo crystal structures, using as a basis the PCA modes from the apo AKE trajectory. The coherent motion described by a small set of the apo PCA modes is shown to be able to produce protein conformations that are quite similar to the holo conformation of the protein. In this sense, apo AKE does encode in its fluctuations information about holo-like conformations.

Electronic and spectroscopic characterizations of SNP isomers

NASA Astrophysics Data System (ADS)

Trabelsi, Tarek; Al Mogren, Muneerah Mogren; Hochlaf, Majdi; Francisco, Joseph S.

2018-02-01

High-level ab initio electronic structure calculations were performed to characterize SNP isomers. In addition to the known linear SNP, cyc-PSN, and linear SPN isomers, we identified a fourth isomer, linear PSN, which is located ˜2.4 eV above the linear SNP isomer. The low-lying singlet and triplet electronic states of the linear SNP and SPN isomers were investigated using a multi-reference configuration interaction method and large basis set. Several bound electronic states were identified. However, their upper rovibrational levels were predicted to pre-dissociate, leading to S + PN, P + NS products, and multi-step pathways were discovered. For the ground states, a set of spectroscopic parameters were derived using standard and explicitly correlated coupled-cluster methods in conjunction with augmented correlation-consistent basis sets extrapolated to the complete basis set limit. We also considered scalar and core-valence effects. For linear isomers, the rovibrational spectra were deduced after generation of their 3D-potential energy surfaces along the stretching and bending coordinates and variational treatments of the nuclear motions.

First-principle modelling of forsterite surface properties: Accuracy of methods and basis sets.

PubMed

Demichelis, Raffaella; Bruno, Marco; Massaro, Francesco R; Prencipe, Mauro; De La Pierre, Marco; Nestola, Fabrizio

2015-07-15

The seven main crystal surfaces of forsterite (Mg2 SiO4 ) were modeled using various Gaussian-type basis sets, and several formulations for the exchange-correlation functional within the density functional theory (DFT). The recently developed pob-TZVP basis set provides the best results for all properties that are strongly dependent on the accuracy of the wavefunction. Convergence on the structure and on the basis set superposition error-corrected surface energy can be reached also with poorer basis sets. The effect of adopting different DFT functionals was assessed. All functionals give the same stability order for the various surfaces. Surfaces do not exhibit any major structural differences when optimized with different functionals, except for higher energy orientations where major rearrangements occur around the Mg sites at the surface or subsurface. When dispersions are not accounted for, all functionals provide similar surface energies. The inclusion of empirical dispersions raises the energy of all surfaces by a nearly systematic value proportional to the scaling factor s of the dispersion formulation. An estimation for the surface energy is provided through adopting C6 coefficients that are more suitable than the standard ones to describe O-O interactions in minerals. A 2 × 2 supercell of the most stable surface (010) was optimized. No surface reconstruction was observed. The resulting structure and surface energy show no difference with respect to those obtained when using the primitive cell. This result validates the (010) surface model here adopted, that will serve as a reference for future studies on adsorption and reactivity of water and carbon dioxide at this interface. © 2015 Wiley Periodicals, Inc.

Scaled Quantum Mechanical scale factors for vibrational calculations using alternate polarized and augmented basis sets with the B3LYP density functional calculation model

NASA Astrophysics Data System (ADS)

Legler, C. R.; Brown, N. R.; Dunbar, R. A.; Harness, M. D.; Nguyen, K.; Oyewole, O.; Collier, W. B.

2015-06-01

The Scaled Quantum Mechanical (SQM) method of scaling calculated force constants to predict theoretically calculated vibrational frequencies is expanded to include a broad array of polarized and augmented basis sets based on the split valence 6-31G and 6-311G basis sets with the B3LYP density functional. Pulay's original choice of a single polarized 6-31G(d) basis coupled with a B3LYP functional remains the most computationally economical choice for scaled frequency calculations. But it can be improved upon with additional polarization functions and added diffuse functions for complex molecular systems. The new scale factors for the B3LYP density functional and the 6-31G, 6-31G(d), 6-31G(d,p), 6-31G+(d,p), 6-31G++(d,p), 6-311G, 6-311G(d), 6-311G(d,p), 6-311G+(d,p), 6-311G++(d,p), 6-311G(2d,p), 6-311G++(2d,p), 6-311G++(df,p) basis sets are shown. The double d polarized models did not perform as well and the source of the decreased accuracy was investigated. An alternate system of generating internal coordinates that uses the out-of plane wagging coordinate whenever it is possible; makes vibrational assignments via potential energy distributions more meaningful. Automated software to produce SQM scaled vibrational calculations from different molecular orbital packages is presented.

Satellite lesions in congenital melanocytic nevi--time for a change of name.

PubMed

Kinsler, Veronica

2011-01-01

The term "satellite lesions" is used in many conditions in dermatology, generally to describe smaller lesions near the edges of a principal lesion. An online medical dictionary gives the definition "a smaller lesion accompanying a main one and situated nearby," and this can apply both macroscopically and microscopically. The implication is that the smaller lesions have spread from the parent lesion. Given this definition and usual understanding of the term its use is not apt in the case of congenital melanocytic nevi (CMN). In the vast majority of cases where the patient is said to have satellite lesions these are not restricted to the area around or near the edge of the principal lesion, and are not necessarily significantly smaller. It seems likely that the early use of the term in this condition is an adaptation of the established and correct use in the context of melanoma. Not only is the term not apt clinically but has no known etiological basis. This leaves us with the question of what to call these lesions in cases of CMN. This proposal is to categorize cases into single or multiple CMN, where multiple is 2 or more nevi of any size at birth. An accurate count or good estimate of the number of lesions at birth should also be recorded, and the largest lesion classified as usual with respect to projected adult size. © 2011 Wiley Periodicals, Inc.

Schema Knowledge Structures for Representing and Understanding Arithmetic Story Problems.

DTIC Science & Technology

1987-03-01

do so on a common unit of measure. Implicit in the CP relation is the concept of one-to- one matching of one element in the problem with the other. As...engages in one-to-one matching , removing one member from each set and setting them apart as a matched pair. The smaller of the two sets is the one...to be critical. As we pointed out earlier, some of the semantic * relations can be present in situations that demand any of * the four arithmetic

CCSDT calculations of molecular equilibrium geometries

NASA Astrophysics Data System (ADS)

Halkier, Asger; Jørgensen, Poul; Gauss, Jürgen; Helgaker, Trygve

1997-08-01

CCSDT equilibrium geometries of CO, CH 2, F 2, HF, H 2O and N 2 have been calculated using the correlation-consistent cc-pVXZ basis sets. Similar calculations have been performed for SCF, CCSD and CCSD(T). In general, bond lengths decrease when improving the basis set and increase when improving the N-electron treatment. CCSD(T) provides an excellent approximation to CCSDT for bond lengths as the largest difference between CCSDT and CCSD(T) is 0.06 pm. At the CCSDT/cc-pVQZ level, basis set deficiencies, neglect of higher-order excitations, and incomplete treatment of core-correlation all give rise to errors of a few tenths of a pm, but to a large extent, these errors cancel. The CCSDT/cc-pVQZ bond lengths deviate on average only by 0.11 pm from experiment.

General contraction of Gaussian basis sets. II - Atomic natural orbitals and the calculation of atomic and molecular properties

NASA Technical Reports Server (NTRS)

Almlof, Jan; Taylor, Peter R.

1990-01-01

A recently proposed scheme for using natural orbitals from atomic configuration interaction wave functions as a basis set for linear combination of atomic orbitals (LCAO) calculations is extended for the calculation of molecular properties. For one-electron properties like multipole moments, which are determined largely by the outermost regions of the molecular wave function, it is necessary to increase the flexibility of the basis in these regions. This is most easily done by uncontracting the outermost Gaussian primitives, and/or by adding diffuse primitives. A similar approach can be employed for the calculation of polarizabilities. Properties which are not dominated by the long-range part of the wave function, such as spectroscopic constants or electric field gradients at the nucleus, can generally be treated satisfactorily with the original atomic natural orbital sets.

Economic communication model set

NASA Astrophysics Data System (ADS)

Zvereva, Olga M.; Berg, Dmitry B.

2017-06-01

This paper details findings from the research work targeted at economic communications investigation with agent-based models usage. The agent-based model set was engineered to simulate economic communications. Money in the form of internal and external currencies was introduced into the models to support exchanges in communications. Every model, being based on the general concept, has its own peculiarities in algorithm and input data set since it was engineered to solve the specific problem. Several and different origin data sets were used in experiments: theoretic sets were estimated on the basis of static Leontief's equilibrium equation and the real set was constructed on the basis of statistical data. While simulation experiments, communication process was observed in dynamics, and system macroparameters were estimated. This research approved that combination of an agent-based and mathematical model can cause a synergetic effect.

Geminal embedding scheme for optimal atomic basis set construction in correlated calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sorella, S., E-mail: sorella@sissa.it; Devaux, N.; Dagrada, M., E-mail: mario.dagrada@impmc.upmc.fr

2015-12-28

We introduce an efficient method to construct optimal and system adaptive basis sets for use in electronic structure and quantum Monte Carlo calculations. The method is based on an embedding scheme in which a reference atom is singled out from its environment, while the entire system (atom and environment) is described by a Slater determinant or its antisymmetrized geminal power (AGP) extension. The embedding procedure described here allows for the systematic and consistent contraction of the primitive basis set into geminal embedded orbitals (GEOs), with a dramatic reduction of the number of variational parameters necessary to represent the many-body wavemore » function, for a chosen target accuracy. Within the variational Monte Carlo method, the Slater or AGP part is determined by a variational minimization of the energy of the whole system in presence of a flexible and accurate Jastrow factor, representing most of the dynamical electronic correlation. The resulting GEO basis set opens the way for a fully controlled optimization of many-body wave functions in electronic structure calculation of bulk materials, namely, containing a large number of electrons and atoms. We present applications on the water molecule, the volume collapse transition in cerium, and the high-pressure liquid hydrogen.« less

Scanning tunneling microscopy image simulation of the rutile (110) TiO2 surface with hybrid functionals and the localized basis set approach

NASA Astrophysics Data System (ADS)

Di Valentin, Cristiana

2007-10-01

In this work we present a simplified procedure to use hybrid functionals and localized atomic basis sets to simulate scanning tunneling microscopy (STM) images of stoichiometric, reduced and hydroxylated rutile (110) TiO2 surface. For the two defective systems it is necessary to introduce some exact Hartree-Fock exchange in the exchange functional in order to correctly describe the details of the electronic structure. Results are compared to the standard density functional theory and planewave basis set approach. Both methods have advantages and drawbacks that are analyzed in detail. In particular, for the localized basis set approach, it is necessary to introduce a number of Gaussian function in the vacuum region above the surface in order to correctly describe the exponential decay of the integrated local density of states from the surface. In the planewave periodic approach, a thick vacuum region is required to achieve correct results. Simulated STM images are obtained for both the reduced and hydroxylated surface which nicely compare with experimental findings. A direct comparison of the two defects as displayed in the simulated STM images indicates that the OH groups should appear brighter than oxygen vacancies in perfect agreement with the experimental STM data.

Third-Order Incremental Dual-Basis Set Zero-Buffer Approach: An Accurate and Efficient Way To Obtain CCSD and CCSD(T) Energies.

PubMed

Zhang, Jun; Dolg, Michael

2013-07-09

An efficient way to obtain accurate CCSD and CCSD(T) energies for large systems, i.e., the third-order incremental dual-basis set zero-buffer approach (inc3-db-B0), has been developed and tested. This approach combines the powerful incremental scheme with the dual-basis set method, and along with the new proposed K-means clustering (KM) method and zero-buffer (B0) approximation, can obtain very accurate absolute and relative energies efficiently. We tested the approach for 10 systems of different chemical nature, i.e., intermolecular interactions including hydrogen bonding, dispersion interaction, and halogen bonding; an intramolecular rearrangement reaction; aliphatic and conjugated hydrocarbon chains; three compact covalent molecules; and a water cluster. The results show that the errors for relative energies are <1.94 kJ/mol (or 0.46 kcal/mol), for absolute energies of <0.0026 hartree. By parallelization, our approach can be applied to molecules of more than 30 atoms and more than 100 correlated electrons with high-quality basis set such as cc-pVDZ or cc-pVTZ, saving computational cost by a factor of more than 10-20, compared to traditional implementation. The physical reasons of the success of the inc3-db-B0 approach are also analyzed.

An historically consistent and broadly applicable MRV system based on LiDAR sampling and Landsat time-series

Treesearch

W. Cohen; H. Andersen; S. Healey; G. Moisen; T. Schroeder; C. Woodall; G. Domke; Z. Yang; S. Stehman; R. Kennedy; C. Woodcock; Z. Zhu; J. Vogelmann; D. Steinwand; C. Huang

2014-01-01

The authors are developing a REDD+ MRV system that tests different biomass estimation frameworks and components. Design-based inference from a costly fi eld plot network was compared to sampling with LiDAR strips and a smaller set of plots in combination with Landsat for disturbance monitoring. Biomass estimation uncertainties associated with these different data sets...

Optimization of auxiliary basis sets for the LEDO expansion and a projection technique for LEDO-DFT.

PubMed

Götz, Andreas W; Kollmar, Christian; Hess, Bernd A

2005-09-01

We present a systematic procedure for the optimization of the expansion basis for the limited expansion of diatomic overlap density functional theory (LEDO-DFT) and report on optimized auxiliary orbitals for the Ahlrichs split valence plus polarization basis set (SVP) for the elements H, Li--F, and Na--Cl. A new method to deal with near-linear dependences in the LEDO expansion basis is introduced, which greatly reduces the computational effort of LEDO-DFT calculations. Numerical results for a test set of small molecules demonstrate the accuracy of electronic energies, structural parameters, dipole moments, and harmonic frequencies. For larger molecular systems the numerical errors introduced by the LEDO approximation can lead to an uncontrollable behavior of the self-consistent field (SCF) process. A projection technique suggested by Löwdin is presented in the framework of LEDO-DFT, which guarantees for SCF convergence. Numerical results on some critical test molecules suggest the general applicability of the auxiliary orbitals presented in combination with this projection technique. Timing results indicate that LEDO-DFT is competitive with conventional density fitting methods. (c) 2005 Wiley Periodicals, Inc.

Setting initial conditions for inflation with reaction-diffusion equation

NASA Astrophysics Data System (ADS)

Bagchi, Partha; Das, Arpan; Dave, Shreyansh S.; Sengupta, Srikumar; Srivastava, Ajit M.

2018-03-01

We discuss the issue of setting appropriate initial conditions for inflation. Specifically, we consider natural inflation model and discuss the fine tuning required for setting almost homogeneous initial conditions over a region of order several times the Hubble size which is orders of magnitude larger than any relevant correlation length for field fluctuations. We then propose to use the special propagating front solutions of reaction-diffusion equations for localized field domains of smaller sizes. Due to very small velocities of these propagating fronts we find that the inflaton field in such a field domain changes very slowly, contrary to naive expectation of rapid roll down to the true vacuum. Continued expansion leads to the energy density in the Hubble region being dominated by the vacuum energy, thereby beginning the inflationary phase. Our results show that inflation can occur even with a single localized field domain of size smaller than the Hubble size. We discuss possible extensions of our results for different inflationary models, as well as various limitations of our analysis (e.g. neglecting self gravity of the localized field domain).

Potential use of duckweed based anaerobic digester effluent as a feed source for heterotrophic growth of micro-algae

NASA Astrophysics Data System (ADS)

Ahmadi, L.; Dupont, R.

2013-12-01

Finding an alternative source of energy for the growing world's demand is a challenging task being considered by many scientists. Various types of renewable energy alternatives are being investigated by researchers around the world. The abundance of duckweed (i.e., Lemna and Wolfia sp.) in wetlands and wastewater lagoons, their rapid growth, and their capacity for nutrient, metal and other contaminant removal from wastewater suggests their potential as an inexpensive source of biomass for biofuel production. Another source of biomass for biofuel and energy production is micro-algae. The large-scale growth of micro-algae can potentially be achieved in a smaller footprint and at a higher rate and lower cost via heterotrophic growth compared to autotrophic growth for specific species that can grow under both conditions. Here we describe two types of research. First, two lab-scale, 5 L anaerobic digesters containing municipal raw wastewater that were set up, maintained and monitored over the course of 6 months using duckweed as the feed source. The pH, salinity, amount of gas production and gas composition were measured on a daily basis. The results from these measurements show that duckweed can be used as a good source of biofuel production in the form of methane gas. The second set of reactors consisted of two 1 L batch fed reactors containing algae (Chlorella vulgaris) grown in the lab environment heterotrophically. The pH and DO were monitored on a daily basis in order to investigate their effect on algae growth. Lipid analysis of the harvested algal biomass was done to investigate the efficiency of harvestable biofuel products. A nutrient solution containing glucose as an energy source was used as the initial feed solution, and the potential substitution of the glucose solution with the organic carbon residue from the duckweed digester effluent was investigated. Methane production, carbon stabilization, and gas composition results from the duckweed fed anaerobic digesters, and the growth and biolipid production of heterotrophic micro-algae fed pure substrate versus residual digester effluent carbon are discussed in detail in this study.

Quantum-Chemical Study of the Adsorption of DMMP and Sarin on gamma-Al2O3

DTIC Science & Technology

2007-02-01

In this and in the following section, ∆Eads is not corrected for zero-point vibrational energy ( ZPE ); however, a counterpoise correction for basis set...Ångstroms and the bond angle is in degrees. Values in parentheses are BSSE-corrected (∆Eads C ) results. ∆Eads has not been corrected for ZPE . b 6-31G...sets. The ∆ Eads C values are given in parentheses. No ZPE corrections have been applied. e The basis sets used were 6-311G(df) for Sarin and for the Al

42 CFR § 512.1 - Basis and scope.

Code of Federal Regulations, 2010 CFR

2017-10-01

...) HEALTH CARE INFRASTRUCTURE AND MODEL PROGRAMS EPISODE PAYMENT MODEL General Provisions § 512.1 Basis and scope. (a) Basis. This part implements the test of episode payment models under section 1115A of the Act... sets forth the following: (1) The participants in each episode payment model. (2) The episodes being...

Daubechies wavelets for linear scaling density functional theory.

PubMed

Mohr, Stephan; Ratcliff, Laura E; Boulanger, Paul; Genovese, Luigi; Caliste, Damien; Deutsch, Thierry; Goedecker, Stefan

2014-05-28

We demonstrate that Daubechies wavelets can be used to construct a minimal set of optimized localized adaptively contracted basis functions in which the Kohn-Sham orbitals can be represented with an arbitrarily high, controllable precision. Ground state energies and the forces acting on the ions can be calculated in this basis with the same accuracy as if they were calculated directly in a Daubechies wavelets basis, provided that the amplitude of these adaptively contracted basis functions is sufficiently small on the surface of the localization region, which is guaranteed by the optimization procedure described in this work. This approach reduces the computational costs of density functional theory calculations, and can be combined with sparse matrix algebra to obtain linear scaling with respect to the number of electrons in the system. Calculations on systems of 10,000 atoms or more thus become feasible in a systematic basis set with moderate computational resources. Further computational savings can be achieved by exploiting the similarity of the adaptively contracted basis functions for closely related environments, e.g., in geometry optimizations or combined calculations of neutral and charged systems.

Selecting Sustainability Indicators for Small to Medium Sized Urban Water Systems Using Fuzzy-ELECTRE.

PubMed

Chhipi-Shrestha, Gyan; Hewage, Kasun; Sadiq, Rehan

2017-03-01

  Urban water systems (UWSs) are challenged by the sustainability perspective. Certain limitations of the sustainability of centralized UWSs and decentralized household level wastewater treatments can be overcome by managing UWSs at an intermediate scale, referred to as small to medium sized UWSs (SMUWSs). SMUWSs are different from large UWSs, mainly in terms of smaller infrastructure, data limitation, smaller service area, and institutional limitations. Moreover, sustainability assessment systems to evaluate the sustainability of an entire UWS are very limited and confined only to large UWSs. This research addressed the gap and has developed a set of 38 applied sustainability performance indicators (SPIs) by using fuzzy-Elimination and Choice Translating Reality (ELECTRE) I outranking method to assess the sustainability of SMUWSs. The developed set of SPIs can be applied to existing and new SMUWSs and also provides a flexibility to include additional SPIs in the future based on the same selection criteria.

On the Interaction between Carbon Dioxide and Nanomaterials with High Accuracy ab initio and DFT Calculations

NASA Astrophysics Data System (ADS)

Vogiatzis, Konstantinos D.; Mavrandonakis, Antreas; Klopper, Wim; Froudakis, George

2009-08-01

The separation, capture and storage of carbon dioxide from the flue gas is an environmental and economical problem of significant importance. Zeolites and activated carbons have been used from the industries in order to reduce the emissions of CO2. A new family of materials, the metal-organic frameworks (MOFs), has been recently proposed as an efficient substitute of the abovementioned materials. In particular, materials based on zinc complexes with imidazo-like aromatic compounds which builds frameworks similar with those of Zeolites (Zeolite-Imidazolium Frameworks, ZIFs), have the potential for efficient separation of CO2 from CO and CH4. [1]. Weak interactions between carbon dioxide and heterocyclic aromatic compounds are being examined with high accuracy ab initio methods. CO2 has zero dipole moment but a significant quadrupole moment enables it to operate as a weak acid or weak base, according to his environment. Nitrogen-containing aromatic compounds act as electron donors, while CO2 acts as an electron acceptor. Electrostatic interactions induce a non-permanent dipole moment on CO2 and the complex is stabilized by in-plane hydrogen bonds between the charged oxygens of CO2 and nearby hydrogen of the aromatic molecule. In addition, dispersion forces from the electron correlation contribute to the interaction energy. By using explicitly correlated methods (MP2-F12/aug-cc-pVTZ) [2] and by adding the contribution from the triples excitations, calculated with a smaller basis (6-311++G**), we reach to an approximate CCSD(T) complete basis set result. [3] Extrapolation schemes were used in order to reach the MP2 basis set limit and compare it with the CCSD(T)/CBS result. Those results are in excellent agreement with the explicitly correlated MP2-F12. In addition, our complexes are being investigated with DFT methods that calculate separately the dispersion energy (DFT-D) [4] and modified MP2 which scaling of spin pair correlation [5]. DFT-D results are in good agreement with CCSD(T)/CBS results, providing us a computational cheap method with high accuracy. The quantization of the interaction is examined by changing the aromaticity of the heterocyclic molecules and by talking into account the electron correlation. [6] The electron density of the nitrogen that binds CO2 is gradually decreasing by substituting carbons with nitrogens in pyridine (pyrimidine, pyrazine, triazine), leading to lower binding energy.

High-level ab initio studies of the complex formed between CO and O2

NASA Astrophysics Data System (ADS)

Grein, Friedrich

2017-05-01

The explicitly correlated CCSD(T)-F12 method with VXZ-F12 basis sets was used to find the most stable structures of the van der Waals CO-O2 complexes. With geometry optimizations performed up to the quadruple-zeta level and basis set extrapolation, the calculated interaction energies for the triplet complexes are 123 cm-1 for the H complex in Cs symmetry (slipped near-parallel structure), 118 cm-1 for the X complex, also in Cs symmetry (perpendicular alignment) and 116 cm-1 for the CO-O2 T complex in C2v symmetry. The corresponding CCSD(T)-F12 results using the aug-cc-pVXZ basis sets are nearly the same. Similar calculations were performed for the CO-O2 singlet complexes, which are shown to have much higher stabilization energies, the highest being 206 cm-1 for the X complex.

General contraction of Gaussian basis sets. Part 2: Atomic natural orbitals and the calculation of atomic and molecular properties

NASA Technical Reports Server (NTRS)

Almloef, Jan; Taylor, Peter R.

1989-01-01

A recently proposed scheme for using natural orbitals from atomic configuration interaction (CI) wave functions as a basis set for linear combination of atomic orbitals (LCAO) calculations is extended for the calculation of molecular properties. For one-electron properties like multipole moments, which are determined largely by the outermost regions of the molecular wave function, it is necessary to increase the flexibility of the basis in these regions. This is most easily done by uncontracting the outmost Gaussian primitives, and/or by adding diffuse primitives. A similar approach can be employed for the calculation of polarizabilities. Properties which are not dominated by the long-range part of the wave function, such as spectroscopic constants or electric field gradients at the nucleus, can generally be treated satisfactorily with the original atomic natural orbital (ANO) sets.

Quantum-chemical investigation of the structures and electronic spectra of the nucleic acid bases at the coupled cluster CC2 level.

PubMed

Fleig, Timo; Knecht, Stefan; Hättig, Christof

2007-06-28

We study the ground-state structures and singlet- and triplet-excited states of the nucleic acid bases by applying the coupled cluster model CC2 in combination with a resolution-of-the-identity approximation for electron interaction integrals. Both basis set effects and the influence of dynamic electron correlation on the molecular structures are elucidated; the latter by comparing CC2 with Hartree-Fock and Møller-Plesset perturbation theory to second order. Furthermore, we investigate basis set and electron correlation effects on the vertical excitation energies and compare our highest-level results with experiment and other theoretical approaches. It is shown that small basis sets are insufficient for obtaining accurate results for excited states of these molecules and that the CC2 approach to dynamic electron correlation is a reliable and efficient tool for electronic structure calculations on medium-sized molecules.

Polyatomic molecular Dirac-Hartree-Fock calculations with Gaussian basis sets

NASA Technical Reports Server (NTRS)

Dyall, Kenneth G.; Faegri, Knut, Jr.; Taylor, Peter R.

1990-01-01

Numerical methods have been used successfully in atomic Dirac-Hartree-Fock (DHF) calculations for many years. Some DHF calculations using numerical methods have been done on diatomic molecules, but while these serve a useful purpose for calibration, the computational effort in extending this approach to polyatomic molecules is prohibitive. An alternative more in line with traditional quantum chemistry is to use an analytical basis set expansion of the wave function. This approach fell into disrepute in the early 1980's due to problems with variational collapse and intruder states, but has recently been put on firm theoretical foundations. In particular, the problems of variational collapse are well understood, and prescriptions for avoiding the most serious failures have been developed. Consequently, it is now possible to develop reliable molecular programs using basis set methods. This paper describes such a program and reports results of test calculations to demonstrate the convergence and stability of the method.

The observed clustering of damaging extratropical cyclones in Europe

NASA Astrophysics Data System (ADS)

Cusack, Stephen

2016-04-01

The clustering of severe European windstorms on annual timescales has substantial impacts on the (re-)insurance industry. Our knowledge of the risk is limited by large uncertainties in estimates of clustering from typical historical storm data sets covering the past few decades. Eight storm data sets are gathered for analysis in this study in order to reduce these uncertainties. Six of the data sets contain more than 100 years of severe storm information to reduce sampling errors, and observational errors are reduced by the diversity of information sources and analysis methods between storm data sets. All storm severity measures used in this study reflect damage, to suit (re-)insurance applications. The shortest storm data set of 42 years provides indications of stronger clustering with severity, particularly for regions off the main storm track in central Europe and France. However, clustering estimates have very large sampling and observational errors, exemplified by large changes in estimates in central Europe upon removal of one stormy season, 1989/1990. The extended storm records place 1989/1990 into a much longer historical context to produce more robust estimates of clustering. All the extended storm data sets show increased clustering between more severe storms from return periods (RPs) of 0.5 years to the longest measured RPs of about 20 years. Further, they contain signs of stronger clustering off the main storm track, and weaker clustering for smaller-sized areas, though these signals are more uncertain as they are drawn from smaller data samples. These new ultra-long storm data sets provide new information on clustering to improve our management of this risk.

Weekday AOD smaller than weekend AOD in eastern China on the basis of the MODIS AOD product

NASA Astrophysics Data System (ADS)

Song, Jingjing; Xia, Xiangao; Zhang, Xiaoling; Che, Huizheng; Li, Xiaojing

2018-05-01

A weekly cycle of surface particulate matter (PM) characterized by smaller values during weekends and larger values during weekdays was reported in eastern China. Whether column-integrated aerosol optical depth (AOD) showed similar weekly cycling as that of PM was debated. The weekly variation of AOD in eastern China was further studied by using the latest MODIS aerosol product (collection 6) with a fine spatial resolution (0.1°) from 2002 to 2015. We used three statistical methods to determine whether the weekly cycle of AOD was significant. AOD during weekdays (Wednesday to Friday) was lower than that during weekends. The maximum and minimum AOD was generally observed on Monday and Wednesday, respectively. This weekly pattern of AOD was in good agreement with previous results based on satellite aerosol products with a coarse spatial resolution, but it was in contrast to that of PM. Further analysis of the AOD weekly variability in 19 provincial cities suggested that AOD during weekdays was smaller than that during weekends in urban regions. Potential causes for the different weekly cycle of PM and AOD in eastern China were discussed.

Probing Intrawire, Interwire, and Diameter-Dependent Variations in Silicon Nanowire Surface Trap Density with Pump-Probe Microscopy.

PubMed

Cating, Emma E M; Pinion, Christopher W; Christesen, Joseph D; Christie, Caleb A; Grumstrup, Erik M; Cahoon, James F; Papanikolas, John M

2017-10-11

Surface trap density in silicon nanowires (NWs) plays a key role in the performance of many semiconductor NW-based devices. We use pump-probe microscopy to characterize the surface recombination dynamics on a point-by-point basis in 301 silicon NWs grown using the vapor-liquid-solid (VLS) method. The surface recombination velocity (S), a metric of the surface quality that is directly proportional to trap density, is determined by the relationship S = d/4τ from measurements of the recombination lifetime (τ) and NW diameter (d) at distinct spatial locations in individual NWs. We find that S varies by as much as 2 orders of magnitude between NWs grown at the same time but varies only by a factor of 2 or three within an individual NW. Although we find that, as expected, smaller-diameter NWs exhibit shorter τ, we also find that smaller wires exhibit higher values of S; this indicates that τ is shorter both because of the geometrical effect of smaller d and because of a poorer quality surface. These results highlight the need to consider interwire heterogeneity as well as diameter-dependent surface effects when fabricating NW-based devices.

A numerical fragment basis approach to SCF calculations.

NASA Astrophysics Data System (ADS)

Hinde, Robert J.

1997-11-01

The counterpoise method is often used to correct for basis set superposition error in calculations of the electronic structure of bimolecular systems. One drawback of this approach is the need to specify a ``reference state'' for the system; for reactive systems, the choice of an unambiguous reference state may be difficult. An example is the reaction F^- + HCl arrow HF + Cl^-. Two obvious reference states for this reaction are F^- + HCl and HF + Cl^-; however, different counterpoise-corrected interaction energies are obtained using these two reference states. We outline a method for performing SCF calculations which employs numerical basis functions; this method attempts to eliminate basis set superposition errors in an a priori fashion. We test the proposed method on two one-dimensional, three-center systems and discuss the possibility of extending our approach to include electron correlation effects.

Is HO3 minimum cis or trans? An analytic full-dimensional ab initio isomerization path.

PubMed

Varandas, A J C

2011-05-28

The minimum energy path for isomerization of HO(3) has been explored in detail using accurate high-level ab initio methods and techniques for extrapolation to the complete basis set limit. In agreement with other reports, the best estimates from both valence-only and all-electron single-reference methods here utilized predict the minimum of the cis-HO(3) isomer to be deeper than the trans-HO(3) one. They also show that the energy varies by less than 1 kcal mol(-1) or so over the full isomerization path. A similar result is found from valence-only multireference configuration interaction calculations with the size-extensive Davidson correction and a correlation consistent triple-zeta basis, which predict the energy difference between the two isomers to be of only Δ = -0.1 kcal mol(-1). However, single-point multireference calculations carried out at the optimum triple-zeta geometry with basis sets of the correlation consistent family but cardinal numbers up to X = 6 lead upon a dual-level extrapolation to the complete basis set limit of Δ = (0.12 ± 0.05) kcal mol(-1). In turn, extrapolations with the all-electron single-reference coupled-cluster method including the perturbative triples correction yield values of Δ = -0.19 and -0.03 kcal mol(-1) when done from triple-quadruple and quadruple-quintuple zeta pairs with two basis sets of increasing quality, namely cc-cpVXZ and aug-cc-pVXZ. Yet, if added a value of 0.25 kcal mol(-1) that accounts for the effect of triple and perturbative quadruple excitations with the VTZ basis set, one obtains a coupled cluster estimate of Δ = (0.14 ± 0.08) kcal mol(-1). It is then shown for the first time from systematic ab initio calculations that the trans-HO(3) isomer is more stable than the cis one, in agreement with the available experimental evidence. Inclusion of the best reported zero-point energy difference (0.382 kcal mol(-1)) from multireference configuration interaction calculations enhances further the relative stability to ΔE(ZPE) = (0.51 ± 0.08) kcal mol(-1). A scheme is also suggested to model the full-dimensional isomerization potential-energy surface using a quadratic expansion that is parametrically represented by a Fourier analysis in the torsion angle. The method illustrated at the raw and complete basis-set limit coupled-cluster levels can provide a valuable tool for a future analysis of the available (incomplete thus far) experimental rovibrational data. This journal is © the Owner Societies 2011

A segmentation approach for a delineation of terrestrial ecoregions

NASA Astrophysics Data System (ADS)

Nowosad, J.; Stepinski, T.

2017-12-01

Terrestrial ecoregions are the result of regionalization of land into homogeneous units of similar ecological and physiographic features. Terrestrial Ecoregions of the World (TEW) is a commonly used global ecoregionalization based on expert knowledge and in situ observations. Ecological Land Units (ELUs) is a global classification of 250 meters-sized cells into 4000 types on the basis of the categorical values of four environmental variables. ELUs are automatically calculated and reproducible but they are not a regionalization which makes them impractical for GIS-based spatial analysis and for comparison with TEW. We have regionalized terrestrial ecosystems on the basis of patterns of the same variables (land cover, soils, landform, and bioclimate) previously used in ELUs. Considering patterns of categorical variables makes segmentation and thus regionalization possible. Original raster datasets of the four variables are first transformed into regular grids of square-sized blocks of their cells called eco-sites. Eco-sites are elementary land units containing local patterns of physiographic characteristics and thus assumed to contain a single ecosystem. Next, eco-sites are locally aggregated using a procedure analogous to image segmentation. The procedure optimizes pattern homogeneity of all four environmental variables within each segment. The result is a regionalization of the landmass into land units characterized by uniform pattern of land cover, soils, landforms, climate, and, by inference, by uniform ecosystem. Because several disjoined segments may have very similar characteristics, we cluster the segments to obtain a smaller set of segment types which we identify with ecoregions. Our approach is automatic, reproducible, updatable, and customizable. It yields the first automatic delineation of ecoregions on the global scale. In the resulting vector database each ecoregion/segment is described by numerous attributes which make it a valuable GIS resource for global ecological and conservation studies.

The national sports safety in secondary schools benchmark (N4SB) study: defining athletic training practice characteristics.

PubMed

McLeod, Tamara C Valovich; Bliven, Kellie C Huxel; Lam, Kenneth C; Bay, R Curtis; Valier, Alison R Snyder; Parsons, John T

2013-01-01

Increased rates of sport participation and sport-related injury have led to greater emphasis on and attention to medical care of student-athletes in the secondary school setting. Access to athletic training services is seen as a critical factor for delivering adequate injury prevention and medical care to student-athletes. However, few data are available regarding practice characteristics of athletic trainers (ATs) in this setting. To characterize the practices of secondary school athletic trainers (ATs). Descriptive study. Web-based survey. A total of 17 558 ATs with current National Athletic Trainers' Association membership were identified for survey distribution. Of these, 4232 ATs indicated that they practiced in the secondary school setting, and 4045 completed some part of the survey. A Web-based survey was used to obtain demographic information about ATs and their secondary schools and characteristics of athletic training practice. Descriptive data regarding the athletic trainer's personal characteristics, secondary school characteristics, and practice patterns are reported as percentages and frequencies. Most respondents were in the early stages of their careers and relatively new to the secondary school practice setting. Nearly two-thirds (62.4%; n = 2522) of respondents had 10 or fewer years of experience as secondary school ATs, 52% (n = 2132) had been certified for 10 or fewer years, and 53.4% (n = 2164) had 10 or fewer years of experience in any practice setting. The majority of respondents (85%) worked in public schools with enrollment of 1000 to 1999 (35.5%) and with football (95.5%). More than half of respondents were employed directly by their school. Most respondents (50.6%) reported an athletic training budget of less than $4000. The majority of ATs performed evaluations (87.5%) on-site all of the time, with a smaller percentage providing treatments (73.3%) or rehabilitation (47.4%) services all of the time. This is the first study to describe secondary school athletic training that reflects national practice trends. To improve the quality of athletic training care and to support and improve current working conditions, the profession must examine how its members practice on a day-to-day basis.

48 CFR 19.502-2 - Total small business set-asides.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 48 Federal Acquisition Regulations System 1 2012-10-01 2012-10-01 false Total small business set... SOCIOECONOMIC PROGRAMS SMALL BUSINESS PROGRAMS Set-Asides for Small Business 19.502-2 Total small business set... contracting officer does not proceed with the small business set-aside and purchases on an unrestricted basis...

48 CFR 19.502-2 - Total small business set-asides.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 48 Federal Acquisition Regulations System 1 2011-10-01 2011-10-01 false Total small business set... SOCIOECONOMIC PROGRAMS SMALL BUSINESS PROGRAMS Set-Asides for Small Business 19.502-2 Total small business set... contracting officer does not proceed with the small business set-aside and purchases on an unrestricted basis...

48 CFR 19.502-2 - Total small business set-asides.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 48 Federal Acquisition Regulations System 1 2013-10-01 2013-10-01 false Total small business set... SOCIOECONOMIC PROGRAMS SMALL BUSINESS PROGRAMS Set-Asides for Small Business 19.502-2 Total small business set... contracting officer does not proceed with the small business set-aside and purchases on an unrestricted basis...

Influence maximization in complex networks through optimal percolation

NASA Astrophysics Data System (ADS)

Morone, Flaviano; Makse, Hernán A.

2015-08-01

The whole frame of interconnections in complex networks hinges on a specific set of structural nodes, much smaller than the total size, which, if activated, would cause the spread of information to the whole network, or, if immunized, would prevent the diffusion of a large scale epidemic. Localizing this optimal, that is, minimal, set of structural nodes, called influencers, is one of the most important problems in network science. Despite the vast use of heuristic strategies to identify influential spreaders, the problem remains unsolved. Here we map the problem onto optimal percolation in random networks to identify the minimal set of influencers, which arises by minimizing the energy of a many-body system, where the form of the interactions is fixed by the non-backtracking matrix of the network. Big data analyses reveal that the set of optimal influencers is much smaller than the one predicted by previous heuristic centralities. Remarkably, a large number of previously neglected weakly connected nodes emerges among the optimal influencers. These are topologically tagged as low-degree nodes surrounded by hierarchical coronas of hubs, and are uncovered only through the optimal collective interplay of all the influencers in the network. The present theoretical framework may hold a larger degree of universality, being applicable to other hard optimization problems exhibiting a continuous transition from a known phase.

Influence maximization in complex networks through optimal percolation.

PubMed

Morone, Flaviano; Makse, Hernán A

2015-08-06

The whole frame of interconnections in complex networks hinges on a specific set of structural nodes, much smaller than the total size, which, if activated, would cause the spread of information to the whole network, or, if immunized, would prevent the diffusion of a large scale epidemic. Localizing this optimal, that is, minimal, set of structural nodes, called influencers, is one of the most important problems in network science. Despite the vast use of heuristic strategies to identify influential spreaders, the problem remains unsolved. Here we map the problem onto optimal percolation in random networks to identify the minimal set of influencers, which arises by minimizing the energy of a many-body system, where the form of the interactions is fixed by the non-backtracking matrix of the network. Big data analyses reveal that the set of optimal influencers is much smaller than the one predicted by previous heuristic centralities. Remarkably, a large number of previously neglected weakly connected nodes emerges among the optimal influencers. These are topologically tagged as low-degree nodes surrounded by hierarchical coronas of hubs, and are uncovered only through the optimal collective interplay of all the influencers in the network. The present theoretical framework may hold a larger degree of universality, being applicable to other hard optimization problems exhibiting a continuous transition from a known phase.

Influence of basis-set size on the X Σ 1 /2 +2 , A Π 1 /2 2 , A Π 3 /2 2 , and B Σ 1 /2 +2 potential-energy curves, A Π 3 /2 2 vibrational energies, and D1 and D2 line shapes of Rb+He

NASA Astrophysics Data System (ADS)

Blank, L. Aaron; Sharma, Amit R.; Weeks, David E.

2018-03-01

The X Σ 1 /2 +2 , A Π 1 /2 2 , A Π 3 /2 2 , and B2Σ1/2 + potential-energy curves for Rb+He are computed at the spin-orbit multireference configuration interaction level of theory using a hierarchy of Gaussian basis sets at the double-zeta (DZ), triple-zeta (TZ), and quadruple-zeta (QZ) levels of valence quality. Counterpoise and Davidson-Silver corrections are employed to remove basis-set superposition error and ameliorate size-consistency error. An extrapolation is performed to obtain a final set of potential-energy curves in the complete basis-set (CBS) limit. This yields four sets of systematically improved X Σ 1 /2 +2 , A Π 1 /2 2 , A Π 3 /2 2 , and B2Σ1/2 + potential-energy curves that are used to compute the A Π 3 /2 2 bound vibrational energies, the position of the D2 blue satellite peak, and the D1 and D2 pressure broadening and shifting coefficients, at the DZ, TZ, QZ, and CBS levels. Results are compared with previous calculations and experimental observation.

Effect of O2 plasma treatment on density-of-states in a-IGZO thin film transistors

NASA Astrophysics Data System (ADS)

Ding, Xingwei; Huang, Fei; Li, Sheng; Zhang, Jianhua; Jiang, Xueyin; Zhang, Zhilin

2017-01-01

This work reports an efficient route for enhancing the performance of amorphous InGaZnO (a-IGZO) thin film transistors (TFT). The mobility was greatly improved by about 38% by means of O2 plasma treatment. Temperature-stress was carried out to investigate the stability and extract the parameters related to activation energy ( E a) and density-of-states (DOS). The DOS was calculated on the basis of the experimentally obtained E a, which can explain the experimental observation. A lower activation energy ( E a, 0.72 eV) and a smaller DOS were obtained in the O2 plasma treatment TFT based on the temperature-dependent transfer curves. The results showed that temperature stability and electrical properties enhancements in a-IGZO thin film transistors were attributed to the smaller DOS. [Figure not available: see fulltext.

Life-History Patterns of Lizards of the World.

PubMed

Mesquita, Daniel O; Costa, Gabriel C; Colli, Guarino R; Costa, Taís B; Shepard, Donald B; Vitt, Laurie J; Pianka, Eric R

2016-06-01

Identification of mechanisms that promote variation in life-history traits is critical to understand the evolution of divergent reproductive strategies. Here we compiled a large life-history data set (674 lizard populations, representing 297 species from 263 sites globally) to test a number of hypotheses regarding the evolution of life-history traits in lizards. We found significant phylogenetic signal in most life-history traits, although phylogenetic signal was not particularly high. Climatic variables influenced the evolution of many traits, with clutch frequency being positively related to precipitation and clutches of tropical lizards being smaller than those of temperate species. This result supports the hypothesis that in tropical and less seasonal climates, many lizards tend to reproduce repeatedly throughout the season, producing smaller clutches during each reproductive episode. Our analysis also supported the hypothesis that viviparity has evolved in lizards as a response to cooler climates. Finally, we also found that variation in trait values explained by clade membership is unevenly distributed among lizard clades, with basal clades and a few younger clades showing the most variation. Our global analyses are largely consistent with life-history theory and previous results based on smaller and scattered data sets, suggesting that these patterns are remarkably consistent across geographic and taxonomic scales.

Resolving Transition Metal Chemical Space: Feature Selection for Machine Learning and Structure-Property Relationships.

PubMed

Janet, Jon Paul; Kulik, Heather J

2017-11-22

Machine learning (ML) of quantum mechanical properties shows promise for accelerating chemical discovery. For transition metal chemistry where accurate calculations are computationally costly and available training data sets are small, the molecular representation becomes a critical ingredient in ML model predictive accuracy. We introduce a series of revised autocorrelation functions (RACs) that encode relationships of the heuristic atomic properties (e.g., size, connectivity, and electronegativity) on a molecular graph. We alter the starting point, scope, and nature of the quantities evaluated in standard ACs to make these RACs amenable to inorganic chemistry. On an organic molecule set, we first demonstrate superior standard AC performance to other presently available topological descriptors for ML model training, with mean unsigned errors (MUEs) for atomization energies on set-aside test molecules as low as 6 kcal/mol. For inorganic chemistry, our RACs yield 1 kcal/mol ML MUEs on set-aside test molecules in spin-state splitting in comparison to 15-20× higher errors for feature sets that encode whole-molecule structural information. Systematic feature selection methods including univariate filtering, recursive feature elimination, and direct optimization (e.g., random forest and LASSO) are compared. Random-forest- or LASSO-selected subsets 4-5× smaller than the full RAC set produce sub- to 1 kcal/mol spin-splitting MUEs, with good transferability to metal-ligand bond length prediction (0.004-5 Å MUE) and redox potential on a smaller data set (0.2-0.3 eV MUE). Evaluation of feature selection results across property sets reveals the relative importance of local, electronic descriptors (e.g., electronegativity, atomic number) in spin-splitting and distal, steric effects in redox potential and bond lengths.

Highly efficient implementation of pseudospectral time-dependent density-functional theory for the calculation of excitation energies of large molecules.

PubMed

Cao, Yixiang; Hughes, Thomas; Giesen, Dave; Halls, Mathew D; Goldberg, Alexander; Vadicherla, Tati Reddy; Sastry, Madhavi; Patel, Bhargav; Sherman, Woody; Weisman, Andrew L; Friesner, Richard A

2016-06-15

We have developed and implemented pseudospectral time-dependent density-functional theory (TDDFT) in the quantum mechanics package Jaguar to calculate restricted singlet and restricted triplet, as well as unrestricted excitation energies with either full linear response (FLR) or the Tamm-Dancoff approximation (TDA) with the pseudospectral length scales, pseudospectral atomic corrections, and pseudospectral multigrid strategy included in the implementations to improve the chemical accuracy and to speed the pseudospectral calculations. The calculations based on pseudospectral time-dependent density-functional theory with full linear response (PS-FLR-TDDFT) and within the Tamm-Dancoff approximation (PS-TDA-TDDFT) for G2 set molecules using B3LYP/6-31G*(*) show mean and maximum absolute deviations of 0.0015 eV and 0.0081 eV, 0.0007 eV and 0.0064 eV, 0.0004 eV and 0.0022 eV for restricted singlet excitation energies, restricted triplet excitation energies, and unrestricted excitation energies, respectively; compared with the results calculated from the conventional spectral method. The application of PS-FLR-TDDFT to OLED molecules and organic dyes, as well as the comparisons for results calculated from PS-FLR-TDDFT and best estimations demonstrate that the accuracy of both PS-FLR-TDDFT and PS-TDA-TDDFT. Calculations for a set of medium-sized molecules, including Cn fullerenes and nanotubes, using the B3LYP functional and 6-31G(**) basis set show PS-TDA-TDDFT provides 19- to 34-fold speedups for Cn fullerenes with 450-1470 basis functions, 11- to 32-fold speedups for nanotubes with 660-3180 basis functions, and 9- to 16-fold speedups for organic molecules with 540-1340 basis functions compared to fully analytic calculations without sacrificing chemical accuracy. The calculations on a set of larger molecules, including the antibiotic drug Ramoplanin, the 46-residue crambin protein, fullerenes up to C540 and nanotubes up to 14×(6,6), using the B3LYP functional and 6-31G(**) basis set with up to 8100 basis functions show that PS-FLR-TDDFT CPU time scales as N(2.05) with the number of basis functions. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

42 CFR 415.1 - Basis and scope.

Code of Federal Regulations, 2010 CFR

2010-10-01

... PROGRAM SERVICES FURNISHED BY PHYSICIANS IN PROVIDERS, SUPERVISING PHYSICIANS IN TEACHING SETTINGS, AND... beneficiaries in providers, physician services in teaching settings, and services of residents. ...

Basis for paraxial surface-plasmon-polariton packets

NASA Astrophysics Data System (ADS)

Martinez-Herrero, Rosario; Manjavacas, Alejandro

2016-12-01

We present a theoretical framework for the study of surface-plasmon polariton (SPP) packets propagating along a lossy metal-dielectric interface within the paraxial approximation. Using a rigorous formulation based on the plane-wave spectrum formalism, we introduce a set of modes that constitute a complete basis set for the solutions of Maxwell's equations for a metal-dielectric interface in the paraxial approximation. The use of this set of modes allows us to fully analyze the evolution of the transversal structure of SPP packets beyond the single plane-wave approximation. As a paradigmatic example, we analyze the case of a Gaussian SPP mode, for which, exploiting the analogy with paraxial optical beams, we introduce a set of parameters that characterize its propagation.

Application of the dual-kinetic-balance sets in the relativistic many-body problem of atomic structure

NASA Astrophysics Data System (ADS)

Beloy, Kyle; Derevianko, Andrei

2008-05-01

The dual-kinetic-balance (DKB) finite basis set method for solving the Dirac equation for hydrogen-like ions [V. M. Shabaev et al., Phys. Rev. Lett. 93, 130405 (2004)] is extended to problems with a non-local spherically-symmetric Dirac-Hartree-Fock potential. We implement the DKB method using B-spline basis sets and compare its performance with the widely- employed approach of Notre Dame (ND) group [W.R. Johnson, S.A. Blundell, J. Sapirstein, Phys. Rev. A 37, 307-15 (1988)]. We compare the performance of the ND and DKB methods by computing various properties of Cs atom: energies, hyperfine integrals, the parity-non-conserving amplitude of the 6s1/2-7s1/2 transition, and the second-order many-body correction to the removal energy of the valence electrons. We find that for a comparable size of the basis set the accuracy of both methods is similar for matrix elements accumulated far from the nuclear region. However, for atomic properties determined by small distances, the DKB method outperforms the ND approach.

Blind compressive sensing dynamic MRI

PubMed Central

Lingala, Sajan Goud; Jacob, Mathews

2013-01-01

We propose a novel blind compressive sensing (BCS) frame work to recover dynamic magnetic resonance images from undersampled measurements. This scheme models the dynamic signal as a sparse linear combination of temporal basis functions, chosen from a large dictionary. In contrast to classical compressed sensing, the BCS scheme simultaneously estimates the dictionary and the sparse coefficients from the undersampled measurements. Apart from the sparsity of the coefficients, the key difference of the BCS scheme with current low rank methods is the non-orthogonal nature of the dictionary basis functions. Since the number of degrees of freedom of the BCS model is smaller than that of the low-rank methods, it provides improved reconstructions at high acceleration rates. We formulate the reconstruction as a constrained optimization problem; the objective function is the linear combination of a data consistency term and sparsity promoting ℓ1 prior of the coefficients. The Frobenius norm dictionary constraint is used to avoid scale ambiguity. We introduce a simple and efficient majorize-minimize algorithm, which decouples the original criterion into three simpler sub problems. An alternating minimization strategy is used, where we cycle through the minimization of three simpler problems. This algorithm is seen to be considerably faster than approaches that alternates between sparse coding and dictionary estimation, as well as the extension of K-SVD dictionary learning scheme. The use of the ℓ1 penalty and Frobenius norm dictionary constraint enables the attenuation of insignificant basis functions compared to the ℓ0 norm and column norm constraint assumed in most dictionary learning algorithms; this is especially important since the number of basis functions that can be reliably estimated is restricted by the available measurements. We also observe that the proposed scheme is more robust to local minima compared to K-SVD method, which relies on greedy sparse coding. Our phase transition experiments demonstrate that the BCS scheme provides much better recovery rates than classical Fourier-based CS schemes, while being only marginally worse than the dictionary aware setting. Since the overhead in additionally estimating the dictionary is low, this method can be very useful in dynamic MRI applications, where the signal is not sparse in known dictionaries. We demonstrate the utility of the BCS scheme in accelerating contrast enhanced dynamic data. We observe superior reconstruction performance with the BCS scheme in comparison to existing low rank and compressed sensing schemes. PMID:23542951

How to calculate H3 better.

PubMed

Pavanello, Michele; Tung, Wei-Cheng; Adamowicz, Ludwik

2009-11-14

Efficient optimization of the basis set is key to achieving a very high accuracy in variational calculations of molecular systems employing basis functions that are explicitly dependent on the interelectron distances. In this work we present a method for a systematic enlargement of basis sets of explicitly correlated functions based on the iterative-complement-interaction approach developed by Nakatsuji [Phys. Rev. Lett. 93, 030403 (2004)]. We illustrate the performance of the method in the variational calculations of H(3) where we use explicitly correlated Gaussian functions with shifted centers. The total variational energy (-1.674 547 421 Hartree) and the binding energy (-15.74 cm(-1)) obtained in the calculation with 1000 Gaussians are the most accurate results to date.

Multi-level basis selection of wavelet packet decomposition tree for heart sound classification.

PubMed

Safara, Fatemeh; Doraisamy, Shyamala; Azman, Azreen; Jantan, Azrul; Abdullah Ramaiah, Asri Ranga

2013-10-01

Wavelet packet transform decomposes a signal into a set of orthonormal bases (nodes) and provides opportunities to select an appropriate set of these bases for feature extraction. In this paper, multi-level basis selection (MLBS) is proposed to preserve the most informative bases of a wavelet packet decomposition tree through removing less informative bases by applying three exclusion criteria: frequency range, noise frequency, and energy threshold. MLBS achieved an accuracy of 97.56% for classifying normal heart sound, aortic stenosis, mitral regurgitation, and aortic regurgitation. MLBS is a promising basis selection to be suggested for signals with a small range of frequencies. Copyright © 2013 The Authors. Published by Elsevier Ltd.. All rights reserved.

Reduced-cost linear-response CC2 method based on natural orbitals and natural auxiliary functions

PubMed Central

Mester, Dávid

2017-01-01

A reduced-cost density fitting (DF) linear-response second-order coupled-cluster (CC2) method has been developed for the evaluation of excitation energies. The method is based on the simultaneous truncation of the molecular orbital (MO) basis and the auxiliary basis set used for the DF approximation. For the reduction of the size of the MO basis, state-specific natural orbitals (NOs) are constructed for each excited state using the average of the second-order Møller–Plesset (MP2) and the corresponding configuration interaction singles with perturbative doubles [CIS(D)] density matrices. After removing the NOs of low occupation number, natural auxiliary functions (NAFs) are constructed [M. Kállay, J. Chem. Phys. 141, 244113 (2014)], and the NAF basis is also truncated. Our results show that, for a triple-zeta basis set, about 60% of the virtual MOs can be dropped, while the size of the fitting basis can be reduced by a factor of five. This results in a dramatic reduction of the computational costs of the solution of the CC2 equations, which are in our approach about as expensive as the evaluation of the MP2 and CIS(D) density matrices. All in all, an average speedup of more than an order of magnitude can be achieved at the expense of a mean absolute error of 0.02 eV in the calculated excitation energies compared to the canonical CC2 results. Our benchmark calculations demonstrate that the new approach enables the efficient computation of CC2 excitation energies for excited states of all types of medium-sized molecules composed of up to 100 atoms with triple-zeta quality basis sets. PMID:28527453

Comparison of some dispersion-corrected and traditional functionals with CCSD(T) and MP2 ab initio methods: Dispersion, induction, and basis set superposition error

NASA Astrophysics Data System (ADS)

Roy, Dipankar; Marianski, Mateusz; Maitra, Neepa T.; Dannenberg, J. J.

2012-10-01

We compare dispersion and induction interactions for noble gas dimers and for Ne, methane, and 2-butyne with HF and LiF using a variety of functionals (including some specifically parameterized to evaluate dispersion interactions) with ab initio methods including CCSD(T) and MP2. We see that inductive interactions tend to enhance dispersion and may be accompanied by charge-transfer. We show that the functionals do not generally follow the expected trends in interaction energies, basis set superposition errors (BSSE), and interaction distances as a function of basis set size. The functionals parameterized to treat dispersion interactions often overestimate these interactions, sometimes by quite a lot, when compared to higher level calculations. Which functionals work best depends upon the examples chosen. The B3LYP and X3LYP functionals, which do not describe pure dispersion interactions, appear to describe dispersion mixed with induction about as accurately as those parametrized to treat dispersion. We observed significant differences in high-level wavefunction calculations in a basis set larger than those used to generate the structures in many of the databases. We discuss the implications for highly parameterized functionals based on these databases, as well as the use of simple potential energy for fitting the parameters rather than experimentally determinable thermodynamic state functions that involve consideration of vibrational states.

Comparison of some dispersion-corrected and traditional functionals with CCSD(T) and MP2 ab initio methods: dispersion, induction, and basis set superposition error.

PubMed

Roy, Dipankar; Marianski, Mateusz; Maitra, Neepa T; Dannenberg, J J

2012-10-07

We compare dispersion and induction interactions for noble gas dimers and for Ne, methane, and 2-butyne with HF and LiF using a variety of functionals (including some specifically parameterized to evaluate dispersion interactions) with ab initio methods including CCSD(T) and MP2. We see that inductive interactions tend to enhance dispersion and may be accompanied by charge-transfer. We show that the functionals do not generally follow the expected trends in interaction energies, basis set superposition errors (BSSE), and interaction distances as a function of basis set size. The functionals parameterized to treat dispersion interactions often overestimate these interactions, sometimes by quite a lot, when compared to higher level calculations. Which functionals work best depends upon the examples chosen. The B3LYP and X3LYP functionals, which do not describe pure dispersion interactions, appear to describe dispersion mixed with induction about as accurately as those parametrized to treat dispersion. We observed significant differences in high-level wavefunction calculations in a basis set larger than those used to generate the structures in many of the databases. We discuss the implications for highly parameterized functionals based on these databases, as well as the use of simple potential energy for fitting the parameters rather than experimentally determinable thermodynamic state functions that involve consideration of vibrational states.

Comparison of some dispersion-corrected and traditional functionals with CCSD(T) and MP2 ab initio methods: Dispersion, induction, and basis set superposition error

PubMed Central

Roy, Dipankar; Marianski, Mateusz; Maitra, Neepa T.; Dannenberg, J. J.

2012-01-01

We compare dispersion and induction interactions for noble gas dimers and for Ne, methane, and 2-butyne with HF and LiF using a variety of functionals (including some specifically parameterized to evaluate dispersion interactions) with ab initio methods including CCSD(T) and MP2. We see that inductive interactions tend to enhance dispersion and may be accompanied by charge-transfer. We show that the functionals do not generally follow the expected trends in interaction energies, basis set superposition errors (BSSE), and interaction distances as a function of basis set size. The functionals parameterized to treat dispersion interactions often overestimate these interactions, sometimes by quite a lot, when compared to higher level calculations. Which functionals work best depends upon the examples chosen. The B3LYP and X3LYP functionals, which do not describe pure dispersion interactions, appear to describe dispersion mixed with induction about as accurately as those parametrized to treat dispersion. We observed significant differences in high-level wavefunction calculations in a basis set larger than those used to generate the structures in many of the databases. We discuss the implications for highly parameterized functionals based on these databases, as well as the use of simple potential energy for fitting the parameters rather than experimentally determinable thermodynamic state functions that involve consideration of vibrational states. PMID:23039587

Error assessment in molecular dynamics trajectories using computed NMR chemical shifts.

PubMed

Koes, David R; Vries, John K

2017-01-01

Accurate chemical shifts for the atoms in molecular mechanics (MD) trajectories can be obtained from quantum mechanical (QM) calculations that depend solely on the coordinates of the atoms in the localized regions surrounding atoms of interest. If these coordinates are correct and the sample size is adequate, the ensemble average of these chemical shifts should be equal to the chemical shifts obtained from NMR spectroscopy. If this is not the case, the coordinates must be incorrect. We have utilized this fact to quantify the errors associated with the backbone atoms in MD simulations of proteins. A library of regional conformers containing 169,499 members was constructed from 6 model proteins. The chemical shifts associated with the backbone atoms in each of these conformers was obtained from QM calculations using density functional theory at the B3LYP level with a 6-311+G(2d,p) basis set. Chemical shifts were assigned to each backbone atom in each MD simulation frame using a template matching approach. The ensemble average of these chemical shifts was compared to chemical shifts from NMR spectroscopy. A large systematic error was identified that affected the 1 H atoms of the peptide bonds involved in hydrogen bonding with water molecules or peptide backbone atoms. This error was highly sensitive to changes in electrostatic parameters. Smaller errors affecting the 13 C a and 15 N atoms were also detected. We believe these errors could be useful as metrics for comparing the force-fields and parameter sets used in MD simulation because they are directly tied to errors in atomic coordinates.

A genome-wide study of common SNPs and CNVs in cognitive performance in the CANTAB

PubMed Central

Need, Anna C.; Attix, Deborah K.; McEvoy, Jill M.; Cirulli, Elizabeth T.; Linney, Kristen L.; Hunt, Priscilla; Ge, Dongliang; Heinzen, Erin L.; Maia, Jessica M.; Shianna, Kevin V.; Weale, Michael E.; Cherkas, Lynn F.; Clement, Gail; Spector, Tim D.; Gibson, Greg; Goldstein, David B.

2009-01-01

Psychiatric disorders such as schizophrenia are commonly accompanied by cognitive impairments that are treatment resistant and crucial to functional outcome. There has been great interest in studying cognitive measures as endophenotypes for psychiatric disorders, with the hope that their genetic basis will be clearer. To investigate this, we performed a genome-wide association study involving 11 cognitive phenotypes from the Cambridge Neuropsychological Test Automated Battery. We showed these measures to be heritable by comparing the correlation in 100 monozygotic and 100 dizygotic twin pairs. The full battery was tested in ∼750 subjects, and for spatial and verbal recognition memory, we investigated a further 500 individuals to search for smaller genetic effects. We were unable to find any genome-wide significant associations with either SNPs or common copy number variants. Nor could we formally replicate any polymorphism that has been previously associated with cognition, although we found a weak signal of lower than expected P-values for variants in a set of 10 candidate genes. We additionally investigated SNPs in genomic loci that have been shown to harbor rare variants that associate with neuropsychiatric disorders, to see if they showed any suggestion of association when considered as a separate set. Only NRXN1 showed evidence of significant association with cognition. These results suggest that common genetic variation does not strongly influence cognition in healthy subjects and that cognitive measures do not represent a more tractable genetic trait than clinical endpoints such as schizophrenia. We discuss a possible role for rare variation in cognitive genomics. PMID:19734545

A genome-wide study of common SNPs and CNVs in cognitive performance in the CANTAB.

PubMed

Need, Anna C; Attix, Deborah K; McEvoy, Jill M; Cirulli, Elizabeth T; Linney, Kristen L; Hunt, Priscilla; Ge, Dongliang; Heinzen, Erin L; Maia, Jessica M; Shianna, Kevin V; Weale, Michael E; Cherkas, Lynn F; Clement, Gail; Spector, Tim D; Gibson, Greg; Goldstein, David B

2009-12-01

Psychiatric disorders such as schizophrenia are commonly accompanied by cognitive impairments that are treatment resistant and crucial to functional outcome. There has been great interest in studying cognitive measures as endophenotypes for psychiatric disorders, with the hope that their genetic basis will be clearer. To investigate this, we performed a genome-wide association study involving 11 cognitive phenotypes from the Cambridge Neuropsychological Test Automated Battery. We showed these measures to be heritable by comparing the correlation in 100 monozygotic and 100 dizygotic twin pairs. The full battery was tested in approximately 750 subjects, and for spatial and verbal recognition memory, we investigated a further 500 individuals to search for smaller genetic effects. We were unable to find any genome-wide significant associations with either SNPs or common copy number variants. Nor could we formally replicate any polymorphism that has been previously associated with cognition, although we found a weak signal of lower than expected P-values for variants in a set of 10 candidate genes. We additionally investigated SNPs in genomic loci that have been shown to harbor rare variants that associate with neuropsychiatric disorders, to see if they showed any suggestion of association when considered as a separate set. Only NRXN1 showed evidence of significant association with cognition. These results suggest that common genetic variation does not strongly influence cognition in healthy subjects and that cognitive measures do not represent a more tractable genetic trait than clinical endpoints such as schizophrenia. We discuss a possible role for rare variation in cognitive genomics.

Monitoring and forecasting of great radiation hazards for spacecraft and aircrafts by online cosmic ray data

NASA Astrophysics Data System (ADS)

Dorman, L. I.

2005-11-01

We show that an exact forecast of great radiation hazard in space, in the magnetosphere, in the atmosphere and on the ground can be made by using high-energy particles (few GeV/nucleon and higher) whose transportation from the Sun is characterized by a much bigger diffusion coefficient than for small and middle energy particles. Therefore, high energy particles come from the Sun much earlier (8-20 min after acceleration and escaping into solar wind) than the main part of smaller energy particles (more than 30-60 min later), causing radiation hazard for electronics and personal health, as well as spacecraft and aircrafts. We describe here principles of an automatic set of programs that begin with "FEP-Search", used to determine the beginning of a large FEP event. After a positive signal from "FEP-Search", the following programs start working: "FEP-Research/Spectrum", and then "FEP-Research/Time of Ejection", "FEP-Research /Source" and "FEP-Research/Diffusion", which online determine properties of FEP generation and propagation. On the basis of the obtained information, the next set of programs immediately start to work: "FEP-Forecasting/Spacecrafts", "FEP-Forecasting/Aircrafts", "FEP-Forecasting/Ground", which determine the expected differential and integral fluxes and total fluency for spacecraft on different orbits, aircrafts on different airlines, and on the ground, depending on altitude and cutoff rigidity. If the level of radiation hazard is expected to be dangerous for high level technology or/and personal health, the following programs will be used "FEP-Alert/Spacecrafts", "FEP-Alert/ Aircrafts", "FEP-Alert/Ground".

Quantum properties of light emitted by dipole nano-laser

NASA Astrophysics Data System (ADS)

Ghannam, Talal

Recent technological advances allow entire optical systems to be lithographically implanted on small silicon chips. These systems include tiny semiconductor lasers that function as light sources for digital optical signals. Future advances will rely on even smaller components. At the theoretical limit of this process, the smallest lasers will have an active medium consisting of a single atom (natural or artificial). Several suggestions for how this can be accomplished have already been published, such as nano-lasers based on photonic crystals and nano wires. In particular, the "dipole nanolaser" consists of a single quantum dot functioning as the active medium. It is optically coupled to a metal nanoparticles that form a resonant cavity. Laser light is generated from the near-field optical signal. The proposed work is a theoretical exploration of the nature of the resulting laser light. The dynamics of the system will be studied and relevant time scales described. These will form the basis for a set of operator equations describing the quantum properties of the emitted light. The dynamics will be studied in both density matrix and quantum Langevin formulations, with attention directed to noise sources. The equations will be linearized and solved using standard techniques. The result of the study will be a set of predicted noise spectra describing the statistics of the emitted light. The goal will be to identify the major noise contributions and suggest methods for suppressing them. This will be done by studying the probability of getting squeezed light from the nanoparticle for the certain scheme of parameters.

How many cents on the dollar? Women and men in product markets.

PubMed

Kricheli-Katz, Tamar; Regev, Tali

2016-02-01

Gender inequality in contemporary U.S. society is a well-documented, widespread phenomenon. However, little is known about gender disparities in product markets. This study is the first to use actual market data to study the behavior of women and men as sellers and buyers and differences in market outcomes. We analyze a unique and large data set containing all eBay auction transactions of most popular products by private sellers between the years 2009 and 2012. Women sellers received a smaller number of bids and lower final prices than did equally qualified men sellers of the exact same product. On average, women sellers received about 80 cents for every dollar a man received when selling the identical new product and 97 cents when selling the same used product. These findings held even after controlling for the sentiments that appear in the text of the sellers' listings. Nonetheless, it is worth noting that this gap varied by the type of the product being sold. As a policy, eBay does not reveal the gender of users. We attribute the price differences to the ability of buyers to discern the gender of the seller. We present results from an experiment that shows that people accurately identify the gender of sellers on the basis of typical information provided in postings. We supplement the analysis with an additional off-eBay experiment showing that, in a controlled setting, people are willing to pay less for money-value gift cards when they are sold by women rather than men.

Engineered protein scaffolds as next-generation antibody therapeutics.

PubMed

Gebauer, Michaela; Skerra, Arne

2009-06-01

Antibodies have been the paradigm of binding proteins with desired specificities for more than one century and during the past decade their recombinant or humanized versions have entered clinical application with remarkable success. Meanwhile, a new generation of receptor proteins was born, which is derived from small and robust non-immunoglobulin "scaffolds" that can be equipped with prescribed binding functions using the methods of combinatorial protein design. Their ongoing development does not only provide valuable insights into the principles of molecular recognition and protein structure-function relationships but also yields novel reagents for medical use. This technology goes hand in hand with our expanding knowledge about the molecular pathologies of cancer, immunological, and infectious diseases. Currently, questions regarding the choice of suitable medically relevant targets with regard to a certain protein scaffold, the methodology for engineering high affinity, arming with effector functions, routes of administration, plasma half-life, and immunogenicity are in the focus. While many protein scaffolds have been proposed during the past years, the technology shows a trend toward consolidation with a smaller set of systems that are being applied against multiple targets and in different settings, with emphasis on the development of drug candidates for therapy or in vivo diagnostics: Adnectins, Affibodies, Anticalins, DARPins, and engineered Kunitz-type inhibitors, among others. Only few data from early clinical studies are available yet, but many more are likely to come in the near future, thus providing a growing basis for assessing the therapeutic potential--but possibly also some limitations--of this exciting new class of protein drugs.

New View on Quiet-Sun Photospheric Dynamics Offered by NST Data

NASA Astrophysics Data System (ADS)

Abramenko, Valentyna; Yurchyshyn, V.; Goode, P. R.

2011-05-01

Recent observations of the quiet sun photosphere obtained with the 1.6 meter New Solar telescope (NST) of Big Bear Solar observatory (BBSO) delivered new information about photospheric fine structures and their dynamics, as well as posing new questions. The 2-hour uninterrupted data set of solar granulation obtained under excellent seeing conditions on August 3, 2010 (with cadence of 10 sec) was the basis for the study. Statistical analysis of automatically detected and tracked magnetic bright points (MBPs) showed that the MBPs population monotonically increases as their size decreases, down to 60-70 km. Our analysis shows that if the smallest magnetic flux tubes exist, their size is still smaller that 60-70 km, which impose strong restrictions on the modeling of these structures. We also found that the distributions of the MBP's size and lifetime do not follow a traditional Gaussian distribution, typical for random processes. Instead, it follows a log-normal distribution, typical for avalanches, catastrophes, stock market data, etc. Our data set also demonstrated that a majority (98.6 %) of MBPs are short live (<2 min). This remarkable fact was not obvious from previous studies because an extremely high time cadence was required. The fact indicates that the majority of MBPs appear for a very short time (tens of seconds), similar to other transient features, for example, chromospheric jets. The most important point here is that these small and short living MBPs significantly increase dynamics (flux emergence, collapse into MBPs, and magnetic flux recycling) of the solar surface magnetic fields.

How many cents on the dollar? Women and men in product markets

PubMed Central

Kricheli-Katz, Tamar; Regev, Tali

2016-01-01

Gender inequality in contemporary U.S. society is a well-documented, widespread phenomenon. However, little is known about gender disparities in product markets. This study is the first to use actual market data to study the behavior of women and men as sellers and buyers and differences in market outcomes. We analyze a unique and large data set containing all eBay auction transactions of most popular products by private sellers between the years 2009 and 2012. Women sellers received a smaller number of bids and lower final prices than did equally qualified men sellers of the exact same product. On average, women sellers received about 80 cents for every dollar a man received when selling the identical new product and 97 cents when selling the same used product. These findings held even after controlling for the sentiments that appear in the text of the sellers’ listings. Nonetheless, it is worth noting that this gap varied by the type of the product being sold. As a policy, eBay does not reveal the gender of users. We attribute the price differences to the ability of buyers to discern the gender of the seller. We present results from an experiment that shows that people accurately identify the gender of sellers on the basis of typical information provided in postings. We supplement the analysis with an additional off-eBay experiment showing that, in a controlled setting, people are willing to pay less for money-value gift cards when they are sold by women rather than men. PMID:26989770

Scaling fixed-field alternating gradient accelerators with a small orbit excursion.

PubMed

Machida, Shinji

2009-10-16

A novel scaling type of fixed-field alternating gradient (FFAG) accelerator is proposed that solves the major problems of conventional scaling and nonscaling types. This scaling FFAG accelerator can achieve a much smaller orbit excursion by taking a larger field index k. A triplet focusing structure makes it possible to set the operating point in the second stability region of Hill's equation with a reasonable sensitivity to various errors. The orbit excursion is about 5 times smaller than in a conventional scaling FFAG accelerator and the beam size growth due to typical errors is at most 10%.

Morphological Characteristics of Round Window Niche in Congenital Aural Atresia and Stenosis Patients.

PubMed

Chen, Keguang; Lyu, Huiying; Xie, Youzhou; Yang, Lin; Zhang, Tianyu; Dai, Peidong

2015-01-01

The aim of this study was to measure the round window niche (RWN) among congenital aural atresia (CAA), congenital aural stenosis (CAS) and control groups and to analyze whether differences exist between them. Computed tomography images of 10 normal subjects (20 ears), 27 CAS patients (30 ears) and 25 CAA patients (30 ears) were analyzed. We measured RWN on the basis of 3-dimensional reconstruction. The anterior wall length and the depth of RWN were smaller in control group than those in the CAS group; furthermore, the anterior wall length and the depth of RWN in CAS group were smaller than those in CAA group (P < 0.05). The posterior wall length of RWN was found smaller in the control group than that in both hCAS and CAA groups (P < 0.05). The superior and inferior wall lengths of RWN were found smaller in control group than those in the CAA group (P < 0.05). There were no statistically significant differences in the sizes of the round window membrane and niche opening or the angle between the plane of the RWN opening and the round window membrane plane among all groups. The RWN walls lengths and its depth tended to be longer with the aggravation of the aural malformations. Our calculation results may provide some information for a better design and a safer implantation of the floating mass transducer in the area of RWN.

Satellite Lesions in Congenital Melanocytic Nevi—Time for a Change of Name

PubMed Central

KINSLER, VERONICA

2011-01-01

Abstract The term “satellite lesions” is used in many conditions in dermatology, generally to describe smaller lesions near the edges of a principal lesion. An online medical dictionary gives the definition “a smaller lesion accompanying a main one and situated nearby,” and this can apply both macroscopically and microscopically. The implication is that the smaller lesions have spread from the parent lesion. Given this definition and usual understanding of the term its use is not apt in the case of congenital melanocytic nevi (CMN). In the vast majority of cases where the patient is said to have satellite lesions these are not restricted to the area around or near the edge of the principal lesion, and are not necessarily significantly smaller. It seems likely that the early use of the term in this condition is an adaptation of the established and correct use in the context of melanoma. Not only is the term not apt clinically but has no known etiological basis. This leaves us with the question of what to call these lesions in cases of CMN. This proposal is to categorise cases into single or multiple CMN, where multiple is 2 or more nevi of any size at birth. An accurate count or good estimate of the number of lesions at birth should also be recorded, and the largest lesion classified as usual with respect to projected adult size. PMID:21418289

Structural ordering of casein micelles on silicon nitride micro-sieves during filtration.

PubMed

Gebhardt, Ronald; Holzmüller, Wolfgang; Zhong, Qi; Müller-Buschbaum, Peter; Kulozik, Ulrich

2011-11-01

The paper reports on the structure and formation of casein micelle deposits on silicon nitride micro-sieves during the frontal filtration. The most frequent radius of the fractionated casein micelles we use is R=60 nm as detected by static light scattering (SLS) and atomic force microscopy (AFM). We estimate the size and size distribution of the casein micelles which pass through the micro-sieve during the filtration process. A sharpening of the size distribution at the beginning of the filtration process (t=40s) is followed by a broadening and a shift of the most frequent radii towards smaller sizes at later times (t=840 s). The size distribution of the micelles deposited on the micro-sieve during filtration is bimodal and consists of the largest and smallest micelles. At larger filtration times, we observe a shift of both deposited size classes towards smaller sizes. The atomic force micrographs of the reference sample reveal a tendency of the casein micelles to order in a hexagonal lattice when deposited on the micro-sieves by solution casting. The deposition of two size classes can be explained by a formation of a mixed hexagonal lattice with large micelles building up the basis lattice and smaller sizes filling octahedral and tetrahedral holes of the lattice. The accompanied compression with increasing thickness of the casein layer could result from preferential deposition of smaller sizes in the course of the filtration. Copyright © 2011 Elsevier B.V. All rights reserved.

Estimation of Δ R/ R values by benchmark study of the Mössbauer Isomer shifts for Ru, Os complexes using relativistic DFT calculations

NASA Astrophysics Data System (ADS)

Kaneko, Masashi; Yasuhara, Hiroki; Miyashita, Sunao; Nakashima, Satoru

2017-11-01

The present study applies all-electron relativistic DFT calculation with Douglas-Kroll-Hess (DKH) Hamiltonian to each ten sets of Ru and Os compounds. We perform the benchmark investigation of three density functionals (BP86, B3LYP and B2PLYP) using segmented all-electron relativistically contracted (SARC) basis set with the experimental Mössbauer isomer shifts for 99Ru and 189Os nuclides. Geometry optimizations at BP86 theory of level locate the structure in a local minimum. We calculate the contact density to the wavefunction obtained by a single point calculation. All functionals show the good linear correlation with experimental isomer shifts for both 99Ru and 189Os. Especially, B3LYP functional gives a stronger correlation compared to BP86 and B2PLYP functionals. The comparison of contact density between SARC and well-tempered basis set (WTBS) indicated that the numerical convergence of contact density cannot be obtained, but the reproducibility is less sensitive to the choice of basis set. We also estimate the values of Δ R/ R, which is an important nuclear constant, for 99Ru and 189Os nuclides by using the benchmark results. The sign of the calculated Δ R/ R values is consistent with the predicted data for 99Ru and 189Os. We obtain computationally the Δ R/ R values of 99Ru and 189Os (36.2 keV) as 2.35×10-4 and -0.20×10-4, respectively, at B3LYP level for SARC basis set.

Quantum-chemical study of model chemisorption structures on copper-containing catalysts. Communicat ion 1. ab-initio calculations of CuCo and CuCo/sup +/

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kuzminskii, M.B.; Bagator'yants, A.A.; Kazanskii, V.B.

1986-08-01

The authors perform ab-initio calculations, by the SCF MO LCAO method, of the electronic and geometric structure of the systems CuCO /SUP n+/ (n=0, 1) and potential curves of CO, depending on the charge state of the copper, with variation of all geometric parameters. The calculations of open-shell electronic states were performed by the unrestricted SCF method in a minimal basis set (I, STO-3G for the C and O, and MINI-1' for the Cu) and in a valence two-exponential basis set (II, MIDI-1 for the C and O, and MIDI'2' for the Cu). The principal results from the calculation inmore » the more flexible basis II are presented and the agreement between the results obtained in the minimal basis I and these data is then analyzed qualitatively.« less

Application of ab initio many-body perturbation theory with Gaussian basis sets to the singlet and triplet excitations of organic molecules

NASA Astrophysics Data System (ADS)

Hamed, Samia; Rangel, Tonatiuh; Bruneval, Fabien; Neaton, Jeffrey B.

Quantitative understanding of charged and neutral excitations of organic molecules is critical in diverse areas of study that include astrophysics and the development of energy technologies that are clean and efficient. The recent use of local basis sets with ab initio many-body perturbation theory in the GW approximation and the Bethe-Saltpeter equation approach (BSE), methods traditionally applied to periodic condensed phases with a plane-wave basis, has opened the door to detailed study of such excitations for molecules, as well as accurate numerical benchmarks. Here, through a series of systematic benchmarks with a Gaussian basis, we report on the extent to which the predictive power and utility of this approach depend critically on interdependent underlying approximations and choices for molecules, including the mean-field starting point (eg optimally-tuned range separated hybrids, pure DFT functionals, and untuned hybrids), the GW scheme, and the Tamm Dancoff approximation. We demonstrate the effects of these choices in the context of Thiels' set while drawing analogies to linear-response time-dependent DFT and making comparisons to best theoretical estimates from higher-order wavefunction-based theories.

Improved flow cytometer measurement of binding assays

NASA Astrophysics Data System (ADS)

Saunders, G. C.

1984-05-01

A method of measuring binding assays is carried out with different size particles wherein the binding assay sample is run through a flow cytometer without separating the sample from the marking agent. The amount of a binding reactant present in a sample is determined by providing particles with a coating of binder and also known quantity of smaller particles with a coating of binder reactant. The smaller particles also contain a fluorescent chemical. The particles are combined with the sample and the binding reaction is allowed to occur for a set length of time followed by combining the smaller particles with the mixture of the particles and the sample produced and allowing the binding reactions to proceed to equilibrium. The fluorescence and light scatter of the combined mixture is then measured as the combined mixture passes through a flow cytometer equipped with a laser to bring about fluorescence, and the number of fluorescent events are compared. A similar method is also provided for determining the amount of antigen present in the sample by providing spheres with an antibody coating and some smaller spheres with an antigen coating.

Electronic Structure and Bonding in Transition Metal Inorganic and Organometallic Complexes: New Basis Sets, Linear Semibridging Carbonyls and Thiocarbonyls, and Oxidative Addition of Molecular Hydrogen to Square - Iridium Complexes.

NASA Astrophysics Data System (ADS)

Sargent, Andrew Landman

Approximate molecular orbital and ab initio quantum chemical techniques are used to investigate the electronic structure, bonding and reactivity of several transition metal inorganic and organometallic complexes. Modest-sized basis sets are developed for the second-row transition metal atoms and are designed for use in geometry optimizations of inorganic and organometallic complexes incorporating these atoms. The basis sets produce optimized equilibrium geometries which are slightly better than those produced with standard 3-21G basis sets, and which are significantly better than those produced with effective core potential basis sets. Linear semibridging carbonyl ligands in heterobimetallic complexes which contain a coordinatively unsaturated late transition metal center are found to accept electron density from, rather than donate electron density to, these centers. Only when the secondary metal center is a coordinatively unsaturated early transition metal center does the semibridging ligand donate electron density to this center. Large holes in the d shell around the metal center are more prominent and prevalent in early than in late transition metal centers, and the importance of filling in these holes outweighs the importance of mitigating the charge imbalance due to the dative metal-metal interaction. Semibridging thiocarbonyl ligands are more effective donors of electron density than the carbonyl ligands since the occupied donor orbitals of pi symmetry are higher in energy. The stereoselectivity of H_2 addition to d^8 square-planar transition metal complexes is controlled by the interactions between the ligands in the plane of addition and the concentrations of electronic charge around the metal center as the complex evolves from a four-coordinate to a six-coordinate species. Electron -withdrawing ligands help stabilize the five-coordinate species while strong electron donor ligands contribute only to the destabilizing repulsive interactions. The relative thermodynamic stabilities of the final complexes can be predicted based on the relative orientations of the strongest sigma-donor ligands.

Carbon-Hydrogen Bond Activation in Hydridotris(pyrazolyl)borate Platinum(IV) Complexes:  Comparison of Density Functionals, Basis Sets, and Bonding Patterns.

PubMed

Vastine, Benjamin Alan; Webster, Charles Edwin; Hall, Michael B

2007-11-01

The reaction mechanism for the cycle beginning with the reductive elimination (RE) of methane from κ(3)-TpPt(IV)(CH3)2H (1) (Tp = hydridotris(pyrazolyl)borate) and subsequent oxidative addition (OA) of benzene to form finally κ(3)-TpPt(IV)(Ph)2H (19) was investigated by density functional theory (DFT). Two mechanistic steps are of particular interest, namely the barrier to C-H coupling (barrier 1 - Ba1) and the barrier to methane release (barrier 2 - Ba2). For 31 density functionals, the calculated values for Ba1 and Ba2 were benchmarked against the experimentally reported values of 26 (Ba1) and 35 (Ba2) kcal·mol(-1), respectively. Specifically, the values for Ba1 and Ba2, calculated at the B3LYP/double-ζ plus polarization level of theory, are 24.6 and 34.3 kcal·mol(-1), respectively. Overall, the best performing functional was BPW91 where the mae associated with the calculated values of the two barriers is 0.68 kcal·mol(-1). The calculated B3LYP values of Ba1 ranged between 20 and 26 kcal·mol(-1) for 12 effective core potential basis sets for platinum and 29 all-electron basis sets for the first row elements. Polarization functions for the first row elements were important for accurate values, but the addition of diffuse functions to non-hydrogen (+) and hydrogen atoms (++) had little effect on the calculated values. Basis set saturation was achieved with APNO basis sets utilized for first-row atoms. Bader's "Atoms in Molecules" was used to analyze the electron density of several complexes, and the electron density at the Pt-Nax bond critical point (trans to the active site for C-H coupling) varied over a wider range than any of the other Pt-N bonds.

Correlation consistent basis sets for lanthanides: The atoms La–Lu

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lu, Qing; Peterson, Kirk A., E-mail: kipeters@wsu.edu

Using the 3rd-order Douglas-Kroll-Hess (DKH3) Hamiltonian, all-electron correlation consistent basis sets of double-, triple-, and quadruple-zeta quality have been developed for the lanthanide elements La through Lu. Basis sets designed for the recovery of valence correlation (defined here as 4f5s5p5d6s), cc-pVnZ-DK3, and outer-core correlation (valence + 4s4p4d), cc-pwCVnZ-DK3, are reported (n = D, T, and Q). Systematic convergence of both Hartree-Fock and correlation energies towards their respective complete basis set (CBS) limits are observed. Benchmark calculations of the first three ionization potentials (IPs) of La through Lu are reported at the DKH3 coupled cluster singles and doubles with perturbative triples,more » CCSD(T), level of theory, including effects of correlation down through the 4s electrons. Spin-orbit coupling is treated at the 2-component HF level. After extrapolation to the CBS limit, the average errors with respect to experiment were just 0.52, 1.14, and 4.24 kcal/mol for the 1st, 2nd, and 3rd IPs, respectively, compared to the average experimental uncertainties of 0.03, 1.78, and 2.65 kcal/mol, respectively. The new basis sets are also used in CCSD(T) benchmark calculations of the equilibrium geometries, atomization energies, and heats of formation for Gd{sub 2}, GdF, and GdF{sub 3}. Except for the equilibrium geometry and harmonic frequency of GdF, which are accurately known from experiment, all other calculated quantities represent significant improvements compared to the existing experimental quantities. With estimated uncertainties of about ±3 kcal/mol, the 0 K atomization energies (298 K heats of formation) are calculated to be (all in kcal/mol): 33.2 (160.1) for Gd{sub 2}, 151.7 (−36.6) for GdF, and 447.1 (−295.2) for GdF{sub 3}.« less

The sensitivity of the Arctic sea ice to orbitally induced insolation changes: a study of the mid-Holocene Paleoclimate Modelling Intercomparison Project 2 and 3 simulations

NASA Astrophysics Data System (ADS)

Berger, M.; Brandefelt, J.; Nilsson, J.

2013-04-01

In the present work the Arctic sea ice in the mid-Holocene and the pre-industrial climates are analysed and compared on the basis of climate-model results from the Paleoclimate Modelling Intercomparison Project phase 2 (PMIP2) and phase 3 (PMIP3). The PMIP3 models generally simulate smaller and thinner sea-ice extents than the PMIP2 models both for the pre-industrial and the mid-Holocene climate. Further, the PMIP2 and PMIP3 models all simulate a smaller and thinner Arctic summer sea-ice cover in the mid-Holocene than in the pre-industrial control climate. The PMIP3 models also simulate thinner winter sea ice than the PMIP2 models. The winter sea-ice extent response, i.e. the difference between the mid-Holocene and the pre-industrial climate, varies among both PMIP2 and PMIP3 models. Approximately one half of the models simulate a decrease in winter sea-ice extent and one half simulates an increase. The model-mean summer sea-ice extent is 11 % (21 %) smaller in the mid-Holocene than in the pre-industrial climate simulations in the PMIP2 (PMIP3). In accordance with the simple model of Thorndike (1992), the sea-ice thickness response to the insolation change from the pre-industrial to the mid-Holocene is stronger in models with thicker ice in the pre-industrial climate simulation. Further, the analyses show that climate models for which the Arctic sea-ice responses to increasing atmospheric CO2 concentrations are similar may simulate rather different sea-ice responses to the change in solar forcing between the mid-Holocene and the pre-industrial. For two specific models, which are analysed in detail, this difference is found to be associated with differences in the simulated cloud fractions in the summer Arctic; in the model with a larger cloud fraction the effect of insolation change is muted. A sub-set of the mid-Holocene simulations in the PMIP ensemble exhibit open water off the north-eastern coast of Greenland in summer, which can provide a fetch for surface waves. This is in broad agreement with recent analyses of sea-ice proxies, indicating that beach-ridges formed on the north-eastern coast of Greenland during the early- to mid-Holocene.

A new species of Lonchophylla Thomas (Chiroptera: Phyllostomidae) from Ecuador

USGS Publications Warehouse

Albuja V., Luis; Gardner, Alfred L.

2005-01-01

We describe Lonchophylla orcesi, sp. nov., from the Choco, a region of high biotic diversity, endemism, and rainfall along the western Andean slopes and Pacific lowlands of Colombia and Ecuador. One of the largest known Lonchophylla, it occurs sympatrically with at least two other species of Lonchophylla including the similar, but somewhat smaller L. robusta. We also recognize L. concava as a Middle American Province species distinct from L. mordax of Brazil and Bolivia on the basis of cranial and dental features.

Current orbital debris environment

NASA Technical Reports Server (NTRS)

Kessler, Donald J.

1989-01-01

NASA has instituted a plan for the definition of activities and resources required over the coming decade for the deepening of current understanding of anthropogenic orbital debris, and its effects on future mission operations. This understanding will be the basis of policy definition and policy implementation efforts. The most immediate requirement is the definition of the debris environment, with emphasis on data for debris sizes smaller than 4 cm. Systems-damage criteria and hypervelocity-impact theory will then be used to define the hazard to specific spacecraft.

High symmetric 18-facet polyhedron nanocrystals of Cu7S4 with a hollow nanocage.

PubMed

Cao, Hongliang; Qian, Xuefeng; Wang, Cheng; Ma, Xiaodong; Yin, Jie; Zhu, Zikang

2005-11-23

On the basis of Kirkendall Effect, high symmetric 18-facet polyhedral nanocrystals of Cu7S4 with a hollow nanocage could be converted from cubic nanocrystals of Cu2O in an aqueous media. The presence of organic additives makes the surface energy of {110} smaller than those of {100} and {111}. The growth of nanocrystals along the normal direction of highest energy surface {100} leads to the formation of a 18-facet polyhedron.

Propulsion element requirements using electrical power system unscheduled power

NASA Technical Reports Server (NTRS)

Zimmermann, Frank; Hodge, Kathy

1989-01-01

The suitability of using the electrical energy from the Space Station's Electrical Power System (EPS) during the periods of peak solar insolation which is currently not specifically allocated (unscheduled power) to produce propulsion propellants, gaseous hydrogen, and oxygen by electrolyzing water is investigated. Reboost propellant requirements are emphasized, but the results are more generally relevant because the balance of recurring propellant requirements are an order of magnitude smaller and the nonrecurring requirements are not significant on an average basis.

Revision of the experimental electron affinity of BO

NASA Astrophysics Data System (ADS)

Rienstra, Jonathan C.; Schaefer, Henry F., III

1997-05-01

The experimental electron affinity of BO has proven questionable. We obtained the electron affinity of BO using the large aug-cc-pVQZ basis with SCF, CISD, CISD+Q, CCSD, and CCSD(T) methods and predict a value of 2.57 eV, or 0.55 eV smaller than the latest experimental value. The 2∑+ to 2Π excitation energy of BO has also been obtained with the CCSD(T) method and found to be 2.82 eV.

Space station orbit maintenance

NASA Technical Reports Server (NTRS)

Kaplan, D. I.; Jones, R. M.

1983-01-01

The orbit maintenance problem is examined for two low-earth-orbiting space station concepts - the large, manned Space Operations Center (SOC) and the smaller, unmanned Science and Applications Space Platform (SASP). Atmospheric drag forces are calculated, and circular orbit altitudes are selected to assure a 90 day decay period in the event of catastrophic propulsion system failure. Several thrusting strategies for orbit maintenance are discussed. Various chemical and electric propulsion systems for orbit maintenance are compared on the basis of propellant resupply requirements, power requirements, Shuttle launch costs, and technology readiness.

Evaluation of B3LYP, X3LYP, and M06-Class Density Functionals for Predicting the Binding Energies of Neutral, Protonated, and Deprotonated Water Clusters.

PubMed

Bryantsev, Vyacheslav S; Diallo, Mamadou S; van Duin, Adri C T; Goddard, William A

2009-04-14

In this paper we assess the accuracy of the B3LYP, X3LYP, and newly developed M06-L, M06-2X, and M06 functionals to predict the binding energies of neutral and charged water clusters including (H2O)n, n = 2-8, 20), H3O(+)(H2O)n, n = 1-6, and OH(-)(H2O)n, n = 1-6. We also compare the predicted energies of two ion hydration and neutralization reactions on the basis of the calculated binding energies. In all cases, we use as benchmarks calculated binding energies of water clusters extrapolated to the complete basis set limit of the second-order Møller-Plesset perturbation theory with the effects of higher order correlation estimated at the coupled-cluster theory with single, double, and perturbative triple excitations in the aug-cc-pVDZ basis set. We rank the accuracy of the functionals on the basis of the mean unsigned error (MUE) between calculated benchmark and density functional theory energies. The corresponding MUE (kcal/mol) for each functional is listed in parentheses. We find that M06-L (0.73) and M06 (0.84) give the most accurate binding energies using very extended basis sets such as aug-cc-pV5Z. For more affordable basis sets, the best methods for predicting the binding energies of water clusters are M06-L/aug-cc-pVTZ (1.24), B3LYP/6-311++G(2d,2p) (1.29), and M06/aug-cc-PVTZ (1.33). M06-L/aug-cc-pVTZ also gives more accurate energies for the neutralization reactions (1.38), whereas B3LYP/6-311++G(2d,2p) gives more accurate energies for the ion hydration reactions (1.69).

Set-Based Design: Fleet Architecture and Design 2030-2035

DTIC Science & Technology

2017-12-01

choose any quantity between 250 - 350 HP for the final system design without suffering the same consequences in PBD. Figure 2 visually compares SBD... comparing the coverages in 2035 to those in 2017. This report does not advocate for a larger or smaller domain grid factor for overall fleet design , as...Distribution is unlimited. SET-BASED DESIGN : FLEET ARCHITECTURE AND DESIGN 2030–2035 by David Alessandria, Isa Al-Jawder, Eric Clow, Carlos

Reinforcement Learning with Orthonormal Basis Adaptation Based on Activity-Oriented Index Allocation

NASA Astrophysics Data System (ADS)

Satoh, Hideki

An orthonormal basis adaptation method for function approximation was developed and applied to reinforcement learning with multi-dimensional continuous state space. First, a basis used for linear function approximation of a control function is set to an orthonormal basis. Next, basis elements with small activities are replaced with other candidate elements as learning progresses. As this replacement is repeated, the number of basis elements with large activities increases. Example chaos control problems for multiple logistic maps were solved, demonstrating that the method for adapting an orthonormal basis can modify a basis while holding the orthonormality in accordance with changes in the environment to improve the performance of reinforcement learning and to eliminate the adverse effects of redundant noisy states.

New separated polynomial solutions to the Zernike system on the unit disk and interbasis expansion.

PubMed

Pogosyan, George S; Wolf, Kurt Bernardo; Yakhno, Alexander

2017-10-01

The differential equation proposed by Frits Zernike to obtain a basis of polynomial orthogonal solutions on the unit disk to classify wavefront aberrations in circular pupils is shown to have a set of new orthonormal solution bases involving Legendre and Gegenbauer polynomials in nonorthogonal coordinates, close to Cartesian ones. We find the overlaps between the original Zernike basis and a representative of the new set, which turn out to be Clebsch-Gordan coefficients.

The Heats of Formation of GaCl3 and its Fragments

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W., Jr.; Arnold, James (Technical Monitor)

1998-01-01

The heats of formation of GaC13 and its fragments are computed. The geometries and frequencies are obtained at the B3LYP level. The CCSD(T) approach is used to solve the correlation problem. The effect of Ga 3d correlation is studied, and found to affect the bond energies by up to 1 kcal/mol. Both basis set extrapolation and bond functions are considered as ways to approach the basis set limit. Spin-orbit and scalar relativistic effects are also considered.

Fourier spatial frequency analysis for image classification: training the training set

NASA Astrophysics Data System (ADS)

Johnson, Timothy H.; Lhamo, Yigah; Shi, Lingyan; Alfano, Robert R.; Russell, Stewart

2016-04-01

The Directional Fourier Spatial Frequencies (DFSF) of a 2D image can identify similarity in spatial patterns within groups of related images. A Support Vector Machine (SVM) can then be used to classify images if the inter-image variance of the FSF in the training set is bounded. However, if variation in FSF increases with training set size, accuracy may decrease as the size of the training set increases. This calls for a method to identify a set of training images from among the originals that can form a vector basis for the entire class. Applying the Cauchy product method we extract the DFSF spectrum from radiographs of osteoporotic bone, and use it as a matched filter set to eliminate noise and image specific frequencies, and demonstrate that selection of a subset of superclassifiers from within a set of training images improves SVM accuracy. Central to this challenge is that the size of the search space can become computationally prohibitive for all but the smallest training sets. We are investigating methods to reduce the search space to identify an optimal subset of basis training images.

Correlation dimension of financial market

NASA Astrophysics Data System (ADS)

Nie, Chun-Xiao

2017-05-01

In this paper, correlation dimension is applied to financial data analysis. We calculate the correlation dimensions of some real market data and find that the dimensions are significantly smaller than those of the simulation data based on geometric Brownian motion. Based on the analysis of the Chinese and US stock market data, the main results are as follows. First, by calculating three data sets for the Chinese and US market, we find that large market volatility leads to a significant decrease in the dimensions. Second, based on 5-min stock price data, we find that the Chinese market dimension is significantly larger than the US market; this shows a significant difference between the two markets for high frequency data. Third, we randomly extract stocks from a stock set and calculate the correlation dimensions, and find that the average value of these dimensions is close to the dimension of the original set. In addition, we analyse the intuitional meaning of the relevant dimensions used in this paper, which are directly related to the average degree of the financial threshold network. The dimension measures the speed of the average degree that varies with the threshold value. A smaller dimension means that the rate of change is slower.

17 CFR 260.4d-7 - Application for exemption from one or more provisions of the Act.

Code of Federal Regulations, 2011 CFR

2011-04-01

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Code of Federal Regulations, 2013 CFR

2013-04-01

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Code of Federal Regulations, 2014 CFR

2014-04-01

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2010-04-01

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2012-04-01

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Determination of Calorific Ability of Fuel Briquettes on the Basis of Oil and Oil Slimes

NASA Astrophysics Data System (ADS)

Fedyaeva, O. A.; Poshelyuzhnaya, E. G.; Rakhmatulina, E. M.; Zakharov, V. A.; Fisenko, T. E.

2018-01-01

Utilization and neutralization of oil slimes is one of important environmental problems of the oil-extracting, oil-processing and petrochemical industry. The easiest and economic way of utilization of oil slimes is their use as a part of the bricketed boiler fuel. In this work the highest calorific ability of crude oil, the oil slimes and fuel briquettes made on their basis is defined. A research problem was carrying out the technical analysis of oil fuels on the content in them analytical moisture, the cindery rest and volatiles. It is established that in comparison with oil slimes crude oil possesses bigger highest calorific ability, has smaller humidity and an ash-content. The highest calorific abilities of the boiler briquettes made of samples of crude oil, oil slimes and peat made 14 - 26 MJ/kg.

Utilization of group theory in studies of molecular clusters

NASA Astrophysics Data System (ADS)

Ocak, Mahir E.

The structure of the molecular symmetry group of molecular clusters was analyzed and it is shown that the molecular symmetry group of a molecular cluster can be written as direct products and semidirect products of its subgroups. Symmetry adaptation of basis functions in direct product groups and semidirect product groups was considered in general and the sequential symmetry adaptation procedure which is already known for direct product groups was extended to the case of semidirect product groups. By using the sequential symmetry adaptation procedure a new method for calculating the VRT spectra of molecular clusters which is named as Monomer Basis Representation (MBR) method is developed. In the MBR method, calculations starts with a single monomer with the purpose of obtaining an optimized basis for that monomer as a linear combination of some primitive basis functions. Then, an optimized basis for each identical monomer is generated from the optimized basis of this monomer. By using the optimized bases of the monomers, a basis is generated generated for the solution of the full problem, and the VRT spectra of the cluster is obtained by using this basis. Since an optimized basis is used for each monomer which has a much smaller size than the primitive basis from which the optimized bases are generated, the MBR method leads to an exponential optimization in the size of the basis that is required for the calculations. Application of the MBR method has been illustrated by calculating the VRT spectra of water dimer by using the SAPT-5st potential surface of Groenenboom et al. The rest of the calculations are in good agreement with both the original calculations of Groenenboom et al. and also with the experimental results. Comparing the size of the optimized basis with the size of the primitive basis, it can be said that the method works efficiently. Because of its efficiency, the MBR method can be used for studies of clusters bigger than dimers. Thus, MBR method can be used for studying the many-body terms and for deriving accurate potential surfaces.

Response to “Comment on ‘Rethinking first-principles electron transport theories with projection operators: The problems caused by partitioning the basis set’” [J. Chem. Phys. 140, 177103 (2014)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Reuter, Matthew G., E-mail: mgreuter@u.northwestern.edu; Harrison, Robert J.

2014-05-07

The thesis of Brandbyge's comment [J. Chem. Phys. 140, 177103 (2014)] is that our operator decoupling condition is immaterial to transport theories, and it appeals to discussions of nonorthogonal basis sets in transport calculations in its arguments. We maintain that the operator condition is to be preferred over the usual matrix conditions and subsequently detail problems in the existing approaches. From this operator perspective, we conclude that nonorthogonal projectors cannot be used and that the projectors must be selected to satisfy the operator decoupling condition. Because these conclusions pertain to operators, the choice of basis set is not germane.

Spectral properties of minimal-basis-set orbitals: Implications for molecular electronic continuum states

NASA Astrophysics Data System (ADS)

Langhoff, P. W.; Winstead, C. L.

Early studies of the electronically excited states of molecules by John A. Pople and coworkers employing ab initio single-excitation configuration interaction (SECI) calculations helped to simulate related applications of these methods to the partial-channel photoionization cross sections of polyatomic molecules. The Gaussian representations of molecular orbitals adopted by Pople and coworkers can describe SECI continuum states when sufficiently large basis sets are employed. Minimal-basis virtual Fock orbitals stabilized in the continuous portions of such SECI spectra are generally associated with strong photoionization resonances. The spectral attributes of these resonance orbitals are illustrated here by revisiting previously reported experimental and theoretical studies of molecular formaldehyde (H2CO) in combination with recently calculated continuum orbital amplitudes.

Parameter and Structure Inference for Nonlinear Dynamical Systems

NASA Technical Reports Server (NTRS)

Morris, Robin D.; Smelyanskiy, Vadim N.; Millonas, Mark

2006-01-01

A great many systems can be modeled in the non-linear dynamical systems framework, as x = f(x) + xi(t), where f() is the potential function for the system, and xi is the excitation noise. Modeling the potential using a set of basis functions, we derive the posterior for the basis coefficients. A more challenging problem is to determine the set of basis functions that are required to model a particular system. We show that using the Bayesian Information Criteria (BIC) to rank models, and the beam search technique, that we can accurately determine the structure of simple non-linear dynamical system models, and the structure of the coupling between non-linear dynamical systems where the individual systems are known. This last case has important ecological applications.

The IPEA dilemma in CASPT2† †Electronic supplementary information (ESI) available: Original data (Table S1) and additional comments for the literature survey; note on symmetry (Table S2), geometries (Table S3), data (Tables S4–S6) and comments (Section S2) for calculations on di-/triatomic molecules; results (Tables S7–S25) and comments (Section S3) for calculations on the organic molecular data set. See DOI: 10.1039/c6sc03759c Click here for additional data file.

PubMed Central

Zobel, J. Patrick

2017-01-01

Multi-configurational second order perturbation theory (CASPT2) has become a very popular method for describing excited-state properties since its development in 1990. To account for systematic errors found in the calculation of dissociation energies, an empirical correction applied to the zeroth-order Hamiltonian, called the IPEA shift, was introduced in 2004. The errors were attributed to an unbalanced description of open-shell versus closed-shell electronic states and is believed to also lead to an underestimation of excitation energies. Here we show that the use of the IPEA shift is not justified and the IPEA should not be used to calculate excited states, at least for organic chromophores. This conclusion is the result of three extensive analyses. Firstly, we survey the literature for excitation energies of organic molecules that have been calculated with the unmodified CASPT2 method. We find that the excitation energies of 356 reference values are negligibly underestimated by 0.02 eV. This value is an order of magnitude smaller than the expected error based on the calculation of dissociation energies. Secondly, we perform benchmark full configuration interaction calculations on 137 states of 13 di- and triatomic molecules and compare the results with CASPT2. Also in this case, the excited states are underestimated by only 0.05 eV. Finally, we perform CASPT2 calculations with different IPEA shift values on 309 excited states of 28 organic small and medium-sized organic chromophores. We demonstrate that the size of the IPEA correction scales with the amount of dynamical correlation energy (and thus with the size of the system), and gets immoderate already for the molecules considered here, leading to an overestimation of the excitation energies. It is also found that the IPEA correction strongly depends on the size of the basis set. The dependency on both the size of the system and of the basis set, contradicts the idea of a universal IPEA shift which is able to compensate for systematic CASPT2 errors in the calculation of excited states. PMID:28572908

Hydrogen peroxide clusters: the role of open book motif in cage and helical structures.

PubMed

Elango, M; Parthasarathi, R; Subramanian, V; Ramachandran, C N; Sathyamurthy, N

2006-05-18

Hartree-Fock (HF) calculations using 6-31G*, 6-311++G(d,p), aug-cc-pVDZ, and aug-cc-pVTZ basis sets show that hydrogen peroxide molecular clusters tend to form hydrogen-bonded cyclic and cage structures along the lines expected of a molecule which can act as a proton donor as well as an acceptor. These results are reiterated by density functional theoretic (DFT) calculations with B3LYP parametrization and also by second-order Møller-Plesset perturbation (MP2) theory using 6-31G* and 6-311++G(d,p) basis sets. Trends in stabilization energies and geometrical parameters obtained at the HF level using 6-311++G(d,p), aug-cc-pVDZ, and aug-cc-pVTZ basis sets are similar to those obtained from HF/6-31G* calculation. In addition, the HF calculations suggest the formation of stable helical structures for larger clusters, provided the neighbors form an open book structure.

Performance of local orbital basis sets in the self-consistent Sternheimer method for dielectric matrices of extended systems

NASA Astrophysics Data System (ADS)

Hübener, H.; Pérez-Osorio, M. A.; Ordejón, P.; Giustino, F.

2012-09-01

We present a systematic study of the performance of numerical pseudo-atomic orbital basis sets in the calculation of dielectric matrices of extended systems using the self-consistent Sternheimer approach of [F. Giustino et al., Phys. Rev. B 81, 115105 (2010)]. In order to cover a range of systems, from more insulating to more metallic character, we discuss results for the three semiconductors diamond, silicon, and germanium. Dielectric matrices of silicon and diamond calculated using our method fall within 1% of reference planewaves calculations, demonstrating that this method is promising. We find that polarization orbitals are critical for achieving good agreement with planewaves calculations, and that only a few additional ζ's are required for obtaining converged results, provided the split norm is properly optimized. Our present work establishes the validity of local orbital basis sets and the self-consistent Sternheimer approach for the calculation of dielectric matrices in extended systems, and prepares the ground for future studies of electronic excitations using these methods.

Accurate ab initio binding energies of the benzene dimer.

PubMed

Park, Young Choon; Lee, Jae Shin

2006-04-20

Accurate binding energies of the benzene dimer at the T and parallel displaced (PD) configurations were determined using the single- and double-coupled cluster method with perturbative triple correction (CCSD(T)) with correlation-consistent basis sets and an effective basis set extrapolation scheme recently devised. The difference between the estimated CCSD(T) basis set limit electronic binding energies for the T and PD shapes appears to amount to more than 0.3 kcal/mol, indicating the PD shape is a more stable configuration than the T shape for this dimer in the gas phase. This conclusion is further strengthened when a vibrational zero-point correction to the electronic binding energies of this dimer is made, which increases the difference between the two configurations to 0.4-0.5 kcal/mol. The binding energies of 2.4 and 2.8 kcal/mol for the T and PD configurations are in good accord with the previous experimental result from ionization potential measurement.

Small Atomic Orbital Basis Set First‐Principles Quantum Chemical Methods for Large Molecular and Periodic Systems: A Critical Analysis of Error Sources

PubMed Central

Sure, Rebecca; Brandenburg, Jan Gerit

2015-01-01

Abstract In quantum chemical computations the combination of Hartree–Fock or a density functional theory (DFT) approximation with relatively small atomic orbital basis sets of double‐zeta quality is still widely used, for example, in the popular B3LYP/6‐31G* approach. In this Review, we critically analyze the two main sources of error in such computations, that is, the basis set superposition error on the one hand and the missing London dispersion interactions on the other. We review various strategies to correct those errors and present exemplary calculations on mainly noncovalently bound systems of widely varying size. Energies and geometries of small dimers, large supramolecular complexes, and molecular crystals are covered. We conclude that it is not justified to rely on fortunate error compensation, as the main inconsistencies can be cured by modern correction schemes which clearly outperform the plain mean‐field methods. PMID:27308221

The complex-scaled multiconfigurational spin-tensor electron propagator method for low-lying shape resonances in Be-, Mg- and Ca-

NASA Astrophysics Data System (ADS)

Tsogbayar, Tsednee; Yeager, Danny L.

2017-01-01

We further apply the complex scaled multiconfigurational spin-tensor electron propagator method (CMCSTEP) for the theoretical determination of resonance parameters with electron-atom systems including open-shell and highly correlated (non-dynamical correlation) atoms and molecules. The multiconfigurational spin-tensor electron propagator method (MCSTEP) developed and implemented by Yeager and his coworkers for real space gives very accurate and reliable ionization potentials and electron affinities. CMCSTEP uses a complex scaled multiconfigurational self-consistent field (CMCSCF) state as an initial state along with a dilated Hamiltonian where all of the electronic coordinates are scaled by a complex factor. CMCSTEP is designed for determining resonances. We apply CMCSTEP to get the lowest 2P (Be-, Mg-) and 2D (Mg-, Ca-) shape resonances using several different basis sets each with several complete active spaces. Many of these basis sets we employ have been used by others with different methods. Hence, we can directly compare results with different methods but using the same basis sets.

Perturbation expansion theory corrected from basis set superposition error. I. Locally projected excited orbitals and single excitations.

PubMed

Nagata, Takeshi; Iwata, Suehiro

2004-02-22

The locally projected self-consistent field molecular orbital method for molecular interaction (LP SCF MI) is reformulated for multifragment systems. For the perturbation expansion, two types of the local excited orbitals are defined; one is fully local in the basis set on a fragment, and the other has to be partially delocalized to the basis sets on the other fragments. The perturbation expansion calculations only within single excitations (LP SE MP2) are tested for water dimer, hydrogen fluoride dimer, and colinear symmetric ArM+ Ar (M = Na and K). The calculated binding energies of LP SE MP2 are all close to the corresponding counterpoise corrected SCF binding energy. By adding the single excitations, the deficiency in LP SCF MI is thus removed. The results suggest that the exclusion of the charge-transfer effects in LP SCF MI might indeed be the cause of the underestimation for the binding energy. (c) 2004 American Institute of Physics.

Computing single step operators of logic programming in radial basis function neural networks

NASA Astrophysics Data System (ADS)

Hamadneh, Nawaf; Sathasivam, Saratha; Choon, Ong Hong

2014-07-01

Logic programming is the process that leads from an original formulation of a computing problem to executable programs. A normal logic program consists of a finite set of clauses. A valuation I of logic programming is a mapping from ground atoms to false or true. The single step operator of any logic programming is defined as a function (Tp:I→I). Logic programming is well-suited to building the artificial intelligence systems. In this study, we established a new technique to compute the single step operators of logic programming in the radial basis function neural networks. To do that, we proposed a new technique to generate the training data sets of single step operators. The training data sets are used to build the neural networks. We used the recurrent radial basis function neural networks to get to the steady state (the fixed point of the operators). To improve the performance of the neural networks, we used the particle swarm optimization algorithm to train the networks.

The National Sports Safety in Secondary Schools Benchmark (N4SB) Study: Defining Athletic Training Practice Characteristics

PubMed Central

McLeod, Tamara C. Valovich; Bliven, Kellie C. Huxel; Lam, Kenneth C.; Bay, R. Curtis; Valier, Alison R. Snyder; Parsons, John T.

2013-01-01

Context: Increased rates of sport participation and sport-related injury have led to greater emphasis on and attention to medical care of student-athletes in the secondary school setting. Access to athletic training services is seen as a critical factor for delivering adequate injury prevention and medical care to student-athletes. However, few data are available regarding practice characteristics of athletic trainers (ATs) in this setting. Objective: To characterize the practices of secondary school athletic trainers (ATs). Design:  Descriptive study. Setting: Web-based survey. Patients or Other Participants: A total of 17 558 ATs with current National Athletic Trainers' Association membership were identified for survey distribution. Of these, 4232 ATs indicated that they practiced in the secondary school setting, and 4045 completed some part of the survey. Main Outcome Measure(s):  A Web-based survey was used to obtain demographic information about ATs and their secondary schools and characteristics of athletic training practice. Descriptive data regarding the athletic trainer's personal characteristics, secondary school characteristics, and practice patterns are reported as percentages and frequencies. Results: Most respondents were in the early stages of their careers and relatively new to the secondary school practice setting. Nearly two-thirds (62.4%; n = 2522) of respondents had 10 or fewer years of experience as secondary school ATs, 52% (n = 2132) had been certified for 10 or fewer years, and 53.4% (n = 2164) had 10 or fewer years of experience in any practice setting. The majority of respondents (85%) worked in public schools with enrollment of 1000 to 1999 (35.5%) and with football (95.5%). More than half of respondents were employed directly by their school. Most respondents (50.6%) reported an athletic training budget of less than $4000. The majority of ATs performed evaluations (87.5%) on-site all of the time, with a smaller percentage providing treatments (73.3%) or rehabilitation (47.4%) services all of the time. Conclusions: This is the first study to describe secondary school athletic training that reflects national practice trends. To improve the quality of athletic training care and to support and improve current working conditions, the profession must examine how its members practice on a day-to-day basis. PMID:23768120

Charge Transfer Rate in Collisions of H + Ions with Si Atoms

NASA Astrophysics Data System (ADS)

Kimura, M.; Sannigrahi, A. B.; Gu, J. P.; Hirsch, G.; Buenker, R. J.; Shimamura, I.

1996-12-01

Charge transfer in Si(3P, 1D) + H+ collisions is studied theoretically by using a semiclassical molecular representation with six molecular channels for the triplet manifold and four channels for the singlet manifold at collision energies above 30 eV, and by using a fully quantum mechanical approach with two molecular channels for both triplet and singlet manifolds below 30 eV. The ab initio potential curves and nonadiabatic coupling matrix elements for the HSi+ system are obtained from multireference single- and double-excitation configuration interaction (MRD-CI) calculations employing a relatively large basis set. The present rate coefficients for charge transfer to Si+(4P) formation resulting from H+ + Si(3P) collisions are found to be large with values from 1 x 10-10 cm-3 s-1 at 1000 K to 1 x 10-8 cm-3 s-1 at 100,000 K. The rate coefficient for Si+(2P) formation, resulting from H+ + Si(3P) collisions, is found to be much smaller because of a larger energy defect from the initial state. These calculated rates are much larger than those reported by Baliunas & Butler, who estimated a value of 10-11 cm-3 s-1 in their coronal plasma study. The present result may be relevant to the description of the silicon ionization equilibrium.

Hydrodynamic cavitation for sonochemical effects.

PubMed

Moholkar, V S; Kumar, P S; Pandit, A B

1999-03-01

A comparative study of hydrodynamic and acoustic cavitation has been made on the basis of numerical solutions of the Rayleigh-Plesset equation. The bubble/cavity behaviour has been studied under both acoustic and hydrodynamic cavitation conditions. The effect of varying pressure fields on the collapse of the cavity (sinusoidal for acoustic and linear for hydrodynamic) and also on the latter's dynamic behaviour has been studied. The variations of parameters such as initial cavity size, intensity of the acoustic field and irradiation frequency in the case of acoustic cavitation, and initial cavity size, final recovery pressure and time for pressure recovery in the case of hydrodynamic cavitation, have been found to have significant effects on cavity/bubble dynamics. The simulations reveal that the bubble/cavity collapsing behaviour in the case of hydrodynamic cavitation is accompanied by a large number of pressure pulses of relatively smaller magnitude, compared with just one or two pulses under acoustic cavitation. It has been shown that hydrodynamic cavitation offers greater control over operating parameters and the resultant cavitation intensity. Finally, a brief summary of the experimental results on the oxidation of aqueous KI solution with a hydrodynamic cavitation set-up is given which supports the conclusion of this numerical study. The methodology presented allows one to manipulate and optimise of specific process, either physical or chemical.

How localized is ``local?'' Efficiency vs. accuracy of O(N) domain decomposition in local orbital based all-electron electronic structure theory

NASA Astrophysics Data System (ADS)

Havu, Vile; Blum, Volker; Scheffler, Matthias

2007-03-01

Numeric atom-centered local orbitals (NAO) are efficient basis sets for all-electron electronic structure theory. The locality of NAO's can be exploited to render (in principle) all operations of the self-consistency cycle O(N). This is straightforward for 3D integrals using domain decomposition into spatially close subsets of integration points, enabling critical computational savings that are effective from ˜tens of atoms (no significant overhead for smaller systems) and make large systems (100s of atoms) computationally feasible. Using a new all-electron NAO-based code,^1 we investigate the quantitative impact of exploiting this locality on two distinct classes of systems: Large light-element molecules [Alanine-based polypeptide chains (Ala)n], and compact transition metal clusters. Strict NAO locality is achieved by imposing a cutoff potential with an onset radius rc, and exploited by appropriately shaped integration domains (subsets of integration points). Conventional tight rc<= 3å have no measurable accuracy impact in (Ala)n, but introduce inaccuracies of 20-30 meV/atom in Cun. The domain shape impacts the computational effort by only 10-20 % for reasonable rc. ^1 V. Blum, R. Gehrke, P. Havu, V. Havu, M. Scheffler, The FHI Ab Initio Molecular Simulations (aims) Project, Fritz-Haber-Institut, Berlin (2006).

Cytoplasmic male sterility in Mimulus hybrids has pleiotropic effects on corolla and pistil traits.

PubMed

Barr, C M; Fishman, L

2011-05-01

The mechanisms underlying genetic associations have important consequences for evolutionary outcomes, but distinguishing linkage from pleiotropy is often difficult. Here, we use a fine mapping approach to determine the genetic basis of association between cytonuclear male sterility and other floral traits in Mimulus hybrids. Previous work has shown that male sterility in hybrids between Mimulus guttatus and Mimulus nasutus is due to interactions between a mitochondrial gene from M. guttatus and two tightly linked nuclear restorer alleles on Linkage Group 7, and that male sterility is associated with reduced corolla size. In the present study, we generated a set of nearly isogenic lines segregating for the restorer region and male sterility, but with unique flanking introgressions. Male-sterile flowers had significantly smaller corollas, longer styles and greater stigmatic exsertion than fertile flowers. Because these effects were significant regardless of the genotypic composition of introgressions flanking the restorer region, they suggest that these floral differences are a direct byproduct of the genetic incompatibility causing anther abortion. In addition, we found a non-significant but intriguing trend for male-sterile plants to produce more seeds per flower than fertile siblings after supplemental pollination. Such pleiotropic effects may underlie the corolla dimorphism frequently observed in gynodioecious taxa and may affect selection on cytoplasmic male sterility genes when they initially arise.

Psychosocial stress as a predictor of injury in elite junior soccer: a latent growth curve analysis.

PubMed

Ivarsson, Andreas; Johnson, Urban; Lindwall, Magnus; Gustafsson, Henrik; Altemyr, Mats

2014-07-01

To investigate by use of a latent growth curve analysis framework whether athletes' individual levels and changes in hassle and uplift levels over a 10-week period could predict injury outcome in an elite junior soccer population. A prospective design with repeated measurement points. Participants were 101 Swedish elite junior soccer players (67 males and 34 females). Ten sets of measures were taken on a weekly basis during which participants completed the Hassles and Uplifts Scale (HUS). Latent growth curve models were used to examine whether the level and change in psychological stress could predict the frequency of injury over the 10-week period. The results show that injury occurrence was significantly associated with both the initial level of daily hassle and the change in daily hassle. High initial daily hassle levels and a smaller decrease in daily hassles were associated with injury occurrence. Moreover, injury occurrence was significantly associated with a greater decrease in daily uplift. The findings highlight the importance of focusing on state variables using prospective designs and appropriate analysis of within-person change to detect complex and dynamic associations across time in injury-prediction research. Copyright © 2013 Sports Medicine Australia. Published by Elsevier Ltd. All rights reserved.

[Application of artificial neural networks in forecasting the number of circulatory system diseases death toll].

PubMed

Zhang, Ying; Shao, Yi; Shang, Kezheng; Wang, Shigong; Wang, Jinyan

2014-09-01

Set up the model of forecasting the number of circulatorys death toll based on back-propagation (BP) artificial neural networks discuss the relationship between the circulatory system diseases death toll meteorological factors and ambient air pollution. The data of tem deaths, meteorological factors, and ambient air pollution within the m 2004 to 2009 in Nanjing were collected. On the basis of analyzing the ficient between CSDDT meteorological factors and ambient air pollution, leutral network model of CSDDT was built for 2004 - 2008 based on factors and ambient air pollution within the same time, and the data of 2009 est the predictive power of the model. There was a closely system diseases relationship between meteorological factors, ambient air pollution and the circulatory system diseases death toll. The ANN model structure was 17 -16 -1, 17 input notes, 16 hidden notes and 1 output note. The training precision was 0. 005 and the final error was 0. 004 999 42 after 487 training steps. The results of forecast show that predict accuracy over 78. 62%. This method is easy to be finished with smaller error, and higher ability on circulatory system death toll on independent prediction, which can provide a new method for forecasting medical-meteorological forecast and have the value of further research.

A Taxonomy of Accountable Care Organizations for Policy and Practice

PubMed Central

Shortell, Stephen M; Wu, Frances M; Lewis, Valerie A; Colla, Carrie H; Fisher, Elliott S

2014-01-01

Objective To develop an exploratory taxonomy of Accountable Care Organizations (ACOs) to describe and understand early ACO development and to provide a basis for technical assistance and future evaluation of performance. Data Sources/Study Setting Data from the National Survey of Accountable Care Organizations, fielded between October 2012 and May 2013, of 173 Medicare, Medicaid, and commercial payer ACOs. Study Design Drawing on resource dependence and institutional theory, we develop measures of eight attributes of ACOs such as size, scope of services offered, and the use of performance accountability mechanisms. Data are analyzed using a two-step cluster analysis approach that accounts for both continuous and categorical data. Principal Findings We identified a reliable and internally valid three-cluster solution: larger, integrated systems that offer a broad scope of services and frequently include one or more postacute facilities; smaller, physician-led practices, centered in primary care, and that possess a relatively high degree of physician performance management; and moderately sized, joint hospital–physician and coalition-led groups that offer a moderately broad scope of services with some involvement of postacute facilities. Conclusions ACOs can be characterized into three distinct clusters. The taxonomy provides a framework for assessing performance, for targeting technical assistance, and for diagnosing potential antitrust violations. PMID:25251146

Electrophysiological brain indices of risk behavior modification induced by contingent feedback.

PubMed

Megías, Alberto; Torres, Miguel Angel; Catena, Andrés; Cándido, Antonio; Maldonado, Antonio

2018-02-01

The main aim of this research was to study the effects of response feedback on risk behavior and the neural and cognitive mechanisms involved, as a function of the feedback contingency. Sixty drivers were randomly assigned to one of three feedback groups: contingent, non-contingent and no feedback. The participants' task consisted of braking or not when confronted with a set of risky driving situations, while their electroencephalographic activity was continuously recorded. We observed that contingent feedback, as opposed to non-contingent feedback, promoted changes in the response bias towards safer decisions. This behavioral modification implied a higher demand on cognitive control, reflected in a larger amplitude of the N400 component. Moreover, the contingent feedback, being predictable and entailing more informative value, gave rise to smaller SPN and larger FRN scores when compared with non-contingent feedback. Taken together, these findings provide a new and complex insight into the neurophysiological basis of the influence of feedback contingency on the processing of decision-making under risk. We suggest that response feedback, when contingent upon the risky behavior, appears to improve the functionality of the brain mechanisms involved in decision-making and can be a powerful tool for reducing the tendency to choose risky options in risk-prone individuals. Copyright © 2018 Elsevier B.V. All rights reserved.

Bioinformatics-Based Identification of Candidate Genes from QTLs Associated with Cell Wall Traits in Populus

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ranjan, Priya; Yin, Tongming; Zhang, Xinye

2009-11-01

Quantitative trait locus (QTL) studies are an integral part of plant research and are used to characterize the genetic basis of phenotypic variation observed in structured populations and inform marker-assisted breeding efforts. These QTL intervals can span large physical regions on a chromosome comprising hundreds of genes, thereby hampering candidate gene identification. Genome history, evolution, and expression evidence can be used to narrow the genes in the interval to a smaller list that is manageable for detailed downstream functional genomics characterization. Our primary motivation for the present study was to address the need for a research methodology that identifies candidatemore » genes within a broad QTL interval. Here we present a bioinformatics-based approach for subdividing candidate genes within QTL intervals into alternate groups of high probability candidates. Application of this approach in the context of studying cell wall traits, specifically lignin content and S/G ratios of stem and root in Populus plants, resulted in manageable sets of genes of both known and putative cell wall biosynthetic function. These results provide a roadmap for future experimental work leading to identification of new genes controlling cell wall recalcitrance and, ultimately, in the utility of plant biomass as an energy feedstock.« less

Two-Photon Absorption Properties of Gold Fluorescent Protein: A Combined Molecular Dynamics and Quantum Chemistry Study.

PubMed

Şimşek, Yusuf; Brown, Alex

2018-06-07

Molecular dynamics (MD) simulations were carried out to obtain the conformational changes of the chromophore in the gold fluorescent protein (PDB ID: 1OXF ). To obtain two-photon absorption (TPA) cross-sections, time dependent density functional theory (TD-DFT) computations were performed for chromophore geometries sampled along the trajectory. The TD-DFT computations used the CAM-B3LYP functional and 6-31+G(d) basis set. Results showed that two dihedral angles change remarkably over the simulation time. TPA cross-sections were found to average 13.82 GM for the excitation to S 1 computed from the equilibrium geometries; however, extending the structures with a water molecule and GLU residue, which make H bonds with the chromophore molecule, increased excitation energies and TPA cross-sections significantly. Besides the effects of the surrounding residues and the dihedrals on the spectroscopic properties, some bond lengths affected the excitation energies and the TPA cross-sections significantly (up to ±25-30%), while the effects of the bond angles were smaller (±5%). Overall the present results provide insight into the effects of the conformational flexibility on TPA (with gold fluorescent protein as a specific example) and suggest that further experimental measurements of TPA for the gold fluorescent protein should be undertaken.

DFT Study of the Oxygen Reduction Reaction Activity on Fe−N4-Patched Carbon Nanotubes: The Influence of the Diameter and Length

PubMed Central

Chen, Xin; Hu, Rui; Bai, Fan

2017-01-01

The influences of diameter and length of the Fe−N4-patched carbon nanotubes (Fe−N4/CNTs) on oxygen reduction reaction (ORR) activity were investigated by density functional theory method using the BLYP/DZP basis set. The results indicate that the stability of the Fe−N4 catalytic site in Fe−N4/CNTs will be enhanced with a larger tube diameter, but reduced with shorter tube length. A tube with too small a diameter makes a Fe−N4 site unstable in acid medium since Fe−N and C−N bonds must be significantly bent at smaller diameters due to hoop strain. The adsorption energy of the ORR intermediates, especially of the OH group, becomes weaker with the increase of the tube diameter. The OH adsorption energy of Fe−N4/CNT with the largest tube diameter is close to that on Pt(111) surface, indicating that its catalytic property is similar to Pt. Electronic structure analysis shows that the OH adsorption energy is mainly controlled by the energy levels of Fe 3d orbital. The calculation results uncover that Fe−N4/CNTs with larger tube diameters and shorter lengths will exhibit better ORR activity and stability. PMID:28772903

Geometrical, electronic, and magnetic properties of CunFe (n=1-12) clusters: A density functional study

NASA Astrophysics Data System (ADS)

Ling, Wang; Dong, Die; Shi-Jian, Wang; Zheng-Quan, Zhao

2015-01-01

The geometrical, electronic, and magnetic properties of small CunFe (n=1-12) clusters have been investigated by using density functional method B3LYP and LanL2DZ basis set. The structural search reveals that Fe atoms in low-energy CunFe isomers tend to occupy the position with the maximum coordination number. The ground state CunFe clusters possess planar structure for n=2-5 and three-dimensional (3D) structure for n=6-12. The electronic properties of CunFe clusters are analyzed through the averaged binding energy, the second-order energy difference and HOMO-LUMO energy gap. It is found that the magic numbers of stability are 1, 3, 7 and 9 for the ground state CunFe clusters. The energy gap of Fe-encapsulated cage clusters is smaller than that of other configurations. The Cu5Fe and Cu7Fe clusters have a very large energy gap (>2.4 eV). The vertical ionization potential (VIP), electron affinity (EA) and photoelectron spectra are also calculated and simulated theoretically for all the ground-state clusters. The magnetic moment analyses for the ground-state CunFe clusters show that Fe atom can enhance the magnetic moment of the host cluster and carries most of the total magnetic moment.

Stimulus edge effects in the measurement of macular pigment using heterochromatic flicker photometry.

PubMed

Smollon, William E; Wooten, Billy R; Hammond, Billy R

2015-11-01

Heterochromatic flicker photometry (HFP) is the most common technique of measuring macular pigment optical density (MPOD). Some data strongly suggest that HFP samples MPOD specifically at the edge of center-fixated circular stimuli. Other data have led to the conclusion that HFP samples over the entire area of the stimulus. To resolve this disparity, MPOD was measured using HFP and a series of solid discs of varying radii (0.25 to 2.0 deg) and with thin annuli corresponding to the edge of those discs. MPOD assessed with the two methods yielded excellent correspondence and linearity: Y=0.01+0.98X , r=0.96. A second set of experiments showed that if a disc stimulus is adjusted for no-flicker (the standard procedure) and simply reduced in size, no flicker is observed despite the higher level of MPOD in the smaller area. Taken together, these results confirm that MPOD is determined at the edge of the measuring stimulus when using stimulus sizes in the range that is in dispute (up to a radius of 0.75 deg). The basis for this edge effect can be explained by quantitative differences in the spatial-temporal properties of the visual field as a function of angular distance from the fixation point.

Nitrogen oxides/sulfur oxides (NOx/SOx) Secondary NAAQS ...

EPA Pesticide Factsheets

This document assesses the policy basis for setting the secondary NOx/SOx NAAQS. To provide the policy assessment information for the Administrator to make a more informed decision about the basis for retaining or revising the secondary NOx/SOx NAAQS.

Correlation consistent basis sets for actinides. II. The atoms Ac and Np-Lr

NASA Astrophysics Data System (ADS)

Feng, Rulin; Peterson, Kirk A.

2017-08-01

New correlation consistent basis sets optimized using the all-electron third-order Douglas-Kroll-Hess (DKH3) scalar relativistic Hamiltonian are reported for the actinide elements Ac and Np through Lr. These complete the series of sets reported previously for Th-U [K. A. Peterson, J. Chem. Phys. 142, 074105 (2015); M. Vasiliu et al., J. Phys. Chem. A 119, 11422 (2015)]. The new sets range in size from double- to quadruple-zeta and encompass both those optimized for valence (6s6p5f7s6d) and outer-core electron correlations (valence + 5s5p5d). The final sets have been contracted for both the DKH3 and eXact 2-component (X2C) Hamiltonians, yielding cc-pVnZ-DK3/cc-pVnZ-X2C sets for valence correlation and cc-pwCVnZ-DK3/cc-pwCVnZ-X2C sets for outer-core correlation (n = D, T, Q in each case). In order to test the effectiveness of the new basis sets, both atomic and molecular benchmark calculations have been carried out. In the first case, the first three atomic ionization potentials (IPs) of all the actinide elements Ac-Lr have been calculated using the Feller-Peterson-Dixon (FPD) composite approach, primarily with the multireference configuration interaction (MRCI) method. Excellent convergence towards the respective complete basis set (CBS) limits is achieved with the new sets, leading to good agreement with experiment, where these exist, after accurately accounting for spin-orbit effects using the 4-component Dirac-Hartree-Fock method. For a molecular test, the IP and atomization energy (AE) of PuO2 have been calculated also using the FPD method but using a coupled cluster approach with spin-orbit coupling accounted for using the 4-component MRCI. The present calculations yield an IP0 for PuO2 of 159.8 kcal/mol, which is in excellent agreement with the experimental electron transfer bracketing value of 162 ± 3 kcal/mol. Likewise, the calculated 0 K AE of 305.6 kcal/mol is in very good agreement with the currently accepted experimental value of 303.1 ± 5 kcal/mol. The ground state of PuO2 is predicted to be the 0 g +5Σ state.

Correlation consistent basis sets for actinides. II. The atoms Ac and Np-Lr.

PubMed

Feng, Rulin; Peterson, Kirk A

2017-08-28

New correlation consistent basis sets optimized using the all-electron third-order Douglas-Kroll-Hess (DKH3) scalar relativistic Hamiltonian are reported for the actinide elements Ac and Np through Lr. These complete the series of sets reported previously for Th-U [K. A. Peterson, J. Chem. Phys. 142, 074105 (2015); M. Vasiliu et al., J. Phys. Chem. A 119, 11422 (2015)]. The new sets range in size from double- to quadruple-zeta and encompass both those optimized for valence (6s6p5f7s6d) and outer-core electron correlations (valence + 5s5p5d). The final sets have been contracted for both the DKH3 and eXact 2-component (X2C) Hamiltonians, yielding cc-pVnZ-DK3/cc-pVnZ-X2C sets for valence correlation and cc-pwCVnZ-DK3/cc-pwCVnZ-X2C sets for outer-core correlation (n = D, T, Q in each case). In order to test the effectiveness of the new basis sets, both atomic and molecular benchmark calculations have been carried out. In the first case, the first three atomic ionization potentials (IPs) of all the actinide elements Ac-Lr have been calculated using the Feller-Peterson-Dixon (FPD) composite approach, primarily with the multireference configuration interaction (MRCI) method. Excellent convergence towards the respective complete basis set (CBS) limits is achieved with the new sets, leading to good agreement with experiment, where these exist, after accurately accounting for spin-orbit effects using the 4-component Dirac-Hartree-Fock method. For a molecular test, the IP and atomization energy (AE) of PuO 2 have been calculated also using the FPD method but using a coupled cluster approach with spin-orbit coupling accounted for using the 4-component MRCI. The present calculations yield an IP 0 for PuO 2 of 159.8 kcal/mol, which is in excellent agreement with the experimental electron transfer bracketing value of 162 ± 3 kcal/mol. Likewise, the calculated 0 K AE of 305.6 kcal/mol is in very good agreement with the currently accepted experimental value of 303.1 ± 5 kcal/mol. The ground state of PuO 2 is predicted to be the Σ0g+5 state.

A Study on Gröbner Basis with Inexact Input

NASA Astrophysics Data System (ADS)

Nagasaka, Kosaku

Gröbner basis is one of the most important tools in recent symbolic algebraic computations. However, computing a Gröbner basis for the given polynomial ideal is not easy and it is not numerically stable if polynomials have inexact coefficients. In this paper, we study what we should get for computing a Gröbner basis with inexact coefficients and introduce a naive method to compute a Gröbner basis by reduced row echelon form, for the ideal generated by the given polynomial set having a priori errors on their coefficients.

A Bayesian spatial model for neuroimaging data based on biologically informed basis functions.

PubMed

Huertas, Ismael; Oldehinkel, Marianne; van Oort, Erik S B; Garcia-Solis, David; Mir, Pablo; Beckmann, Christian F; Marquand, Andre F

2017-11-01

The dominant approach to neuroimaging data analysis employs the voxel as the unit of computation. While convenient, voxels lack biological meaning and their size is arbitrarily determined by the resolution of the image. Here, we propose a multivariate spatial model in which neuroimaging data are characterised as a linearly weighted combination of multiscale basis functions which map onto underlying brain nuclei or networks or nuclei. In this model, the elementary building blocks are derived to reflect the functional anatomy of the brain during the resting state. This model is estimated using a Bayesian framework which accurately quantifies uncertainty and automatically finds the most accurate and parsimonious combination of basis functions describing the data. We demonstrate the utility of this framework by predicting quantitative SPECT images of striatal dopamine function and we compare a variety of basis sets including generic isotropic functions, anatomical representations of the striatum derived from structural MRI, and two different soft functional parcellations of the striatum derived from resting-state fMRI (rfMRI). We found that a combination of ∼50 multiscale functional basis functions accurately represented the striatal dopamine activity, and that functional basis functions derived from an advanced parcellation technique known as Instantaneous Connectivity Parcellation (ICP) provided the most parsimonious models of dopamine function. Importantly, functional basis functions derived from resting fMRI were more accurate than both structural and generic basis sets in representing dopamine function in the striatum for a fixed model order. We demonstrate the translational validity of our framework by constructing classification models for discriminating parkinsonian disorders and their subtypes. Here, we show that ICP approach is the only basis set that performs well across all comparisons and performs better overall than the classical voxel-based approach. This spatial model constitutes an elegant alternative to voxel-based approaches in neuroimaging studies; not only are their atoms biologically informed, they are also adaptive to high resolutions, represent high dimensions efficiently, and capture long-range spatial dependencies, which are important and challenging objectives for neuroimaging data. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Exploring biorthonormal transformations of pair-correlation functions in atomic structure variational calculations

NASA Astrophysics Data System (ADS)

Verdebout, S.; Jönsson, P.; Gaigalas, G.; Godefroid, M.; Froese Fischer, C.

2010-04-01

Multiconfiguration expansions frequently target valence correlation and correlation between valence electrons and the outermost core electrons. Correlation within the core is often neglected. A large orbital basis is needed to saturate both the valence and core-valence correlation effects. This in turn leads to huge numbers of configuration state functions (CSFs), many of which are unimportant. To avoid the problems inherent to the use of a single common orthonormal orbital basis for all correlation effects in the multiconfiguration Hartree-Fock (MCHF) method, we propose to optimize independent MCHF pair-correlation functions (PCFs), bringing their own orthonormal one-electron basis. Each PCF is generated by allowing single- and double-excitations from a multireference (MR) function. This computational scheme has the advantage of using targeted and optimally localized orbital sets for each PCF. These pair-correlation functions are coupled together and with each component of the MR space through a low dimension generalized eigenvalue problem. Nonorthogonal orbital sets being involved, the interaction and overlap matrices are built using biorthonormal transformation of the coupled basis sets followed by a counter-transformation of the PCF expansions. Applied to the ground state of beryllium, the new method gives total energies that are lower than the ones from traditional complete active space (CAS)-MCHF calculations using large orbital active sets. It is fair to say that we now have the possibility to account for, in a balanced way, correlation deep down in the atomic core in variational calculations.

Crystal structure, spectroscopic studies and quantum mechanical calculations of 2-[((3-iodo-4-methyl)phenylimino)methyl]-5-nitrothiophene.

PubMed

Özdemir Tarı, Gonca; Gümüş, Sümeyye; Ağar, Erbil

2015-04-15

The title compound, 2-[((3-iodo-4-methyl)phenylimino)methyl]-5-nitrothiophene, C12H9O2N2I1S1, was synthesized and characterized by IR, UV-Vis and single-crystal X-ray diffraction technique. The molecular structure was optimized at the B3LYP, B3PW91 and PBEPBE levels of the density functional method (DFT) with the 6-311G+(d,p) basis set. Using the TD-DFT method, the electronic absorption spectra of the title compound was computed in both the gas phase and ethanol solvent. The harmonic vibrational frequencies of the title compound were calculated using the same methods with the 6-311G+(d,p) basis set. The calculated results were compared with the experimental determination results of the compound. The energetic behavior such as the total energy, atomic charges, dipole moment of the title compound in solvent media were examined using the B3LYP, B3PW91 and PBEPBE methods with the 6-311G+(d,p) basis set by applying the Onsager and the polarizable continuum model (PCM). The molecular orbitals (FMOs) analysis, the molecular electrostatic potential map (MEP) and the nonlinear optical properties (NLO) for the title compound were obtained with the same levels of theory. And then thermodynamic properties for the title compound were obtained using the same methods with the 6-311G(d,p) basis set. Copyright © 2015 Elsevier B.V. All rights reserved.

Method and basis set dependence of anharmonic ground state nuclear wave functions and zero-point energies: application to SSSH.

PubMed

Kolmann, Stephen J; Jordan, Meredith J T

2010-02-07

One of the largest remaining errors in thermochemical calculations is the determination of the zero-point energy (ZPE). The fully coupled, anharmonic ZPE and ground state nuclear wave function of the SSSH radical are calculated using quantum diffusion Monte Carlo on interpolated potential energy surfaces (PESs) constructed using a variety of method and basis set combinations. The ZPE of SSSH, which is approximately 29 kJ mol(-1) at the CCSD(T)/6-31G* level of theory, has a 4 kJ mol(-1) dependence on the treatment of electron correlation. The anharmonic ZPEs are consistently 0.3 kJ mol(-1) lower in energy than the harmonic ZPEs calculated at the Hartree-Fock and MP2 levels of theory, and 0.7 kJ mol(-1) lower in energy at the CCSD(T)/6-31G* level of theory. Ideally, for sub-kJ mol(-1) thermochemical accuracy, ZPEs should be calculated using correlated methods with as big a basis set as practicable. The ground state nuclear wave function of SSSH also has significant method and basis set dependence. The analysis of the nuclear wave function indicates that SSSH is localized to a single symmetry equivalent global minimum, despite having sufficient ZPE to be delocalized over both minima. As part of this work, modifications to the interpolated PES construction scheme of Collins and co-workers are presented.

Method and basis set dependence of anharmonic ground state nuclear wave functions and zero-point energies: Application to SSSH

NASA Astrophysics Data System (ADS)

Kolmann, Stephen J.; Jordan, Meredith J. T.

2010-02-01

One of the largest remaining errors in thermochemical calculations is the determination of the zero-point energy (ZPE). The fully coupled, anharmonic ZPE and ground state nuclear wave function of the SSSH radical are calculated using quantum diffusion Monte Carlo on interpolated potential energy surfaces (PESs) constructed using a variety of method and basis set combinations. The ZPE of SSSH, which is approximately 29 kJ mol-1 at the CCSD(T)/6-31G∗ level of theory, has a 4 kJ mol-1 dependence on the treatment of electron correlation. The anharmonic ZPEs are consistently 0.3 kJ mol-1 lower in energy than the harmonic ZPEs calculated at the Hartree-Fock and MP2 levels of theory, and 0.7 kJ mol-1 lower in energy at the CCSD(T)/6-31G∗ level of theory. Ideally, for sub-kJ mol-1 thermochemical accuracy, ZPEs should be calculated using correlated methods with as big a basis set as practicable. The ground state nuclear wave function of SSSH also has significant method and basis set dependence. The analysis of the nuclear wave function indicates that SSSH is localized to a single symmetry equivalent global minimum, despite having sufficient ZPE to be delocalized over both minima. As part of this work, modifications to the interpolated PES construction scheme of Collins and co-workers are presented.

Highly correlated configuration interaction calculations on water with large orbital bases

DOE Office of Scientific and Technical Information (OSTI.GOV)

Almora-Díaz, César X., E-mail: xalmora@fisica.unam.mx

2014-05-14

A priori selected configuration interaction (SCI) with truncation energy error [C. F. Bunge, J. Chem. Phys. 125, 014107 (2006)] and CI by parts [C. F. Bunge and R. Carbó-Dorca, J. Chem. Phys. 125, 014108 (2006)] are used to approximate the total nonrelativistic electronic ground state energy of water at fixed experimental geometry with CI up to sextuple excitations. Correlation-consistent polarized core-valence basis sets (cc-pCVnZ) up to sextuple zeta and augmented correlation-consistent polarized core-valence basis sets (aug-cc-pCVnZ) up to quintuple zeta quality are employed. Truncation energy errors range between less than 1 μhartree, and 100 μhartree for the largest orbital set. Coupledmore » cluster CCSD and CCSD(T) calculations are also obtained for comparison. Our best upper bound, −76.4343 hartree, obtained by SCI with up to sextuple excitations with a cc-pCV6Z basis recovers more than 98.8% of the correlation energy of the system, and it is only about 3 kcal/mol above the “experimental” value. Despite that the present energy upper bounds are far below all previous ones, comparatively large dispersion errors in the determination of the extrapolated energies to the complete basis set do not allow to determine a reliable estimation of the full CI energy with an accuracy better than 0.6 mhartree (0.4 kcal/mol)« less

Monitoring and modeling of runoff from a natural and an urbanized part of a small stream catchment

NASA Astrophysics Data System (ADS)

Kalicz, P.; Kucsara, M.; Gribovszki, Z.; Erős, M.; Csáfordi, P.

2012-04-01

Runoff processes in natural catchments are significantly different compared to urbanized areas. Human impacts are manifested in high amount of paved surfaces like roofs, roads, parking plots and the compacted soils of quasi natural areas like public gardens and parks. Decay of permeability and storage capacity both induce higher amount of runoff. The common practice to treat the increased volume of runoff is to collect in pipes and drain to a stream as soon as possible. These interventions induce flash floods with smaller time of concentration and higher flood peaks as normal food waves therefore strongly load discharge capacity of stream channel. Streams in urban areas are strongly modified and regulated. Sometimes the stream channel are dredged out to increase the discharge capacity. In worst case some smaller brooks are crowded with lid to increase urbanized habitat. Many climate change scenarios predict higher probability of heavy storm events, therefore increasing volume of runoff induces higher demands of strongly modified and enormous concrete channels. This study presents one year monitoring of a small stream comparing runoff from natural, rural and urban sections. In this paper we also introduce the process of a model setup and an evaluation to investigate the weak points of a stream section in urbanized areas. The pilot area of this research is the Rák Brook which is the second largest stream of city Sopron (western Hungary). The natural headwater catchment is long-term research area of Hidegvíz Valley Project, therefore we had a good basis to extend the research catchment monitoring in the direction of urbanized lower part of the stream. Seven monitoring points are established along the longitudinal section of the stream. In each point the water stage is recorded continuously beside several other water quality parameters. These data sets help the later validation of the hydrodynamic model.

An ab initio benchmark study of the H + CO --> HCO reaction

NASA Technical Reports Server (NTRS)

Woon, D. E.

1996-01-01

The H + CO --> HCO reaction has been characterized with correlation consistent basis sets at five levels of theory in order to benchmark the sensitivities of the barrier height and reaction ergicity to the one-electron and n-electron expansions of the electronic wave function. Single and multireference methods are compared and contrasted. The coupled cluster method RCCSD(T) was found to be in very good agreement with Davidson-corrected internally-contracted multireference configuration interaction (MRCI+Q). Second-order Moller-Plesset perturbation theory (MP2) was also employed. The estimated complete basis set (CBS) limits for the barrier height (in kcal/mol) for the five methods, including harmonic zero-point energy corrections, are MP2, 4.66; RCCSD, 4.78; RCCSD(T), 4.15; MRCI, 5.10; and MRCI+Q, 4.07. Similarly, the estimated CBS limits for the ergicity of the reaction are: MP2, -17.99; RCCSD, -13.34; RCCSD(T), -13.79; MRCI, -11.46; and MRCI+Q, -13.70. Additional basis set explorations for the RCCSD(T) method demonstrate that aug-cc-pVTZ sets, even with some functions removed, are sufficient to reproduce the CBS limits to within 0.1-0.3 kcal/mol.

Explicitly correlated coupled-cluster theory using cusp conditions. II. Treatment of connected triple excitations.

PubMed

Köhn, Andreas

2010-11-07

The coupled-cluster singles and doubles method augmented with single Slater-type correlation factors (CCSD-F12) determined by the cusp conditions (also denoted as SP ansatz) yields results close to the basis set limit with only small overhead compared to conventional CCSD. Quantitative calculations on many-electron systems, however, require to include the effect of connected triple excitations at least. In this contribution, the recently proposed [A. Köhn, J. Chem. Phys. 130, 131101 (2009)] extended SP ansatz and its application to the noniterative triples correction CCSD(T) is reviewed. The approach allows to include explicit correlation into connected triple excitations without introducing additional unknown parameters. The explicit expressions are presented and analyzed, and possible simplifications to arrive at a computationally efficient scheme are suggested. Numerical tests based on an implementation obtained by an automated approach are presented. Using a partial wave expansion for the neon atom, we can show that the proposed ansatz indeed leads to the expected (L(max)+1)(-7) convergence of the noniterative triples correction, where L(max) is the maximum angular momentum in the orbital expansion. Further results are reported for a test set of 29 molecules, employing Peterson's F12-optimized basis sets. We find that the customary approach of using the conventional noniterative triples correction on top of a CCSD-F12 calculation leads to significant basis set errors. This, however, is not always directly visible for total CCSD(T) energies due to fortuitous error compensation. The new approach offers a thoroughly explicitly correlated CCSD(T)-F12 method with improved basis set convergence of the triples contributions to both total and relative energies.

Exploring the spatio-temporal neural basis of face learning

PubMed Central

Yang, Ying; Xu, Yang; Jew, Carol A.; Pyles, John A.; Kass, Robert E.; Tarr, Michael J.

2017-01-01

Humans are experts at face individuation. Although previous work has identified a network of face-sensitive regions and some of the temporal signatures of face processing, as yet, we do not have a clear understanding of how such face-sensitive regions support learning at different time points. To study the joint spatio-temporal neural basis of face learning, we trained subjects to categorize two groups of novel faces and recorded their neural responses using magnetoencephalography (MEG) throughout learning. A regression analysis of neural responses in face-sensitive regions against behavioral learning curves revealed significant correlations with learning in the majority of the face-sensitive regions in the face network, mostly between 150–250 ms, but also after 300 ms. However, the effect was smaller in nonventral regions (within the superior temporal areas and prefrontal cortex) than that in the ventral regions (within the inferior occipital gyri (IOG), midfusiform gyri (mFUS) and anterior temporal lobes). A multivariate discriminant analysis also revealed that IOG and mFUS, which showed strong correlation effects with learning, exhibited significant discriminability between the two face categories at different time points both between 150–250 ms and after 300 ms. In contrast, the nonventral face-sensitive regions, where correlation effects with learning were smaller, did exhibit some significant discriminability, but mainly after 300 ms. In sum, our findings indicate that early and recurring temporal components arising from ventral face-sensitive regions are critically involved in learning new faces. PMID:28570739

The Genetics of Resistance to Morinda Fruit Toxin During the Postembryonic Stages in Drosophila sechellia

PubMed Central

Huang, Yan; Erezyilmaz, Deniz

2015-01-01

Although a great deal has been learned regarding the genetic changes that give rise to adaptation in bacteria and yeast, an understanding of how new complex traits arise in multicellular organisms is far less complete. Many phytophagous insect species are ecological specialists that have adapted to utilize a single host plant. Drosophila sechellia is a specialist that utilizes the ripe fruit of Morinda citrifolia, which is toxic to its sibling species, D. simulans. Here we apply multiplexed shotgun genotyping and QTL analysis to examine the genetic basis of resistance to M. citrifolia fruit toxin in interspecific hybrids. We identify a locus of large effect on the third chromosome (QTL-IIIsima) in the D. simulans backcross that was not detected in previous analyses. We also identify a highly significant QTL of large effect on the X chromosome, QTL-Xsim. Additional smaller-effect loci were also identified in the D. simulans and D. sechellia backcrosses. We did not detect significant epistasis between loci. Instead, our analysis reveals large and smaller-effect loci that contribute to M. citrifolia resistance additively. The additive effect of each locus suggests that partial resistance to lower levels of M. citrifolia toxin could be passed through introgression from D. sechellia to D. simulans in nature. The identification of the major effect loci, QTL-IIIsima and QTL-Xsim, is an important step toward identifying the molecular basis of adaptation in a multicellular organism. PMID:26224784

Exploring the spatio-temporal neural basis of face learning.

PubMed

Yang, Ying; Xu, Yang; Jew, Carol A; Pyles, John A; Kass, Robert E; Tarr, Michael J

2017-06-01

Humans are experts at face individuation. Although previous work has identified a network of face-sensitive regions and some of the temporal signatures of face processing, as yet, we do not have a clear understanding of how such face-sensitive regions support learning at different time points. To study the joint spatio-temporal neural basis of face learning, we trained subjects to categorize two groups of novel faces and recorded their neural responses using magnetoencephalography (MEG) throughout learning. A regression analysis of neural responses in face-sensitive regions against behavioral learning curves revealed significant correlations with learning in the majority of the face-sensitive regions in the face network, mostly between 150-250 ms, but also after 300 ms. However, the effect was smaller in nonventral regions (within the superior temporal areas and prefrontal cortex) than that in the ventral regions (within the inferior occipital gyri (IOG), midfusiform gyri (mFUS) and anterior temporal lobes). A multivariate discriminant analysis also revealed that IOG and mFUS, which showed strong correlation effects with learning, exhibited significant discriminability between the two face categories at different time points both between 150-250 ms and after 300 ms. In contrast, the nonventral face-sensitive regions, where correlation effects with learning were smaller, did exhibit some significant discriminability, but mainly after 300 ms. In sum, our findings indicate that early and recurring temporal components arising from ventral face-sensitive regions are critically involved in learning new faces.

Not all numbers are equal: preferences and biases among children and adults when generating random sequences.

PubMed

Towse, John N; Loetscher, Tobias; Brugger, Peter

2014-01-01

We investigate the number preferences of children and adults when generating random digit sequences. Previous research has shown convincingly that adults prefer smaller numbers when randomly choosing between responses 1-6. We analyze randomization choices made by both children and adults, considering a range of experimental studies and task configurations. Children - most of whom are between 8 and 11~years - show a preference for relatively large numbers when choosing numbers 1-10. Adults show a preference for small numbers with the same response set. We report a modest association between children's age and numerical bias. However, children also exhibit a small number bias with a smaller response set available, and they show a preference specifically for the numbers 1-3 across many datasets. We argue that number space demonstrates both continuities (numbers 1-3 have a distinct status) and change (a developmentally emerging bias toward the left side of representational space or lower numbers).

Comet/Asteroid Protection System (CAPS): A Space-Based System Concept for Revolutionizing Earth Protection and Utilization of Near-Earth Objects

NASA Technical Reports Server (NTRS)

Mazanek, Daniel D.; Roithmayr, Carlos M.; Antol, Jeffrey; Kay-Bunnell, Linda; Werner, Martin R.; Park, Sang-Young; Kumar, Renjith R.

2002-01-01

There exists an infrequent, but significant hazard to life and property due to impacting asteroids and comets. There is currently no specific search for long-period comets, smaller near-Earth asteroids, or smaller short-period comets. These objects represent a threat with potentially little or no warning time using conventional ground-based telescopes. These planetary bodies also represent a significant resource for commercial exploitation, long-term sustained space exploration, and scientific research. The Comet/Asteroid Protection System (CAPS) would expand the current detection effort to include long-period comets, as well as small asteroids and short-period comets capable of regional destruction. A space-based detection system, despite being more costly and complex than Earth-based initiatives, is the most promising way of expanding the range of detectable objects, and surveying the entire celestial sky on a regular basis. CAPS is a future spacebased system concept that provides permanent, continuous asteroid and comet monitoring, and rapid, controlled modification of the orbital trajectories of selected bodies. CAPS would provide an orbit modification system capable of diverting kilometer class objects, and modifying the orbits of smaller asteroids for impact defense and resource utilization. This paper provides a summary of CAPS and discusses several key areas and technologies that are being investigated.